;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015-2023 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2016, 2017 Ben Woodcroft ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2017 Raoul Bonnal ;;; Copyright © 2018 Vijayalakshmi Vedantham ;;; Copyright © 2018 Sahithi Yarlagadda ;;; Copyright © 2018 Sandeep Subramanian ;;; Copyright © 2018 Charlie Ritter ;;; Copyright © 2018 Konrad Hinsen ;;; Copyright © 2018, 2020-2023 Mădălin Ionel Patrașcu ;;; Copyright © 2018 Laura Lazzati ;;; Copyright © 2018 Leo Famulari ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2018, 2019 Brett Gilio ;;; Copyright © 2019 Nicolò Balzarotti ;;; Copyright © 2019, 2020, 2021, 2022 Wiktor Żelazny ;;; Copyright © 2019 Arne Babenhauserheide ;;; Copyright © 2019, 2020, 2023 Efraim Flashner ;;; Copyright © 2020 Todor Kondić ;;; Copyright © 2020 Danjela Lura ;;; Copyright © 2020 Naga Malleswari ;;; Copyright © 2020 Eric Brown ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Rafael Luque Leiva ;;; Copyright © 2020, 2021 Lars-Dominik Braun ;;; Copyright © 2020 Vinicius Monego ;;; Copyright © 2020 Antoine Côté ;;; Copyright © 2020 Arun Isaac ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020, 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2020 Aniket Patil ;;; Copyright © 2021 Marcel Schilling ;;; Copyright © 2021 Guillaume Le Vaillant ;;; Copyright © 2022, 2023 Navid Afkhami ;;; Copyright © 2022 Greg Hogan ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . (define-module (gnu packages cran) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system r) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) #:use-module (gnu packages compression) #:use-module (gnu packages crypto) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages libevent) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) #:use-module (gnu packages node) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages ssh) #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages tcl) #:use-module (gnu packages tex) #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages uglifyjs) #:use-module (gnu packages version-control) #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) (define-public r-aer (package (name "r-aer") (version "1.2-10") (source (origin (method url-fetch) (uri (cran-uri "AER" version)) (sha256 (base32 "1p6vxr0220lim5i4gwsvphqrfd65zbs8h3qydz4gipca9asmy2k5")))) (properties `((upstream-name . "AER"))) (build-system r-build-system) (propagated-inputs (list r-car r-formula r-lmtest r-sandwich r-survival r-zoo)) (home-page "https://cran.r-project.org/package=AER") (synopsis "Applied econometrics with R") (description "This package provides functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette \"AER\" for a package overview.)") ;; Either version of the GPL (license (list license:gpl2 license:gpl3)))) (define-public r-afpt (package (name "r-afpt") (version "1.1.0.4") (source (origin (method url-fetch) (uri (cran-uri "afpt" version)) (sha256 (base32 "15pa4p78p6r478l05481lzx6z4ahswj728s1sb3xp3pvn6rv4jfj")))) (properties `((upstream-name . "afpt"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/MarcoKlH/afpt-r/") (synopsis "Tools for modelling of animal flight performance") (description "This package allows estimation and modelling of flight costs in animal (vertebrate) flight, implementing the aerodynamic power model. Flight performance is estimated based on basic morphological measurements such as body mass, wingspan and wing area. @code{Afpt} can be used to make predictions on how animals should adjust their flight behaviour and wingbeat kinematics to varying flight conditions.") (license license:gpl3+))) (define-public r-aod (package (name "r-aod") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "aod" version)) (sha256 (base32 "0zh8sjzbsq3sjzayv8wa0n1vh654g47xkxklgzxcsy3xpy55w95p")))) (properties `((upstream-name . "aod"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=aod") (synopsis "Analysis of overdispersed data") (description "This package provides a set of functions to analyze overdispersed counts or proportions. Most of the methods are already available elsewhere but are scattered in different packages. The proposed functions should be considered as complements to more sophisticated methods such as @dfn{generalized estimating equations} (GEE) or @dfn{generalized linear mixed effect models} (GLMM).") (license license:gpl2+))) (define-public r-brio (package (name "r-brio") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "brio" version)) (sha256 (base32 "1s0q1qk3w3fwf7gn4xfwhf8i8yqqb6z096x6xqsj8av8924z7fqc")))) (properties `((upstream-name . "brio"))) (build-system r-build-system) (home-page "https://github.com/r-lib/brio") (synopsis "Basic R input output") (description "This package provides functions to handle basic input output. These functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.") (license license:expat))) (define-public r-broom-helpers (package (name "r-broom-helpers") (version "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "broom.helpers" version)) (sha256 (base32 "14vaqxv12yrvqllp8552nx68wk2qfjcy1iy7bajkspgdpwsjzhfd")))) (properties `((upstream-name . "broom.helpers"))) (build-system r-build-system) (propagated-inputs (list r-broom r-cli r-dplyr r-labelled r-lifecycle r-purrr r-rlang r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://larmarange.github.io/broom.helpers/") (synopsis "Helpers for Model Coefficients Tibbles") (description "This package provides suite of functions to work with regression model @code{broom::tidy()} tibbles. The suite includes functions to group regression model terms by variable, insert reference and header rows for categorical variables, add variable labels, and more.") (license license:gpl3+))) (define-public r-ca (package (name "r-ca") (version "0.71.1") (source (origin (method url-fetch) (uri (cran-uri "ca" version)) (sha256 (base32 "095lk7p2b9835hc3a03c4019wg0baf0dhz6c2vqpaq1m9k4jy304")))) (properties `((upstream-name . "ca"))) (build-system r-build-system) (home-page "http://www.carme-n.org/") (synopsis "Simple, multiple and joint correspondence analysis") (description "This is a package for computation and visualization of simple, multiple and joint correspondence analysis.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-cachem (package (name "r-cachem") (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "cachem" version)) (sha256 (base32 "1hj5gw040pdrl3iwvwbgyrs91jcar0pwr3kmf23wwpb1zqcsk77a")))) (properties `((upstream-name . "cachem"))) (build-system r-build-system) (propagated-inputs (list r-fastmap r-rlang)) (home-page "https://cachem.r-lib.org/") (synopsis "Cache R objects with automatic pruning") (description "This package provides key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.") (license license:expat))) (define-public r-caic4 (package (name "r-caic4") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "cAIC4" version)) (sha256 (base32 "1qg73g0g029wkzpmp0fgvyfz8p1k3x38yqx0404cpb3dxj4n4hcg")))) (properties `((upstream-name . "cAIC4"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-matrix r-mgcv r-mvtnorm r-nlme r-rlrsim)) (home-page "https://cran.r-project.org/package=cAIC4") (synopsis "Conditional AIC for lme4 and nlme") (description "This package estimates conditional Akaike information in mixed-effect models. These models are fitted using @code{(g)lmer()} from lme4, @code{lme()} from nlme, and @code{gamm()} from mgcv. The provided functions facilitate the computation of the conditional Akaike information for model evaluation.") (license license:gpl2+))) (define-public r-castor (package (name "r-castor") (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "castor" version)) (sha256 (base32 "0caw206hndfzypj33w6npvppdc5hhq1q71wriqd0ck9f238rfi3c")))) (properties `((upstream-name . "castor"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-matrix r-naturalsort r-rcpp r-rspectra)) (home-page "https://cran.r-project.org/package=castor") (synopsis "Efficient phylogenetics on large trees") (description "This tool supports analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. In addition, this tool takes care of calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format.") (license license:gpl2+))) (define-public r-changepoint (package (name "r-changepoint") (version "2.2.4") (source (origin (method url-fetch) (uri (cran-uri "changepoint" version)) (sha256 (base32 "16v4p2c9zi2w3anwf5y9snl5dy1g5aidiqz1vn2p64qhfvg6yqxc")))) (properties `((upstream-name . "changepoint"))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://github.com/rkillick/changepoint/") (synopsis "Methods for changepoint detection") (description "Changepoint implements various mainstream and specialised changepoint methods. These methods are suitable for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included as well.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-celestial (package (name "r-celestial") (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "celestial" version)) (sha256 (base32 "1gls0qvr8mxz79lsmk76v253f747g0cqys8p8wjmpijs8r0pyr4z")))) (properties `((upstream-name . "celestial"))) (build-system r-build-system) (propagated-inputs (list r-nistunits r-pracma r-rann)) (home-page "https://cran.r-project.org/package=celestial") (synopsis "Collection of common astronomical conversion routines and functions") (description "This package contains a number of common astronomy conversion routines, particularly the HMS and degrees schemes, which can be fiddly to convert between on mass due to the textural nature of the former. It allows users to coordinate match datasets quickly. It also contains functions for various cosmological calculations.") (license license:gpl3))) ;; The package sources include multiple non-minified JavaScript files and the ;; v5.1.0 variant of d3.js. The d3.js file is not minified. (define-public r-chromomap (package (name "r-chromomap") (version "4.1.1") (source (origin (method url-fetch) (uri (cran-uri "chromoMap" version)) (sha256 (base32 "1067h5d6jdbm811n7ayikhqfbcqmxbz5jgp05vf1sbln7qgn9l43")))) (properties `((upstream-name . "chromoMap"))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-htmlwidgets)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=chromoMap") (synopsis "Interactive genomic visualization of biological data") (description "This package provides interactive, configurable and graphics visualization of the chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the \"chromosome heatmap\" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.") (license (list license:gpl3 license:isc)))) ;for bundled d3js (define-public r-consort (package (name "r-consort") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "consort" version)) (sha256 (base32 "03xkypy4r84mdif6m331c27haxnyi1s87vvj2f83xxw0m0s5im5j")))) (properties `((upstream-name . "consort"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/adayim/consort/") (synopsis "Create Consort Diagrams") (description "To make it easy to create CONSORT diagrams for the transparent reporting of participant allocation in randomized, controlled clinical trials. This is done by creating a standardized disposition data, and using this data as the source for the creation a standard CONSORT diagram. Human effort by supplying text labels on the node can also be achieved.") (license license:expat))) (define-public r-collapse (package (name "r-collapse") (version "2.0.9") (source (origin (method url-fetch) (uri (cran-uri "collapse" version)) (sha256 (base32 "0c9cz1dqrgd3gss9cr40a3rh014av0w8gfhq35lq1knyik6bhk28")))) (properties `((upstream-name . "collapse"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://sebkrantz.github.io/collapse/") (synopsis "Advanced and fast data transformation") (description "This is a C/C++ based package for advanced data transformation and statistical computing in R that is extremely fast, class-agnostic, robust and programmer friendly. Core functionality includes a rich set of S3 generic grouped and weighted statistical functions for vectors, matrices and data frames, which provide efficient low-level vectorizations, @code{OpenMP} multithreading, and skip missing values by default. These are integrated with fast grouping and ordering algorithms (also callable from C), and efficient data manipulation functions. The package also provides a flexible and rigorous approach to time series and panel data in R. It further includes fast functions for common statistical procedures, detailed (grouped, weighted) summary statistics, powerful tools to work with nested data, fast data object conversions, functions for memory efficient R programming, and helpers to effectively deal with variable labels, attributes, and missing data.") (license (list license:gpl2+)))) (define-public r-collections (package (name "r-collections") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "collections" version)) (sha256 (base32 "003zlp5s2ilq3pq0imlp7p46jkfihwzg1hkkgk7378ikcbwnz17z")))) (properties `((upstream-name . "collections"))) (build-system r-build-system) (home-page "https://github.com/randy3k/collections") (synopsis "High performance container data types") (description "This package provides high performance container data types such as queues, stacks, deques, dicts and ordered dicts.") (license license:expat))) (define-public r-correlation (package (name "r-correlation") (version "0.8.4") (source (origin (method url-fetch) (uri (cran-uri "correlation" version)) (sha256 (base32 "07fz7wmvrcd6b023jhj3bsrvg4w6i7f1v99jslm0gj84vzmnqzbs")))) (properties `((upstream-name . "correlation"))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight r-parameters)) (native-inputs (list r-knitr)) (home-page "https://easystats.github.io/correlation/") (synopsis "Methods for correlation analysis") (description "This is a lightweight package for computing different kinds of correlations. These correlations include partial correlations, Bayesian correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more.") (license license:gpl3))) (define-public r-cplm (package (name "r-cplm") (version "0.7-12") (source (origin (method url-fetch) (uri (cran-uri "cplm" version)) (sha256 (base32 "1m0b0jksl1y90q4sdhjspby4hafxxdgra8sbicd5rsrwq4hzwyxc")))) (properties `((upstream-name . "cplm"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; GET_SLOT is only found in Rdefines.h (add-after 'unpack 'compatibility (lambda _ (substitute* "src/common.h" (("#include " m) (string-append m "\n#include ")))))))) (propagated-inputs (list r-biglm r-coda r-ggplot2 r-matrix r-minqa r-nlme r-reshape2 r-statmod r-tweedie)) (home-page "https://github.com/actuaryzhang/cplm") (synopsis "Compound Poisson linear models") (description "The Tweedie compound Poisson distribution is a mixture of a degenerate distribution at the origin and a continuous distribution on the positive real line. It has been applied in a wide range of fields in which continuous data with exact zeros regularly arise. The cplm package provides likelihood based and Bayesian procedures for fitting common Tweedie compound Poisson linear models. In particular, models with hierarchical structures or extra zero inflation can be handled. Further, the package implements the Gini index based on an ordered version of the Lorenz curve as a robust model comparison tool involving zero-inflated and highly skewed distributions.") (license license:gpl2+))) (define-public r-curry (package (name "r-curry") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "curry" version)) (sha256 (base32 "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29")))) (properties `((upstream-name . "curry"))) (build-system r-build-system) (home-page "https://github.com/thomasp85/curry") (synopsis "Partial function application") (description "Partial application is the process of reducing the arity of a function by fixing one or more arguments, thus creating a new function lacking the fixed arguments. The @code{curry} package provides three different ways of performing partial function application by fixing arguments from either end of the argument list (currying and tail currying) or by fixing multiple named arguments (partial application). This package provides this functionality through the @code{%<%}, @code{%-<%}, and @code{%><%} operators which allows for a programming style comparable to modern functional languages. Compared to other implementations such a @code{purrr::partial()} the operators in @code{curry} composes functions with named arguments, aiding in autocomplete etc.") (license license:gpl2+))) (define-public r-datawizard (package (name "r-datawizard") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 "0d01akddrbvdf16rvws3fh4pjl64myxn7is4qv2szm7hp6wjb4p5")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs (list r-insight)) (native-inputs (list r-knitr)) (home-page "https://easystats.github.io/datawizard/") (synopsis "Easy data wrangling") (description "This package provides a lightweight package to easily manipulate, clean, transform, and prepare your data for analysis. It also forms the data wrangling backend for the packages in the @code{easystats} ecosystem.") (license license:gpl3))) (define-public r-dbscan (package (name "r-dbscan") (version "1.1-12") (source (origin (method url-fetch) (uri (cran-uri "dbscan" version)) (sha256 (base32 "1snfcf5jy3chh5nmvn7ashhlyv35nkajlfrlk9kzpy4jnfyv3y2n")))) (properties `((upstream-name . "dbscan"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/mhahsler/dbscan") (synopsis "Density-based spatial clustering of applications with noise") (description "This package provides a fast reimplementation of several density-based algorithms of the DBSCAN family. It includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and @dfn{hierarchical DBSCAN} (HDBSCAN), the ordering algorithm @dfn{ordering points to identify the clustering structure} (OPTICS), shared nearest neighbor clustering, and the outlier detection algorithms @dfn{local outlier factor} (LOF) and @dfn{global-local outlier score from hierarchies} (GLOSH). The implementations use the kd-tree data structure for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.") (license license:gpl2+))) (define-public r-diffobj (package (name "r-diffobj") (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "diffobj" version)) (sha256 (base32 "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q")))) (properties `((upstream-name . "diffobj"))) (build-system r-build-system) (propagated-inputs (list r-crayon)) (native-inputs (list r-knitr)) (home-page "https://github.com/brodieG/diffobj") (synopsis "Diffs for R objects") (description "Generate a colorized diff of two R objects for an intuitive visualization of their differences.") (license license:gpl2+))) (define-public r-dirichletreg (package (name "r-dirichletreg") (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "DirichletReg" version)) (sha256 (base32 "1ql5mwb7zb06y9j6inrlngq7c15as4j17wd8kc71fxs0a2jdj7xi")))) (properties `((upstream-name . "DirichletReg"))) (build-system r-build-system) (propagated-inputs (list r-formula r-maxlik)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=DirichletReg") (synopsis "Dirichlet regression") (description "This package implements Dirichlet regression models.") (license license:gpl2+))) (define-public r-dirmult (package (name "r-dirmult") (version "0.1.3-5") (source (origin (method url-fetch) (uri (cran-uri "dirmult" version)) (sha256 (base32 "05whzhl81nyag7321hw98xa63r440s9bgj1764346yvm9bvzjqi4")))) (properties `((upstream-name . "dirmult"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=dirmult") (synopsis "Estimation in Dirichlet-Multinomial distribution") (description "This package estimates the parameters in Dirichlet-Multinomial and computes log-likelihoods.") (license license:gpl2+))) (define-public r-dixontest (package (name "r-dixontest") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "dixonTest" version)) (sha256 (base32 "0gz39s1z987bg56vwrpcs14wzyf7p07s7l7z9napz0i38564wsdq")))) (properties `((upstream-name . "dixonTest"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=dixonTest") (synopsis "Dixon's ratio test for outlier detection") (description "For outlier detection in small and normally distributed samples the ratio test of Dixon (Q-test) can be used. Density, distribution function, quantile function and random generation for Dixon's ratio statistics are provided as wrapper functions. The core applies McBane's Fortran functions that use Gaussian quadrature for a numerical solution.") (license license:gpl3))) (define-public r-dmwr2 (package (name "r-dmwr2") (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "DMwR2" version)) (sha256 (base32 "1vzfbz2k05j8r2hpig3d2grb99rnnh2s1sviii3prcyqicxfh0i9")))) (properties `((upstream-name . "DMwR2"))) (build-system r-build-system) (propagated-inputs (list r-class r-dbi r-dplyr r-quantmod r-readr r-rpart r-xts r-zoo)) (home-page "https://github.com/ltorgo/DMwR2") (synopsis "Functions and data for the second edition of \"Data Mining with R\"") (description "This package provides functions and data accompanying the second edition of the book \"Data Mining with R, learning with case studies\" by Luis Torgo, published by CRC Press.") (license license:gpl2+))) (define-public r-earlywarnings (package (name "r-earlywarnings") (version "1.1.29") (source (origin (method url-fetch) (uri (cran-uri "earlywarnings" version)) (sha256 (base32 "1xa9rijqqxa5l253dg8dn1jjhdakf8krl5rflq5v9gybfyrq1885")))) (properties `((upstream-name . "earlywarnings"))) (build-system r-build-system) (propagated-inputs (list r-fields r-ggplot2 r-kendall r-kernsmooth r-knitr r-lmtest r-moments r-nortest r-quadprog r-som r-spam r-tgp r-tseries)) (native-inputs (list r-knitr)) (home-page "https://www.early-warning-signals.org") (synopsis "Early warning signals for critical transitions in time series") (description "This package offers methods for estimating statistical changes in time series. These are used for identifying nearby critical transitions.") (license license:bsd-2))) (define-public r-embedsom (package (name "r-embedsom") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "EmbedSOM" version)) (sha256 (base32 "0k4hja5y7qd0n3gfaxzxrz4wpxc1w9d4d4xbb63rq2nfk3lj7a42")))) (properties `((upstream-name . "EmbedSOM"))) (build-system r-build-system) (propagated-inputs (list r-fnn r-ggplot2 r-igraph r-matrix r-rtsne r-umap r-uwot)) (native-inputs (list r-knitr)) (home-page "https://github.com/exaexa/EmbedSOM") (synopsis "Fast embedding guided by self-organizing map") (description "This package provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. It is designed to work with FlowSOM and flow-cytometry use-cases.") (license license:gpl3+))) (define-public r-emdist (package (name "r-emdist") (version "0.3-3") (source (origin (method url-fetch) (uri (cran-uri "emdist" version)) (sha256 (base32 "0jmnz612pjad3p1zk0qiljcbf0zbxfi4zcw2jqwg8ncjsifhr3mp")))) (properties `((upstream-name . "emdist"))) (build-system r-build-system) (home-page "https://www.rforge.net/emd") (synopsis "Earth mover's distance") (description "This package provides tools to calculate the Earth Mover's Distance (EMD).") (license license:expat))) (define-public r-gfonts (package (name "r-gfonts") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "gfonts" version)) (sha256 (base32 "19ja087k767bq71v2w4jcpynd62ysrqmjf6rpfnmmd40aanyxqkj")))) (properties `((upstream-name . "gfonts"))) (build-system r-build-system) (propagated-inputs (list r-crayon r-crul r-glue r-htmltools r-jsonlite r-shiny)) (native-inputs (list r-knitr)) (home-page "https://dreamrs.github.io/gfonts/") (synopsis "Offline Google fonts for Markdown and Shiny") (description "This package lets you download Google fonts and generate CSS to use in rmarkdown documents and Shiny applications. Some popular fonts are included and ready to use.") (license license:gpl3))) (define-public r-ggalt (package (name "r-ggalt") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "ggalt" version)) (sha256 (base32 "0ssa274d41vhd6crzjz7jqzbwgnjimxwxl23p2cx35aqs5wdfjpc")))) (properties `((upstream-name . "ggalt"))) (build-system r-build-system) (propagated-inputs (list r-ash r-dplyr r-extrafont r-ggplot2 r-gtable r-kernsmooth r-maps r-mass r-plotly r-proj4 r-rcolorbrewer r-scales r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/hrbrmstr/ggalt") (synopsis "Geometries, coordinate systems, fonts and more for ggplot2") (description "This package provides a compendium of new geometries, coordinate systems, statistical transformations, scales and fonts for ggplot2, including splines, 1d and 2d densities, univariate average shifted histograms, a new map coordinate system based on the PROJ.4-library along with @code{geom_cartogram()} that mimics the original functionality of @code{geom_map()}, formatters for \"bytes\", a @code{stat_stepribbon()} function, increased @code{plotly} compatibility and the @code{StateFace} open source font ProPublica. Further new functionality includes lollipop charts, dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.") (license license:agpl3))) (define-public r-ggbreak (package (name "r-ggbreak") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "ggbreak" version)) (sha256 (base32 "14rx16v66xd0fjlywi89dq9dbw41zn7hpq14wgvf0178cxdp2fw4")))) (properties `((upstream-name . "ggbreak"))) (build-system r-build-system) (propagated-inputs (list r-aplot r-ggfun r-ggplot2 r-ggplotify r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/YuLab-SMU/ggbreak") (synopsis "Set axis break for ggplot2") (description "This package provides an implementation of scale functions for setting axis breaks of a ggplot.") (license license:artistic2.0))) (define-public r-ggdist (package (name "r-ggdist") (version "3.3.1") (source (origin (method url-fetch) (uri (cran-uri "ggdist" version)) (sha256 (base32 "0agr1l65s7vimdb88a7n3ahr6pp9ng5zf9mypdic26vhaaifh1b7")))) (properties `((upstream-name . "ggdist"))) (build-system r-build-system) (propagated-inputs (list r-cli r-distributional r-dplyr r-ggplot2 r-glue r-numderiv r-quadprog r-rcpp r-rlang r-scales r-tibble r-tidyselect r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://mjskay.github.io/ggdist/") (synopsis "Visualizations of distributions and uncertainty") (description "This package provides primitives for visualizing distributions using ggplot2 that are particularly tuned for visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as bootstrap distributions or Bayesian posterior samples) are easily visualized.") (license license:gpl3+))) (define-public r-ggfittext (package (name "r-ggfittext") (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "ggfittext" version)) (sha256 (base32 "1z06q55igv6nibc72hll93cpp80mfg3yqfqbi967832nfj7wll7a")))) (properties `((upstream-name . "ggfittext"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridtext r-shades r-stringi)) (native-inputs (list r-knitr)) (home-page "https://wilkox.org/ggfittext/") (synopsis "Ggfittext is a ggplot2 extension for fitting text into boxes") (description "Ggfittext is a ggplot2 extension for fitting text into boxes.") (license license:gpl2))) (define-public r-ggstats (package (name "r-ggstats") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "ggstats" version)) (sha256 (base32 "1jcydapwarl1cxinm80rjmmli8vmlid8alnh6w484bh7nwzmcsic")))) (properties `((upstream-name . "ggstats"))) (build-system r-build-system) (propagated-inputs (list r-broom-helpers r-cli r-dplyr r-forcats r-ggplot2 r-lifecycle r-magrittr r-patchwork r-purrr r-rlang r-scales r-stringr r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://larmarange.github.io/ggstats/") (synopsis "Extension to ggplot2 for plotting stats") (description "This package provides new statistics, new geometries and new positions for ggplot2 and a suite of functions to facilitate the creation of statistical plots.") (license license:gpl3+))) (define-public r-ggstatsplot (package (name "r-ggstatsplot") (version "0.12.2") (source (origin (method url-fetch) (uri (cran-uri "ggstatsplot" version)) (sha256 (base32 "0nriqsfk48ijkkg06i87zp2frp7yz3c4gfmfgfig6v8mcmj19zwr")))) (properties `((upstream-name . "ggstatsplot"))) (build-system r-build-system) (propagated-inputs (list r-correlation r-datawizard r-dplyr r-ggcorrplot r-ggplot2 r-ggrepel r-ggside r-ggsignif r-glue r-insight r-paletteer r-parameters r-patchwork r-performance r-purrr r-rlang r-statsexpressions r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://indrajeetpatil.github.io/ggstatsplot/") (synopsis "Based plots with statistical details") (description "This package generates graphics with embedded details from statistical tests. Statistical tests included in the plots themselves. It provides an easier syntax to generate information-rich plots for statistical analysis of continuous or categorical data. Currently, it supports the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian versions of t-test/ANOVA, correlation analyses, contingency table analysis, meta-analysis, and regression analyses.") (license license:gpl3))) (define-public r-glmpca (package (name "r-glmpca") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "glmpca" version)) (sha256 (base32 "02xjf0gg52925hw9nw2j0znfmzfzfwbv0fxjl9d2fy9j63drr2h4")))) (properties `((upstream-name . "glmpca"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (native-inputs (list r-knitr)) (home-page "https://github.com/willtownes/glmpca") (synopsis "Dimension Reduction of Non-Normally Distributed Data") (description "This package implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.") (license license:lgpl3+))) (define-public r-googledrive (package (name "r-googledrive") (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "googledrive" version)) (sha256 (base32 "10pv70nvsqh1yc12g5fj7avfihjzpj02m8s9f8sb0c1np9s4z2qb")))) (properties `((upstream-name . "googledrive"))) (build-system r-build-system) (propagated-inputs (list r-cli r-gargle r-glue r-httr r-jsonlite r-lifecycle r-magrittr r-pillar r-purrr r-rlang r-tibble r-uuid r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://googledrive.tidyverse.org") (synopsis "Interface to Google Drive") (description "This package lets you manage Google Drive files from R.") (license license:expat))) (define-public r-googlevis (package (name "r-googlevis") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "googleVis" version)) (sha256 (base32 "067jcwbq0a06wbpaa46ngjs3hkpvz8q6v8019f15yr58kq2k2n9k")))) (properties `((upstream-name . "googleVis"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://mages.github.io/googleVis/") (synopsis "R interface to Google Charts") (description "The @code{googleVis} package provides an interface between R and the Google Charts API. Google Charts offer interactive charts which can be embedded into web pages. The functions of the @code{googleVis} package allow the user to visualise data stored in R data frames with Google Charts without uploading the data to Google. The output of a @code{googleVis} function is HTML code that contains the data and references to JavaScript functions hosted by Google. @code{googleVis} makes use of the internal R HTTP server to display the output locally.") (license license:gpl2+))) (define-public r-gson (package (name "r-gson") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "gson" version)) (sha256 (base32 "10d3v543bvsyrwg3dm04xpzxjvmba1d1fhcf2zfb3l36pvjvxp8l")))) (properties `((upstream-name . "gson"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-rlang r-tidyr)) (home-page "https://cran.r-project.org/package=gson") (synopsis "Base Class and Methods for 'gson' Format") (description "This package proposes a new file format named @code{gson} for storing gene set and related information, and provides read, write and other utilities to process this file format.") (license license:artistic2.0))) (define-public r-guix-install (package (name "r-guix-install") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "guix.install" version)) (sha256 (base32 "0s3wb5781yc43c9zwrn7i87zcbrlx7xr0ms0v9hvgs7qsv02id9j")))) (properties `((upstream-name . "guix.install"))) (build-system r-build-system) (propagated-inputs (list r-runit)) (home-page "https://github.com/BIMSBbioinfo/guix.install") (synopsis "Install R packages with GNU Guix") (description "This R package provides a single procedure @code{guix.install()}, which allows users to install R packages via Guix right from within their running R session. If the requested R package does not exist in Guix at this time, the package and all its missing dependencies will be imported recursively and the generated package definitions will be written to @file{~/.Rguix/packages.scm}. This record of imported packages can be used later to reproduce the environment, and to add the packages in question to a proper Guix channel (or Guix itself). @code{guix.install()} not only supports installing packages from CRAN, but also from Bioconductor or even arbitrary git or mercurial repositories, replacing the need for installation via @code{devtools}.") (license license:gpl3+))) (define-public r-gunifrac (package (name "r-gunifrac") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "GUniFrac" version)) (sha256 (base32 "1yw0d8hb7s662xy0dny9ygvx9gwh7yj8dxw4897zy7zyjhzim95f")))) (properties `((upstream-name . "GUniFrac"))) (build-system r-build-system) (propagated-inputs (list r-ape r-dirmult r-foreach r-ggplot2 r-ggrepel r-inline r-mass r-matrix r-matrixstats r-modeest r-rcpp r-rmutil r-statmod r-vegan)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=GUniFrac") (synopsis "Generalized UniFrac distances and methods for microbiome data analysis") (description "This package provides a suite of methods for powerful and robust microbiome data analysis, including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, @dfn{Geometric Mean of Pairwise Ratios} (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature- based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: @itemize @item PERMANOVA using the Freedman-Lane permutation scheme, @item PERMANOVA omnibus test using multiple matrices, and @item analytical approach to approximating PERMANOVA p-value. @end itemize Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.") (license license:gpl3))) (define-public r-gwasexacthw (package (name "r-gwasexacthw") (version "1.01") (source (origin (method url-fetch) (uri (cran-uri "GWASExactHW" version)) (sha256 (base32 "19qmk8h7kxmn9kzw0x4xns5p3qqz27xkqq4q6zmh4jzizd0fsl78")))) (properties `((upstream-name . "GWASExactHW"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=GWASExactHW") (synopsis "Exact Hardy-Weinburg testing for Genome Wide Association Studies") (description "This package contains a function to do exact Hardy-Weinburg testing (using Fisher's test) for SNP genotypes as typically obtained in a @dfn{Genome Wide Association Study} (GWAS).") (license license:gpl3))) (define-public r-gwidgets2 (package (name "r-gwidgets2") (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "gWidgets2" version)) (sha256 (base32 "1ifljpdazzmwf3mgkg9g76365n2cmw8dd3da161fpvw84xxyznfl")))) (properties `((upstream-name . "gWidgets2"))) (build-system r-build-system) (propagated-inputs (list r-digest)) (home-page "https://github.com/gWidgets3/gWidgets2") (synopsis "Rewrite of gWidgets API for simplified GUI construction") (description "This package provides a re-implementation of the @code{gWidgets} API. The API is defined in this package. A second, toolkit-specific package is required to use it.") (license license:gpl3+))) (define-public r-gwidgets2tcltk (package (name "r-gwidgets2tcltk") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "gWidgets2tcltk" version)) (sha256 (base32 "02ic4avpa33dnqsnm1mzg7ci1psngk1p169pqf259szf6v39qf8h")))) (properties `((upstream-name . "gWidgets2tcltk"))) (build-system r-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-before 'install 'start-x-server (lambda _ ;; Tests require a running X server. (system "Xvfb :1 +extension GLX &") (setenv "DISPLAY" ":1")))))) (propagated-inputs (list r-digest r-gwidgets2 r-memoise)) (native-inputs (list xorg-server-for-tests)) (home-page "https://github.com/jverzani/gWidgets2tcltk") (synopsis "Toolkit implementation of gWidgets2 for tcltk") (description "This package is a port of the @code{gWidgets2} API for the @code{tcltk} package.") (license license:gpl2+))) (define-public r-ids (package (name "r-ids") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ids" version)) (sha256 (base32 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn")))) (properties `((upstream-name . "ids"))) (build-system r-build-system) (propagated-inputs (list r-openssl r-uuid)) (native-inputs (list r-knitr)) (home-page "https://github.com/richfitz/ids") (synopsis "Generate random identifiers") (description "This package lets you generate random or human readable and pronounceable identifiers.") (license license:expat))) (define-public r-googlesheets4 (package (name "r-googlesheets4") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "googlesheets4" version)) (sha256 (base32 "1kzwhs9zrx1i4kqhdqrkzyhnwx25j8j2pcg7ja2dxfalihs67k65")))) (properties `((upstream-name . "googlesheets4"))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-cli r-curl r-gargle r-glue r-googledrive r-httr r-ids r-lifecycle r-magrittr r-purrr r-rematch2 r-rlang r-tibble r-vctrs r-withr)) (home-page "https://github.com/tidyverse/googlesheets4") (synopsis "Access Google Sheets using the Sheets API V4") (description "This package lets you interact with Google Sheets through the @url{https://developers.google.com/sheets/api,Sheets API v4}. This package can read and write both the metadata and the cell data in a Sheet.") (license license:expat))) (define-public r-pma (package (name "r-pma") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "PMA" version)) (sha256 (base32 "1rhiylm3jfarnqdkv7nwg536sgsa30ic80dk9byks9w0wf4mn59s")))) (properties `((upstream-name . "PMA"))) (build-system r-build-system) (home-page "https://github.com/bnaras/PMA") (synopsis "Penalized multivariate analysis") (description "This package performs penalized multivariate analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis.") (license license:gpl2+))) (define-public r-prettydoc (package (name "r-prettydoc") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "prettydoc" version)) (sha256 (base32 "0aa89jnqhz0l69inrgm1f1riq5bm3ksb8wjl8d4x2f320adsd50h")) (snippet '(for-each delete-file '("inst/resources/js/auto-render.min.js" "inst/resources/js/katex.min.js"))))) (properties `((upstream-name . "prettydoc"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/resources/js/" (call-with-values (lambda () (unzip2 `((,(search-input-file inputs "dist/katex.js") "katex.min.js") (,(search-input-file inputs "dist/contrib/auto-render.js") "auto-render.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (inputs (list pandoc)) (propagated-inputs (list r-rmarkdown)) (native-inputs (list esbuild r-knitr r-rmarkdown (let ((version "0.12.0")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/KaTeX/KaTeX") (commit (string-append "v" version)))) (file-name (git-file-name "js-katex" version)) (sha256 (base32 "0pdfw28affnfpqpnf244acf5rkxdy2gk63669myy7ysg4z0i1n8j")))))) (home-page "https://github.com/yixuan/prettydoc") (synopsis "Create pretty documents from R markdown") (description "This is a package for creating tiny yet beautiful documents and vignettes from R Markdown. The package provides the @code{html_pretty} output format as an alternative to the @code{html_document} and @code{html_vignette} engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported.") (license license:asl2.0))) (define-public r-profmem (package (name "r-profmem") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "profmem" version)) (sha256 (base32 "0gg6ja0ifwn9jj42rw1gnyil55sl9r2y5rjb6yjcvqwd5arajp3l")))) (properties `((upstream-name . "profmem"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-before 'install 'set-HOME (lambda _ ;; Needed for building vignettes (setenv "HOME" "/tmp")))))) (native-inputs (list r-r-rsp r-markdown)) ;for vignettes (home-page "https://github.com/HenrikBengtsson/profmem") (synopsis "Simple memory profiling for R") (description "This package provides a simple and light-weight API for memory profiling of R expressions. The profiling is built on top of R's built-in memory profiler @code{utils::Rprofmem()}, which records every memory allocation done by R (also native code).") (license license:lgpl2.1+))) (define-public r-proj4 (package (name "r-proj4") (version "1.0-14") (source (origin (method url-fetch) (uri (cran-uri "proj4" version)) (sha256 (base32 "1dh059lhw32vn0hxlp6sxb6m8hjdgmm01djq6vfncrhkjbd73mfk")))) (properties `((upstream-name . "proj4"))) (build-system r-build-system) (inputs (list proj-7 zlib)) (native-inputs (list pkg-config)) (home-page "https://www.rforge.net/proj4/") (synopsis "Simple interface to the PROJ.4 cartographic projections library") (description "This package provides a simple interface to lat/long projection and datum transformation of the PROJ.4 cartographic projections library. It allows transformation of geographic coordinates from one projection and/or datum to another.") (license license:gpl2))) (define-public r-rorcid (package (name "r-rorcid") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "rorcid" version)) (sha256 (base32 "1d0s5w48ksyj152nc4xq5w0nsimab8jc5fgspdwnbas2g8a52igr")))) (properties `((upstream-name . "rorcid"))) (build-system r-build-system) (propagated-inputs (list r-crul r-data-table r-fauxpas r-httr r-jsonlite r-tibble r-xml2)) (home-page "https://github.com/ropensci/rorcid") (synopsis "Interface to the @url{Orcid.org, https://orcid.org} API") (description "This package provides an API for @url{Orcid.org, https://orcid.org}. Functions include searching for people, searching by DOI, or searching by Orcid ID.") (license license:expat))) (define-public r-ruv (package (name "r-ruv") (version "0.9.7.1") (source (origin (method url-fetch) (uri (cran-uri "ruv" version)) (sha256 (base32 "1n4q9mrp9f644spbns6bbnzmlabrg90hwkdfg3hnm3rxp9b4xid0")))) (properties `((upstream-name . "ruv"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-scales)) (home-page "https://cran.r-project.org/web/packages/ruv/index.html") (synopsis "Detect and remove unwanted variation using negative controls") (description "This package implements the RUV (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are RUV-2, RUV-4, RUV-inv, RUV-rinv, RUV-I, and RUV-III, along with various supporting algorithms.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-waldo (package (name "r-waldo") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "waldo" version)) (sha256 (base32 "019fvypq36kwvr2znlr0fd9f2ihb08rgigf6ypdybry5n8daxkc2")))) (properties `((upstream-name . "waldo"))) (build-system r-build-system) (propagated-inputs (list r-cli r-diffobj r-fansi r-glue r-rematch2 r-rlang r-tibble)) (home-page "https://github.com/r-lib/waldo") (synopsis "Find differences between R objects") (description "Compare complex R objects and reveal the key differences. This package was designed particularly for use in testing packages where being able to quickly isolate key differences makes understanding test failures much easier.") (license license:expat))) (define-public r-wheatmap (package (name "r-wheatmap") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "wheatmap" version)) (sha256 (base32 "064idlrnb85xxav39gp3n854fic6514khvazrf5d0x48crpzyvdp")))) (properties `((upstream-name . "wheatmap"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://github.com/zwdzwd/wheatmap") (synopsis "Incrementally build complex plots using natural semantics") (description "This package lets you build complex plots, heatmaps in particular, using natural semantics. Bigger plots can be assembled using directives such as @code{LeftOf}, @code{RightOf}, @code{TopOf}, and @code{Beneath} and more. Other features include clustering, dendrograms and integration with ggplot2 generated grid objects. This package is particularly designed for bioinformaticians to assemble complex plots for publication.") (license license:gpl3))) (define-public r-rticles (package (name "r-rticles") (version "0.26") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 "0v1sji223iifqmq9hakr1wcgzfca52nvmh3vbi6s6d309qc77vkk")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs (list r-knitr r-lifecycle r-rmarkdown r-tinytex r-xfun r-yaml)) (home-page "https://github.com/rstudio/rticles") (synopsis "Article formats for R Markdown") (description "This package provides a suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.") (license license:gpl3))) (define-public r-babelwhale (package (name "r-babelwhale") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "babelwhale" version)) (sha256 (base32 "0m5q83ykz5w1fsjsk2vyrnv21cg4n075kbvfvw4k22c61p78shdl")))) (properties `((upstream-name . "babelwhale"))) (build-system r-build-system) (propagated-inputs (list r-crayon r-digest r-dplyr r-dynutils r-fs r-glue r-processx r-purrr)) (home-page "https://github.com/dynverse/babelwhale") (synopsis "Talking to Docker and Singularity containers") (description "This package provides a unified interface to interact with Docker and Singularity containers. You can execute a command inside a container, mount a volume or copy a file.") (license license:expat))) (define-public r-bench (package (name "r-bench") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "bench" version)) (sha256 (base32 "05zky7l6103gabv9y0g3qlx8sgkq1sn9yl9jd3x8834cmlh67bmz")))) (properties `((upstream-name . "bench"))) (build-system r-build-system) (propagated-inputs (list r-glue r-pillar r-profmem r-rlang r-tibble)) (home-page "https://bench.r-lib.org/") (synopsis "High precision timing of R expressions") (description "This package provides tools to accurately benchmark and analyze execution times for R expressions.") (license license:expat))) (define-public r-benchmarkmedata (package (name "r-benchmarkmedata") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "benchmarkmeData" version)) (sha256 (base32 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-tibble)) (home-page "https://github.com/csgillespie/benchmarkme-data") (synopsis "Data set for the @code{benchmarkme} package") (description "This package contains the data set for the crowd-sourced benchmarks from running the @code{benchmarkme} package.") (license license:gpl2+))) (define-public r-benchmarkme (package (name "r-benchmarkme") (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "benchmarkme" version)) (sha256 (base32 "0qaz8wy3n08k9lr8qljk5i8z8db18scbdc8m734aymd307h00w8x")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-benchmarkmedata r-doparallel r-dplyr r-foreach r-httr r-matrix r-stringr r-tibble)) (home-page "https://csgillespie.github.io/benchmarkme/") (synopsis "Crowd-sourced system benchmarks") (description "This package provides functionality to benchmark your CPU and compare against other CPUs. Also provides functions for obtaining system specifications, such as RAM, CPU type, and R version.") (license license:gpl2+))) (define-public r-bestnormalize (package (name "r-bestnormalize") (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "bestNormalize" version)) (sha256 (base32 "1lryl23jvf51n7ka58ncwhjglk0zzm18wik962h403j4mph1jjly")))) (properties `((upstream-name . "bestNormalize"))) (build-system r-build-system) (propagated-inputs (list r-butcher r-doparallel r-dorng r-dplyr r-foreach r-generics r-lambertw r-nortest r-purrr r-recipes r-tibble)) (native-inputs (list r-knitr)) (home-page "https://petersonr.github.io/bestNormalize/") (synopsis "Normalizing transformation functions") (description "Estimate a suite of normalizing transformations, including a new adaptation of a technique based on ranks which can guarantee normally distributed transformed data if there are no ties: @dfn{ordered quantile normalization} (ORQ). ORQ normalization combines a rank-mapping approach with a shifted logit approximation that allows the transformation to work on data outside the original domain. It is also able to handle new data within the original domain via linear interpolation. The package is built to estimate the best normalizing transformation for a vector consistently and accurately. It implements the Box-Cox transformation, the Yeo-Johnson transformation, three types of Lambert WxF transformations, and the ordered quantile normalization transformation. It estimates the normalization efficacy of other commonly used transformations, and it allows users to specify custom transformations or normalization statistics. Finally, functionality can be integrated into a machine learning workflow via recipes.") (license license:gpl3))) (define-public r-bezier (package (name "r-bezier") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "bezier" version)) (sha256 (base32 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bezier/") (synopsis "Bezier curve and spline toolkit") (description "This package is a toolkit for working with Bezier curves and splines. The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.") (license license:gpl2+))) (define-public r-biglm (package (name "r-biglm") (version "0.9-2.1") (source (origin (method url-fetch) (uri (cran-uri "biglm" version)) (sha256 (base32 "0iy9xr2bq42wlizgwlz7w5kh9206yqkw9h2cr6mcsmizgjg3rkvd")))) (properties `((upstream-name . "biglm"))) (build-system r-build-system) (propagated-inputs (list r-dbi)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=biglm") (synopsis "Bounded memory linear and generalized linear models") (description "The biglm package lets you create a linear model object that uses only code{p^2} memory for @code{p} variables. It can be updated with more data using @code{update}. This allows linear regression on data sets larger than memory.") ;; Expanded from GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-bwstest (package (name "r-bwstest") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "BWStest" version)) (sha256 (base32 "1chlszmshda84000jj4q5j2swflj512vfj3h97361aphzhkwri2b")))) (properties `((upstream-name . "BWStest"))) (build-system r-build-system) (propagated-inputs (list r-memoise r-rcpp)) (home-page "https://github.com/shabbychef/BWStest") (synopsis "Baumgartner Weiss Schindler Test of equal distributions") (description "This package performs the Baumgartner-Weiss-Schindler two-sample test of equal probability distributions (doi:10.2307/2533862). It also performs similar rank-based tests for equal probability distributions due to Neuhauser (doi:10.1080/10485250108832874) and Murakami (doi:10.1080/00949655.2010.551516).") (license license:lgpl3))) (define-public r-v8 (package (name "r-v8") (version "4.4.1") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 "129spn531m9arz7v8vyfsrvc69hg0w39fdnhjxrcrww37l9xcvav")))) (properties `((upstream-name . "V8") (updater-extra-inputs . ("libnode")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'find-v8 (lambda* (#:key inputs #:allow-other-keys) (substitute* "configure" (("^PKG_LIBS=.*") (string-append "PKG_LIBS=" (assoc-ref inputs "libnode") "/lib/libnode.so.108\n"))) (setenv "INCLUDE_DIR" (string-append (assoc-ref inputs "libnode") "/include/node")) (setenv "LIB_DIR" (string-append (assoc-ref inputs "libnode") "/lib"))))))) (inputs (list libnode zlib)) (propagated-inputs (list r-curl r-jsonlite r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://jeroen.cran.dev/V8") (synopsis "Embedded JavaScript and WebAssembly engine for R") (description "This package provides an R interface to V8: Google's JavaScript and WebAssembly engine.") (license license:expat))) (define-public r-venn (package (name "r-venn") (version "1.12") (source (origin (method url-fetch) (uri (cran-uri "venn" version)) (sha256 (base32 "07bjv0m21gljdr3sj1z9rp6xhgxspah9j1m3a8rskvlwv6dvd1pd")))) (properties `((upstream-name . "venn"))) (build-system r-build-system) (propagated-inputs (list r-admisc)) (home-page "https://github.com/dusadrian/venn") (synopsis "Draw Venn diagrams") (description "This package provides a close to zero dependency package to draw and display Venn diagrams up to 7 sets, and any Boolean union of set intersections.") (license license:gpl3+))) (define-public r-rvenn (package (name "r-rvenn") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "RVenn" version)) (sha256 (base32 "016m00xv59lkwm2is32v5nr4lw5a1ymdnz34r3ffflcv9bfrc6n4")))) (properties `((upstream-name . "RVenn"))) (build-system r-build-system) (propagated-inputs (list r-ggforce r-ggplot2 r-magrittr r-pheatmap r-purrr r-rlang r-vegan)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=RVenn") (synopsis "Set operations for many sets") (description "The base functions for set operations in @code{R} can be used for only two sets. This package @code{RVenn} provides functions for dealing with multiple sets. It uses @code{purr} to find the union, intersection and difference of three or more sets. This package also provides functions for pairwise set operations among several sets. Further, based on @code{ggplot2} and @code{ggforce}, a Venn diagram can be drawn for two or three sets. For bigger data sets, a clustered heatmap showing the presence or absence of the elements of the sets can be drawn based on the @code{pheatmap} package. Finally, enrichment test can be applied to two sets whether an overlap is statistically significant or not.") (license license:gpl3))) (define-public r-dot (package (name "r-dot") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "DOT" version)) (sha256 (base32 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i")))) (properties `((upstream-name . "DOT"))) (build-system r-build-system) (propagated-inputs (list r-v8)) (home-page "http://haghish.com/dot") (synopsis "Render and Export DOT Graphs in R") (description "This package provides tools to render DOT diagram markup language in R and also provides the possibility to export the graphs in PostScript and SVG (Scalable Vector Graphics) formats. In addition, it supports literate programming packages such as @code{knitr} and @code{rmarkdown}.") (license license:expat))) (define-public r-carrier (package (name "r-carrier") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "carrier" version)) (sha256 (base32 "155zna5bv6ybb6hr3lsv8dn67lkbbvn3dbihfw2s6ajkzvms9x13")))) (properties `((upstream-name . "carrier"))) (build-system r-build-system) (propagated-inputs (list r-lobstr r-rlang)) (home-page "https://github.com/r-lib/carrier") (synopsis "Isolate functions for remote execution") (description "Sending functions to remote processes can be wasteful of resources because they carry their environments with them. With this package, it is easy to create functions that are isolated from their environment. These isolated functions, also called crates, print to the console with their total size and can be easily tested locally before being sent to a remote.") (license license:gpl3))) (define-public r-climaemet (package (name "r-climaemet") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "climaemet" version)) (sha256 (base32 "1276pxs3w610v6m8j5h206xxgwvm2wwma73jpvn7s3rcxycs32m5")))) (properties `((upstream-name . "climaemet"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-httr r-jsonlite r-rappdirs r-readr r-rlang r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://ropenspain.github.io/climaemet/") (synopsis "Climate AEMET Tools") (description "This package provides tools to download the climatic data of the Spanish Meteorological Agency (AEMET) directly from R using their API and create scientific graphs (climate charts, trend analysis of climate time series, temperature and precipitation anomalies maps, warming stripes graphics, climatograms, etc.).") (license license:gpl3))) (define-public r-climatol (package (name "r-climatol") (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "climatol" version)) (sha256 (base32 "0hz5j9wg3c2bd2v4q0mv01v7wwd6v650fbcvrl4zqxd9w55kmggs")))) (properties `((upstream-name . "climatol"))) (build-system r-build-system) (home-page "http://www.climatol.eu/") (synopsis "Climate tools") (description "This package provides functions for the quality control, homogenization and missing data infilling of climatological series, and to obtain climatological summaries and grids from the results. Also functions to draw wind-roses and Walter&Lieth climate diagrams are included.") (license license:gpl2+))) (define-public r-clipr (package (name "r-clipr") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") (description "This package provides simple utility functions to read from and write to the system clipboards.") (license license:gpl3))) (define-public r-clock (package (name "r-clock") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "clock" version)) (sha256 (base32 "0x58xhngpd2rj7da9gr1x1zwz4rliza7aakfadkqsc4c7wxpmral")))) (properties `((upstream-name . "clock"))) (build-system r-build-system) (propagated-inputs (list r-cli r-cpp11 r-lifecycle r-rlang r-tzdb r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://clock.r-lib.org") (synopsis "Date-Time types and tools") (description "This package provides a comprehensive library for date-time manipulations using a new family of orthogonal date-time classes (durations, time points, zoned-times, and calendars) that partition responsibilities so that the complexities of time zones are only considered when they are really needed. Capabilities include: date-time parsing, formatting, arithmetic, extraction and updating of components, and rounding.") (license license:expat))) (define-public r-clvalid (package (name "r-clvalid") (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "clValid" version)) (sha256 (base32 "18aiyjhnh5mfdxbzns4cy0r8bymfikhwkybpn4g04qhli5ls8z83")))) (properties `((upstream-name . "clValid"))) (build-system r-build-system) (propagated-inputs (list r-class r-cluster)) (home-page "https://cran.r-project.org/package=clValid") (synopsis "Validation of clustering results") (description "Statistical and biological validation of clustering results. This package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and BSI. Further information can be found in Brock, G et al. (2008) .") (license license:lgpl3))) (define-public r-dlm (package (name "r-dlm") (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "dlm" version)) (sha256 (base32 "0mxfakryagyg2idjhw1ydp4xqk57s3z17cv69hj16lisx8q43pc9")))) (properties `((upstream-name . "dlm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=dlm") (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models") (description "This package provides routines for Maximum likelihood, Kalman filtering and smoothing, and Bayesian analysis of Normal linear State Space models, also known as Dynamic Linear Models.") (license license:gpl2+))) (define-public r-zcompositions (package (name "r-zcompositions") (version "1.5.0-1") (source (origin (method url-fetch) (uri (cran-uri "zCompositions" version)) (sha256 (base32 "0sx6i03iyg4jxmjiyzkssz3i6c8nv29wwhbl7yd0wxapwpakmlj8")))) (properties `((upstream-name . "zCompositions"))) (build-system r-build-system) (propagated-inputs (list r-mass r-nada r-truncnorm)) (home-page "https://github.com/Japal/zCompositions") (synopsis "Treatment of zeros, left-censored and missing values in compositional data") (description "This is an R package for the imputation of left-censored data under a compositional approach. The implemented methods consider aspects of relevance for a compositional approach such as scale invariance, subcompositional coherence or preserving the multivariate relative structure of the data. Based on solid statistical frameworks, it comprises the ability to deal with single and varying censoring thresholds, consistent treatment of closed and non-closed data, exploratory tools, multiple imputation, @dfn{Markov Chain Monte Carlo} (MCMC), robust and non-parametric alternatives, and recent proposals for count data.") (license license:gpl2+))) (define-public r-zoo (package (name "r-zoo") (version "1.8-12") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 "1f1g7f362sidh99n2pcgnj8iwsn7hnjgpdnkrqml5qzrd0k8dhz6")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (home-page "https://zoo.R-Forge.R-project.org/") (synopsis "S3 infrastructure for regular and irregular time series") (description "This package contains an S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors.") (license license:gpl2+))) (define-public r-fontawesome (package (name "r-fontawesome") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "fontawesome" version)) (sha256 (base32 "1jaw3jz9jz8v7msqv76f234vhrkcy21xgva81m0d313hf6ly4gfs")))) (properties `((upstream-name . "fontawesome"))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-rlang)) (home-page "https://github.com/rstudio/fontawesome") (synopsis "Easily work with Font Awesome icons") (description "Easily and flexibly insert Font Awesome icons into R Markdown documents and Shiny apps. These icons can be inserted into HTML content through inline SVG tags or @code{i} tags. There is also a utility function for exporting Font Awesome icons as PNG images for those situations where raster graphics are needed.") (license license:expat))) (define-public r-fingerprint (package (name "r-fingerprint") (version "3.5.7") (source (origin (method url-fetch) (uri (cran-uri "fingerprint" version)) (sha256 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic")))) (properties `((upstream-name . "fingerprint"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fingerprint") (synopsis "Functions to Operate on Binary Fingerprint Data") (description "This package provides functions to manipulate binary fingerprints of arbitrary length. A fingerprint is represented by an object of S4 class @code{fingerprint}. The bitwise logical functions in R are overridden so that they can be used directly with @code{fingerprint} objects. A number of distance metrics are also available. Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded. Arbitrary fingerprint formats can be handled via line handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-fpeek (package (name "r-fpeek") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "fpeek" version)) (sha256 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii")))) (properties `((upstream-name . "fpeek"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/davidgohel/fpeek") (synopsis "Check text files content at a glance") (description "This package provides tools to help working with text files. It can return the number of lines; print the first and last lines; convert encoding. Operations are made without reading the entire file before starting, resulting in good performances with large files.") (license license:expat))) (define-public r-ggalluvial (package (name "r-ggalluvial") (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "ggalluvial" version)) (sha256 (base32 "0wax853pi3ghqv5alfkx9rgfb3sm3sqh3miklwvn22bh1s44q14h")))) (properties `((upstream-name . "ggalluvial"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-lazyeval r-rlang r-tidyr r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://corybrunson.github.io/ggalluvial/") (synopsis "Alluvial plots for ggplot2") (description "This package provides alluvial plots for @code{ggplot2}. Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables.") (license license:gpl3))) (define-public r-ggpp (package (name "r-ggpp") (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 "0xnjbxd1lkg85c2hsx7cgxqsqb3dc0pma8jwdlqfgg7d519d60xa")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-glue r-gridextra r-lubridate r-magrittr r-mass r-polynom r-rlang r-scales r-stringr r-tibble r-xts r-zoo)) (native-inputs (list r-knitr)) (home-page "https://docs.r4photobiology.info/ggpp/") (synopsis "Grammar extensions to ggplot2") (description "This package contains extensions to ggplot2. @enumerate @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add insets to plots using native data coordinates, while @code{geom_table_npc}, @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc} coordinates through new aesthetics @code{npcx} and @code{npcy}. @item Statistics: select observations based on 2D density. @item Positions: radial nudging away from a center point and nudging away from a line or curve. @end enumerate ") (license license:gpl2+))) (define-public r-ggprism (package (name "r-ggprism") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "ggprism" version)) (sha256 (base32 "0ycklp7764cw65hqh9r61im8vqfd7sjayyw1gvprxzg7k217gnl3")))) (properties `((upstream-name . "ggprism"))) (build-system r-build-system) (propagated-inputs (list r-digest r-ggplot2 r-glue r-gtable r-rlang r-scales r-tibble)) (native-inputs (list r-knitr)) (home-page "https://csdaw.github.io/ggprism/") (synopsis "ggplot2 extension inspired by GraphPad Prism") (description "This package provides various themes, palettes, and other functions that are used to customise ggplots to look like they were made in GraphPad Prism. The Prism-look is achieved with @code{theme_prism()} and @code{scale_fill|colour_prism()}, axes can be changed with custom guides like @code{guide_prism_minor()}, and significance indicators added with @code{add_pvalue()}.") (license license:gpl3+))) (define-public r-ggrastr (package (name "r-ggrastr") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "ggrastr" version)) (sha256 (base32 "1l90mlb6bqq98ifmlbs5481vch9inmzdnvnz192adklrr9nl09yb")))) (properties `((upstream-name . "ggrastr"))) (build-system r-build-system) (propagated-inputs (list r-cairo r-ggbeeswarm r-ggplot2 r-png r-ragg)) (native-inputs (list r-knitr)) (home-page "https://github.com/VPetukhov/ggrastr") (synopsis "Rasterize layers for ggplot2") (description "Rasterize only specific layers of a ggplot2 plot while simultaneously keeping all labels and text in vector format. This allows users to keep plots within the reasonable size limit without losing vector properties of the scale-sensitive information.") (license license:expat))) (define-public r-ggvenn (package (name "r-ggvenn") (version "0.1.10") (source (origin (method url-fetch) (uri (cran-uri "ggvenn" version)) (sha256 (base32 "0gl7z8hrn2wmmb59fvfv2hsw40p629aj086dv0kwlv162zqidqfd")))) (properties `((upstream-name . "ggvenn"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2)) (home-page "https://cran.r-project.org/package=ggvenn") (synopsis "Draw Venn diagram with ggplot2") (description "This package offers an easy to use way to draw a Venn diagram with @code{ggplot2}.") (license license:expat))) (define-public r-ggvenndiagram (package (name "r-ggvenndiagram") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggVennDiagram" version)) (sha256 (base32 "0ngvvmz2mxh4v98wg3xqpmz1p1cpk3qsdvszcjzb1yhhway211a5")))) (properties `((upstream-name . "ggVennDiagram"))) (build-system r-build-system) (propagated-inputs (list r-aplot r-dplyr r-forcats r-ggplot2 r-tibble r-venn r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/gaospecial/ggVennDiagram") (synopsis "Implementention of the Venn diagram using ggplot2") (description "This package implements easy-to-use functions to generate 2-7 sets Venn plot in publication quality. @code{ggVennDiagram} plot Venn using well-defined geometry dataset and @code{ggplot2}. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package @code{venn}. We provide internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in three components: set edges, set labels, and regions. From version 1.0, it is possible to customize these components as you demand in ordinary @code{ggplot2} grammar.") (license license:gpl3))) (define-public r-lmds (package (name "r-lmds") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "lmds" version)) (sha256 (base32 "130azb0nc2wwxv0qi8v5s4rd02p9lc92zwn634pv7b8awbw81i65")))) (properties `((upstream-name . "lmds"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-dynutils r-irlba r-matrix)) (home-page "https://github.com/dynverse/lmds") (synopsis "Landmark multi-dimensional scaling") (description "This package provides a fast dimensionality reduction method scalable to large numbers of samples. @dfn{Landmark Multi-Dimensional Scaling} (LMDS) is an extension of classical Torgerson MDS, but rather than calculating a complete distance matrix between all pairs of samples, only the distances between a set of landmarks and the samples are calculated.") (license license:gpl3))) (define-public r-lmodel2 (package (name "r-lmodel2") (version "1.7-3") (source (origin (method url-fetch) (uri (cran-uri "lmodel2" version)) (sha256 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb")))) (properties `((upstream-name . "lmodel2"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=lmodel2") (synopsis "Model II regression") (description "This package computes model II simple linear regression using @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major axis} (SMA), and @dfn{ranged major axis} (RMA).") (license license:gpl2))) (define-public r-ggpmisc (package (name "r-ggpmisc") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 "1j49q1fbihxir5q5llqwyga111j3lggifzjk3cvq8lphim4c3jia")))) (build-system r-build-system) (propagated-inputs (list r-confintr r-dplyr r-generics r-ggplot2 r-ggpp r-lmodel2 r-lubridate r-mass r-multcomp r-multcompview r-plyr r-polynom r-quantreg r-rlang r-scales r-splus2r r-tibble)) (native-inputs (list r-knitr)) (home-page "https://www.r4photobiology.info/") (synopsis "Miscellaneous Extensions to @code{ggplot2}") (description "This package provides extensions to @code{ggplot2}, respecting the grammar of its graphics paradigm.") (license license:gpl2+))) (define-public r-ggside (package (name "r-ggside") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "ggside" version)) (sha256 (base32 "0qj564rqxw8fn5h00wwmkvk6p3x60r64gpvxw9yrb5lvcykgsj8q")))) (properties `((upstream-name . "ggside"))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-glue r-gtable r-rlang r-scales r-tibble r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ggside") (synopsis "Side grammar graphics that extends @code{ggplot2}") (description "The grammar of graphics as shown in @code{ggplot2} has provided an expressive API for users to build plots. This package @{ggside} extends @code{ggplot2} by allowing users to add graphical information about one of the main panel's axis using a familiar @code{ggplot2} style API with tidy data. This package is particularly useful for visualizing metadata on a discrete axis, or summary graphics on a continuous axis such as a boxplot or a density distribution.") (license license:expat))) (define-public r-gprofiler (package (name "r-gprofiler") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs (list r-plyr r-rcurl)) (home-page "https://cran.r-project.org/web/packages/gProfileR/") (synopsis "Interface to the g:Profiler toolkit") (description "This package provides tools for functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the @code{g:Profiler} toolkit.") (license license:gpl2+))) (define-public r-gprofiler2 (package (name "r-gprofiler2") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "gprofiler2" version)) (sha256 (base32 "1zbfvpb4qqj6vipz0ps4pyy14h6rc4jaqfa8q4zrbhi5vvw9805r")))) (properties `((upstream-name . "gprofiler2"))) (build-system r-build-system) (propagated-inputs (list r-crosstalk r-dplyr r-ggplot2 r-gridextra r-jsonlite r-plotly r-rcurl r-tidyr r-viridislite)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/gprofiler2/") (synopsis "Interface to the g:Profiler toolset") (description "This package provides a toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}. The main tools are: @enumerate @item @code{g:GOSt}, functional enrichment analysis and visualization of gene lists; @item @code{g:Convert}, gene/protein/transcript identifier conversion across various namespaces; @item @code{g:Orth}, orthology search across species; @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions, genes and variant effects. @end enumerate This package is an R interface corresponding to the 2019 update of @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and higher.") (license license:gpl2+))) (define-public r-oenb (package (name "r-oenb") (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "oenb" version)) (sha256 (base32 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5")))) (properties `((upstream-name . "oenb"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-xml)) (native-inputs (list r-knitr)) (home-page "https://github.com/franzmohr/oenb") (synopsis "Tools for the OeNB Data Web Service") (description "Tools to access data from the data web service of the @acronym{OeNB, Oesterreichische Nationalbank}, @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.") (license license:gpl2+))) (define-public r-oompadata (package (name "r-oompadata") (version "3.1.3") (source (origin (method url-fetch) (uri (cran-uri "oompaData" version)) (sha256 (base32 "0gdp7bghgpz3q0h06w8r926x7wkpcvkpyf0v5qfi1qixbpvk5fdf")))) (properties `((upstream-name . "oompaData"))) (build-system r-build-system) (home-page "https://oompa.r-forge.r-project.org/") (synopsis "Data to illustrate OOMPA algorithms") (description "OOMPA offers R packages for gene expression and proteomics analysis. OOMPA uses S4 classes to construct object-oriented tools with a consistent user interface. All higher level analysis tools in OOMPA are compatible with the eSet classes defined in BioConductor. The lower level processing tools offer an alternative to parts of BioConductor, but can also be used to enhance existing BioConductor packages.") (license license:asl2.0))) (define-public r-oompabase (package (name "r-oompabase") (version "3.2.9") (source (origin (method url-fetch) (uri (cran-uri "oompaBase" version)) (sha256 (base32 "1cmw2s5dznmv675484jgvkzgvi6vhg0zbxsq6zhpqsisf672pjhl")))) (properties `((upstream-name . "oompaBase"))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://oompa.r-forge.r-project.org/") (synopsis "Class unions, matrix operations, and color schemes for OOMPA") (description "This package preloads class unions for defining/loading core OOMPA tools. It also includes vectorized operations for row-by-row means, variances, and t-tests. Finally, it provides new colorschemes.") (license license:asl2.0))) (define-public r-orgmassspecr (package (name "r-orgmassspecr") (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "OrgMassSpecR" version)) (sha256 (base32 "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8")))) (properties `((upstream-name . "OrgMassSpecR"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://OrgMassSpec.github.io/") (synopsis "Organic or biological mass spectrometry data analysis") (description "This package @code{OrgMassSpecR} is an extension of the @code{R} statistical computing language. It contains functions to assist with organic or biological mass spectrometry data analysis. Mass spectral libraries are available as companion packages.") (license license:bsd-2))) (define-public r-scales (package (name "r-scales") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 (base32 "122qyd88qr8cc8h3k46xpygm00inqpm55zdy0b7535958imhygmk")))) (build-system r-build-system) (propagated-inputs (list r-cli r-farver r-glue r-labeling r-lifecycle r-munsell r-r6 r-rcolorbrewer r-rlang r-viridislite)) (home-page "https://github.com/hadley/scales") (synopsis "Scale functions for visualization") (description "This package provides graphical scales that map data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends.") (license license:expat))) (define-public r-swagger (package (name "r-swagger") (version "3.33.1") (source (origin (method url-fetch) (uri (cran-uri "swagger" version)) (sha256 (base32 "1ldgmy5vjzd11z5yl5a518wkw6y0l469b2zf0lp12hk19jq6k0sj")))) (properties `((upstream-name . "swagger"))) (build-system r-build-system) (home-page "https://github.com/rstudio/swagger") (synopsis "Dynamically generate documentation from a Swagger-compliant API") (description "This package provides a collection of HTML, JavaScript, and CSS assets that dynamically generate beautiful documentation from a Swagger compliant API.") (license license:asl2.0))) (define-public r-pacman (package (name "r-pacman") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "pacman" version)) (sha256 (base32 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy")))) (build-system r-build-system) (propagated-inputs (list r-remotes)) (home-page "https://github.com/trinker/pacman") (synopsis "Package Management Tool") (description "This package provides tools to more conveniently perform tasks associated with add-on packages. @code{pacman} conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.") (license license:gpl2))) (define-public r-pagoda2 (package (name "r-pagoda2") (version "1.0.11") (source (origin (method url-fetch) (uri (cran-uri "pagoda2" version)) (sha256 (base32 "13x2l7hcvd6975921c5hba8hm2qijkslviszfizah8wxynhbayy1")))) (properties `((upstream-name . "pagoda2"))) (build-system r-build-system) (propagated-inputs (list r-dendsort r-drat r-fastcluster r-igraph r-irlba r-magrittr r-mass r-matrix r-mgcv r-n2r r-plyr r-r-utils r-r6 r-rcpp r-rcpparmadillo r-rcppeigen r-rcppprogress r-rjson r-rlang r-rmtstat r-rook r-rtsne r-sccore r-urltools)) (home-page "https://github.com/kharchenkolab/pagoda2") (synopsis "Single cell analysis and differential expression") (description "The package offers functions for analyzing and interactively exploring large-scale single-cell RNA-seq datasets. Pagoda2 primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. pagoda2 was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos.") (license license:gpl3))) (define-public r-pals (package (name "r-pals") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "pals" version)) (sha256 (base32 "0z6lkvkq7b3wsxvizljf08sjqrdcj33p5kdx6074pc5jv36dylhb")))) (properties `((upstream-name . "pals"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-dichromat r-mapproj r-maps)) (native-inputs (list r-knitr)) (home-page "https://kwstat.github.io/pals/") (synopsis "Color palettes, color maps, and tools to evaluate them") (description "This package provides a comprehensive collection of color palettes, color maps, and tools to evaluate them.") (license license:gpl3))) (define-public r-paralleldist (package (name "r-paralleldist") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "parallelDist" version)) (sha256 (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih")))) (properties `((upstream-name . "parallelDist"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel)) (home-page "https://github.com/alexeckert/parallelDist") (synopsis "Parallel Distance Matrix Computation using multiple threads") (description "This package provides a fast parallelized alternative to R's native @code{dist} function to calculate distance matrices for continuous, binary, and multi-dimensional input matrices, which supports a broad variety of predefined distance functions from other R packages, as well as user- defined functions written in C++. For ease of use, the @code{parDist} function extends the signature of the @code{dist} function and uses the same parameter naming conventions as distance methods of existing R packages.") (license license:gpl2+))) (define-public r-paramhelpers (package (name "r-paramhelpers") (version "1.14.1") (source (origin (method url-fetch) (uri (cran-uri "ParamHelpers" version)) (sha256 (base32 "088sl3az4ysq8cyw82brdn9xm5yy7rqskxih462d1m5hi62gyl04")))) (properties `((upstream-name . "ParamHelpers"))) (build-system r-build-system) (propagated-inputs (list r-backports r-bbmisc r-checkmate r-fastmatch)) (home-page "https://paramhelpers.mlr-org.com") (synopsis "Helpers for parameters in black-box optimization, tuning, and machine learning") (description "This is a package for parameter description and operations in optimization, tuning and machine learning. Parameters can be described (type, constraints, defaults, etc.), combined to parameter sets and can in general be programmed on. A useful @code{OptPath} object (archive) to log function evaluations is also provided.") (license license:bsd-2))) (define-public r-parallelmap (package (name "r-parallelmap") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "parallelMap" version)) (sha256 (base32 "1qg7zpz5sd9jp8wzjqahkhipwj1jn192llwg06q4gv9mlcsac261")))) (properties `((upstream-name . "parallelMap"))) (build-system r-build-system) (propagated-inputs (list r-bbmisc r-checkmate)) (home-page "https://parallelmap.mlr-org.com") (synopsis "Unified interface to parallelization backends") (description "This package provides a unified parallelization framework for multiple backends. This package is designed for internal package and interactive usage. The main operation is parallel mapping over lists. It supports local, multicore, mpi and BatchJobs mode. It allows tagging of the parallel operation with a level name that can be later selected by the user to switch on parallel execution for exactly this operation.") (license license:bsd-2))) (define-public r-pheatmap (package (name "r-pheatmap") (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "pheatmap" version)) (sha256 (base32 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) (build-system r-build-system) (propagated-inputs (list r-gtable r-rcolorbrewer r-scales)) (home-page "https://cran.r-project.org/web/packages/pheatmap") (synopsis "Pretty heatmaps") (description "This package provides an implementation of heatmaps that offers more control over dimensions and appearance.") (license license:gpl2+))) (define-public r-philentropy (package (name "r-philentropy") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "philentropy" version)) (sha256 (base32 "0gmycszk86mc9clmxfdrspqh5z0g3cw2cgzaaqngxx38h68x99is")))) (properties `((upstream-name . "philentropy"))) (build-system r-build-system) (propagated-inputs (list r-kernsmooth r-poorman r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/drostlab/philentropy") (synopsis "Similarity and distance quantification between probability functions") (description "This package computes optimized distance and similarity measures for comparing probability functions (Drost (2018) ). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.") (license license:gpl2))) (define-public r-pnwcolors (package (name "r-pnwcolors") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "PNWColors" version)) (sha256 (base32 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj")))) (properties `((upstream-name . "PNWColors"))) (build-system r-build-system) (home-page "https://github.com/jakelawlor/PNWColors") (synopsis "Color palettes for data visualizations") (description "This package provides color palettes. They are checked for colorblind accessibility from hue, saturation, and lightness value scaling using the Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.") (license license:cc0))) (define-public r-plotfunctions (package (name "r-plotfunctions") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "plotfunctions" version)) (sha256 (base32 "0asmxw8283fpvl83h478j5nyg59xqifqaa8f2f6l199gvvswhhg2")))) (properties `((upstream-name . "plotfunctions"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://jacolienvanrij.com/tutorials.html") (synopsis "Various functions to facilitate visualization of data and analysis") (description "When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions.") (license license:gpl2+))) (define-public r-plumber (package (name "r-plumber") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "plumber" version)) (sha256 (base32 "1k0y7ylc8bld16imn86g0i0dmxmr3kmh9ax4ys0yrxqzrvji7z3g")))) (properties `((upstream-name . "plumber"))) (build-system r-build-system) (propagated-inputs (list r-crayon r-ellipsis r-httpuv r-jsonlite r-lifecycle r-magrittr r-mime r-promises r-r6 r-rlang r-sodium r-stringi r-swagger r-webutils)) (home-page "https://www.rplumber.io") (synopsis "API generator for R") (description "This package gives you the ability to automatically generate and serve an HTTP API from R functions using the annotations in the R documentation around your functions.") (license license:expat))) (define-public r-polychrome (package (name "r-polychrome") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "Polychrome" version)) (sha256 (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg")))) (properties `((upstream-name . "Polychrome"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-scatterplot3d)) (native-inputs (list r-knitr)) (home-page "https://oompa.r-forge.r-project.org/") (synopsis "Qualitative palettes with many colors") (description "This package provides tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors. See Coombes and colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.") (license license:asl2.0))) (define-public r-polylabelr (package (name "r-polylabelr") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "polylabelr" version)) (sha256 (base32 "01b2v0l5g8nxwbd6nwqv8ahypgh6gfhd4qabg75brlj7z1iyfzf2")))) (properties `((upstream-name . "polylabelr"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/jolars/polylabelr") (synopsis "Finding pole of inaccessibility (visual center) of a polygon") (description "This package provides a wrapper around the @code{C++} library @code{ polylabel} from @code{Mapbox}, providing an efficient routine for finding the approximate pole of inaccessibility of a polygon, which usually serves as an excellent candidate for labeling of a polygon.") (license license:expat))) (define-public r-poorman (package (name "r-poorman") (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "poorman" version)) (sha256 (base32 "1amlcbgfnm6yh7lmlzhs7aalv4mdm2ir3s2kpx33ppnz7hlii508")))) (properties `((upstream-name . "poorman"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://nathaneastwood.github.io/poorman/") (synopsis "Dependency-free recreation of dplyr") (description "This package provides a replication of key functionality from @code{dplyr} and the wider @code{tidyverse} using only @code{base}.") (license license:expat))) (define-public r-ecosolver (package (name "r-ecosolver") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "ECOSolveR" version)) (sha256 (base32 "1izc8dwj438wpkmdmhwnnhkijz5skig4gwxgr6f1bzmj08bfv515")))) (properties `((upstream-name . "ECOSolveR"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://bnaras.github.io/ECOSolveR/") (synopsis "Embedded conic solver in R") (description "This package provides an R interface to the @dfn{Embedded COnic Solver} (ECOS), an efficient and robust C library for convex problems. Conic and equality constraints can be specified in addition to integer and boolean variable constraints for mixed-integer problems. This R interface is inspired by the Python interface and has similar calling conventions.") (license license:gpl3+))) (define-public r-ecp (package (name "r-ecp") (version "3.1.5") (source (origin (method url-fetch) (uri (cran-uri "ecp" version)) (sha256 (base32 "17m2m3nz7kqzjw2bkkp6c1a3zhwjq2c5mw9pk5g0ma274iiqj8wy")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/web/packages/ecp/") (synopsis "Multiple change-point analysis of multivariate data") (description "This package implements various procedures for finding multiple change-points. Two methods make use of dynamic programming and pruning, with no distributional assumptions other than the existence of certain absolute moments in one method. Hierarchical and exact search methods are included. All methods return the set of estimated change-points as well as other summary information.") (license license:gpl2+))) (define-public r-ellipsis (package (name "r-ellipsis") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "ellipsis" version)) (sha256 (base32 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9")))) (build-system r-build-system) (propagated-inputs (list r-rlang)) (home-page "https://github.com/hadley/ellipsis") (synopsis "Tools for working with additional arguments") (description "In S3 generics, it's useful to take @code{...} so that methods can have additional arguments. But this flexibility comes at a cost: misspelled arguments will be silently ignored. The @code{ellipsis} package is an experiment that allows a generic to warn if any arguments passed in @code{...} are not used.") (license license:gpl3))) (define-public r-ga (package (name "r-ga") (version "3.2.3") (source (origin (method url-fetch) (uri (cran-uri "GA" version)) (sha256 (base32 "0q0br75zklnp0g3j98x6lll5fhyayxqzaqs3hc2z39s2imwi2fpb")))) (properties `((upstream-name . "GA"))) (build-system r-build-system) (propagated-inputs (list r-cli r-crayon r-foreach r-iterators r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://luca-scr.github.io/GA/") (synopsis "Genetic algorithms for stochastic optimisation") (description "Flexible general-purpose toolbox implementing genetic algorithms (GAs) for stochastic optimisation. Binary, real-valued, and permutation representations are available to optimize a fitness function, i.e., a function provided by users depending on their objective function. Several genetic operators are available and can be combined to explore the best settings for the current task. Furthermore, users can define new genetic operators and easily evaluate their performances. Local search using general-purpose optimisation algorithms can be applied stochastically to exploit interesting regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.") (license license:gpl2+))) (define-public r-grr (package (name "r-grr") (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "grr" version)) (sha256 (base32 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/grr") (synopsis "Alternative implementations of base R functions") (description "This package provides alternative implementations of some base R functions, including @code{sort}, @code{order}, and @code{match}. The functions are simplified but can be faster or have other advantages.") (license license:gpl3))) (define-public r-matrixtests (package (name "r-matrixtests") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "matrixTests" version)) (sha256 (base32 "0d7i00cxzszfdnjm8q5b72ildic8nig6fbw7rba6acdnllpp7sza")))) (properties `((upstream-name . "matrixTests"))) (build-system r-build-system) (propagated-inputs (list r-matrixstats)) (home-page "https://github.com/karoliskoncevicius/matrixTests") (synopsis "Statistical hypothesis tests on rows and columns of matrices") (description "This package offers quick statistical hypothesis testing for matrix rows/columns. The main goals are speed through vectorization, detailed and user-friendly output, and compatibility with tests implemented in R.") (license license:gpl2))) (define-public r-matrix-utils (package (name "r-matrix-utils") (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "Matrix.utils" version)) (sha256 (base32 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb")))) (properties `((upstream-name . "Matrix.utils"))) (build-system r-build-system) (propagated-inputs (list r-grr r-matrix)) (home-page "https://github.com/cvarrichio/Matrix.utils") (synopsis "Data.frame-Like Operations on Sparse and Dense Matrix Objects") (description "This package implements data manipulation methods such as @code{cast}, @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like objects.") (license license:gpl3))) (define-public r-mblm (package (name "r-mblm") (version "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "mblm" version)) (sha256 (base32 "1fipb3bryaimr30lcxsxrn0ymv24z39swca7s4z7p9xcfg3ban1b")))) (properties `((upstream-name . "mblm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mblm/index.html") (synopsis "Median-based linear models") (description "This package provides linear models based on Theil-Sen single median and Siegel repeated medians. They are very robust (29 or 50 percent breakdown point, respectively), and if no outliers are present, the estimators are very similar to OLS.") (license license:gpl2+))) (define-public r-mboost (package (name "r-mboost") (version "2.9-9") (source (origin (method url-fetch) (uri (cran-uri "mboost" version)) (sha256 (base32 "1apcd90xsr9hl5f1szhyibdx61zi4p6s9bvag8bdk2yj4kqq6fmz")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-matrix r-nnls r-partykit r-quadprog r-stabs r-survival)) (home-page "https://github.com/boost-R/mboost") (synopsis "Model-based boosting") (description "This package provides a functional gradient descent algorithm (boosting) for optimizing general risk functions utilizing component-wise (penalised) least squares estimates or regression trees as base-learners for fitting generalized linear, additive and interaction models to potentially high-dimensional data.") (license license:gpl2))) (define-public r-mc2d (package (name "r-mc2d") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "mc2d" version)) (sha256 (base32 "07h2gvmdfqjydikxksbqhikihg46fv6xyn8vk5kyni6x75gp9abk")))) (properties `((upstream-name . "mc2d"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggpubr r-mvtnorm)) (home-page "https://cran.r-project.org/package=mc2d") (synopsis "Tools for two-dimensional monte-carlo simulations") (description "This is a framework for construction and analysis of 2D Monte-Carlo simulations. In addition, this package includes various distributions.") (license license:gpl2+))) (define-public r-mclogit (package (name "r-mclogit") (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "mclogit" version)) (sha256 (base32 "0sbglgak6jhhpx65jnj59hbpvzs8qjsdjc4w02z0m5j9hrnmzp4s")))) (properties `((upstream-name . "mclogit"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-memisc)) (home-page "https://www.elff.eu/software/mclogit/") (synopsis "Multinomial logit models, with or without random effects or overdispersion") (description "This package provides estimators for multinomial logit models in their conditional logit and baseline logit variants, with or without random effects, with or without overdispersion. Random effects models are estimated using the PQL technique (based on a Laplace approximation) or the MQL technique (based on a Solomon-Cox approximation). Estimates should be treated with caution if the group sizes are small.") (license license:gpl2))) (define-public r-shadowtext (package (name "r-shadowtext") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "shadowtext" version)) (sha256 (base32 "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15")))) (properties `((upstream-name . "shadowtext"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/GuangchuangYu/shadowtext/") (synopsis "Shadow text grob and layer") (description "This package implements @code{shadowtextGrob()} for @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}. These functions draw text grob with background shadow.") (license license:artistic2.0))) (define-public r-sys (package (name "r-sys") (version "3.4.2") (source (origin (method url-fetch) (uri (cran-uri "sys" version)) (sha256 (base32 "1cz57jkc159zfgffvcdb40wv9avb5id7pdvgx8q1hs7vy1kcxgdp")))) (build-system r-build-system) (home-page "https://github.com/jeroen/sys") (synopsis "Powerful and reliable tools for running system commands in R") (description "This package provides drop-in replacements for the base @code{system2()} function with fine control and consistent behavior across platforms. It supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. The package also provides functions for evaluating expressions inside a temporary fork. Such evaluations have no side effects on the main R process, and support reliable interrupts and timeouts. This provides the basis for a sandboxing mechanism.") (license license:expat))) (define-public r-ashr (package (name "r-ashr") (version "2.2-63") (source (origin (method url-fetch) (uri (cran-uri "ashr" version)) (sha256 (base32 "1japskxfdsg91jwgf5knlwy9iaq4ziqvyvlvjch1y3ygsdz9b8bz")))) (properties `((upstream-name . "ashr"))) (build-system r-build-system) (propagated-inputs (list r-etrunct r-invgamma r-matrix r-mixsqp r-rcpp r-squarem r-truncnorm)) (native-inputs (list r-knitr)) (home-page "https://github.com/stephens999/ashr") (synopsis "Methods for adaptive shrinkage, using empirical bayes") (description "This package implements an empirical Bayes approach for large-scale hypothesis testing and false discovery rate estimation.") (license license:gpl3+))) (define-public r-askpass (package (name "r-askpass") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "askpass" version)) (sha256 (base32 "1vrcb69gf5hc8rggc9m7wv19crz5mkl7f08cipy0ykckh6bkc8mr")))) (build-system r-build-system) (propagated-inputs (list r-sys)) (home-page "https://github.com/jeroen/askpass") (synopsis "Safe password entry for R") (description "This package provides cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key.") (license license:expat))) (define-public r-astsa (package (name "r-astsa") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "astsa" version)) (sha256 (base32 "0rnbacq5vbnlzfssj13ixgkg0d1wixh2m3dcsi66c63wx65rm3d3")))) (properties `((upstream-name . "astsa"))) (build-system r-build-system) (home-page "https://github.com/nickpoison/astsa/") (synopsis "Applied statistical time series analysis") (description "This package provides data sets and scripts to accompany Time Series Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2017, @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data Analysis Approach Using R. Chapman-Hall, 2019, @url{https://doi.org/10.1201/9780429273285}.") (license license:gpl3))) (define-public r-vegan (package (name "r-vegan") (version "2.6-4") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 "01hxlb5sy0d28ajq993fqs4z0qjcyl610d0ahjyjpbkrpszd92jx")))) (build-system r-build-system) (native-inputs (list r-knitr ; needed for vignettes gfortran)) (propagated-inputs (list r-cluster r-lattice r-mass r-mgcv r-permute)) (home-page "https://cran.r-project.org/web/packages/vegan") (synopsis "Functions for community ecology") (description "The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.") (license license:gpl2+))) (define-public r-tgp (package (name "r-tgp") (version "2.4-22") (source (origin (method url-fetch) (uri (cran-uri "tgp" version)) (sha256 (base32 "0gpndjq2xiic6fb5187f4hgrqj3477pd83caajnw3yy9wan4vly6")))) (properties `((upstream-name . "tgp"))) (build-system r-build-system) (propagated-inputs (list r-maptree)) (home-page "https://bobby.gramacy.com/r_packages/tgp/") (synopsis "Bayesian treed Gaussian process models") (description "R-tgb provides Bayesian nonstationary regression and treed Gaussian processes. In addition, it provides visualization functions, tree drawing, sensitivity analysis, multi-resolution models, and sequential experimental design tools, including ALM, ALC, and expected improvement for optimizing noisy black-box functions.") (license license:lgpl2.0+))) (define-public r-tgstat (package (name "r-tgstat") (version "2.3.25") (source (origin (method url-fetch) (uri (cran-uri "tgstat" version)) (sha256 (base32 "07hdw3n4l88nr0x2a2qnjich4cfihgd0fk65ar3crgdahjcv9vn4")))) (properties `((upstream-name . "tgstat"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=tgstat") (synopsis "Amos Tanay's Group High Performance Statistical Utilities") (description "This package provides a collection of high-performance utilities. It can be used to compute distances, correlations, autocorrelations, clustering, and other tasks. It also contains a graph clustering algorithm described in MetaCell analysis of single-cell RNA-seq data using K-nn graph partitions.") (license license:gpl2))) (define-public r-tidyft (package (name "r-tidyft") (version "0.5.7") (source (origin (method url-fetch) (uri (cran-uri "tidyft" version)) (sha256 (base32 "00qcsr2sx8fwyil384vgppx0q72qjrkj7h5nv4mdxdi8f9h6ph2r")))) (properties `((upstream-name . "tidyft"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-fst r-stringr)) (native-inputs (list r-knitr)) (home-page "https://github.com/hope-data-science/tidyft") (synopsis "Fast and memory efficient data operations in tidy syntax") (description "Tidyft is an extension of @code{data.table}. It uses modifification by reference whenever possible. This toolkit is designed for big data analysis in high-performance desktop or laptop computers. The syntax of the package is similar or identical to tidyverse.") (license license:expat))) (define-public r-tidyverse (package (name "r-tidyverse") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "tidyverse" version)) (sha256 (base32 "1r980y6d4a5brvxwdx41qzi8f3fck36c5l89sd3k4csna09jsg1x")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cli r-conflicted r-dbplyr r-dplyr r-dtplyr r-forcats r-ggplot2 r-googledrive r-googlesheets4 r-haven r-hms r-httr r-jsonlite r-lubridate r-magrittr r-modelr r-pillar r-purrr r-ragg r-readr r-readxl r-reprex r-rlang r-rstudioapi r-rvest r-stringr r-tibble r-tidyr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://tidyverse.tidyverse.org") (synopsis "Install and load packages from the \"Tidyverse\"") (description "The @code{tidyverse} is a set of packages that work in harmony because they share common data representations and API design. This package is designed to make it easy to install and load multiple tidyverse packages in a single step.") (license license:gpl3))) (define-public r-tkrplot (package (name "r-tkrplot") (version "0.0-27") (source (origin (method url-fetch) (uri (cran-uri "tkrplot" version)) (sha256 (base32 "19bj4wn1fs4wrx5k4gakhpz4q59fgx0584wyaw7hnh0ljj8i34n9")))) (properties `((upstream-name . "tkrplot"))) (build-system r-build-system) (inputs (list libx11)) (home-page "https://cran.r-project.org/package=tkrplot") (synopsis "Place R graphics in a Tk widget") (description "The tkrplot package lets you place R graphics in a @dfn{Tk, cross-platform graphical user interface toolkit} widget.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-rvest (package (name "r-rvest") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 (base32 "07hws9infwchy19smrcd9m6c0jii0bdn335yxqk3ramgj5ryyrd4")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-httr r-lifecycle r-magrittr r-rlang r-selectr r-tibble r-withr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/rvest") (synopsis "Simple web scraping for R") (description "@code{r-rvest} helps you scrape information from web pages. It is designed to work with @code{magrittr} to make it easy to express common web scraping tasks, inspired by libraries like @code{BeautifulSoup}.") (license license:gpl3))) (define-public r-selectr (package (name "r-selectr") (version "0.4-2") (source (origin (method url-fetch) (uri (cran-uri "selectr" version)) (sha256 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m")))) (build-system r-build-system) (propagated-inputs (list r-stringr r-r6)) (home-page "https://sjp.co.nz/projects/selectr/") (synopsis "Translate CSS selectors to XPath expressions") (description "@code{r-selectr} translates a CSS3 selector into an equivalent XPath expression. This allows you to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package @code{cssselect}.") (license license:bsd-3))) (define-public r-relations (package (name "r-relations") (version "0.6-13") (source (origin (method url-fetch) (uri (cran-uri "relations" version)) (sha256 (base32 "1nnr0kcr3whbwzi36sg7wn46jp7r0hfkvcwlybvjsjhczcvc6ngq")))) (properties `((upstream-name . "relations"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-sets r-slam)) (home-page "https://cran.r-project.org/package=relations") (synopsis "Data structures and algorithms for relations") (description "This package provides data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.") (license license:gpl2))) (define-public r-repmis (package (name "r-repmis") (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "repmis" version)) (sha256 (base32 "0z5mjbsl24yjbl0aawr35grcal44rf2xbwv1hy7bdkms94ix79b5")))) (properties `((upstream-name . "repmis"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-before 'install 'change-home-dir (lambda _ ;; Change from /homeless-shelter to /tmp for write permission. (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-data-table r-digest r-httr r-plyr r-r-cache)) (home-page "https://cran.r-project.org/package=repmis") (synopsis "Miscellaneous tools for reproducible research") (description "This package is a colletion of tools to load R packages and automatically generate BibTeX files citing them as well as load and cache plain-text and Excel formatted data stored on GitHub, and from other sources.") (license license:gpl3+))) (define-public r-reprex (package (name "r-reprex") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 "0ld90pkw2r7z115xdnyqk4p39vnxrc8jnn57sl4bkpg5frczw38a")))) (build-system r-build-system) (propagated-inputs (list r-callr r-cli r-clipr r-fs r-glue r-knitr r-lifecycle r-rlang r-rmarkdown r-rstudioapi r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidyverse/reprex") (synopsis "Prepare reproducible R code examples for sharing") (description "This package provides a convenience wrapper that uses the @code{rmarkdown} package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites or email. @code{reprex} also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.") (license license:expat))) (define-public r-reordercluster (package (name "r-reordercluster") (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "ReorderCluster" version)) (sha256 (base32 "0zq143xvv2br7016f9b1501ymcpkjqm3al1dn5qfm21axyi2p1iq")))) (build-system r-build-system) (propagated-inputs (list r-gplots r-gtools r-rcpp)) (home-page "https://cran.r-project.org/web/packages/ReorderCluster") (synopsis "Reordering the dendrogram according to the class labels") (description "This package provides tools for performing the leaf reordering for the dendrogram that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together.") (license license:gpl3+))) (define-public r-callr (package (name "r-callr") (version "3.7.3") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 "0knh5yxhxwjz96kbjrq524w4j8cac10k6mghhmblq79s0zgzwysn")))) (build-system r-build-system) (propagated-inputs (list r-r6 r-processx)) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") (description "It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This package does exactly that.") (license license:expat))) (define-public r-deming (package (name "r-deming") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "deming" version)) (sha256 (base32 "1yx3qrbik6jpqgsi0gqgc7y2cra13qlisg2gq8rvnv57nvcvb421")))) (properties `((upstream-name . "deming"))) (build-system r-build-system) (propagated-inputs (list r-boot)) (home-page "https://cran.r-project.org/package=deming") (synopsis "Deming, Theil-Sen, Passing-Bablock and Total Least Squares regression") (description "This package implements generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.") (license license:lgpl2.0+))) (define-public r-depmixs4 (package (name "r-depmixs4") (version "1.5-0") (source (origin (method url-fetch) (uri (cran-uri "depmixS4" version)) (sha256 (base32 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8")))) (propagated-inputs (list r-nnet r-nlme r-mass r-rsolnp)) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/depmixS4/") (synopsis "Dependent Mixture Models") (description "This package fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models.") (license license:gpl2+))) (define-public r-readxl (package (name "r-readxl") (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 "0j2rkb012h0kvcm8n3817lgfir52dvmkwaxn7mij71gbxz6vpzky")))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-cpp11 r-progress r-tibble)) (native-inputs (list r-knitr)) (home-page "https://readxl.tidyverse.org") (synopsis "Read Excel files") (description "This package lets you import Excel files into R. It supports @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via the embedded @code{RapidXML} C++ library.") ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and ;; 'rapidxml' which is Boost. (license (list license:gpl3 license:bsd-2 license:boost1.0)))) (define-public r-model4you (package (name "r-model4you") (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "model4you" version)) (sha256 (base32 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8")))) (build-system r-build-system) (propagated-inputs (list r-formula r-ggplot2 r-gridextra r-partykit r-sandwich r-survival)) (home-page "https://cran.r-project.org/web/packages/model4you/") (synopsis "Stratified and personalised models based on trees and forests") (description "This package provides procedures for model-based trees for subgroup analyses in clinical trials and model-based forests for the estimation and prediction of personalised treatment effects. Currently partitioning of linear models, @code{lm()}, generalised linear models, @code{glm()}, and Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is supported for the trees and a test for parameter heterogeneity is provided for the personalised models.") (license license:gpl2+))) (define-public r-modelenv (package (name "r-modelenv") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "modelenv" version)) (sha256 (base32 "1pnc3bs2fzanqzjv2y8a7yy6s8hmwwsccjc8pvifff5kp557a6di")))) (properties `((upstream-name . "modelenv"))) (build-system r-build-system) (propagated-inputs (list r-glue r-rlang r-tibble r-vctrs)) (home-page "https://github.com/tidymodels/modelenv") (synopsis "Tools for registering models for use in tidymodels") (description "This is a developer-focused, low dependency package in @code{tidymodels} that provides functions to register how models are to be used. Functions to register models are complimented with accessor functions to retrieve registered model information to aid in model fitting and error handling.") (license license:expat))) (define-public r-modelr (package (name "r-modelr") (version "0.1.11") (source (origin (method url-fetch) (uri (cran-uri "modelr" version)) (sha256 (base32 "1lvv6gac3g4x1d58chbvlxlkd77qz21a3rlb64jvzwycx43dbswl")))) (build-system r-build-system) (propagated-inputs (list r-broom r-magrittr r-purrr r-rlang r-tibble r-tidyr r-tidyselect r-vctrs)) (home-page "https://github.com/tidyverse/modelr") (synopsis "Helper functions for modelling in pipelines") (description "Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.") (license license:gpl3))) (define-public r-morpho (package (name "r-morpho") (version "2.12") (source (origin (method url-fetch) (uri (cran-uri "Morpho" version)) (sha256 (base32 "1hg1jr0y11v93mqg2kn8n841nbsiffhyyr2kswj7kk664vlpril0")))) (properties `((upstream-name . "Morpho"))) (build-system r-build-system) (propagated-inputs (list r-bezier r-colorramps r-doparallel r-foreach r-jsonlite r-mass r-matrix r-rcpp r-rcpparmadillo r-rgl r-rvcg r-sf)) (home-page "https://github.com/zarquon42b/Morpho") (synopsis "Calculations and visualizations related to geometric morphometrics") (description "This package provides a toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.") (license license:gpl2))) (define-public r-hgnchelper (package (name "r-hgnchelper") (version "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "HGNChelper" version)) (sha256 (base32 "0qwkk5658j4j6w2wgvxkp38cyvscjp93d3zc7gb97vcihqx0ngxa")))) (properties `((upstream-name . "HGNChelper"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/waldronlab/HGNChelper") (synopsis "Identification and correction of invalid gene symbols for human and mouse") (description "This package provides a set of R functions for identifying and correcting HGNC human gene symbols. In addition, you can identify MGI mouse gene symbols, which have been converted to date format by Excel, withdrawn, or aliased. It also contains functions for reversibly converting between HGNC symbols and valid R names.") (license license:gpl2+))) (define-public r-hmm (package (name "r-hmm") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "HMM" version)) (sha256 (base32 "03b548bnwqpnd7zypb4gvy9chyi5li2hp99a9vrh4qszxg2ihas7")))) (properties `((upstream-name . "HMM"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/HMM/") (synopsis "Hidden Markov Models") (description "This package provides an easy to use library to setup, apply and make inference with discrete time and discrete space hidden Markov models.") (license license:gpl2+))) (define-public r-hiddenmarkov (package (name "r-hiddenmarkov") (version "1.8-13") (source (origin (method url-fetch) (uri (cran-uri "HiddenMarkov" version)) (sha256 (base32 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/") (synopsis "Hidden markov models for R") (description "This package contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. The algorithms are based of those of Walter Zucchini.") (license license:gpl2+))) (define-public r-httpuv (package (name "r-httpuv") (version "1.6.13") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 "0prvd2mv4rliqm0ldaldd6yjxy04qvxnqyhfxlk2c1lanmxzjvnb")) (modules '((guix build utils))) ;; Cannot unbundle http-parser, because it contains local ;; modifications. (snippet '(delete-file-recursively "src/libuv")))) (build-system r-build-system) (inputs (list libuv-for-r-httpuv zlib)) (propagated-inputs (list r-later r-promises r-r6 r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://github.com/rstudio/httpuv") (synopsis "HTTP and WebSocket server library for R") (description "The httpuv package provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone.") ;; This package includes third-party code that was originally released ;; under various non-copyleft licenses. Full licensing information can be ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE (license license:gpl3+))) (define-public r-httr2 (package (name "r-httr2") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "httr2" version)) (sha256 (base32 "0jaajfr1hr6bzb1vz2nw2csl2l09kbq619vsq5yrlchcarpjv1fb")))) (properties `((upstream-name . "httr2"))) (build-system r-build-system) (propagated-inputs (list r-cli r-curl r-glue r-lifecycle r-magrittr r-openssl r-r6 r-rappdirs r-rlang r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://httr2.r-lib.org") (synopsis "Perform HTTP requests and process the responses") (description "This package provides tools for creating and modifying HTTP requests, then performing them and processing the results. @code{httr2} is a re-imagining of @code{httr} that uses a pipe-based interface and solves more of the problems that API wrapping packages face.") (license license:expat))) (define-public r-jade (package (name "r-jade") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "JADE" version)) (sha256 (base32 "0m90rnhr5vkdv1xswr5c0j06ngzvmg73nd0kmg9m9r6a6ddddcyl")))) (properties `((upstream-name . "JADE"))) (build-system r-build-system) (propagated-inputs (list r-clue)) (home-page "https://cran.r-project.org/package=JADE") (synopsis "Blind source separation methods") (description "In this package Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other @dfn{blind source separation} (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given. The package is described in Miettinen, Nordhausen and Taskinen (2017) .") (license license:gpl2+))) (define-public r-job (package (name "r-job") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "job" version)) (sha256 (base32 "0d7pw3q5lqlgmav1vx63y8l6gdav96656bg378wj001rx5gx052h")))) (properties `((upstream-name . "job"))) (build-system r-build-system) (propagated-inputs (list r-digest r-rstudioapi)) (home-page "https://cran.r-project.org/package=job") (synopsis "Run code as an RStudio job") (description "Call @code{job::job({})} to run R code as an RStudio job and keep your console free in the meantime. This allows for a productive workflow while testing (multiple) long-running chunks of code. It can also be used to organize results using the RStudio Jobs GUI or to test code in a clean environment. Two RStudio Addins can be used to run selected code as a job.") (license license:expat))) (define-public r-jsonify (package (name "r-jsonify") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "jsonify" version)) (sha256 (base32 "0bxgyj5b1hnijq5315g050giixy4k5mjz2zdx8yil0igb5ifji9p")))) (properties `((upstream-name . "jsonify"))) (build-system r-build-system) (propagated-inputs (list r-rapidjsonr r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=jsonify") (synopsis "Convert between R objects and JavaScript Object Notation (JSON)") (description "This package enables conversions between R objects and JavaScript Object Notation (JSON) using the rapidjsonr library.") (license license:expat))) (define-public r-jsonlite (package (name "r-jsonlite") (version "1.8.8") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 "196an37f118qw43vyfaygh01dirh3hyz84ix8bbs6fsck0b17qkx")))) (build-system r-build-system) (native-inputs (list r-knitr r-r-rsp)) (home-page "https://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") (description "The jsonlite package provides a fast JSON parser and generator optimized for statistical data and the web. It offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. In addition to converting JSON data from/to R objects, jsonlite contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.") (license license:expat))) (define-public r-servr (package (name "r-servr") (version "0.28") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 "10nl6aal2kr0k1j7yfpggcxpjxby6z5hhc6wb4nkqhy2w5qi6g26")))) (build-system r-build-system) (propagated-inputs (list r-httpuv r-jsonlite r-mime r-xfun)) (home-page "https://github.com/yihui/servr") (synopsis "Simple HTTP server to serve static files or dynamic documents") (description "Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.") (license license:expat))) (define-public r-howmany (package (name "r-howmany") (version "0.3-1") (source (origin (method url-fetch) (uri (cran-uri "howmany" version)) (sha256 (base32 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/howmany/") (synopsis "Lower bound for the number of correct rejections") (description "When testing multiple hypotheses simultaneously, this package provides functionality to calculate a lower bound for the number of correct rejections (as a function of the number of rejected hypotheses), which holds simultaneously -with high probability- for all possible number of rejections. As a special case, a lower bound for the total number of false null hypotheses can be inferred. Dependent test statistics can be handled for multiple tests of associations. For independent test statistics, it is sufficient to provide a list of p-values.") (license license:gpl2+))) (define-public r-htmltools (package (name "r-htmltools") (version "0.5.7") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 "11mkk26pjck6r2w2nv6niy90c6l13g64zi01s3j4jgq634kdic7c")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-digest r-ellipsis r-fastmap r-rlang)) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description "This package provides tools for HTML generation and output in R.") (license license:expat))) (define-public r-htmlwidgets (package (name "r-htmlwidgets") (version "1.6.4") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 "1l0f7bz2icixsrgg5fg8k09mv0nq9vn5ch1fywkaqpa8605qzc3w")))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-jsonlite r-knitr r-rmarkdown r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ramnathv/htmlwidgets") (synopsis "HTML Widgets for R") (description "HTML widgets is a framework for creating HTML widgets that render in various contexts including the R console, R Markdown documents, and Shiny web applications.") (license license:expat))) (define-public r-htmltable (package (name "r-htmltable") (version "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 (base32 "039nnxnvw5l284n7w8q0hnplm0b58nwhsrpjfi5asg61f9hxv0va")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda* (#:key inputs #:allow-other-keys) (minify (assoc-ref inputs "js-jquery") #:target "inst/htmlwidgets/lib/jquery/jquery.min.js")))))) (propagated-inputs (list r-checkmate r-htmltools r-htmlwidgets r-knitr r-magrittr r-rstudioapi r-stringr)) (native-inputs `(("esbuild" ,esbuild) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.7.1.js") (sha256 (base32 "1zicjv44sx6n83vrkd2lwnlbf7qakzh3gcfjw0lhq48b5z55ma3q")))) ("r-knitr" ,r-knitr))) (home-page "http://gforge.se/packages/") (synopsis "Advanced tables for Markdown/HTML") (description "This package provides functions to build tables with advanced layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying CSS-structure is simple in order to maximize compatibility with word processors such as LibreOffice. The package also contains a few text formatting functions that help outputting text compatible with HTML or LaTeX.") (license license:gpl3+))) (define-public r-curl (package (name "r-curl") (version "5.2.0") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 "12gldddkfkdwm6h0lb1pjrcpqc9kmqwfwz18wn9brilzbw8s9nxz")))) (properties `((upstream-name . "curl") (updater-extra-inputs . ("curl")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases ;; The environment variable CURL_CA_BUNDLE is only respected when ;; running Windows, so we disable the platform checks. ;; This can be removed once the libcurl has been patched. (add-after 'unpack 'allow-CURL_CA_BUNDLE (lambda _ (substitute* "R/onload.R" (("if \\(!grepl\\(\"mingw\".*") "if (FALSE)\n")) (substitute* "src/handle.c" (("/\\* Only set" m) (string-append "\ const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\"); if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); } " m)))))))) (inputs (list curl zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/jeroenooms/curl") (synopsis "HTTP client for R") (description "The @code{curl()} and @code{curl_download()} functions provide highly configurable drop-in replacements for base @code{url()} and @code{download.file()} with better performance, support for encryption, gzip compression, authentication, and other @code{libcurl} goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces.") (license license:expat))) (define-public r-hwriter (package (name "r-hwriter") (version "1.3.2.1") (source (origin (method url-fetch) (uri (cran-uri "hwriter" version)) (sha256 (base32 "1wxnv8h9cs65m3z01dpnnkgn2cpwfsck70g1jz9nbkr7mdaa4bzd")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/hwriter") (synopsis "Output R objects in HTML format") (description "This package provides easy-to-use and versatile functions to output R objects in HTML format.") (license license:lgpl2.1+))) (define-public r-rjson (package (name "r-rjson") (version "0.2.21") (source (origin (method url-fetch) (uri (cran-uri "rjson" version)) (sha256 (base32 "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rjson") (synopsis "JSON library for R") (description "This package provides functions to convert R objects into JSON objects and vice-versa.") (license license:gpl2+))) (define-public r-fastdummies (package (name "r-fastdummies") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "fastDummies" version)) (sha256 (base32 "0sm02pxbabckxpi3mn36h5bz2wx5pyx7a1dhc2abc4c7fwpihsng")))) (properties `((upstream-name . "fastDummies"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/jacobkap/fastDummies") (synopsis "Create dummy columns and rows from categorical variables") (description "This package creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through @code{model.matrix()}.") (license license:expat))) (define-public r-fastmap (package (name "r-fastmap") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "fastmap" version)) (sha256 (base32 "0wvibiy16i30nzg5k80md68lpz7g6iwbl02j4fyqmbhns2fq08rn")))) (properties `((upstream-name . "fastmap"))) (build-system r-build-system) (home-page "https://r-lib.github.io/fastmap/") (synopsis "Fast implementation of a key-value store") (description "This package provides a fast implementation of a key-value store. Environments are commonly used as key-value stores, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.") (license license:expat))) (define-public r-fastghquad (package (name "r-fastghquad") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "fastGHQuad" version)) (sha256 (base32 "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w")))) (properties `((upstream-name . "fastGHQuad"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/awblocker/fastGHQuad") (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature") (description "This package implements numerically-stable Gauss-Hermite quadrature rules and utility functions for adaptive GH quadrature.") (license license:expat))) (define-public r-rstpm2 (package (name "r-rstpm2") (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "rstpm2" version)) (sha256 (base32 "07q3n9hv8azwiipggyb6ykhvb8qy10s4nkp5irv76d54fsl7jq2y")))) (properties `((upstream-name . "rstpm2"))) (build-system r-build-system) (propagated-inputs (list r-bbmle r-bh r-desolve r-fastghquad r-mgcv r-mvtnorm r-rcpp r-rcpparmadillo r-survival)) (native-inputs (list gfortran)) (home-page "https://github.com/mclements/rstpm2") (synopsis "Link-based survival models") (description "This package provides R implementations of @dfn{generalized survival models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov multi-state models.") ;; One of these licenses (license (list license:gpl2 license:gpl3)))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-jquerylib (package (name "r-jquerylib") (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "jquerylib" version)) (sha256 (base32 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h")) (snippet '(for-each delete-file '("inst/lib/1.12.4/jquery-1.12.4.min.js" "inst/lib/2.2.4/jquery-2.2.4.min.js" "inst/lib/3.6.0/jquery-3.6.0.min.js"))))) (properties `((upstream-name . "jquerylib"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/lib/" (call-with-values (lambda () (unzip2 `(("1.12.4/jquery-1.12.4.js" "1.12.4/jquery-1.12.4.min.js") ("2.2.4/jquery-2.2.4.js" "2.2.4/jquery-2.2.4.min.js") ("3.6.0/jquery-3.6.0.js" "3.6.0/jquery-3.6.0.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-htmltools)) (native-inputs (list esbuild)) (home-page "https://cran.r-project.org/package=jquerylib") (synopsis "Obtain jQuery as an HTML dependency object") (description "Obtain any major version of jQuery and use it in any webpage generated by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't need to use this package directly, but other R packages (e.g. shiny, rmarkdown, etc.) depend on this package to avoid bundling redundant copies of jQuery.") (license license:expat))) (define-public r-jqr (package (name "r-jqr") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "jqr" version)) (sha256 (base32 "1w6806yx763xb0xaqh8ms20gz4h1y3c2s11lgsq3x8h6bahimn5s")))) (properties `((upstream-name . "jqr"))) (build-system r-build-system) (inputs (list jq)) (propagated-inputs (list r-lazyeval r-magrittr)) (native-inputs (list pkg-config)) (home-page "https://docs.ropensci.org/jqr/") (synopsis "R client for jq, a JSON Processor") (description "This package provides an R client for @command{jq}, a JSON processor. @command{jq} allows the following with JSON data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.") (license license:expat))) (define-public r-safetensors (package (name "r-safetensors") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "safetensors" version)) (sha256 (base32 "0xvg5y2sd7gzcal0qqgxbx8vcvmy50jm0j2ajr8iw3wyy5qpyvkp")))) (properties `((upstream-name . "safetensors"))) (build-system r-build-system) (propagated-inputs (list r-cli r-jsonlite r-r6 r-rlang)) (home-page "https://github.com/mlverse/safetensors") (synopsis "Safetensors file format") (description "This package provides a file format for storing tensors that is secure (doesn't allow for code execution), fast and simple to implement. @code{safetensors} also enables cross language and cross frameworks compatibility making it an ideal format for storing machine learning model weights.") (license license:expat))) (define-public r-sass (package (name "r-sass") (version "0.4.8") (source (origin (method url-fetch) (uri (cran-uri "sass" version)) (sha256 (base32 "0364ndnmlqrga3k4c1hfy1894k5wpm9srf9201g9zb92rlq2kfj2")))) (properties `((upstream-name . "sass"))) (build-system r-build-system) (propagated-inputs (list r-fs r-htmltools r-r6 r-rappdirs r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/sass") (synopsis "Syntactically Awesome Style Sheets (SASS)") (description "This package provides an SCSS compiler, powered by the libsass library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the Sass CSS extension language, which is stable, powerful, and CSS compatible.") (license license:expat))) (define-public r-saver (package (name "r-saver") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "SAVER" version)) (sha256 (base32 "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158")))) (properties `((upstream-name . "SAVER"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-glmnet r-iterators r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/mohuangx/SAVER") (synopsis "Recovery of gene expression profile in noisy and sparse scRNA-seq data") (description "This package is an implementation of a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. In @dfn{single-cell RNA sequencing} (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. This package @dfn{single-cell analysis via expression recovery} (SAVER) implements an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.") (license license:gpl2))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-bslib (package (name "r-bslib") (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 "1nrix6i5ailhhlnnv9b2rymvy0c0w3szg9f5r0d5z2fksypka9v4")) (snippet '(for-each delete-file '("inst/components/dist/components.min.js" "inst/components/dist/web-components.min.js" "inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" "inst/lib/bs3/assets/javascripts/bootstrap.min.js" "inst/lib/bs4/dist/js/bootstrap.bundle.min.js" "inst/lib/bs5/dist/js/bootstrap.bundle.min.js"))))) (properties `((upstream-name . "bslib"))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/" (for-each (match-lambda ((source . target) (minify source #:target target))) `(("components/dist/components.js" . "components/dist/components.min.js") ("components/dist/web-components.js" . "components/dist/web-components.min.js") ("lib/bs-a11y-p/plugins/js/bootstrap-accessibility.js" . "lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js") ("lib/bs3/assets/javascripts/bootstrap.js" . "lib/bs3/assets/javascripts/bootstrap.min.js") (,(assoc-ref inputs "js-bootstrap4-bundle") . "lib/bs4/dist/js/bootstrap.bundle.min.js") (,(assoc-ref inputs "js-bootstrap5-bundle") . "lib/bs5/dist/js/bootstrap.bundle.min.js"))))))))) (propagated-inputs (list r-base64enc r-cachem r-htmltools r-jquerylib r-jsonlite r-lifecycle r-memoise r-mime r-rlang r-sass)) (native-inputs `(("esbuild" ,esbuild) ("js-bootstrap4-bundle" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js") (sha256 (base32 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1")))) ("js-bootstrap5-bundle" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.3.1/dist/js/bootstrap.bundle.js") (sha256 (base32 "1bp0a2fin80hwxvd260r1jk57snsgz74vahid64yb2sgj0rlmj8a")))))) (home-page "https://rstudio.github.io/bslib/") (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") (description "This package simplifies custom CSS styling of both shiny and rmarkdown via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their various Bootswatch themes. An interactive widget is also provided for previewing themes in real time.") (license license:expat))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-shiny (package (name "r-shiny") (version "1.8.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/rstudio/shiny") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0rfrch2147yhp2vkr3198gn1ww00ckzcw4i6rywfl38c6fdw9vr1")) (snippet '(for-each delete-file '("inst/www/shared/bootstrap/js/bootstrap.min.js" "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO "inst/www/shared/datatables/js/jquery.dataTables.min.js" "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js" "inst/www/shared/highlight/highlight.pack.js" "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js" "inst/www/shared/jquery.min.js" "inst/www/shared/jqueryui/jquery-ui.min.js" "inst/www/shared/legacy/jquery.min.js" "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js" "inst/www/shared/selectize/js/selectize.min.js" "inst/www/shared/shiny.min.js" "inst/www/shared/showdown/compressed/showdown.js" "inst/www/shared/strftime/strftime-min.js"))))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases '(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda* (#:key inputs #:allow-other-keys) (let ((replace-file (lambda (old new) (format #t "replacing ~a with ~a\n" old new) (symlink new old)))) ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ ;; contain just data. They are not minified code, so we don't ;; replace them. (with-directory-excursion "inst/www/shared" (replace-file "strftime/strftime-min.js" (search-input-file inputs "/share/javascript/strftime.min.js")) (replace-file "highlight/highlight.pack.js" (search-input-file inputs "/share/javascript/highlight.min.js")) (replace-file "datatables/js/jquery.dataTables.min.js" (search-input-file inputs "/share/javascript/jquery.dataTables.min.js")) (replace-file "selectize/js/selectize.min.js" (search-input-file inputs "/share/javascript/selectize.min.js")) (for-each (match-lambda ((source . target) (minify source #:target target))) `(("jqueryui/jquery-ui.js" . "jqueryui/jquery-ui.min.js") ("datepicker/js/bootstrap-datepicker.js" . "datepicker/js/bootstrap-datepicker.min.js") ("ionrangeslider/js/ion.rangeSlider.js" . "ionrangeslider/js/ion.rangeSlider.min.js") ("bootstrap/js/bootstrap.js" . "bootstrap/js/bootstrap.min.js") (,(assoc-ref inputs "js-bootstrap-accessibility") . "bootstrap/accessibility/js/bootstrap-accessibility.min.js") ("shiny.js" . "shiny.min.js") ("jquery.js" . "jquery.min.js") ("legacy/jquery.js" . "legacy/jquery.min.js") ("selectize/accessibility/js/selectize-plugin-a11y.js" . "selectize/accessibility/js/selectize-plugin-a11y.min.js") ("showdown/src/showdown.js" . "showdown/compressed/showdown.js")))))))))) (propagated-inputs (list r-bslib r-cachem r-commonmark r-crayon r-ellipsis r-fastmap r-fontawesome r-glue r-htmltools r-httpuv r-jsonlite r-later r-lifecycle r-mime r-promises r-r6 r-rlang r-sourcetools r-withr r-xtable)) (inputs (list js-datatables js-selectize js-strftime js-highlight)) (native-inputs `(("esbuild" ,esbuild) ("gfortran" ,gfortran) ("js-bootstrap-accessibility" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\ v1.0.7/_site/plugins/js/bootstrap-accessibility.js") (sha256 (base32 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8")))))) (home-page "https://shiny.rstudio.com") (synopsis "Easy interactive web applications with R") (description "Makes it incredibly easy to build interactive web applications with R. Automatic \"reactive\" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.") (license license:artistic2.0))) (define-public r-shinyhelper (package (name "r-shinyhelper") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "shinyhelper" version)) (sha256 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp")))) (properties `((upstream-name . "shinyhelper"))) (build-system r-build-system) (propagated-inputs (list r-markdown r-shiny)) (home-page "https://cran.r-project.org/package=shinyhelper") (synopsis "Easily add Markdown help files to shiny app elements") (description "This package creates a lightweight way to add markdown helpfiles to Shiny apps, using modal dialog boxes, with no need to observe each help button separately.") (license license:gpl3))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-shinytree (package (name "r-shinytree") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "shinyTree" version)) (sha256 (base32 "0krffsgdv99cvyzdspb9l7cdnq1vibsbmpd4w48r5pi4v8jbvfj6")) (snippet ;; Delete minified JavaScript '(for-each delete-file '("inst/www/jsTree-3.3.7/libs/require.js" "inst/www/jsTree-3.3.7/libs/jquery.js" "inst/www/jsTree-3.3.7/jstree.min.js"))))) (properties `((upstream-name . "shinyTree"))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases '(modify-phases %standard-phases (add-after 'unpack 'replace-minified-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/jsTree-3.3.7/" (symlink (search-input-file inputs "/share/javascript/require.min.js") "libs/require.js") (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-jquery") "libs/jquery.js") ("jstree.js" "jstree.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr)) (inputs (list js-requirejs)) (native-inputs `(("esbuild" ,esbuild) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.3.1.js") (sha256 (base32 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))))) (home-page "https://cran.r-project.org/web/packages/shinyTree/") (synopsis "jsTree bindings for Shiny") (description "This package exposes R bindings to jsTree, a JavaScript library that supports interactive trees, to enable rich, editable trees in Shiny.") (license license:expat))) (define-public r-shinydashboard (package (name "r-shinydashboard") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'generate-minified-javascript (lambda _ (with-directory-excursion "inst/AdminLTE" (let ((target "app.min.js") (source "app.js")) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs (list r-htmltools r-promises r-shiny)) (native-inputs (list esbuild)) (home-page "https://rstudio.github.io/shinydashboard/") (synopsis "Create dashboards with shiny") (description "This package provides an extension to the Shiny web application framework for R, making it easy to create attractive dashboards.") ;; This package includes software that was released under the Expat ;; license, but the whole package is released under GPL version 2 or ;; later. (license license:gpl2+))) (define-public r-shinyfiles (package (name "r-shinyfiles") (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 (base32 "11kjq0vw5c98lzrg80m9w917lkgw5im2h9wgk1b84vlaxrjy2wja")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs (list r-fs r-htmltools r-jsonlite r-shiny r-tibble)) (home-page "https://github.com/thomasp85/shinyFiles") (synopsis "Server-side file system viewer for Shiny") (description "This package provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to \"download\" files to a temporary location. Both file and folder selection as well as file saving is available.") (license license:gpl2+))) (define-public r-shinythemes (package (name "r-shinythemes") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "shinythemes" version)) (sha256 (base32 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip")))) (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) (propagated-inputs (list r-shiny)) (home-page "https://rstudio.github.io/shinythemes/") (synopsis "Themes for Shiny") (description "This package provides themes for use with Shiny. It includes several Bootstrap themes, which are packaged for use with Shiny applications.") ;; The package is released under version 3 of the GPL, but it includes ;; source files that are covered by the Expat license. It also includes ;; fonts under SIL or the ASL. (license (list license:gpl3 license:expat license:silofl1.1 license:asl2.0)))) ;; The package sources include minified variants of d3.js and non-minified ;; source code of d3-jetpack. (define-public r-d3r (package (name "r-d3r") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 "1dcm53y3jpyswr6y368xhdnn1nkchixf4wkxnsb2mk9lzccb44y4")) (snippet '(for-each delete-file '("inst/www/d3/v3/dist/d3.min.js" "inst/www/d3/v4/dist/d3.min.js" "inst/www/d3/v5/dist/d3.min.js" "inst/www/d3/v6/dist/d3.min.js" "inst/www/d3/v7/dist/d3.min.js"))))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/d3/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "d3.v3.js") "v3/dist/d3.min.js") (,(assoc-ref inputs "d3.v4.js") "v4/dist/d3.min.js") (,(assoc-ref inputs "d3.v5.js") "v5/dist/d3.min.js") (,(assoc-ref inputs "d3.v6.js") "v6/dist/d3.min.js") (,(assoc-ref inputs "d3.v7.js") "v7/dist/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-dplyr r-htmltools r-tidyr)) (native-inputs `(("esbuild" ,esbuild) ("d3.v3.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v3.js") (sha256 (base32 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))) ("d3.v5.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v5.js") (sha256 (base32 "177ypw6mjrp2ch9lj6znibwacwrvm4ypjxflsxsnl2sigx5dcwic")))) ("d3.v6.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v6.js") (sha256 (base32 "13hick3glizzm442b9swlwz584rzwwvhpq9qvfbh3m5jay10wxw0")))) ("d3.v7.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v7.js") (sha256 (base32 "1m4i3kqzkz7w06sp9zqcy9f88xpdhi7cqih3phdrf4yjmfk1pfjg")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description "This package provides a suite of functions to help ease the use of the d3.js visualization library in R. These helpers include @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame} R objects into the JSON format that the d3.js library expects.") (license license:bsd-3))) ;; We use the latest commit here because the last release was in 2016 while ;; the latest commit was in 2018. (define-public r-sankeyd3 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc") (revision "1")) (package (name "r-sankeyd3") (version (git-version "0.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/fbreitwieser/sankeyD3") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) (build-system r-build-system) (propagated-inputs (list r-d3r r-htmlwidgets r-shiny r-magrittr)) (home-page "https://github.com/fbreitwieser/sankeyD3") (synopsis "Sankey network graphs from R") (description "This package provides an R library to generate Sankey network graphs in R and Shiny via the D3 visualization library.") ;; The R code is licensed under GPLv3+. It includes the non-minified ;; JavaScript source code of d3-sankey, which is released under the ;; 3-clause BSD license. (license (list license:gpl3+ license:bsd-3))))) (define-public r-wesanderson (package (name "r-wesanderson") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "wesanderson" version)) (sha256 (base32 "0kjyz5mrkrirg2glf57b0rhxj2fdp1m6q8zx947y0jg1w425cbn9")))) (properties `((upstream-name . "wesanderson"))) (build-system r-build-system) (home-page "https://github.com/karthik/wesanderson") (synopsis "Wes Anderson color palette generator") (description "This package provides color palettes that have been generated mostly from Wes Anderson movies.") (license license:expat))) (define-public r-gg-gap (package (name "r-gg-gap") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "gg.gap" version)) (sha256 (base32 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h")))) (properties `((upstream-name . "gg.gap"))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-ggplot2)) (home-page "https://github.com/ChrisLou-bioinfo/gg.gap") (synopsis "Define segments on the y-axis for ggplot2") (description "The @code{gg.gap} function enables you to define segments for the y-axis in a ggplot2 plot.") (license license:gpl3))) (define-public r-mbess (package (name "r-mbess") (version "4.9.3") (source (origin (method url-fetch) (uri (cran-uri "MBESS" version)) (sha256 (base32 "05ph8dwigwn0c4qg8smqhsjijvsvfawbzvm74mqpasi8qifz8nd3")))) (properties `((upstream-name . "MBESS"))) (build-system r-build-system) (propagated-inputs (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools)) (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html") (synopsis "Methods for designing research studies") (description "This package implements methods that are useful in designing research studies and analyzing data, with particular emphasis on methods that are developed for or used within the behavioral, educational, and social sciences (broadly defined). That being said, many of the methods implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a suite of functions for a variety of related topics, such as effect sizes, confidence intervals for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size planning (from the @dfn{accuracy in parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk point estimation perspectives), mediation analysis, various properties of distributions, and a variety of utility functions.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-homologene (package (name "r-homologene") (version "1.4.68.19.3.27") (source (origin (method url-fetch) (uri (cran-uri "homologene" version)) (sha256 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh")))) (properties `((upstream-name . "homologene"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-purrr r-r-utils r-readr)) (home-page "https://github.com/oganm/homologene") (synopsis "Quick access to homologene and gene annotation updates") (description "This package provides a wrapper for the homologene database by the National Center for Biotechnology Information (NCBI). It allows searching for gene homologs across species. The package also includes an updated version of the homologene database where gene identifiers and symbols are replaced with their latest (at the time of submission) version and functions to fetch latest annotation data to keep updated.") (license license:expat))) (define-public r-ggtern (package (name "r-ggtern") (version "3.4.2") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 (base32 "1xmh0gi81xrzkgjlbxb3jl9mrj407q7ykm4wpdbmd4gdswv20y61")))) (properties `((upstream-name . "ggtern"))) (build-system r-build-system) (propagated-inputs (list r-compositions r-ggplot2 r-gridextra r-gtable r-hexbin r-latex2exp r-lattice r-mass r-plyr r-proto r-scales)) (home-page "http://www.ggtern.com") (synopsis "Extension to ggplot2 for ternary diagrams") (description "This package extends the functionality of ggplot2, providing the capability to plot ternary diagrams for (a subset of) the ggplot2 geometries. Additionally, ggtern has implemented several new geometries which are unavailable to the standard ggplot2 release.") (license license:gpl2))) (define-public r-tablerdash (package (name "r-tablerdash") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "tablerDash" version)) (sha256 (base32 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm")) (snippet '(begin ;; Delete minified JavaScript (for-each delete-file '("inst/tablerDash-0.1.0/require.min.js" "inst/bootstrap-4.0.0/bootstrap.bundle.min.js")) #true)))) (properties `((upstream-name . "tablerDash"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-requirejs") "tablerDash-0.1.0/require.min.js") (,(assoc-ref inputs "js-bootstrap") "bootstrap-4.0.0/bootstrap.bundle.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets)))) #t))))) (propagated-inputs (list r-htmltools r-knitr r-shiny)) (native-inputs `(("esbuild" ,esbuild) ("js-requirejs" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js") (sha256 (base32 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds")))) ("js-bootstrap" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/twbs/bootstrap/\ v4.0.0/dist/js/bootstrap.bundle.js") (sha256 (base32 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj")))))) (home-page "https://rinterface.github.io/tablerDash/") (synopsis "Tabler API for Shiny") (description "This package provides an R interface to the @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap 4 dashboard template. There are different layouts available such as a one page dashboard or a multi-page template, where the navigation menu is contained in the navigation bar.") (license license:gpl2+))) (define-public r-spelling (package (name "r-spelling") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "spelling" version)) (sha256 (base32 "0vr5mgw9grnsnzsc29al72p05z786hnd6b9c6wq0c0dabk5szm2g")))) (properties `((upstream-name . "spelling"))) (build-system r-build-system) (propagated-inputs (list r-commonmark r-hunspell r-knitr r-xml2)) (home-page "https://docs.ropensci.org/spelling/") (synopsis "Tools for spell checking in R") (description "This is an R package for spell checking common document formats including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes utilities to automate checking of documentation and vignettes as a unit test during @code{R CMD check}. Both British and American English are supported out of the box and other languages can be added. In addition, packages may define a wordlist to allow custom terminology without having to abuse punctuation.") (license license:expat))) (define-public r-crosstalk (package (name "r-crosstalk") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "crosstalk" version)) (sha256 (base32 "1w8lc3hcd1nlw541880vs3agk2i6bilyapnq9lcs3mfn2s2g0338")) (snippet '(for-each delete-file (list "inst/lib/jquery/jquery.min.js" "inst/lib/ionrangeslider/js/ion.rangeSlider.min.js" "inst/lib/selectize/js/selectize.min.js" "inst/www/js/crosstalk.min.js"))))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/" (copy-file (search-input-file inputs "/share/javascript/selectize.min.js") "lib/selectize/js/selectize.min.js") (for-each (match-lambda ((source . target) (minify source #:target target))) `(("lib/jquery/jquery.js" . "lib/jquery/jquery.min.js") ("lib/ionrangeslider/js/ion.rangeSlider.js" . "lib/ionrangeslider/js/ion.rangeSlider.min.js") ("www/js/crosstalk.js" . "www/js/crosstalk.min.js"))))))))) (propagated-inputs (list r-htmltools r-jsonlite r-lazyeval r-r6)) (native-inputs (list esbuild js-selectize)) (home-page "https://rstudio.github.io/crosstalk/") (synopsis "Inter-widget interactivity for HTML widgets") (description "This package provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e., static @code{.html} files). It currently supports linked brushing and filtering.") (license license:expat))) (define-public r-rook (package (name "r-rook") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "Rook" version)) (sha256 (base32 "0qjziszrrwsp1mbykps3yf5r98q83cyd4jzpgi7gvbsd2ssy96n7")))) (properties `((upstream-name . "Rook"))) (build-system r-build-system) (propagated-inputs (list r-brew)) (home-page "https://cran.r-project.org/web/packages/Rook") (synopsis "Web server interface for R") (description "This package contains the Rook specification and convenience software for building and running Rook applications. A Rook application is an R reference class object that implements a @code{call} method or an R closure that takes exactly one argument, an environment, and returns a list with three named elements: the @code{status}, the @code{headers}, and the @code{body}.") (license license:gpl2))) (define-public r-miniui (package (name "r-miniui") (version "0.1.1.1") (source (origin (method url-fetch) (uri (cran-uri "miniUI" version)) (sha256 (base32 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) (properties `((upstream-name . "miniUI"))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-shiny)) (home-page "https://cran.r-project.org/web/packages/miniUI/") (synopsis "Shiny UI widgets for small screens") (description "This package provides UI widget and layout functions for writing Shiny apps that work well on small screens.") (license license:gpl3))) (define-public r-feather (package (name "r-feather") (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "feather" version)) (sha256 (base32 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh")))) (build-system r-build-system) (propagated-inputs (list r-hms r-rcpp r-tibble)) (home-page "https://github.com/wesm/feather") (synopsis "R Bindings to the Feather API") (description "Read and write feather files, a lightweight binary columnar data store designed for maximum speed.") (license license:asl2.0))) (define-public r-mapdata (package (name "r-mapdata") (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "mapdata" version)) (sha256 (base32 "1m2r4c8f7fp900g3sdjbfxxnxjla86hn75jd8hi96ms188p0j8b0")))) (properties `((upstream-name . "mapdata"))) (build-system r-build-system) (propagated-inputs (list r-maps)) (home-page "https://cran.r-project.org/package=mapdata") (synopsis "Extra map databases") (description "This is a supplement to the @code{maps} package providing the larger and/or higher-resolution databases.") (license license:gpl2))) (define-public r-maps (package (name "r-maps") (version "3.4.2") (source (origin (method url-fetch) (uri (cran-uri "maps" version)) (sha256 (base32 "032b8348k8vjhwj0d58v7akjkvfpvqzfva0nl7acyy8pky47prak")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/maps") (synopsis "Draw geographical maps") (description "This package provides an R module for display of maps. Projection code and larger maps are in separate packages (@code{mapproj} and @code{mapdata}).") (license license:gpl2))) (define-public r-mapproj (package (name "r-mapproj") (version "1.2.11") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 "0z9lhv006pw4mwqlghvgvv66ga958bs6n1k6fmqjdpirr4f20bfv")))) (build-system r-build-system) (propagated-inputs (list r-maps)) (home-page "https://cran.r-project.org/web/packages/mapproj") (synopsis "Map projection in R") (description "This package converts latitude/longitude into projected coordinates.") (license (list license:gpl2 ; The R interface license:lpl1.02)))) ; The C code (define-public r-rgooglemaps (package (name "r-rgooglemaps") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 "197q5i2sky824dwq0x4hhrpkrsd1b6f9qg06mjlwb89mv4vnrzhl")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs (list r-png)) (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") (synopsis "Use Google Maps in R") (description "This package serves two purposes: @enumerate @item Provide a comfortable R interface to query the Google server for static maps, and @item Use the map as a background image to overlay plots within R. This requires proper coordinate scaling. @end enumerate\n") (license license:gpl2+))) (define-public r-gensa (package (name "r-gensa") (version "1.1.12") (source (origin (method url-fetch) (uri (cran-uri "GenSA" version)) (sha256 (base32 "0m5y0hmhcc40d9a24pz5iqw5diip7sn7bih5s01x5dvqqasnx6vk")))) (properties `((upstream-name . "GenSA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=GenSA") (synopsis "Generalized simulated annealing") (description "This package performs search for the global minimum of a very complex non-linear objective function with a very large number of optima.") (license license:gpl2))) (define-public r-geosphere (package (name "r-geosphere") (version "1.5-18") (source (origin (method url-fetch) (uri (cran-uri "geosphere" version)) (sha256 (base32 "1h6sqvxwxv22js6hz4s8sjk50ygw0y34icbbbdb2v36ca3q6zzwr")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp)) (home-page "https://cran.r-project.org/web/packages/geosphere") (synopsis "Spherical trigonometry") (description "This package computes spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.") (license license:gpl3+))) (define-public r-jpeg (package (name "r-jpeg") (version "0.1-10") (source (origin (method url-fetch) (uri (cran-uri "jpeg" version)) (sha256 (base32 "1jkqj58hj33ar9wyl7c1cnj3h42icq7crmjk93n933q8qc4zdnf8")))) (build-system r-build-system) (inputs (list libjpeg-turbo)) (home-page "https://www.rforge.net/jpeg/") (synopsis "Read and write JPEG images with R") (description "This package provides a way to read, write and display bitmap images stored in the JPEG format with R. It can read and write both files and in-memory raw vectors.") (license license:gpl2+))) (define-public r-ggmap (package (name "r-ggmap") (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggmap" version)) (sha256 (base32 "1x9lqx0mizqiyxzgg8pgkbi8qmbn2a0zsq5r5riknvh6ghskkrhd")))) (build-system r-build-system) (propagated-inputs (list r-bitops r-cli r-digest r-dplyr r-ggplot2 r-glue r-httr r-jpeg r-magrittr r-plyr r-png r-purrr r-rlang r-scales r-stringr r-tibble r-tidyr)) (home-page "https://github.com/dkahle/ggmap") (synopsis "Spatial visualization with ggplot2") (description "This package provides a collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.") (license license:gpl2))) (define-public r-haven (package (name "r-haven") (version "2.5.4") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 "0dd83v3bfs7and9ydx35m8zw0md3wgchwpnvj6yllixa6yxk25cy")) (modules '((guix build utils))) (snippet ;; unvendor readstat '(delete-file-recursively "src/readstat")))) (build-system r-build-system) (properties '((updater-extra-inputs . ("readstat")))) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'unbundle-readstat (lambda _ ;; We’re not building readstat. (substitute* "configure" (("^PKG_CONFIG_NAME=\"zlib\"") "PKG_CONFIG_NAME=\"readstat zlib\"") (("^PKG_LIBS=\"-lz\"") "PKG_LIBS=\"-lz -lreadstat\"\n") (("exit 1") ""))))))) ;don't be so dramatic! (inputs (list readstat zlib)) (native-inputs (list pkg-config r-knitr)) (propagated-inputs (list r-cli r-cpp11 r-forcats r-hms r-lifecycle r-readr r-rlang r-tibble r-tidyselect r-vctrs)) (home-page "https://haven.tidyverse.org") (synopsis "Import and export SPSS, Stata and SAS files") (description "This package lets you import foreign statistical formats into R via the @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (license license:expat))) (define-public r-amap (package (name "r-amap") (version "0.8-19") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 "000r5705lq2mc15skin07dfxjf5816nbfy4gqkya1sv99dlfljbk")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") (synopsis "Another multidimensional analysis package") (description "This package provides tools for clustering and principal component analysis (with robust methods, and parallelized functions).") (license license:gpl2+))) (define-public r-ape (package (name "r-ape") (version "5.7-1") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 "0yh5wl7nydhwwc82h6yr8wcacc2f791pp05w8fg65anq309cf2cb")))) (build-system r-build-system) (propagated-inputs (list r-digest r-lattice r-nlme r-rcpp)) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description "This package provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, and several other tools.") (license license:gpl2+))) (define-public r-abbyyr (package (name "r-abbyyr") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "abbyyR" version)) (sha256 (base32 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r")))) (properties `((upstream-name . "abbyyR"))) (build-system r-build-system) (propagated-inputs (list r-curl r-httr r-plyr r-progress r-readr r-xml)) (home-page "https://github.com/soodoku/abbyyR") (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") (description "This package provides tools to get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily OCR images, barcodes, forms, documents with machine readable zones, e.g. passports and get the results in a variety of formats including plain text and XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (license license:expat))) (define-public r-colorspace (package (name "r-colorspace") (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 (base32 "0k31hazd2rq5lyg3y89y2v5jqadz2qlxd1bhvj89q4aldfxql1q4")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") (description "This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.") (license license:bsd-3))) (define-public r-glue (package (name "r-glue") (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 "1p4699p68k9f8d76bmgx5xabay6xjrcgajckzqxyn6icym8ipx8s")))) (build-system r-build-system) (properties ;; knitr depends on glue, so we can't add knitr here to build the ;; vignettes. '((updater-ignored-native-inputs . ("r-knitr")))) (home-page "https://github.com/tidyverse/glue") (synopsis "Interpreted string literals") (description "This package provides an implementation of interpreted string literals, inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (license license:expat))) (define-public r-glmnetutils (package (name "r-glmnetutils") (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "glmnetUtils" version)) (sha256 (base32 "0rh07i9j6bxiqcl84d8jnn7dzqdwfdzak7w8bf4j4521r24mwm01")))) (properties `((upstream-name . "glmnetUtils"))) (build-system r-build-system) (propagated-inputs (list r-glmnet r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/hongooi73/glmnetUtils") (synopsis "Streamline the process of fitting elastic net models with glmnet") (description "This package provides a collection of tools to streamline the process of fitting elastic net models with @code{glmnet}. In addition to providing a formula interface, it also features a function @code{cva.glmnet} to do crossvalidation for both α and λ, as well as some utility functions.") (license license:gpl2))) (define-public r-paletteer (package (name "r-paletteer") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "paletteer" version)) (sha256 (base32 "1mm0k651356cjasv7wibscw82m1k8mwpp4xafpv66dsq24h28ikl")))) (properties `((upstream-name . "paletteer"))) (build-system r-build-system) (propagated-inputs (list r-prismatic r-rematch2 r-rlang r-rstudioapi)) (home-page "https://github.com/EmilHvitfeldt/paletteer") (synopsis "Comprehensive collection of color palettes") (description "The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This package aims to collect all color palettes across the R ecosystem under the same package with a streamlined API.") (license license:gpl3))) (define-public r-palmerpenguins (package (name "r-palmerpenguins") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "palmerpenguins" version)) (sha256 (base32 "1d1h3bfx750is4qqj4w00rcigk9rrdy69bvd5bgqz5y7ls5x8h1a")))) (properties `((upstream-name . "palmerpenguins"))) (build-system r-build-system) (home-page "https://allisonhorst.github.io/palmerpenguins/") (synopsis "Palmer Archipelago (Antarctica) penguin data") (description "This package includes size measurements, clutch observations, and blood isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. Data were collected and made available by Dr. Kristen Gorman and the Palmer Station Long Term Ecological Research (LTER) Program.") (license license:cc0))) (define-public r-pastecs (package (name "r-pastecs") (version "1.3.21") (source (origin (method url-fetch) (uri (cran-uri "pastecs" version)) (sha256 (base32 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) (build-system r-build-system) (propagated-inputs (list r-boot)) (home-page "https://github.com/phgrosjean/pastecs") (synopsis "Analysis of space-time ecological series") (description "This package provides functions for regulation, decomposition and analysis of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER initiative to bring PASSTEC 2000 functionalities to R.") (license license:gpl2+))) (define-public r-partykit (package (name "r-partykit") (version "1.2-20") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 "1np0sa7fx7wvwxbpk5lpgbdpz0xwcvppq0sc52nifx1dxnirll33")))) (build-system r-build-system) (propagated-inputs (list r-formula r-inum r-libcoin r-mvtnorm r-rpart r-survival)) (home-page "https://partykit.R-Forge.R-project.org/partykit") (synopsis "Toolkit for recursive partytioning") (description "This package provides a toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models.") (license license:gpl2+))) (define-public r-plogr (package (name "r-plogr") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "plogr" version)) (sha256 (base32 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/plogr") (synopsis "R bindings for the plog C++ logging library") (description "This package provides the header files for a stripped-down version of the plog header-only C++ logging library, and a method to log to R's standard error stream.") (license license:expat))) (define-public r-pls (package (name "r-pls") (version "2.8-3") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 (base32 "1qvbwr567vxywpfsl7cb15lpwxpd04kf01nzk1v8dm4csf6p5sz6")))) (build-system r-build-system) (home-page "https://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") (description "The pls package implements multivariate regression methods: Partial Least Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports: @itemize @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd} @item multi-response models (or @dfn{PLS2}) @item flexible cross-validation @item Jackknife variance estimates of regression coefficients @item extensive and flexible plots: scores, loadings, predictions, coefficients, (R)MSEP, R², and correlation loadings @item formula interface, modelled after @code{lm()}, with methods for predict, print, summary, plot, update, etc. @item extraction functions for coefficients, scores, and loadings @item MSEP, RMSEP, and R² estimates @item multiplicative scatter correction (@dfn{MSC}) @end itemize\n") (license license:gpl2))) (define-public r-ps (package (name "r-ps") (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 (base32 "0knblkdrdqbmcv9zmp5096k4vfvvbjzl6zizjyabk5spqpikmg0s")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") (description "The ps package implements an API to list, query, and manipulate system processes. Most of its code is based on the @code{psutil} Python package.") (license license:bsd-3))) (define-public r-pkgbuild (package (name "r-pkgbuild") (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 "0rci20gj2x0bgjy51jp8i4gld6arsigj7lhdkpwvdyhadjsyv0qm")))) (build-system r-build-system) (propagated-inputs (list r-callr r-cli r-desc r-processx r-r6)) (home-page "https://github.com/r-pkgs/pkgbuild") (synopsis "Find tools needed to build R packages") (description "This package provides functions used to build R packages. It locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.") (license license:gpl3))) (define-public r-pkgload (package (name "r-pkgload") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 "1ki6k7l7dpb6bncvvcndrv5764jb1adrzs5iaxicakfsija4pc30")))) (build-system r-build-system) (propagated-inputs (list r-cli r-crayon r-desc r-fs r-glue r-pkgbuild r-rlang r-rprojroot r-withr)) (home-page "https://github.com/r-lib/pkgload") (synopsis "Simulate package installation and attach") (description "This package simulates the process of installing a package and then attaching it. This is a key part of the @code{devtools} package as it allows you to rapidly iterate while developing a package.") (license license:gpl3))) (define-public r-pvclust (package (name "r-pvclust") (version "2.2-0") (source (origin (method url-fetch) (uri (cran-uri "pvclust" version)) (sha256 (base32 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq")))) (build-system r-build-system) (home-page "https://github.com/shimo-lab/pvclust") (synopsis "Hierarchical clustering with P-values via multiscale bootstrap resampling") (description "This package provides an implementation of multiscale bootstrap resampling for assessing the uncertainty in hierarchical cluster analysis. It provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability) value for each cluster in a dendrogram.") (license license:gpl2+))) (define-public r-rcpp (package (name "r-rcpp") (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 (base32 "1l1b0q2r6q2bjr4wvj98kp9844fyrsn2ppx339v05vmy8g65jwqc")))) (build-system r-build-system) (home-page "https://www.rcpp.org") (synopsis "Seamless R and C++ integration") (description "The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the @code{Rcpp Gallery} site at , the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) (define-public r-rcppde (package (name "r-rcppde") (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "RcppDE" version)) (sha256 (base32 "1846pl9gxikycdvwfgy1gw41z0fx4ycjp5p4295v8k2pgvlqw8sa")))) (properties `((upstream-name . "RcppDE"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/package=RcppDE") (synopsis "Global optimization by differential evolution in C++") (description "This package provides an iteration of the @code{DEoptim} function. It performs global optimization by differential evolution.") (license license:gpl2+))) (define-public r-rcppdist (package (name "r-rcppdist") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "RcppDist" version)) (sha256 (base32 "02g57xwfipdcljv06krhm02dbqn9kfyj2km6rdg0a7vq9prwdz1x")))) (properties `((upstream-name . "RcppDist"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/duckmayr/RcppDist") (synopsis "Integration of additional probability distributions") (description "RcppDist provides a header-only C++ library with functions for additional statistical distributions that can be called from C++ when writing code using Rcpp or RcppArmadillo. Functions are available that return a @code{NumericVector} as well as doubles, and for multivariate or matrix distributions, Armadillo vectors and matrices.") (license license:gpl2+))) (define-public r-rcppml (package (name "r-rcppml") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "RcppML" version)) (sha256 (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j")))) (properties `((upstream-name . "RcppML"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) (native-inputs (list r-knitr)) (home-page "https://github.com/zdebruine/RcppML") (synopsis "Rcpp machine learning library") (description "This package provides fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices.") (license license:gpl2+))) (define-public r-rcppspdlog (package (name "r-rcppspdlog") (version "0.0.16") (source (origin (method url-fetch) (uri (cran-uri "RcppSpdlog" version)) (sha256 (base32 "12xryg2mp00nxmpchf0lki43c13c1vsda14pcc4dcfplamwkhlza")))) (properties `((upstream-name . "RcppSpdlog"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-simplermarkdown)) (home-page "https://github.com/eddelbuettel/rcppspdlog") (synopsis "R and C++ interfaces to spdlog C++ header library for logging") (description "The spdlog library is a widely-used and very capable header-only C++ library for logging. This package includes its headers as an R package to permit other R packages to deploy it via a simple @code{LinkingTo: RcppSpdlog}. As of version 0.0.9, it also provides both simple R logging functions and compiled functions callable by other packages.") (license license:gpl2+))) (define-public r-rcppthread (package (name "r-rcppthread") (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "RcppThread" version)) (sha256 (base32 "1997ka0dd36d79fb4crqq0ar3bgzdv4mw5hd6v2pmq7555g0qiz9")))) (properties `((upstream-name . "RcppThread"))) (build-system r-build-system) (native-inputs (list r-r-rsp)) (home-page "https://github.com/tnagler/RcppThread") (synopsis "R threading in C++") (description "This package provides a C++11-style thread class and thread pool that can safely be interrupted from R.") (license license:expat))) (define-public r-rcppnumerical (package (name "r-rcppnumerical") (version "0.6-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 "11nph9fz1bzb0pcvh6xx4cb94090ahwpj21zmbi06m4pibb1a1rg")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis"Numerical computing libraries integration with @code{Rcpp}") (description "This package provides a collection of libraries for numerical computing (numerical integration, optimization, etc.) and their integration with @code{Rcpp}.") (license license:gpl2+))) (define-public r-rcppxptrutils (package (name "r-rcppxptrutils") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "RcppXPtrUtils" version)) (sha256 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l")))) (properties `((upstream-name . "RcppXPtrUtils"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/Enchufa2/RcppXPtrUtils") (synopsis "XPtr add-ons for Rcpp") (description "This package provides the means to compile user-supplied C++ functions with Rcpp and retrieve an @code{XPtr} that can be passed to other C++ components.") (license license:expat))) (define-public r-bb (package (name "r-bb") (version "2019.10-1") (source (origin (method url-fetch) (uri (cran-uri "BB" version)) (sha256 (base32 "0kf9sfsm3n036a8a8gjfpc9qdryvadb019kqjh80n1szdv7bdl04")))) (properties `((upstream-name . "BB"))) (build-system r-build-system) (propagated-inputs (list r-quadprog)) (home-page "https://publichealth.jhu.edu/") (synopsis "Solving and optimizing large-scale nonlinear systems") (description "This package implements Barzilai-Borwein spectral methods for solving nonlinear system of equations, and for optimizing nonlinear objective functions subject to simple constraints.") (license license:gpl3))) (define-public r-bindr (package (name "r-bindr") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "bindr" version)) (sha256 (base32 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/bindr") (synopsis "Parametrized active bindings") (description "This package provides a simple interface for creating active bindings where the bound function accepts additional arguments.") (license license:expat))) (define-public r-bindrcpp (package (name "r-bindrcpp") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "bindrcpp" version)) (sha256 (base32 "1yn9is89r76ay314s216whr0igych4r78kjz85amhwgfb9wawbb6")))) (build-system r-build-system) (propagated-inputs (list r-bindr r-plogr r-rcpp)) (home-page "https://github.com/krlmlr/bindrcpp") (synopsis "Rcpp interface to active bindings") (description "This package provides an easy way to fill an environment with active bindings that call a C++ function.") (license license:expat))) (define-public r-auc (package (name "r-auc") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "AUC" version)) (sha256 (base32 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3")))) (properties `((upstream-name . "AUC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AUC") (synopsis "Compute the area under the curve of selected measures") (description "This package includes functions to compute the area under the curve of selected measures: the area under the sensitivity curve (AUSEC), the area under the specificity curve (AUSPC), the area under the accuracy curve (AUACC), and the area under the receiver operating characteristic curve (AUROC). The curves can also be visualized. Support for partial areas is provided.") (license license:gpl2+))) (define-public r-calibrate (package (name "r-calibrate") (version "1.7.7") (source (origin (method url-fetch) (uri (cran-uri "calibrate" version)) (sha256 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/calibrate") (synopsis "Calibration of scatterplot and biplot axes") (description "This is a package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots.") (license license:gpl2))) (define-public r-shape (package (name "r-shape") (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/shape") (synopsis "Functions for plotting graphical shapes") (description "This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...") (license license:gpl3+))) (define-public r-globaloptions (package (name "r-globaloptions") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "GlobalOptions" version)) (sha256 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7")))) (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/GlobalOptions") (synopsis "Generate functions to get or set global options") (description "This package provides more controls on the option values such as validation and filtering on the values, making options invisible or private.") (license license:gpl2+))) (define-public r-circlize (package (name "r-circlize") (version "0.4.15") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn")))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-globaloptions r-shape)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/circlize") (synopsis "Circular visualization") (description "Circular layout is an efficient way to visualise huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. Its flexibility is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.") (license license:gpl2+))) (define-public r-rcircos (package (name "r-rcircos") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "RCircos" version)) (sha256 (base32 "1z0aam60p1b6q7csn50rrwdilm07myr05bw54s9ah8idzyxc7gav")))) (properties `((upstream-name . "RCircos"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RCircos/") (synopsis "Circos 2D track plot") (description "This package provides a simple and flexible way to generate Circos 2D track plot images. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics packages that comes with the base installation.") (license license:gpl2+))) (define-public r-ctrdata (package (name "r-ctrdata") (version "1.16.0") (source (origin (method url-fetch) (uri (cran-uri "ctrdata" version)) (sha256 (base32 "13n5c7znlxkwqlv04vd5ynbkbq8f28dzbr3y66966971xnf7yhsm")))) (properties `((upstream-name . "ctrdata"))) (build-system r-build-system) (propagated-inputs (list r-clipr r-curl r-dplyr r-httr r-jqr r-jsonlite r-lubridate r-nodbi r-readr r-stringi r-tibble r-v8 r-xml2 r-zip)) (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/package=ctrdata") (synopsis "Retrieve and analyze clinical trials in public registers") (description "This package provides a system for querying, retrieving and analyzing protocol- and results-related information on clinical trials from three public registers, the European Union Clinical Trials Register (EUCTR), ClinicalTrials.gov (CTGOV) and the ISRCTN. Trial information is downloaded, converted and stored in a database. Functions are included to identify deduplicated records, to easily find and extract variables (fields) of interest even from complex nesting as used by the registers, and to update previous queries. The package can be used for meta-analysis and trend-analysis of the design and conduct as well as for results of clinical trials.") (license license:expat))) (define-public r-ctrialsgov (package (name "r-ctrialsgov") (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "ctrialsgov" version)) (sha256 (base32 "0hdh1fdfaja8amf7fkvk1c6yif703132bvacq0j9pk5jr97czgpw")))) (properties `((upstream-name . "ctrialsgov"))) (build-system r-build-system) (propagated-inputs (list r-dbi r-dplyr r-ggplot2 r-htmlwidgets r-lubridate r-matrix r-plotly r-purrr r-rlang r-stringi r-tibble)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ctrialsgov") (synopsis "Query data from U.S. National Library of Medicine's Clinical Trials Database") (description "This package provides tools to query the U.S. National Library of Medicine's Clinical Trials database. Functions are provided for a variety of techniques for searching the data using range queries, categorical filtering, and by searching for full-text keywords. Minimal graphical tools are also provided for interactively exploring the constructed data.") (license license:expat))) (define-public r-powerlaw (package (name "r-powerlaw") (version "0.70.6") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs (list r-pracma)) (native-inputs (list r-knitr)) (home-page "https://github.com/csgillespie/poweRlaw") (synopsis "Tools for the analysis of heavy tailed distributions") (description "This package provides an implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.") ;; Any of these GPL versions. (license (list license:gpl2 license:gpl3)))) (define-public r-ptw (package (name "r-ptw") (version "1.9-16") (source (origin (method url-fetch) (uri (cran-uri "ptw" version)) (sha256 (base32 "0rma3h9ksc5qigdvk5vappb4ipd4rpk64wckzcxvxspakr5w71vy")))) (properties `((upstream-name . "ptw"))) (build-system r-build-system) (propagated-inputs (list r-rcppde)) (home-page "https://github.com/rwehrens/ptw") (synopsis "Parametric time warping") (description "Parametric time warping aligns patterns. It aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: @acronym{RMS, Root Mean Square} error and @acronym{WCC, Weighted Cross Correlation}. Both warping of peak profiles and of peak lists are supported.") (license license:gpl2+))) (define-public r-compare (package (name "r-compare") (version "0.2-6") (source (origin (method url-fetch) (uri (cran-uri "compare" version)) (sha256 (base32 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/compare") (synopsis "Comparing objects for differences") (description "This package provides functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.") (license license:gpl2+))) (define-public r-dendextend (package (name "r-dendextend") (version "1.17.1") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 "08g5z5qyrn2nkw1jw5520sval4jf9l6invqwvzsv8dkjkq8nxsc7")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-magrittr r-viridis)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/dendextend") (synopsis "Extending 'dendrogram' functionality in R") (description "This package offers a set of functions for extending @code{dendrogram} objects in R, letting you visualize and compare trees of hierarchical clusterings. You can adjust a tree's graphical parameters (the color, size, type, etc of its branches, nodes and labels) and visually and statistically compare different dendrograms to one another.") ;; Any of these versions (license (list license:gpl2 license:gpl3)))) (define-public r-dendsort (package (name "r-dendsort") (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "dendsort" version)) (sha256 (base32 "0rs7y471wrhkgibxdmfh5xhp3pa004rrlm2w08b6qli5gq4im5d2")))) (properties `((upstream-name . "dendsort"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/evanbiederstedt/dendsort") (synopsis "Modular leaf ordering methods for dendrogram nodes") (description "This package represents an implementation of functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different distance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.") ;; Any of these versions (license (list license:gpl2 license:gpl3)))) (define-public r-getoptlong (package (name "r-getoptlong") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs (list perl)) (propagated-inputs (list r-crayon r-globaloptions r-rjson)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/GetoptLong") (synopsis "Parsing command-line arguments and variable interpolation") (description "This is yet another command-line argument parser which wraps the powerful Perl module @code{Getopt::Long} and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.") (license license:gpl2+))) (define-public r-fastmatch (package (name "r-fastmatch") (version "1.1-4") (source (origin (method url-fetch) (uri (cran-uri "fastmatch" version)) (sha256 (base32 "0symkcmyrqvz6hkawr40ga808rb3w4hy9ssfsi5ri8hykjn4r4cs")))) (build-system r-build-system) (home-page "https://www.rforge.net/fastmatch") (synopsis "Fast match function") (description "This package provides a fast @code{match} replacement for cases that require repeated look-ups. It is slightly faster that R's built-in @code{match} function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.") (license license:gpl2))) (define-public r-ff (package (name "r-ff") (version "4.0.12") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 "1gs1zf3x0clnim7qlrkhlsjf2xgry5ybqnh8ipa2kzhhk9d3bbq8")))) (build-system r-build-system) (propagated-inputs (list r-bit)) (home-page "https://ff.r-forge.r-project.org/") (synopsis "Memory-efficient storage of large data on disk and access functions") (description "This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.") ;; error Architecture not supported. (supported-systems (delete "aarch64-linux" %supported-systems)) (license license:gpl2))) (define-public r-ffbase (package (name "r-ffbase") (version "0.13.3") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; R 4.3.0 removed the typedef for Sint, which used to be just int. (add-after 'unpack 'r-compatibility (lambda _ (substitute* '("src/grouprunningcumsum.c" "src/grouprunningcumsumindex.c") (("\\bSint ") "int "))))))) (propagated-inputs (list r-bit r-fastmatch r-ff)) (home-page "https://github.com/edwindj/ffbase") (synopsis "Basic statistical functions for package 'ff'") (description "This package extends the out of memory vectors of @code{ff} with statistical functions and other utilities to ease their usage.") (license license:gpl3))) (define-public r-prettyunits (package (name "r-prettyunits") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "prettyunits" version)) (sha256 (base32 "1smcxrfsz6cxym9h8iaiqrrw5bzp2bbpmf05zr8y70jw59zg4ngh")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/prettyunits") (synopsis "Pretty, human readable formatting of quantities") (description "This package provides tools for pretty, human readable formatting of quantities.") (license license:expat))) (define-public r-princurve (package (name "r-princurve") (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "princurve" version)) (sha256 (base32 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/rcannood/princurve") (synopsis "Fit a principal curve in arbitrary dimension") (description "This package provides procedures for fitting a principal curve to a data matrix in arbitrary dimensions.") (license license:gpl2))) (define-public r-prismatic (package (name "r-prismatic") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "prismatic" version)) (sha256 (base32 "013i0mq4n8s2zbzvfrz1vjcn2a6l98bamslkcv1a3cn70gpphja9")))) (properties `((upstream-name . "prismatic"))) (build-system r-build-system) (propagated-inputs (list r-farver)) (home-page "https://github.com/EmilHvitfeldt/prismatic") (synopsis "Color manipulation tools") (description "Manipulate and visualize colors in a intuitive, low-dependency and functional way.") (license license:expat))) (define-public r-reshape (package (name "r-reshape") (version "0.8.9") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br")))) (build-system r-build-system) (propagated-inputs (list r-plyr)) (home-page "http://had.co.nz/reshape") (synopsis "Flexibly reshape data") (description "Flexibly restructure and aggregate data using just two functions: @code{melt} and @code{cast}. This package provides them.") (license license:expat))) (define-public r-restrserve (package (name "r-restrserve") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "RestRserve" version)) (sha256 (base32 "1xfcp0y9l31815g1jk33mnkb6z68qpjl0gb4fj7f4578kx3v1c8p")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-digest r-jsonlite r-mime r-r6 r-rcpp r-rserve r-uuid)) (native-inputs (list r-knitr)) (home-page "https://restrserve.org") (synopsis "R web API framework") (description "RestRserve is an R web API framework for building high-performance AND robust microservices and app backends. With Rserve backend on UNIX-like systems it is parallel by design. It will handle incoming requests in parallel - each request in a separate fork.") (license license:gpl2+))) (define-public r-progress (package (name "r-progress") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "progress" version)) (sha256 (base32 "0xljky4ad2jbbcfrcyh48li461pc5b2wk210n4x5rs2di6dhfaza")))) (build-system r-build-system) (propagated-inputs (list r-crayon r-hms r-prettyunits r-r6)) (home-page "https://github.com/gaborcsardi/progress") (synopsis "Terminal progress bars") (description "This package provides configurable progress bars. They may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The package also provides a C++ API, that works with or without Rcpp.") (license license:expat))) (define-public r-ggally (package (name "r-ggally") (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 "1pc0mcxhj3mz8ac6r1sqfxw1wkamikjal54z7pb1mairsr3hpqnw")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs (list openssl)) (propagated-inputs (list r-dplyr r-ggplot2 r-ggstats r-gtable r-lifecycle r-magrittr r-plyr r-progress r-rcolorbrewer r-rlang r-scales r-tidyr)) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description "The R package ggplot2 is a plotting system based on the grammar of graphics. GGally extends ggplot2 by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.") (license license:gpl2+))) (define-public r-proxy (package (name "r-proxy") (version "0.4-27") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 "0gsng2aggnljl4z82la9hpnd26hngzhj8fizx4wx22npqjj93694")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") (description "This package provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.") (license license:gpl2))) (define-public r-sp (package (name "r-sp") (version "2.1-2") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 "1i8d7sbccnhiw7pkmg89v98abjad45psyxccz1acbq4z5ykb9nxz")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/sp") (synopsis "Classes and methods for spatial data") (description "This package provides classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.") (license license:gpl2+))) (define-public r-lambertw (package (name "r-lambertw") (version "0.6.9-1") (source (origin (method url-fetch) (uri (cran-uri "LambertW" version)) (sha256 (base32 "19j6vjhywyzmrf7rsrx5kf0hg8cpk1gn8al24q813jzp0vsv9ljj")))) (properties `((upstream-name . "LambertW"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-lamw r-mass r-rcolorbrewer r-rcpp r-reshape2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=LambertW") (synopsis "Probabilistic models to analyze and Gaussianize heavy-tailed, skewed data") (description "Lambert W x F distributions are a generalized framework to analyze skewed, heavy-tailed data. It is based on an input/output system, where the output random variable (RV) Y is a non-linearly transformed version of an input RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed). The transformed RV Y has a Lambert W x F distribution. This package contains functions to model and analyze skewed, heavy-tailed data the Lambert Way: simulate random samples, estimate parameters, compute quantiles, and plot/ print results nicely. The most useful function is @code{Gaussianize}, which works similarly to @code{scale}, but actually makes the data Gaussian. A do-it-yourself toolkit allows users to define their own Lambert W x @code{MyFavoriteDistribution} and use it in their analysis right away.") (license license:gpl2+))) (define-public r-lamw (package (name "r-lamw") (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "lamW" version)) (sha256 (base32 "0jq3xq2ll4lpj8f5aqwazqlb978nzyk7hln4iwlzrlkkcqc35qm1")))) (properties `((upstream-name . "lamW"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppparallel)) (home-page "https://github.com/aadler/lamW") (synopsis "Lambert-W function") (description "This package implements both real-valued branches of the Lambert-W function (Corless et al, 1996) without the need for installing the entire GSL.") (license license:bsd-2))) (define-public r-laplacesdemon (package (name "r-laplacesdemon") (version "16.1.6") (source (origin (method url-fetch) (uri (cran-uri "LaplacesDemon" version)) (sha256 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap")))) (properties `((upstream-name . "LaplacesDemon"))) (build-system r-build-system) (home-page "https://github.com/LaplacesDemonR/LaplacesDemon") (synopsis "Complete environment for Bayesian inference") (description "This package provides a complete environment for Bayesian inference using a variety of different samplers.") (license license:expat))) (define-public r-rmtstat (package (name "r-rmtstat") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "RMTstat" version)) (sha256 (base32 "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v")))) (properties `((upstream-name . "RMTstat"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RMTstat") (synopsis "Distributions, statistics and tests derived from random matrix theory") (description "This package provides functions for working with the Tracy-Widom laws and other distributions related to the eigenvalues of large Wishart matrices.") (license license:bsd-3))) (define-public r-rmpi (package (name "r-rmpi") (version "0.7-2") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 "1vrf6bakx9i73sdgggpxzl1lxjn68b8pwvmk69d56lnya2gzm4c5")))) (properties `((upstream-name . "Rmpi") (updater-extra-inputs . ("openmpi")))) (build-system r-build-system) (arguments (list #:configure-flags '(list "--configure-args=\"--with-Rmpi-type=OPENMPI\"") #:phases #~(modify-phases %standard-phases (add-before 'install 'mpi-setup #$%openmpi-setup)))) (inputs (list openmpi)) (native-inputs (list pkg-config)) (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") (synopsis "R interface to message-passing interface (MPI)") (description "This package provides an interface (wrapper) to MPI APIs. It also provides an interactive R manager and worker environment.") (license license:gpl2+))) (define-public r-rmumps (package (name "r-rmumps") (version "5.2.1-26") (source (origin (method url-fetch) (uri (cran-uri "rmumps" version)) (sha256 (base32 "16ii9yg20xkxhsqszay42s4cr29k74av5d9d1d28kmpw6cjh2r2c")))) (properties `((upstream-name . "rmumps"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (native-inputs (list gfortran)) (home-page "https://www.mumps-solver.org/") (synopsis "Wrapper for MUMPS library") (description "Some basic features of @acronym{MUMPS, Multifrontal Massively Parallel sparse direct Solver} are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving. Third part ordering libraries are included and can be used: PORD, METIS, SCOTCH.") (license license:gpl2+))) (define-public r-lmoments (package (name "r-lmoments") (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "Lmoments" version)) (sha256 (base32 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw")))) (properties `((upstream-name . "Lmoments"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "http://www.tilastotiede.fi/juha_karvanen.html") (synopsis "L-moments and quantile mixtures") (description "This package contains functions to estimate L-moments and trimmed L-moments from the data. It also contains functions to estimate the parameters of the normal polynomial quantile mixture and the Cauchy polynomial quantile mixture from L-moments and trimmed L-moments.") (license license:gpl2))) (define-public r-distillery (package (name "r-distillery") (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b")))) (build-system r-build-system) (home-page "https://ral.ucar.edu/staff/ericg/") (synopsis "Functions for confidence intervals and object information") (description "This package provides some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with the packages extRemes and SpatialVx.") (license license:gpl2+))) (define-public r-etrunct (package (name "r-etrunct") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "etrunct" version)) (sha256 (base32 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr")))) (properties `((upstream-name . "etrunct"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/etrunct") (synopsis "Computes moments of univariate truncated T distribution") (description "This package computes moments of univariate truncated T distribution. There is only one exported function, @code{e_trunct}, which should be seen for details.") (license license:expat))) (define-public r-evd (package (name "r-evd") (version "2.3-6.1") (source (origin (method url-fetch) (uri (cran-uri "evd" version)) (sha256 (base32 "0wc95hfj0gwkyghipdrhwd3s6q2agh9x2wy6y7dr6mjw7wnmjb36")))) (properties `((upstream-name . "evd"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=evd") (synopsis "Functions for extreme value distributions") (description "This package extends simulation, distribution, quantile and density functions to univariate and multivariate parametric extreme value distributions, and provides fitting functions which calculate maximum likelihood estimates for univariate and bivariate maxima models, and for univariate and bivariate threshold models.") (license license:gpl3))) (define-public r-evmix (package (name "r-evmix") (version "2.12") (source (origin (method url-fetch) (uri (cran-uri "evmix" version)) (sha256 (base32 "02rabc9snci00s1x7h0svfr66lmw1wjcdg0149wc52mnccsdaivf")))) (properties `((upstream-name . "evmix"))) (build-system r-build-system) (propagated-inputs (list r-gsl r-mass r-sparsem)) (home-page "http://www.math.canterbury.ac.nz/~c.scarrott/evmix.shtml") (synopsis "Extreme value threshold estimation and uncertainty quantification") (description "This package provides the usual distribution functions, maximum likelihood inference and model diagnostics for univariate stationary extreme value mixture models. Also, there are provided kernel density estimation including various boundary corrected kernel density estimation methods and a wide choice of kernels, with cross-validation likelihood based bandwidth estimator. Reasonable consistency with the base functions in the evd package is provided, so that users can safely interchange most code.") (license license:gpl3))) ;; This package contains minified JavaScript: jExcel CE Spreadsheet, ;; version 3.9.1. It is not clear how to obtain this particular ;; version as there is no tag for 3.9.1. There only is 3.6.1 and ;; 4.2.0 at https://github.com/jspreadsheet/ce. (define-public r-excelr (package (name "r-excelr") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "excelR" version)) (sha256 (base32 "1pb4sy54zjv5vrh7gjjv7qlpab74km6mfsmfyl0yhmr0jx01hrw0")) (snippet '(delete-file "inst/htmlwidgets/lib/jexcel/js/jexcel.min.js")))) (properties `((upstream-name . "excelR"))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/jexcel/js" (minify (search-input-file inputs "/dist/jexcel.js") #:target "jexcel.min.js"))))))) (propagated-inputs (list r-htmlwidgets r-jsonlite)) (native-inputs (list esbuild ;; There is no tag for this particular commit, but comparison of ;; the contents of the JavaScript files point to this commit as the ;; most likely source. (let* ((commit "8af1960f76e6803bebc5750013d2ebe95354e88a") (version (git-version "3.9.1" "0" commit))) (origin (method git-fetch) (uri (git-reference (url "https://github.com/jspreadsheet/ce") (commit commit))) (file-name (git-file-name "jexcel" version)) (sha256 (base32 "1zk0wc4h0vax7zgimhwqq2icrvjr84agm3qv42l16gim7gq7fqfq")))))) (home-page "https://github.com/Swechhya/excelR") (synopsis "Wrapper of the JavaScript library jExcel") (description "This package provides an R interface to the jExcel library to create web-based interactive tables and spreadsheets compatible with spreadsheet software.") (license license:expat))) (define-public r-extremes (package (name "r-extremes") (version "2.1-3") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 "0h1w177vz3z58vbqrfbiqapf9z2qsd7gcbv8fnbyn0i5akfz1k71")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs (list r-distillery r-lmoments)) (home-page "https://www.assessment.ucar.edu/toolkit/") (synopsis "Extreme value analysis") (description "ExtRemes is a suite of functions for carrying out analyses on the extreme values of a process of interest; be they block maxima over long blocks or excesses over a high threshold.") (license license:gpl2+))) (define-public r-lmtest (package (name "r-lmtest") (version "0.9-40") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 "15yr2kx08wy085bnziqmj1p6hf9mg3qp2a8465jk2df6di6hsh34")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/lmtest") (synopsis "Testing linear regression models") (description "This package provides a collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.") ;; Either version is okay (license (list license:gpl2 license:gpl3)))) (define-public r-idr (package (name "r-idr") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "idr" version)) (sha256 (base32 "1r6icxf0c0y9wvihwmkk5xqscr1qhacqk3w2076kjm2993f10fbb")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/idr/") (synopsis "Irreproducible discovery rate") (description "This is a package for estimating the copula mixture model and plotting correspondence curves in \"Measuring reproducibility of high-throughput experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel") (license license:gpl2+))) (define-public r-inext (package (name "r-inext") (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "iNEXT" version)) (sha256 (base32 "1yfvadvdwgby047svj9sjwkm7hhrni2ifn6d2g5bv9djcvi22msh")))) (properties `((upstream-name . "iNEXT"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-reshape2)) (native-inputs (list r-knitr)) (home-page "http://chao.stat.nthu.edu.tw/wordpress/software_download/") (synopsis "Interpolation and extrapolation for species diversity") (description "This package provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation curves for species diversity (Hill numbers) based on individual-based abundance data or sampling-unit- based incidence data; see Chao and others (2014, Ecological Monographs) for pertinent theory and methodologies, and Hsieh, Ma and Chao (2016, Methods in Ecology and Evolution) for an introduction of the R package.") (license license:gpl3+))) (define-public r-inline (package (name "r-inline") (version "0.3.19") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") (description "This package provides functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and @code{.Call} calling conventions.") ;; Any version of the LGPL. (license license:lgpl3+))) (define-public r-inum (package (name "r-inum") (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "inum" version)) (sha256 (base32 "1gbbsffbzxjrgi8yw21fl35fsbx7ns8hdrhja50byfqvnghbg5p6")))) (build-system r-build-system) (propagated-inputs (list r-libcoin)) (home-page "https://cran.r-project.org/web/packages/inum/") (synopsis "Interval and enum-type representation of vectors") (description "This package provides an enum-type representation of vectors and representation of intervals, including a method of coercing variables in data frames.") (license license:gpl2))) (define-public r-invgamma (package (name "r-invgamma") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "invgamma" version)) (sha256 (base32 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a")))) (properties `((upstream-name . "invgamma"))) (build-system r-build-system) (home-page "https://github.com/dkahle/invgamma") (synopsis "Inverse gamma distribution") (description "This package provides a light weight implementation of the standard distribution functions for the inverse gamma distribution, wrapping those for the gamma distribution in the @code{stats} package.") (license license:gpl2))) (define-public r-bdsmatrix (package (name "r-bdsmatrix") (version "1.3-6") (source (origin (method url-fetch) (uri (cran-uri "bdsmatrix" version)) (sha256 (base32 "1g300x11rv56f826mbv7mbb67a5xz3dv74hpjc18jh3q8gap3j7r")))) (properties `((upstream-name . "bdsmatrix"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bdsmatrix/") (synopsis "Routines for block diagonal symmetric matrices") (description "This package provides procedures to work with block diagonal symmetric matrices, a special case of sparse matrices.") (license license:lgpl2.0))) (define-public r-bbmle (package (name "r-bbmle") (version "1.0.25.1") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 "02xnfmjr5ax5pc69jkxmygkwvb68flrf1x8pxfw0hk7y37w0qanr")))) (build-system r-build-system) (propagated-inputs (list r-bdsmatrix r-lattice r-mass r-matrix r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description "This package provides methods and functions for fitting maximum likelihood models in R. This package modifies and extends the @code{mle} classes in the @code{stats4} package.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-emdbook (package (name "r-emdbook") (version "1.3.13") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 "069w10i1590bcyzv4kfsg7wsr1yl9nlsyj6yvys088xll5z4n116")))) (build-system r-build-system) (propagated-inputs (list r-bbmle r-coda r-lattice r-mass r-plyr)) (home-page "https://www.math.mcmaster.ca/bolker/emdbook") (synopsis "Support functions and data for \"Ecological Models and Data\"") (description "This package provides auxiliary functions and data sets for \"Ecological Models and Data\", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).") ;; Any GPL version (license (list license:gpl2 license:gpl3)))) (define-public r-lpsolve (package (name "r-lpsolve") (version "5.6.20") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 "1nr1vjz6ma42kxbcay4g9j30r9srkbw79f06sdnc68sid2h0dziz")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") (synopsis "R interface to Lp_solve to solve linear/integer programs") (description "Lp_solve is software for solving linear, integer and mixed integer programs. This implementation supplies a \"wrapper\" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems.") (license license:lgpl2.0))) (define-public r-limsolve (package (name "r-limsolve") (version "1.5.7") (source (origin (method url-fetch) (uri (cran-uri "limSolve" version)) (sha256 (base32 "1waqkkipks8h4h5lpn0xw0077hwpz963q42h7xv6f70p07zncxq4")))) (properties `((upstream-name . "limSolve"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-mass r-quadprog)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/limSolve") (synopsis "Solving linear inverse models") (description "This package provides functions that: @enumerate @item find the minimum/maximum of a linear or quadratic function, @item sample an underdetermined or overdetermined system, @item solve a linear system Ax=B for the unknown x. @end enumerate It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.") ;; Any GPL version. (license (list license:gpl2+ license:gpl3+)))) (define-public r-littler (package (name "r-littler") (version "0.3.19") (source (origin (method url-fetch) (uri (cran-uri "littler" version)) (sha256 (base32 "02b5lfdhajngs2l0fgy47zn7zn68qbx6m41cs5yzzi80qdfapkz1")))) (properties `((upstream-name . "littler") (updater-extra-inputs . ("icu4c" "zlib")))) (build-system r-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'install 'install-executable (lambda _ (install-file "inst/bin/r" (string-append #$output "/bin"))))))) (inputs (list icu4c zlib)) (native-inputs (list r-simplermarkdown)) (home-page "https://github.com/eddelbuettel/littler") (synopsis "R at the command-line via r") (description "This package provides a scripting and command-line front-end is provided by r (aka littler) as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both shebang-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard pipelines. In other words, r provides the R language without the environment.") (license license:gpl2+))) (define-public r-fitdistrplus (package (name "r-fitdistrplus") (version "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 "0gdm06anjmihfj1d0yiqy36d887kmc0d8553pjl1f90bf4mly9r6")))) (build-system r-build-system) (propagated-inputs (list r-mass r-survival)) (native-inputs (list r-knitr)) (home-page "https://riskassessment.r-forge.r-project.org") (synopsis "Fitting a parametric distribution from data") (description "This package extends the @code{fitdistr} function of the MASS package with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left-censored, right-censored and interval-censored values, with several lower and upper bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.") (license license:gpl2+))) (define-public r-energy (package (name "r-energy") (version "1.7-11") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 "04b55ckmaqbnlpifg4w7smvly03kqycklvbg9x8d4yf902q8z7y2")))) (build-system r-build-system) (propagated-inputs (list r-boot r-gsl r-rcpp)) (home-page "https://cran.r-project.org/web/packages/energy") (synopsis "Multivariate inference via the energy of data") (description "This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.") (license license:gpl2+))) (define-public r-envstats (package (name "r-envstats") (version "2.8.1") (source (origin (method url-fetch) (uri (cran-uri "EnvStats" version)) (sha256 (base32 "19nnab201yalxbgpvpp5lkgqs0m17b5plsswmaxbvdv4mag2p58j")))) (properties `((upstream-name . "EnvStats"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-mass r-nortest)) (home-page "https://github.com/alexkowa/EnvStats") (synopsis "Package for environmental statistics, including US EPA guidance") (description "This is a package for graphical and statistical analyses of environmental data, with a focus on analyzing chemical concentrations and physical parameters, usually in the context of mandated environmental monitoring. It provides major environmental statistical methods found in the literature and regulatory guidance documents, with extensive help that explains what these methods do, how to use them, and where to find them in the literature. It comes with numerous built-in data sets from regulatory guidance documents and environmental statistics literature. It includes scripts reproducing analyses presented in the book \"EnvStats: An R Package for Environmental Statistics\" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, @url{https://link.springer.com/book/10.1007/978-1-4614-8456-1}).") (license license:gpl3+))) (define-public r-suppdists (package (name "r-suppdists") (version "1.1-9.7") (source (origin (method url-fetch) (uri (cran-uri "SuppDists" version)) (sha256 (base32 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb")))) (properties `((upstream-name . "SuppDists"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/SuppDists") (synopsis "Supplementary distributions") (description "This package provides ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. In addition two random number generators of George Marsaglia are included.") (license license:gpl2+))) (define-public r-kpmt (package (name "r-kpmt") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "kpmt" version)) (sha256 (base32 "15d26khc0v3kc1c7l1avqp48pfqmc6xj32029mv7myivr41ashk3")))) (properties `((upstream-name . "kpmt"))) (build-system r-build-system) (propagated-inputs (list r-matrixstats)) (home-page "https://cran.r-project.org/package=kpmt") (synopsis "Known population median test") (description "This package provides functions that implement the known population median test.") (license license:expat))) (define-public r-ksamples (package (name "r-ksamples") (version "1.2-10") (source (origin (method url-fetch) (uri (cran-uri "kSamples" version)) (sha256 (base32 "13ap5ggid3w3s3k5mzz1ir31j96hjg6msa2s1hcy66zv242wqrid")))) (properties `((upstream-name . "kSamples"))) (build-system r-build-system) (propagated-inputs (list r-suppdists)) (home-page "https://cran.r-project.org/web/packages/kSamples") (synopsis "K-Sample rank tests and their combinations") (description "This package provides tools to compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples.") (license license:gpl2+))) (define-public r-cvst (package (name "r-cvst") (version "0.2-3") (source (origin (method url-fetch) (uri (cran-uri "CVST" version)) (sha256 (base32 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg")))) (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs (list r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/CVST") (synopsis "Fast cross-validation via sequential testing") (description "This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.") (license license:gpl2+))) (define-public r-cvxr (package (name "r-cvxr") (version "1.0-11") (source (origin (method url-fetch) (uri (cran-uri "CVXR" version)) (sha256 (base32 "0alp1g4bszxqcrjbn54bz1zswg8y10372fwwlbi0jjazycw9cap9")))) (properties `((upstream-name . "CVXR"))) (build-system r-build-system) (propagated-inputs (list r-bit64 r-ecosolver r-gmp r-matrix r-osqp r-r6 r-rcpp r-rcppeigen r-rmpfr r-scs)) (native-inputs (list r-knitr)) (home-page "https://cvxr.rbind.io") (synopsis "Disciplined convex optimization") (description "This package provides an object-oriented modeling language for @dfn{disciplined convex programming} (DCP) as described in Fu, Narasimhan, and Boyd (2020, ). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided.") (license license:asl2.0))) (define-public r-squarem (package (name "r-squarem") (version "2021.1") (source (origin (method url-fetch) (uri (cran-uri "SQUAREM" version)) (sha256 (base32 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6")))) (properties `((upstream-name . "SQUAREM"))) (build-system r-build-system) (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html") (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms") (description "This package provides algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette.") (license license:gpl2+))) (define-public r-progressr (package (name "r-progressr") (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 (base32 "1bsqcarh38z86klcm5iaqmf6akgy5gaii7797c27ymx5g7w9ja4s")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs (list r-digest)) (home-page "https://progressr.futureverse.org") (synopsis "Inclusive, unifying API for progress updates") (description "This package provides a minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates.") (license license:gpl3+))) (define-public r-lava (package (name "r-lava") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 "023av1mz4hr1lqv8cpbx0j1y3c7ljyns35rm838c618b6pqps22f")))) (build-system r-build-system) (propagated-inputs (list r-future-apply r-numderiv r-progressr r-squarem r-survival)) (native-inputs (list r-knitr)) (home-page "https://github.com/kkholst/lava") (synopsis "Latent variable models") (description "This package provides tools for the estimation and simulation of latent variable models.") (license license:gpl3))) (define-public r-drat (package (name "r-drat") (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "drat" version)) (sha256 (base32 "13v7dj2688ix6j9nzhvf8q9ynfihwzkppfdjkis6q1r5m4nikya3")))) (properties `((upstream-name . "drat"))) (build-system r-build-system) (native-inputs (list r-simplermarkdown)) (home-page "https://github.com/eddelbuettel/drat") (synopsis "Drat R archive template") (description "This package helps you with creation and use of R repositories via helper functions to insert packages into a repository, and to add repository information to the current R session. Two primary types of repositories are supported: gh-pages at GitHub, as well as local repositories on either the same machine or a local network. Drat is a recursive acronym: Drat R Archive Template.") (license license:gpl2+))) (define-public r-drr (package (name "r-drr") (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "DRR" version)) (sha256 (base32 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk")))) (properties `((upstream-name . "DRR"))) (build-system r-build-system) (propagated-inputs (list r-cvst r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/DRR") (synopsis "Dimensionality reduction via regression") (description "This package provides an implementation of dimensionality reduction via regression using Kernel Ridge Regression.") (license license:gpl3))) (define-public r-prodlim (package (name "r-prodlim") (version "2023.08.28") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 "1s2xalxfq2q6a9ssz01vzpldpa98q3cl5icap0k2xr5v72gj40l0")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-diagram r-kernsmooth r-lava r-rcpp r-survival)) (home-page "https://cran.r-project.org/web/packages/prodlim") (synopsis "Product-limit estimation for censored event history analysis") (description "This package provides a fast and user-friendly implementation of nonparametric estimators for censored event history (survival) analysis with the Kaplan-Meier and Aalen-Johansen methods.") (license license:gpl2+))) (define-public r-dimred (package (name "r-dimred") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 "05zlkf6hjdqqr1sgw7ww9f17vjnsiqfaj9kvdvi146phh53v2zls")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs (list r-drr r-magrittr)) (native-inputs (list r-knitr)) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description "This package provides a collection of dimensionality reduction techniques from R packages and provides a common interface for calling the methods.") (license license:gpl3))) (define-public r-timechange (package (name "r-timechange") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "timechange" version)) (sha256 (base32 "1wgpab9dvmvkfb1p1arj0knb8qal9hazbhx5jkpxl8r10l420q1x")))) (properties `((upstream-name . "timechange"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) (home-page "https://github.com/vspinu/timechange/") (synopsis "Efficient manipulation of Date-Times") (description "This package provides efficient routines for manipulation of date-time objects while accounting for time-zones and daylight saving times. The package includes utilities for updating of date-time components (year, month, day etc.), modification of time-zones, rounding of date-times, period addition and subtraction etc. Parts of the CCTZ source code, released under the Apache 2.0 License, are included in this package.") (license license:gpl3))) (define-public r-timedate (package (name "r-timedate") (version "4032.109") (source (origin (method url-fetch) (uri (cran-uri "timeDate" version)) (sha256 (base32 "0n5rzi3bb1wjpqcgpxcagjy815vy8ksjzpkkjzs3333yljyl2a20")))) (properties `((upstream-name . "timeDate"))) (build-system r-build-system) (home-page "https://www.rmetrics.org") (synopsis "Chronological and calendar objects") (description "This package provides an environment for teaching \"Financial Engineering and Computational Finance\" and for managing chronological and calendar objects.") (license license:gpl2+))) (define-public r-magic (package (name "r-magic") (version "1.6-1") (source (origin (method url-fetch) (uri (cran-uri "magic" version)) (sha256 (base32 "0xkrrg5qk62pfqx0avijdjaljzslpwd0hv2m52qnqwrbx5xfqyfa")))) (build-system r-build-system) (propagated-inputs (list r-abind)) (home-page "https://github.com/RobinHankin/magic.git") (synopsis "Create and investigate magic squares") (description "This package provides a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.") (license license:gpl2))) (define-public r-magicaxis (package (name "r-magicaxis") (version "2.2.14") (source (origin (method url-fetch) (uri (cran-uri "magicaxis" version)) (sha256 (base32 "1gqnivn6qjmf7axdi0pff6a40clklbipcr6qvm6ivzqbqhpbcb7v")))) (properties `((upstream-name . "magicaxis"))) (build-system r-build-system) (propagated-inputs (list r-celestial r-mapproj r-mass r-plotrix r-rann r-sm)) (home-page "https://cran.r-project.org/package=magicaxis") (synopsis "Scientific plotting with minor-tick and log minor-tick support") (description "This package provides functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.") (license license:gpl3))) (define-public r-rmysql (package (name "r-rmysql") (version "0.10.27") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 "1axz0pqvpqs028p2j7awmgdwpignl7m3hqd1fv3vkgfrkil5nwzi")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs (list `(,mariadb "dev") zlib)) (propagated-inputs (list r-dbi)) (home-page "https://github.com/r-dbi/RMySQL") (synopsis "Database interface and MySQL driver for R") (description "This package provides a DBI interface to MySQL / MariaDB. The RMySQL package contains an old implementation based on legacy code from S-PLUS which is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.") (license license:gpl2))) (define-public r-rpmm (package (name "r-rpmm") (version "1.25") (source (origin (method url-fetch) (uri (cran-uri "RPMM" version)) (sha256 (base32 "1j48dh434wfhfzka0l21w6f73qlwfm70r9gdddhn504i2d5m4jph")))) (properties `((upstream-name . "RPMM"))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/package=RPMM") (synopsis "Recursively partitioned mixture model") (description "This package provides a recursively partitioned mixture model for Beta and Gaussian mixtures. This is a model-based clustering algorithm that returns a hierarchy of classes, similar to hierarchical clustering, but also similar to finite mixture models.") (license license:gpl2+))) (define-public r-rpostgresql (package (name "r-rpostgresql") (version "0.7-6") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 "0b1dmx5pcd4v1xg25ihxilkga3zdblb1xy896ik5fdkaidq3jn9q")))) (properties '((upstream-name . "RPostgreSQL") (updater-extra-inputs . ("postgresql")))) (build-system r-build-system) (inputs (list postgresql)) (propagated-inputs (list r-dbi)) (home-page "https://github.com/tomoakin/RPostgreSQL") (synopsis "R interface to the PostgreSQL database system") (description "This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems.") ;; The whole package is released under GPL version 2. It includes code ;; under the PostgreSQL license. (license license:gpl2))) (define-public r-rpostgres (package (name "r-rpostgres") (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "RPostgres" version)) (sha256 (base32 "1ld03r9rzfxx6gzy3yn8jhzp9sp2qd9wydpxz955ggjxwdklpvnr")))) (properties `((upstream-name . "RPostgres"))) (build-system r-build-system) (inputs (list postgresql)) (propagated-inputs (list r-bit64 r-blob r-cpp11 r-dbi r-hms r-lubridate r-plogr r-withr)) (native-inputs (list pkg-config r-knitr)) (home-page "https://rpostgres.r-dbi.org") (synopsis "Rcpp Interface to PostgreSQL") (description "This package provides a fully @code{DBI}-compliant @code{Rcpp}-backed interface to @code{PostgreSQL}, a relational database.") (license license:gpl3))) (define-public r-linprog (package (name "r-linprog") (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "linprog" version)) (sha256 (base32 "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1")))) (build-system r-build-system) (propagated-inputs (list r-lpsolve)) (home-page "https://linprog.r-forge.r-project.org/") (synopsis "Linear programming and optimization") (description "This package can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm.") (license license:gpl2+))) (define-public r-geometry (package (name "r-geometry") (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 "0fq1sbjlc02idfsnvily7hgi6zgjvrjh7c57wz166k8vyl2l484n")))) (build-system r-build-system) (propagated-inputs (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress)) (home-page "https://geometry.r-forge.r-project.org/") (synopsis "Mesh generator and surface tessellator") (description "This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this. Currently the package only gives access to Delaunay triangulation and convex hull computation.") ;; The Qhull sources are included and are distributed under a custom ;; non-copyleft license. The R sources are released under GPL version 2. (license (list license:gpl2 (license:non-copyleft "http://www.qhull.org/COPYING.txt"))))) (define-public r-ddalpha (package (name "r-ddalpha") (version "1.3.15") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 "1vgyg1c2ir93nsbh4xlm774b6rhx14pyr069dpcl9vwcx2j989qc")))) (build-system r-build-system) (propagated-inputs (list r-bh r-class r-geometry r-mass r-rcpp r-robustbase r-sfsmisc)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ddalpha") (synopsis "Depth-Based classification and calculation of data depth") (description "This package contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.") (license license:gpl2))) (define-public r-gower (package (name "r-gower") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "gower" version)) (sha256 (base32 "1z0mhfp8xp7rk9i820pkvspm6mwih24g6b5rqs63m37sbs79ssi9")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/gower") (synopsis "Gower's distance") (description "This package provides tools to compute Gower's distance (or similarity) coefficient between records, and to compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.") (license license:gpl3))) (define-public r-rcpproll (package (name "r-rcpproll") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppRoll" version)) (sha256 (base32 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) (properties `((upstream-name . "RcppRoll"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppRoll") (synopsis "Efficient rolling and windowed operations") (description "This package provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.") (license license:gpl2+))) (define-public r-ipred (package (name "r-ipred") (version "0.9-14") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 "0dcgabbqk7lb8pfqs06ix87caf5c9p6kcppi5sskv76h8z43vj41")))) (build-system r-build-system) (propagated-inputs (list r-class r-mass r-nnet r-prodlim r-rpart r-survival)) (home-page "https://cran.r-project.org/web/packages/ipred") (synopsis "Improved predictors") (description "This package provides improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.") (license license:gpl2+))) (define-public r-psych (package (name "r-psych") (version "2.3.12") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 "0q8qms180gxk7wlm8li3j5r8rwniqj01xfm00gkvkc8q9djcsm8p")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mnormt r-nlme)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/psych/") (synopsis "Procedures for psychological, psychometric, and personality research") (description "This package provides a general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics.") (license license:gpl2+))) (define-public r-generics (package (name "r-generics") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "generics" version)) (sha256 (base32 "0lyhhwik0w7m5h3fbwl2f52gc1v2g6g6h6sc47sa9f58pxin213m")))) (build-system r-build-system) (home-page "https://github.com/r-lib/generics") (synopsis "Common S3 generics not provided by base R methods") (description "In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics that are not provided by base R methods related to model fitting.") (license license:gpl2))) (define-public r-broom (package (name "r-broom") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 "14fr17cvpy6jzdffzrf46xah70xcq2nkbjyxmkyzwbz3kvpdsxwx")))) (build-system r-build-system) (propagated-inputs (list r-backports r-dplyr r-ellipsis r-generics r-glue r-lifecycle r-purrr r-rlang r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") (description "This package provides tools to convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like @code{dplyr}, @code{tidyr} and @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which summarizes a model's statistical findings such as coefficients of a regression; @code{augment}, which adds columns to the original data such as predictions, residuals and cluster assignments; and @code{glance}, which provides a one-row summary of model-level statistics.") (license license:expat))) (define-public r-recipes (package (name "r-recipes") (version "1.0.9") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 "146p9ij2i4rmzaa5v76lm7z8iaw5wqb47i9cqf4a0q7xsgqvf6hi")))) (build-system r-build-system) (propagated-inputs (list r-cli r-clock r-dplyr r-ellipsis r-generics r-glue r-gower r-hardhat r-ipred r-lifecycle r-lubridate r-magrittr r-matrix r-purrr r-rlang r-tibble r-tidyr r-tidyselect r-timedate r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description "Recipes is an extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis \"steps\". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.") (license license:gpl2))) (define-public r-pdist (package (name "r-pdist") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "pdist" version)) (sha256 (base32 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406")))) (build-system r-build-system) (home-page "https://github.com/jeffwong/pdist") (synopsis "Partitioned distance function") (description "Pdist computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling @code{dist}, but this creates unnecessary computation by computing the distances between a row of X and another row of X, and likewise for Y. Pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.") (license license:gpl3+))) (define-public r-ggrepel (package (name "r-ggrepel") (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 "1alcrw304bn6c2i64rxxjkzk3il19gq30gyj3sb4blradkjh1rni")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-rlang r-scales r-withr)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/slowkow/ggrepel") (synopsis "Repulsive text and label geometries for ggplot2") (description "This package provides text and label geometries for ggplot2 that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.") (license license:gpl3))) (define-public r-coro (package (name "r-coro") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "coro" version)) (sha256 (base32 "0wvxdpdh3xrskz5s5wfkva856x849knx1jigbf0ff6s6n6qjjxsf")))) (properties `((upstream-name . "coro"))) (build-system r-build-system) (propagated-inputs (list r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/coro") (synopsis "Coroutines for R") (description "This package provides coroutines for R, a family of functions that can be suspended and resumed later on. This includes async functions (which await) and generators (which yield). Async functions are based on the concurrency framework of the @code{promises} package. Generators are based on a dependency free iteration protocol defined in @code{coro} and are compatible with iterators from the @code{reticulate} package.") (license license:expat))) (define-public r-corrplot (package (name "r-corrplot") (version "0.92") (source (origin (method url-fetch) (uri (cran-uri "corrplot" version)) (sha256 (base32 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/taiyun/corrplot") (synopsis "Visualization of a correlation matrix") (description "This package provides a graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including choosing color, text labels, color labels, layout, etc.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-stable (package (name "r-stable") (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "stable" version)) (sha256 (base32 "194xsa291v5f0jya1c3aigbclg8cci427ffpb8brxamm6n57hf12")))) (properties `((upstream-name . "stable"))) (build-system r-build-system) (propagated-inputs (list r-rmutil)) (home-page "https://www.commanster.eu/rcode.html") (synopsis "Probability functions and regression models for stable distributions") (description "This package provides density, distribution, quantile and hazard functions of a stable variate, as well as generalized regression models for the parameters of a stable distribution.") (license license:gpl2+))) (define-public r-statip (package (name "r-statip") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "statip" version)) (sha256 (base32 "0kymc3ds1nx0h11ffmm3vmqr1w34gd0k788vf72x2v45h8c1ma2n")))) (properties `((upstream-name . "statip"))) (build-system r-build-system) (propagated-inputs (list r-clue r-rpart)) (home-page "https://github.com/paulponcet/statip") (synopsis "Statistical functions for probability distributions and regression") (description "This package provides a collection of miscellaneous statistical functions for: @itemize @item probability distributions, @item probability density estimation, @item most frequent value estimation, @item other statistical measures of location, @item construction of histograms, @item calculation of the Hellinger distance, @item use of classical kernels, and @item univariate piecewise-constant regression. @end itemize") (license license:gpl3))) (define-public r-statsexpressions (package (name "r-statsexpressions") (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "statsExpressions" version)) (sha256 (base32 "0ixchra1vjqhnzi4r0db1bmjk3h1xqcqc6pymxdjxz3jqbsmmy7n")))) (properties `((upstream-name . "statsExpressions"))) (build-system r-build-system) (propagated-inputs (list r-afex r-bayesfactor r-correlation r-datawizard r-dplyr r-effectsize r-glue r-insight r-magrittr r-parameters r-performance r-pmcmrplus r-purrr r-rlang r-tibble r-tidyr r-withr r-wrs2 r-zeallot)) (native-inputs (list r-knitr)) (home-page "https://indrajeetpatil.github.io/statsExpressions/") (synopsis "Dataframes and expressions with statistical details") (description "This package provides tools for creating detailed dataframes for common statistical approaches and tests. These include parametric, nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation analyses, contingency table analyses, and meta-analyses. The functions are pipe-friendly and provide a consistent syntax to work with tidy data. These dataframes additionally contain expressions with statistical details, and can be used in graphing packages. This package also forms the statistical processing backend for ggstatsplot.") (license license:gpl3))) (define-public r-strawr (package (name "r-strawr") (version "0.0.91") (source (origin (method url-fetch) (uri (cran-uri "strawr" version)) (sha256 (base32 "1nbcn20g3f3f5x9sscj3020n5h4iaphr70s90n2fz31vc4snzq2m")))) (properties `((upstream-name . "strawr"))) (build-system r-build-system) (inputs (list curl zlib)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/aidenlab/straw/tree/master/R") (synopsis "Fast implementation of reading / dumping of .hic files") (description "This package provides an API for efficient @file{.hic} file data extraction with programmatic matrix access. It doesn't store the pointer data for all the matrices, only the one queried, and currently it only supports matrices.") (license license:expat))) (define-public r-stringdist (package (name "r-stringdist") (version "0.9.12") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 "1i365vwjx8kk47wzry8d3zhzrlv51hn76s2ipk9vi121zx939171")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") (description "This package implements an approximate string matching version of R's native @code{match} function. It can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.") (license license:gpl3+))) (define-public r-uchardet (package (name "r-uchardet") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "uchardet" version)) (sha256 (base32 "0m3xy807smqdxhkhd9cwrcf3ljlyvfmnkd7831qzpgcadam2jcdj")))) (properties `((upstream-name . "uchardet"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://artemklevtsov.gitlab.io/uchardet") (synopsis "Universal character encoding detector") (description "This package provides R bindings to the uchardet encoding detector library from Mozilla. It takes a sequence of bytes in an unknown character encoding without any additional information, and attempts to get the encoding of the text. All return names of the encodings are iconv-compatible.") (license license:gpl2))) (define-public r-ucminf (package (name "r-ucminf") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ucminf" version)) (sha256 (base32 "10ycpzxx73div9vpzmkhy524yd47kzmpl7ajpm248clsv6ivngpd")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ucminf/") (synopsis "General-purpose unconstrained non-linear optimization") (description "This package provides an implementation of an algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of @code{ucminf} is designed for easy interchange with the package @code{optim}.") (license license:gpl2+))) (define-public r-usedist (package (name "r-usedist") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "usedist" version)) (sha256 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj")))) (properties `((upstream-name . "usedist"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=usedist") (synopsis "Distance matrix utilities") (description "This package provides functions to re-arrange, extract, and work with distances.") (license license:gpl3))) (define-public r-useful (package (name "r-useful") (version "1.2.6.1") (source (origin (method url-fetch) (uri (cran-uri "useful" version)) (sha256 (base32 "1gb9hqvbm6pr56dfqlsgz26lan7xargfsm8jpdja18mpgli2gyvc")))) (properties `((upstream-name . "useful"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-dplyr r-ggplot2 r-magrittr r-matrix r-plyr r-purrr r-scales)) (home-page "https://github.com/jaredlander/useful") (synopsis "Collection of handy, useful functions") (description "This package provides a set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing parts of a @code{data.frame}, constructing formulas from text and building design and response matrices.") (license license:bsd-3))) (define-public r-ordinal (package (name "r-ordinal") (version "2023.12-4") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 "18lzpmf36vvc3krk7jqz7naikhrcdyplj2z9y6xgzlnzhgcjln7m")))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix r-nlme r-numderiv r-ucminf)) (home-page "https://github.com/runehaubo/ordinal") (synopsis "Regression models for ordinal data") (description "This package provides an implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered models. Estimation is via maximum likelihood and mixed models are fitted with the Laplace approximation and adaptive Gauss-Hermite quadrature.") (license license:gpl2+))) (define-public r-jomo (package (name "r-jomo") (version "2.7-6") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 "1np2sw0kq21kdhkv227pz2rqvpxg06r3mk93ggkrz5nl45ajmyiz")))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-mass r-ordinal r-survival r-tibble)) (home-page "https://cran.r-project.org/web/packages/jomo/") (synopsis "Multilevel Joint Modelling Multiple Imputation") (description "Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation @url{Carpenter and Kenward (2013), http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.") (license license:gpl2))) (define-public r-pan (package (name "r-pan") (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 "0liwcym035174h6c4b9ddmqxa3vkpkk3alyr9psk8yhv7i61hzp3")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pan/") (synopsis "Multiple imputation for multivariate panel or clustered data") (description "This package implements multiple imputation for multivariate panel or clustered data.") (license license:gpl3))) (define-public r-mitml (package (name "r-mitml") (version "0.4-5") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 "1szfw993ma4qn377bab08bkvm4s0sxs5x2hdcj9kgk47661fqsh5")))) (build-system r-build-system) (propagated-inputs (list r-haven r-jomo r-pan)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/mitml/") (synopsis "Tools for multiple imputation in multilevel modeling") (description "This package provides tools for multiple imputation of missing data in multilevel modeling. It includes a user-friendly interface to the packages pan and jomo, and several functions for visualization, data management and the analysis of multiply imputed data sets.") (license license:gpl2+))) (define-public r-mice (package (name "r-mice") (version "3.16.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 "0h20lirk2257y3i1ww5y2pqp9lc21ilmf8yykmz36h55hm8jiw19")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cpp11 r-dplyr r-generics r-glmnet r-lattice r-mitml r-nnet r-rcpp r-rlang r-rpart r-tidyr)) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") (description "Multiple imputation using @dfn{Fully Conditional Specification} (FCS) implemented by the MICE algorithm as described in @url{Van Buuren and Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.") ;; Any of these two versions. (license (list license:gpl2 license:gpl3)))) (define-public r-truncnorm (package (name "r-truncnorm") (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "truncnorm" version)) (sha256 (base32 "0267gvcg6mmf28x26z6njw373prwpaq8aqkd6aavyhrjsv2aqmji")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/truncnorm/") (synopsis "Truncated normal distribution") (description "This package provides functions for the truncated normal distribution with mean equal to @code{mean} and standard deviation equal to @code{sd}. It includes density, distribution, quantile, and expected value functions, as well as a random generation function.") (license license:gpl2))) (define-public r-truncdist (package (name "r-truncdist") (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "truncdist" version)) (sha256 (base32 "02ihw4ixhadwr3sqm6r264i8vpcaz8pn69vkzabd8fwqvn5vcj5q")))) (properties `((upstream-name . "truncdist"))) (build-system r-build-system) (propagated-inputs (list r-evd)) (home-page "https://cran.r-project.org/package=truncdist") (synopsis "Truncated random variables") (description "This package provides a collection of tools to evaluate probability density functions, cumulative distribution functions, quantile functions and random numbers for truncated random variables. These functions are provided to also compute the expected value and variance. @acronym{Q-Q, quantile–quantile} plots can be produced. All the probability functions in the stats, stats4 and evd packages are automatically available for truncation.") (license license:gpl2+))) (define-public r-rsolnp (package (name "r-rsolnp") (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "Rsolnp" version)) (sha256 (base32 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii")))) (properties `((upstream-name . "Rsolnp"))) (build-system r-build-system) (propagated-inputs (list r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/Rsolnp/") (synopsis "General non-linear optimization") (description "The Rsolnp package implements a general non-linear augmented Lagrange multiplier method solver, a @dfn{sequential quadratic programming} (SQP) based solver).") ;; Any version of the GPL. (license license:gpl2+))) (define-public r-hardyweinberg (package (name "r-hardyweinberg") (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs (list r-mice r-nnet r-rcpp r-rsolnp)) (home-page "https://cran.r-project.org/package=HardyWeinberg") (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") (description "This package contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of diallelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.") (license license:gpl2+))) (define-public r-sm (package (name "r-sm") (version "2.2-5.7.1") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 "0mql7rlm8wkdwmx1lv7pscdk9ibvsdpfdv8bpaz1hv2gn4pc637a")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") (synopsis "Smoothing methods for nonparametric regression and density estimation") (description "This is software accompanying the book 'Applied Smoothing Techniques for Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford University Press. It provides smoothing methods for nonparametric regression and density estimation") (license license:gpl2+))) (define-public r-smoof (package (name "r-smoof") (version "1.6.0.3") (source (origin (method url-fetch) (uri (cran-uri "smoof" version)) (sha256 (base32 "1cazhnd0m5jjzixaqgqh2h3rsa2sw3k8slj5cmgm8v47aaqn91mg")))) (properties `((upstream-name . "smoof"))) (build-system r-build-system) (propagated-inputs (list r-bbmisc r-checkmate r-ggplot2 r-paramhelpers r-rcpp r-rcpparmadillo)) (home-page "https://jakobbossek.github.io/smoof/") (synopsis "Single and multi-objective optimization test functions") (description "This tool generates high number of both single- and multi-objective test functions. These functions are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.") (license license:bsd-2))) (define-public r-smurf (package (name "r-smurf") (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "smurf" version)) (sha256 (base32 "1gpzzj67x0i70vw1x4rv56mhk2b74ynvdsy93rzmdk6b2h3dvv46")))) (properties `((upstream-name . "smurf"))) (build-system r-build-system) (propagated-inputs (list r-catdata r-glmnet r-mass r-matrix r-mgcv r-rcolorbrewer r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://gitlab.com/TReynkens/smurf") (synopsis "Sparse multi-type regularized feature modeling") (description "The @code{smurf} package contains the implementation of the @dfn{Sparse Multi-type Regularized Feature} (SMuRF) modeling algorithm to fit @dfn{generalized linear models} (GLMs) with multiple types of predictors via regularized maximum likelihood. Next to the fitting procedure, following functionality is available: @itemize @item Selection of the regularization tuning parameter lambda using three different approaches: in-sample, out-of-sample or using cross-validation. @item S3 methods to handle the fitted object including visualization of the coefficients and a model summary. @end itemize") (license license:gpl2+))) (define-public r-venndiagram (package (name "r-venndiagram") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "VennDiagram" version)) (sha256 (base32 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7")))) (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs (list r-futile-logger)) (home-page "https://cran.r-project.org/web/packages/VennDiagram/") (synopsis "Generate High-Resolution Venn and Euler Plots") (description "This package provides a set of functions to generate high-resolution Venn and Euler plots. It includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.") (license license:gpl2+))) (define-public r-vioplot (package (name "r-vioplot") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 "1db7g0378jbcd6ssb7afff4y4r0v472qnb625hfwixx4wf1v8aap")))) (build-system r-build-system) (propagated-inputs (list r-sm r-zoo)) (native-inputs (list r-knitr)) (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") (synopsis "Violin plot") (description "This package provides a violin plot, which is a combination of a box plot and a kernel density plot.") (license license:bsd-3))) (define-public r-rsofia (package (name "r-rsofia") (version "1.1") (source (origin (method url-fetch) ;; This package has been removed from CRAN, so we can ;; only fetch it from the archives. (uri (string-append "https://cran.r-project.org/src/" "contrib/Archive/RSofia/RSofia_" version ".tar.gz")) (sha256 (base32 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn")))) (properties `((upstream-name . "RSofia"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") (synopsis "Port of sofia-ml to R") (description "This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.") (license license:asl2.0))) (define-public r-xts (package (name "r-xts") (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 "0pc23na5lrzfchd4i22p035y1krjpddi0iw6i78lhbhns330ff9c")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://github.com/joshuaulrich/xts") (synopsis "Extensible time series") (description "This package provides for uniform handling of R's different time-based data classes by extending @code{zoo}, maximizing native format information preservation and allowing for user-level customization and extension, while simplifying cross-class interoperability.") (license license:gpl2+))) (define-public r-performanceanalytics (package (name "r-performanceanalytics") (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "PerformanceAnalytics" version)) (sha256 (base32 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq")))) (properties `((upstream-name . "PerformanceAnalytics"))) (build-system r-build-system) (propagated-inputs (list r-quadprog r-xts r-zoo)) (home-page "https://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.") ;; Either version may be picked. (license (list license:gpl2 license:gpl3)))) (define-public r-laeken (package (name "r-laeken") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mass)) (home-page "https://cran.r-project.org/web/packages/laeken/") (synopsis "Estimation of indicators on social exclusion and poverty") (description "This package provides tools for the estimation of indicators on social exclusion and poverty, as well as an implementation of Pareto tail modeling for empirical income distributions.") (license license:gpl2+))) (define-public r-vcd (package (name "r-vcd") (version "1.4-12") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 "127dkln826ah5ydp3pmd5bqyns9m9m6yrjnmn7fir4r9al8yycf9")))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-lmtest r-mass)) (home-page "https://cran.r-project.org/web/packages/vcd/") (synopsis "Visualizing categorical data") (description "This package provides visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was originally inspired by the book \"Visualizing Categorical Data\" by Michael Friendly and is now the main support package for a new book, \"Discrete Data Analysis with R\" by Michael Friendly and David Meyer (2015).") (license license:gpl2))) (define-public r-vcfr (package (name "r-vcfr") (version "1.15.0") (source (origin (method url-fetch) (uri (cran-uri "vcfR" version)) (sha256 (base32 "1yj91cphin232m09wrpj8l27vxblyryh658siakz55hxjs5y85yz")))) (build-system r-build-system) (native-inputs (list r-knitr)) (inputs (list zlib)) (propagated-inputs (list r-ape r-dplyr r-magrittr r-memuse r-pinfsc50 r-rcpp r-stringr r-tibble r-vegan r-viridislite)) (home-page "https://github.com/knausb/vcfR") (synopsis "Manipulate and visualize VCF data") (description "This package facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R, a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file. It also may be converted into other popular R objects. This package provides a link between VCF data and familiar R software.") (license license:gpl3))) (define-public r-rvcg (package (name "r-rvcg") (version "0.22.2") (source (origin (method url-fetch) (uri (cran-uri "Rvcg" version)) (sha256 (base32 "077p4c16nqi6ayxv1i31cr6sw9fwnxpmfkmrrhzh02khpi2c2jg5")))) (properties `((upstream-name . "Rvcg"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppeigen)) (home-page "https://github.com/zarquon42b/Rvcg") (synopsis "Manipulations of triangular meshes based on the VCGLIB API") (description "This is a package for operations on triangular meshes based on VCGLIB. This package integrates nicely with the R-package rgl to render the meshes processed by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is a library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes.") (license license:gpl2+))) (define-public r-ica (package (name "r-ica") (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "ica" version)) (sha256 (base32 "0rdqd3kz2cv3xvf6yz55bwhsg3k7j90d450i3azs2xkbn4q3aka7")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ica/") (synopsis "Independent component analysis") (description "This package provides tools for @dfn{Independent Component Analysis} (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization of Eigenmatrices} (JADE).") (license license:gpl2+))) (define-public r-ips (package (name "r-ips") (version "0.0.11") (source (origin (method url-fetch) (uri (cran-uri "ips" version)) (sha256 (base32 "02jxanfhsjrabj33nwjv71vdc87hiyzikyqrfdj9ix6dky6lm199")))) (properties `((upstream-name . "ips"))) (build-system r-build-system) (propagated-inputs (list r-ape r-phangorn r-plyr r-seqinr r-xml)) (home-page "https://cran.r-project.org/package=ips") (synopsis "Interfaces to phylogenetic software in R") (description "This package provides functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.") (license license:gpl3))) (define-public r-dtw (package (name "r-dtw") (version "1.23-1") (source (origin (method url-fetch) (uri (cran-uri "dtw" version)) (sha256 (base32 "0vc2is1hf1g0sw92kzl8mddck264qwiqgm5q2wkcwwz65fss7mkf")))) (build-system r-build-system) (propagated-inputs (list r-proxy)) (home-page "https://dtw.r-forge.r-project.org/") (synopsis "Dynamic Time Warping Algorithms") (description "This package provides a comprehensive implementation of @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on.") (license license:gpl2+))) (define-public r-sdmtools (package (name "r-sdmtools") (version "1.1-221.2") (source (origin (method url-fetch) (uri (cran-uri "SDMTools" version)) (sha256 (base32 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh")))) (properties `((upstream-name . "SDMTools"))) (build-system r-build-system) (propagated-inputs (list r-r-utils)) (home-page "https://www.rforge.net/SDMTools/") (synopsis "Species distribution modelling tools") (description "This package provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.") (license license:gpl3+))) (define-public r-scatterplot3d (package (name "r-scatterplot3d") (version "0.3-44") (source (origin (method url-fetch) (uri (cran-uri "scatterplot3d" version)) (sha256 (base32 "1hkfislhzx05y5qqa7pvrils3qf9rhxbf37lkpsjbn9yihs0i70w")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/scatterplot3d/") (synopsis "3D scatter plot") (description "This package provides an implementation of scatter plots for plotting. a three dimensional point cloud.") (license license:gpl2))) (define-public r-ggridges (package (name "r-ggridges") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 "18bmbq5pd751hnw8rpvshvapg09630i2pqpwk5a3yhgz4hwa8xvm")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description "Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) (define-public r-ggjoy (package (name "r-ggjoy") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggjoy" version)) (sha256 (base32 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggridges)) (home-page "https://github.com/clauswilke/ggjoy") (synopsis "Joyplots in ggplot2") (description "Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) (define-public r-gss (package (name "r-gss") (version "2.2-7") (source (origin (method url-fetch) (uri (cran-uri "gss" version)) (sha256 (base32 "0siz9xmfiirkg8sb0amzyp7k1mjbgz8jmsmlc8schw65093i84rv")))) (properties `((upstream-name . "gss"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=gss") (synopsis "General smoothing splines") (description "This package provides a comprehensive collection for structural multivariate function estimation using smoothing splines.") (license license:gpl2+))) (define-public r-cli (package (name "r-cli") (version "3.6.2") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 "0lg131q9l8wpnggc3jlrjl1ri3dw0d1pi4nr1zlnlaqvf7ilj1sc")))) (build-system r-build-system) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") (description "This package provides a suite of tools designed to build attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (license license:expat))) (define-public r-argparser (package (name "r-argparser") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") (description "This package provides a cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script.") (license license:gpl3+))) (define-public r-aricode (package (name "r-aricode") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "aricode" version)) (sha256 (base32 "02nrw66jfpzf6dy0zy21sbdjxjc8c11iv9fkjqj5akzb7wskk9qh")))) (properties `((upstream-name . "aricode"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) (home-page "https://github.com/jchiquet/aricode") (synopsis "Efficient computations of standard clustering comparison measures") (description "This package implements an efficient O(n) algorithm based on bucket-sorting for fast computation of standard clustering comparison measures. Available measures include @dfn{adjusted Rand index} (ARI), @dfn{normalized information distance} (NID), @dfn{normalized mutual information} (NMI), @dfn{adjusted mutual information} (AMI), @dfn{normalized variation information} (NVI) and entropy.") (license license:gpl3+))) (define-public r-attempt (package (name "r-attempt") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "attempt" version)) (sha256 (base32 "1ylgg7jcp8wqmxgf1mydnvh26k0mr8jyjla4hw06730r40yrs58m")))) (properties `((upstream-name . "attempt"))) (build-system r-build-system) (propagated-inputs (list r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/ColinFay/attempt") (synopsis "Tools for defensive programming") (description "This package provides tools for defensive programming. It is inspired by @code{purrr} mappers and based on @code{rlang}. Attempt extends and facilitates defensive programming by providing a consistent grammar, and a set of functions for common tests and conditions. Attempt only depends on @code{rlang}, and focuses on speed, so it can be integrated with other functions and used in the data analysis.") (license license:expat))) (define-public r-debugme (package (name "r-debugme") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "debugme" version)) (sha256 (base32 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) (build-system r-build-system) (propagated-inputs (list r-crayon)) (home-page "https://github.com/r-lib/debugme#readme") (synopsis "Debug R packages") (description "This package allows the user to specify debug messages as special string constants, and control debugging of packages via environment variables.") (license license:expat))) (define-public r-processx (package (name "r-processx") (version "3.8.3") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 "0cfq6pq8rg0vhjfgvf48hfvngbn1g6hv28b6pgxh55xqh8acbn0s")))) (build-system r-build-system) (propagated-inputs (list r-ps r-r6)) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description "This package provides portable tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes and their children; restart processes. It can read the standard output and error of the processes, using non-blocking connections. @code{processx} can poll a process for standard output or error, with a timeout. It can also poll several processes at once.") (license license:expat))) (define-public r-timeseries (package (name "r-timeseries") (version "4032.109") (source (origin (method url-fetch) (uri (cran-uri "timeSeries" version)) (sha256 (base32 "07vkppp9azbrn0lv1xhi4s3vpy4mglhysp7d250fl08b9rc4f32y")))) (properties `((upstream-name . "timeSeries"))) (build-system r-build-system) (propagated-inputs (list r-timedate)) (home-page "https://r-forge.r-project.org/scm/viewvc.php/pkg/timeSeries/?root=rmetrics") (synopsis "Metrics for financial time series objects") (description "This package implements S4 classes and various tools for financial time series. Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions are provided.") (license license:gpl2+))) (define-public r-tsp (package (name "r-tsp") (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 "1263ay3dar2mzm89nf31gl7n8d983qjiy4qwz7sgv8vwkbz0pg9h")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) (home-page "https://cran.r-project.org/web/packages/TSP/") (synopsis "Traveling salesperson problem (TSP)") (description "This package provides basic infrastructure and some algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the traveling salesman problem).") (license license:gpl3))) (define-public r-qap (package (name "r-qap") (version "0.1-2") (source (origin (method url-fetch) (uri (cran-uri "qap" version)) (sha256 (base32 "19adb1bw46pcnmmhqz2jklr0vmma3llxajqp0j9mqfksmsisv927")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic assignment problem} (QAP). Currently only a simulated annealing heuristic is available.") (license license:gpl3))) (define-public r-gclus (package (name "r-gclus") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "gclus" version)) (sha256 (base32 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/gclus/") (synopsis "Clustering graphics") (description "This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices of merit, ordering functions, and enhanced versions of @code{pairs} and @code{parcoord} which color panels according to their merit level.") (license license:gpl2+))) (define-public r-webchem (package (name "r-webchem") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "webchem" version)) (sha256 (base32 "06b9i9jipg564zyw4gkgiidz7501rlp40hxm4z3k5mzy148lr5vq")))) (properties `((upstream-name . "webchem"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-data-tree r-dplyr r-httr r-jsonlite r-purrr r-rlang r-rvest r-stringr r-tibble r-xml2)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/webchem/") (synopsis "Chemical information from the web") (description "This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.") (license license:expat))) (define-public r-webshot (package (name "r-webshot") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 "04xrrf72323sgzsdkbl05p2fdsi486i9avrrxvw0l3n8r8y92xfn")))) (build-system r-build-system) (propagated-inputs (list r-callr r-jsonlite r-magrittr)) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description "Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and screenshot static as well as interactive R Markdown documents.") (license license:gpl2))) (define-public r-seriation (package (name "r-seriation") (version "1.5.4") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 "17rk4674r5knfgqyik9gbz6yj42qv6h79j2prw79glc1ym99qcyj")))) (build-system r-build-system) (propagated-inputs (list r-ca r-cluster r-colorspace r-foreach r-gclus r-mass r-qap r-registry r-tsp r-vegan)) (native-inputs (list gfortran)) (home-page "https://s2.smu.edu/IDA/seriation/") (synopsis "Infrastructure for ordering objects using seriation") (description "This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).") (license license:gpl3))) (define-public r-xfun (package (name "r-xfun") (version "0.41") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 "00ivgr557ja8l33lvawrivfhgj1xbjmdi4dj07zybwa1y6wc6x13")))) (build-system r-build-system) (properties ;; knitr itself depends on xfun '((updater-ignored-native-inputs . ("r-knitr")))) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") (description "This package provides miscellaneous functions commonly used in other packages maintained by Yihui Xie.") (license license:expat))) (define-public r-utf8 (package (name "r-utf8") (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 "0zbv2s5dkzxim3ydyk12479m28f68mak9m50v396in4wpm5q53s1")))) (build-system r-build-system) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description "This package provides tools to process and print UTF-8 encoded international text (Unicode). Input, validate, normalize, encode, format, and display.") (license license:asl2.0))) (define-public r-zeallot (package (name "r-zeallot") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "zeallot" version)) (sha256 (base32 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3")))) (build-system r-build-system) (home-page "https://github.com/nteetor/zeallot") (synopsis "Multiple, unpacking, and destructuring assignment") (description "This package provides a @code{%<-%} operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.") (license license:expat))) (define-public r-zlog (package (name "r-zlog") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "zlog" version)) (sha256 (base32 "0fi9aqrmikdg5ibwhn82kslj4lxih03vm27jmi14m73h09yy4in5")))) (properties `((upstream-name . "zlog"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zlog") (synopsis "Transformation for laboratory easurements") (description "The @code{zlog} package offers functions to transform laboratory measurements into standardised z or @math{z(log)-values}. Therefore the lower and upper reference limits are needed. If these are not known they could be estimated from a given sample.") (license license:gpl3+))) (define-public r-vctrs (package (name "r-vctrs") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 "00p4r1z4xc05m25y0qa7svr67lbypcfqyp2b0ja9asgx90i7s5j3")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) (properties ;; We can't have r-knitr among the inputs here, because r-vctrs ends up ;; being an eventual input to r-knitr. '((updater-ignored-native-inputs . ("r-knitr")))) (home-page "https://github.com/r-lib/vctrs") (synopsis "Vector helpers") (description "There are three main goals to the @code{vctrs} package: @enumerate @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to @code{length()} and @code{class()}. These definitions are paired with a framework for type-coercion and size-recycling. @item To define type- and size-stability as desirable function properties, use them to analyse existing base function, and to propose better alternatives. This work has been particularly motivated by thinking about the ideal properties of @code{c()}, @code{ifelse()}, and @code{rbind()}. @item To provide a new @code{vctr} base class that makes it easy to create new S3 vectors. @code{vctrs} provides methods for many base generics in terms of a few new @code{vctrs} generics, making implementation considerably simpler and more robust. @end enumerate\n") (license license:gpl3))) (define-public r-pillar (package (name "r-pillar") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 "1k3sp37dpn46d2xbq621alpvzgnm06x5qb87nk169y47q23b8gpj")))) (build-system r-build-system) (propagated-inputs (list r-cli r-fansi r-glue r-lifecycle r-rlang r-utf8 r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description "This package provides a @code{pillar} generic designed for formatting columns of data using the full range of colours provided by modern terminals.") (license license:gpl3))) (define-public r-pinfsc50 (package (name "r-pinfsc50") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "pinfsc50" version)) (sha256 (base32 "1gs9x328qqvqwx3k4z9jgzq5zb6g8kdz4430n96v7zb78p7jf5lp")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pinfsc50/") (synopsis "Genomic data for the plant pathogen Phytophthora infestans") (description "This package contains genomic data for the plant pathogen Phytophthora infestans. It includes a variant file, a sequence file and an annotation file. This package is intended to be used as example data for packages that work with genomic data.") (license license:gpl2+))) (define-public r-piton (package (name "r-piton") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "piton" version)) (sha256 (base32 "1krf6zi238m275nxjlpyayv8y2drbgs2kg19dpkqm0lmlz5y5ar8")))) (properties `((upstream-name . "piton"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/Ironholds/piton") (synopsis "Parsing expression grammars in Rcpp") (description "This package provides a wrapper around the Parsing Expression Grammar Template Library, a C++11 library for generating parsing expression grammars, that makes it accessible within Rcpp. With this, developers can implement their own grammars and easily expose them in R packages.") (license license:expat))) (define-public r-uuid (package (name "r-uuid") (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 "1z9a4b7hkymkwjq69d00myy5xw8kl9g99f4m2y4lxqqjz0a0lwbk")))) (build-system r-build-system) (home-page "https://www.rforge.net/uuid") (synopsis "Tools for generating and handling of UUIDs") (description "This package provides tools for generating and handling of @dfn{Universally Unique Identifiers} (UUIDs).") (license license:expat))) (define-public r-tinytex (package (name "r-tinytex") (version "0.49") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 "0i9icscy5n6p6w3f4v2z3cznywrrv2l6xyyhb0k1fpa4cpn6j4cl")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description "This package provides helper functions to install and maintain the LaTeX distribution named TinyTeX, a lightweight, cross-platform, portable, and easy-to-maintain version of TeX Live. This package also contains helper functions to compile LaTeX documents, and install missing LaTeX packages automatically.") (license license:expat))) (define-public r-tinytest (package (name "r-tinytest") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "tinytest" version)) (sha256 (base32 "0x0w1fiqd98vmpz8yrp9ig0ry1wfr16g6bkjzd2a8sq9gn417z7n")))) (properties `((upstream-name . "tinytest"))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/tinytest") (synopsis "Lightweight unit testing framework") (description "This package provides a lightweight unit testing framework. Main features: @enumerate @item install tests with the package; @item test results are treated as data that can be stored and manipulated; @item test files are R scripts interspersed with test commands, that can be programmed over; @item fully automated build-install-test sequence for packages; @item skip tests when not run locally (e.g. on CRAN); @item flexible and configurable output printing; @item compare computed output with output stored with the package; @item run tests in parallel; @item extensible by other packages; @item report side effects. @end enumerate ") (license license:gpl3))) (define-public r-n2r (package (name "r-n2r") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "N2R" version)) (sha256 (base32 "12bv7xx6j6222qgpv6g61i68017fz0x6fjg9a9k5yhgw3zk05hpk")))) (properties `((upstream-name . "N2R"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen r-rcppspdlog)) (home-page "https://github.com/kharchenkolab/N2R") (synopsis "Fast and scalable approximate k-Nearest Neighbor search methods") (description "This package implements methods to perform fast approximate K-nearest neighbor search on the input matrix. The algorithm is based on the N2 implementation of an approximate nearest neighbor search using hierarchical @acronym{NSW, Navigable Small World} graphs.") (license license:asl2.0))) (define-public r-nestedcv (package (name "r-nestedcv") (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "nestedcv" version)) (sha256 (base32 "1f725r2f00ldp6pdk3ncvwxm4c2asz6rjs6g8afwh6plxwfkcjq8")))) (properties `((upstream-name . "nestedcv"))) (build-system r-build-system) (propagated-inputs (list r-caret r-data-table r-doparallel r-foreach r-ggplot2 r-glmnet r-magrittr r-matrixstats r-matrixtests r-proc r-rfast r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/myles-lewis/nestedcv") (synopsis "Nested cross-validation with glmnet and caret") (description "This package implements nested cross-validation applied to the @code{glmnet} and @code{caret} packages. With glmnet this includes cross-validation of elastic net alpha parameter. A number of feature selection filter functions (t-test, Wilcoxon test, ANOVA, Pearson/Spearman correlation, random forest, ReliefF) for feature selection are provided and can be embedded within the outer loop of the nested CV. Nested CV can be also be performed with the @code{caret} package giving access to the large number of prediction methods available in @code{caret}.") (license license:expat))) (define-public r-network (package (name "r-network") (version "1.18.2") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 "0yx20v3izm7037cx5swc19966z97w7q9xw4p2p6skfyap4nqjcxz")))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-statnet-common r-tibble)) (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description "This package provides tools to create and modify network objects. The @code{network} class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) (define-public r-nistunits (package (name "r-nistunits") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "NISTunits" version)) (sha256 (base32 "0km9l3k9p35sb1qrhrz4ijjsdihvsp6j7cz5kh46lgf7nn6xdk7a")))) (properties `((upstream-name . "NISTunits"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=NISTunits") (synopsis "Fundamental physical constants and unit conversions") (description "This package provides fundamental physical constants (quantity, value, uncertainty, unit) for @acronym{SI, International System of Units} and non-SI units, plus unit conversions based on the data from @acronym{NIST, National Institute of Standards and Technology}, USA.") (license license:gpl3+))) (define-public r-stabs (package (name "r-stabs") (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "stabs" version)) (sha256 (base32 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/hofnerb/stabs") (synopsis "Stability selection with error control") (description "This package provides resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting. Both, standard stability selection (Meinshausen & Buhlmann, 2010) and complementary pairs stability selection with improved error bounds (Shah & Samworth, 2013) are implemented. The package can be combined with arbitrary user specified variable selection approaches.") (license license:gpl2))) (define-public r-rle (package (name "r-rle") (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "rle" version)) (sha256 (base32 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40")))) (properties `((upstream-name . "rle"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rle/") (synopsis "Common functions for run-length encoded vectors") (description "This package provides common @code{base} and @code{stats} methods for @code{rle} objects, aiming to make it possible to treat them transparently as vectors.") (license license:gpl3))) (define-public r-statnet-common (package (name "r-statnet-common") (version "4.9.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 "1mrdzhxxrr6a0hwxczs40f8ppkdimlki1gbg6f3kv69s6rpdr1d4")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) (propagated-inputs (list r-coda)) (home-page "https://statnet.org") (synopsis "R scripts and utilities used by the Statnet software") (description "This package provides non-statistical utilities used by the software developed by the Statnet Project.") (license license:gpl3))) (define-public r-statcheck (package (name "r-statcheck") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "statcheck" version)) (sha256 (base32 "1hibrynbgsym4hma8isby8kwb8gab9d4bx7m43qj4zayrl6b8scx")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr r-rlang r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/statcheck/") (synopsis "Extract statistics from articles and recompute p-values") (description "This package can automatically extract statistical null-hypothesis significant testing (NHST) results from articles and recompute the p-values based on the reported test statistic and degrees of freedom to detect possible inconsistencies.") (license license:gpl2))) (define-public r-sna (package (name "r-sna") (version "2.7-2") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 "1kd7qxdc8wy8d385yddj6rs0xc6lkn8hpra3wy4r7svzjqk4c8bv")))) (build-system r-build-system) (propagated-inputs (list r-network r-statnet-common)) (home-page "https://statnet.org") (synopsis "Tools for social network analysis") (description "This package provides a range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.") (license license:gpl2+))) (define-public r-tfisher (package (name "r-tfisher") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "TFisher" version)) (sha256 (base32 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx")))) (properties `((upstream-name . "TFisher"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-mvtnorm r-sn)) (home-page "https://cran.r-project.org/web/packages/TFisher/") (synopsis "Optimal thresholding Fisher's p-value combination method") (description "This package provides the @dfn{cumulative distribution function} (CDF), quantile, and statistical power calculator for a collection of thresholding Fisher's p-value combination methods, including Fisher's p-value combination method, truncated product method and, in particular, soft-thresholding Fisher's p-value combination method which is proven to be optimal in some context of signal detection. The p-value calculator for the omnibus version of these tests are also included.") (license license:gpl2))) (define-public r-ttr (package (name "r-ttr") (version "0.24.4") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 "1102f4i776asqb281mq20ymhzhcp12gn9nr3rm0jzblv6nf2nww9")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs (list r-curl r-xts r-zoo)) (home-page "https://github.com/joshuaulrich/TTR") (synopsis "Technical trading rules") (description "This package provides functions and data to construct technical trading rules with R.") (license license:gpl2))) (define-public r-leaflet-providers (package (name "r-leaflet-providers") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "leaflet.providers" version)) (sha256 (base32 "0rl69bfx2l10x80rl8cppqch3fnd05sk9w29h8589jc8h3ffmkn5")))) (properties `((upstream-name . "leaflet.providers"))) (build-system r-build-system) (propagated-inputs (list r-htmltools)) (home-page "https://github.com/rstudio/leaflet.providers") (synopsis "Leaflet map tile providers") (description "This package contains third-party map tile provider information from Leaflet.js, to be used with the @code{leaflet} R package. Additionally, @code{leaflet.providers} enables users to retrieve up-to-date provider information between package updates.") (license license:bsd-2))) ;; This package contains a lot of minified JavaScript with unclear provenance. ;; When upgrading please make sure that all minified JavaScript files are ;; removed in a snippet and that the replacement sources correspond to the ;; original minified scripts. (define-public r-leaflet (package (name "r-leaflet") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "leaflet" version)) (sha256 (base32 "1gfsf7bsmp418zv4gpk5i1xg5vvgqwpdkznnvj5x0mk4rcqk1i81")) (snippet '(for-each delete-file (list "inst/htmlwidgets/lib/leaflet/leaflet.js" "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js" "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js" "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js" "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js" "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js" "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js" "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js" "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js" "inst/legacy/www/leaflet.js"))))) (properties `((upstream-name . "leaflet"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) ;; The inst directory contains some minified JavaScript files. ;; Regenerate them from sources. (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet")) (with-directory-excursion "inst/" (call-with-values (lambda () (unzip2 `(("/tmp/leaflet-src.js" "htmlwidgets/lib/leaflet/leaflet.js") (,(assoc-ref inputs "js-leaflet-measure") "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js") (,(assoc-ref inputs "js-leaflet-omnivore") "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js") ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js" "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js") (,(assoc-ref inputs "js-bootstrap3") "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js") ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js" "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js") (,(string-append (assoc-ref inputs "js-leaflet-markercluster") "/dist/leaflet.markercluster-src.js") "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js") (,(assoc-ref inputs "js-leaflet-markercluster-freezable") "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js") (,(assoc-ref inputs "js-leaflet-markercluster-layersupport") "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js") (,(assoc-ref inputs "js-proj4leaflet") "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js") ("legacy/www/leaflet-src.js" "legacy/www/leaflet.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (native-inputs `(("esbuild" ,esbuild) ("unzip" ,unzip) ("js-bootstrap3" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js") (sha256 (base32 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha")))) ("js-leaflet" ,(origin (method url-fetch) (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip") (sha256 (base32 "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f")))) ("js-leaflet-omnivore" ,(origin (method url-fetch) (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/" "leaflet-omnivore/v0.3.1/leaflet-omnivore.js")) (sha256 (base32 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) ("js-leaflet-markercluster" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/Leaflet/Leaflet.markercluster.git") (commit "v1.1.0"))) (file-name (git-file-name "js-leaflet-markercluster" "1.1.0")) (sha256 (base32 "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1")))) ("js-leaflet-markercluster-freezable" ,(origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/" "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js")) (file-name "leaflet-markercluster-freezable.js") (sha256 (base32 "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k")))) ("js-leaflet-markercluster-layersupport" ,(origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/" "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js")) (file-name "leaflet-markercluster-layersupport.js") (sha256 (base32 "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff")))) ("js-leaflet-measure" ,(origin (method url-fetch) (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js") (file-name "js-leaflet-measure-1.5.2.js") (sha256 (base32 "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0")))) ("js-proj4leaflet" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js") (file-name "js-proj4leaflet-1.0.2.js") (sha256 (base32 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab")))))) (propagated-inputs (list r-crosstalk r-htmltools r-htmlwidgets r-jquerylib r-leaflet-providers r-magrittr r-png r-raster r-rcolorbrewer r-scales r-sp r-viridis r-xfun)) (home-page "https://rstudio.github.io/leaflet/") (synopsis "Create interactive web maps with the JavaScript Leaflet library") (description "Create and customize interactive maps using the Leaflet JavaScript library and the @code{htmlwidgets} package. These maps can be used directly from the R console, from RStudio, in Shiny applications and R Markdown documents.") (license license:gpl3))) (define-public r-leaps (package (name "r-leaps") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "leaps" version)) (sha256 (base32 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/leaps/") (synopsis "Regression subset selection") (description "This package provides tools for regression subset selection, including exhaustive search.") (license license:gpl2+))) (define-public r-splus2r (package (name "r-splus2r") (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "splus2R" version)) (sha256 (base32 "16r13bbijq7lz3c8qn7dnb4h8fc3vbcahyah2zij888p470vqljn")))) (properties `((upstream-name . "splus2R"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/splus2R/") (synopsis "Supplemental S-PLUS functionality in R") (description "Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.") (license license:gpl2))) (define-public r-ifultools (package (name "r-ifultools") (version "2.0-26") (source (origin (method url-fetch) (uri (cran-uri "ifultools" version)) (sha256 (base32 "1lkmzrh65j6vdb8523axxk9gig5q4zxy08wiqsp16w482d2q2sl1")))) (build-system r-build-system) (arguments (list #:phases `(modify-phases %standard-phases (add-after 'unpack 'compatibility (lambda _ ;; These definitions are no longer part of R since 4.2.0. See ;; https://cran.r-project.org/doc/manuals/r-devel/NEWS.html for ;; details. (substitute* "inst/include/ut_RS.h" (("#include \"R.h\"" m) (string-append "\ #define R_PROBLEM_BUFSIZE 4096 #define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf, #define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf, #define ERROR ),error(R_problem_buf);} #define WARNING(x) ),warning(R_problem_buf);} #define WARN WARNING(NULL) " m)))))))) (propagated-inputs (list r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/ifultools/") (synopsis "Insightful research tools") (description "This package provides C code used by the wmtsa, fractal, and sapa R packages.") (license license:gpl2))) (define-public r-sapa (package (name "r-sapa") (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "sapa" version)) (sha256 (base32 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc")))) (build-system r-build-system) (propagated-inputs (list r-ifultools r-splus2r)) (home-page "https://cran.r-project.org/web/packages/sapa/") (synopsis "Spectral analysis for physical applications") (description "This package provides software for the book Spectral Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.") (license license:gpl2))) (define-public r-aggregation (package (name "r-aggregation") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "aggregation" version)) (sha256 (base32 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/aggregation/") (synopsis "Methods for p-value aggregation") (description "This package contains functionality for performing the following methods of p-value aggregation: Fisher's method, the Lancaster method (weighted Fisher's method), and Sidak correction.") (license license:gpl3))) (define-public r-quantmod (package (name "r-quantmod") (version "0.4.25") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 "0cjvz6hd4q0fd87d54wxfaka3awi9jzj8a7x72jawkdxbza9c61z")))) (build-system r-build-system) (propagated-inputs (list r-curl r-jsonlite r-ttr r-xts r-zoo)) (home-page "https://cran.r-project.org/web/packages/quantmod/") (synopsis "Quantitative financial modelling framework") (description "This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.") (license license:gpl3))) (define-public r-tseries (package (name "r-tseries") (version "0.10-55") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 "03jb2ij4jyhrbygi0gha549vq262kx1ffjmy12rf0gak0qmq5iwp")))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-quadprog r-quantmod r-zoo)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tseries/") (synopsis "Time series analysis and computational finance") (description "This package provides functions relating to time series analysis and computational finance.") (license license:gpl2))) (define-public r-wmtsa (package (name "r-wmtsa") (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "wmtsa" version)) (sha256 (base32 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) (build-system r-build-system) (propagated-inputs (list r-ifultools r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/wmtsa/") (synopsis "Wavelet methods for time series analysis") (description "This package provides software to accompany the book \"Wavelet Methods for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge University Press, 2000.") (license license:gpl2))) (define-public r-tsa (package (name "r-tsa") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 "14g58s2w7wma1fgcg3b51267b3676zrv0w8v4hpypxygz023d9bx")))) (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs (list r-leaps r-locfit r-mgcv r-tseries)) (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description "This package contains R functions and datasets detailed in the book \"Time Series Analysis with Applications in R (second edition)\" by Jonathan Cryer and Kung-Sik Chan.") (license license:gpl2+))) (define-public r-extradistr (package (name "r-extradistr") (version "1.10.0") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 "1ad3xp4axbbid9i9vd4q8iccs3g3917yic2mas37mfwm5in4l9pl")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/twolodzko/extraDistr") (synopsis "Additional univariate and multivariate distributions") (description "This package implements density, distribution functions, quantile functions and random generation functions for a large number of univariate and multivariate distributions.") (license license:gpl2))) (define-public r-fbasics (package (name "r-fbasics") (version "4032.96") (source (origin (method url-fetch) (uri (cran-uri "fBasics" version)) (sha256 (base32 "14461d6ac8hcn1x3srh45a4s5imafqb0xy8bn5l6d0qwhw4njmg1")))) (properties `((upstream-name . "fBasics"))) (build-system r-build-system) (propagated-inputs (list r-gss r-mass r-spatial r-stabledist r-timedate r-timeseries)) (home-page "https://r-forge.r-project.org/scm/viewvc.php/pkg/fBasics/?root=rmetrics") (synopsis "Metrics for markets and basic statistics") (description "This package provides a collection of functions to explore and to investigate basic properties of financial returns and related quantities. The covered fields include techniques of explorative data analysis and the investigation of distributional properties, including parameter estimation and hypothesis testing. Even more, there are several utility functions for data handling and management.") (license license:gpl2+))) (define-public r-fractal (package (name "r-fractal") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "fractal" version)) (sha256 (base32 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) (build-system r-build-system) (propagated-inputs (list r-ifultools r-mass r-sapa r-scatterplot3d r-splus2r r-wmtsa)) (home-page "https://cran.r-project.org/web/packages/fractal/") (synopsis "Fractal time series modeling and analysis") (description "This package provides tools for stochastic fractal and deterministic chaotic time series analysis.") (license license:gpl2))) (define-public r-fresh (package (name "r-fresh") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "fresh" version)) (sha256 (base32 "1787mm6w2s5x9scxy7r9cb77rgpmy4ngwkn4z8g3gs48mrab4bd9")))) (properties `((upstream-name . "fresh"))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-rstudioapi r-sass r-shiny)) (native-inputs (list r-knitr)) (home-page "https://github.com/dreamRs/fresh") (synopsis "Create custom Bootstrap themes to use in Shiny") (description "Customize Bootstrap and Bootswatch themes, like colors, fonts, grid layout, to use in Shiny applications, rmarkdown documents and flexdashboard.") (license license:gpl3))) (define-public r-urca (package (name "r-urca") (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "urca" version)) (sha256 (base32 "1wg9f691pif59xds43gnnw77mmzc9xpnhhvaksk2b0szffvaifj3")))) (build-system r-build-system) (propagated-inputs (list r-nlme)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/urca/") (synopsis "Unit root and cointegration tests for time series data") (description "This package provides unit root and cointegration tests encountered in applied econometric analysis.") (license license:gpl2+))) (define-public r-cubature (package (name "r-cubature") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 "0r9n4xpm3ssjn3vywzlgh3naynzp1cxvjsd0pvah04k115b7i0jx")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/bnaras/cubature") (synopsis "Adaptive multivariate integration over hypercubes") (description "This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both @code{hcubature} and @code{pcubature} routines in addition to a vector interface.") ;; The included cubature C library is released under GPLv2+, but the ;; wrapper declares the license to be GPLv3+. (license (list license:gpl2+ license:gpl3+)))) (define-public r-trend (package (name "r-trend") (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "trend" version)) (sha256 (base32 "0991fp6kjk704rfg0l1m7kwbck9fj1rg27zy4llm5ikczd55w05h")))) (build-system r-build-system) (propagated-inputs (list r-extradistr)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/trend/") (synopsis "Non-parametric trend tests and change-point detection") (description "The analysis of environmental data often requires the detection of trends and change-points. This package includes tests for trend detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman correlation trend test), change-point detection (Lanzante's test procedures, Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two sample Robust Rank-Order Distributional Test.") (license license:gpl3))) (define-public r-expm (package (name "r-expm") (version "0.999-9") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 "1m7yiya3hyv6l87qi0vj9s9cmajnig7ah08id9y4yg4dr95278c3")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran)) (home-page "https://r-forge.r-project.org/projects/expm/") (synopsis "Tools for matrix exponentials and related quantities") (description "This package provides tools for the computation of the matrix exponential, logarithm, square root, and related quantities.") (license license:gpl2+))) (define-public r-exposition (package (name "r-exposition") (version "2.8.23") (source (origin (method url-fetch) (uri (cran-uri "ExPosition" version)) (sha256 (base32 "0x9400ggmgrnaish0cfgnyvw549g4ibfv9aj6vzq7j68n58vq405")))) (properties `((upstream-name . "ExPosition"))) (build-system r-build-system) (propagated-inputs (list r-prettygraphs)) (home-page "https://cran.r-project.org/package=ExPosition") (synopsis "Exploratory analysis with the singular value decomposition") (description "This package provides a variety of descriptive multivariate analyses with the singular value decomposition, such as principal components analysis, correspondence analysis, and multidimensional scaling. See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) .") (license license:gpl2))) (define-public r-complexplus (package (name "r-complexplus") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "complexplus" version)) (sha256 (base32 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) (build-system r-build-system) (propagated-inputs (list r-expm r-matrix)) (home-page "https://cran.r-project.org/web/packages/complexplus/") (synopsis "Functions of complex or real variables") (description "This package extends several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.") (license license:gpl2))) (define-public r-complexupset (package (name "r-complexupset") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "ComplexUpset" version)) (sha256 (base32 "1sk4v5kc2wkgfaws0hjlp30mngm907r5gz1iglf68j46lfs9jbsv")))) (properties `((upstream-name . "ComplexUpset"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-ggplot2 r-patchwork r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/krassowski/complex-upset") (synopsis "Create complex UpSet plots using ggplot2 components") (description "@code{UpSet} plots are an improvement over Venn Diagram for set overlap visualizations. Striving to bring the best of the @code{UpSetR} and ggplot2, this package offers a way to create complex overlap visualisations, using simple and familiar tools.") (license license:expat))) (define-public r-phontools (package (name "r-phontools") (version "0.2-2.2") (source (origin (method url-fetch) (uri (cran-uri "phonTools" version)) (sha256 (base32 "0r5ylbxvzpa23yys4rxdlglfc5jq997ziw6yf8v9jyavy4p1ppkx")))) (properties `((upstream-name . "phonTools"))) (build-system r-build-system) (home-page "http://www.santiagobarreda.com/rscripts.html") (synopsis "Tools for phonetic and acoustic analyses") (description "This package contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.") (license license:bsd-2))) (define-public r-np (package (name "r-np") (version "0.60-17") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 "0dkz8aing2zdah83sjs874cxgwyzx82x60idziqfbhjf4g5mfyfr")))) (build-system r-build-system) (propagated-inputs (list r-boot r-cubature r-quadprog r-quantreg)) (home-page "https://github.com/JeffreyRacine/R-Package-np") (synopsis "Non-parametric kernel smoothing methods for mixed data types") (description "This package provides non-parametric (and semi-parametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-powerplus (package (name "r-powerplus") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "powerplus" version)) (sha256 (base32 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) (build-system r-build-system) (propagated-inputs (list r-complexplus r-expm r-mass r-matrix r-phontools)) (home-page "https://cran.r-project.org/web/packages/powerplus/") (synopsis "Exponentiation operations") (description "This package provides tools for the computation of matrix and scalar exponentiation.") (license license:gpl2))) (define-public r-egg (package (name "r-egg") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "egg" version)) (sha256 (base32 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m")))) (properties `((upstream-name . "egg"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-gtable)) (home-page "https://cran.r-project.org/web/packages/egg") (synopsis "Extensions for ggplot2") (description "This package provides miscellaneous functions to help customize ggplot2 objects. High-level functions are provided to post-process ggplot2 layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. Other functions include a custom @code{geom}, and helper functions to enforce symmetric scales or add tags to facetted plots.") (license license:gpl3))) (define-public r-heatmap3 (package (name "r-heatmap3") (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "heatmap3" version)) (sha256 (base32 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r")))) (build-system r-build-system) (propagated-inputs (list r-fastcluster)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/heatmap3/") (synopsis "Improved heatmap package") (description "This package provides an improved heatmap package. It is completely compatible with the original R function @code{heatmap}, and provides more powerful and convenient features.") (license license:gpl2+))) (define-public r-heatmaply (package (name "r-heatmaply") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 "1crdm7avxv3zx59byz2fqbcw95728crwf9cckjb9gal1065xv95c")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-colorspace r-dendextend r-egg r-ggplot2 r-htmlwidgets r-magrittr r-plotly r-rcolorbrewer r-reshape2 r-scales r-seriation r-viridis r-webshot)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=heatmaply") (synopsis "Interactive cluster heat maps using plotly") (description "This package enables you to create interactive cluster heatmaps that can be saved as a stand-alone HTML file, embedded in R Markdown documents or in a Shiny app, and made available in the RStudio viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A heatmap is a popular graphical method for visualizing high-dimensional data, in which a table of numbers is encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by dendrograms.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-h5 (package (name "r-h5") (version "0.9.9") (source (origin (method url-fetch) (uri (cran-uri "h5" version)) (sha256 (base32 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs (list zlib hdf5)) (native-inputs (list which)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/mannau/h5") (synopsis "Interface to the HDF5 Library") (description "This package provides an S4 interface to the HDF5 library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The HDF5 format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.") (license license:bsd-2))) (define-public r-cgdsr (package (name "r-cgdsr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "cgdsr" version)) (sha256 (base32 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) (build-system r-build-system) (propagated-inputs (list r-httr r-r-methodss3 r-r-oo)) (home-page "https://github.com/cBioPortal/cgdsr") (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") (description "This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).") (license license:lgpl3))) (define-public r-cqrreg (package (name "r-cqrreg") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "cqrReg" version)) (sha256 (base32 "1788hnm1qd5mv5bcizz2h170jg6954sfggjnfqcwfwg167px0df2")))) (properties `((upstream-name . "cqrReg"))) (build-system r-build-system) (propagated-inputs (list r-quantreg r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/package=cqrReg") (synopsis "Quantile, composite quantile regression and regularized versions") (description "Estimate @dfn{quantile regression} (QR) and @dfn{composite quantile regression} (cqr) and with adaptive lasso penalty using @dfn{interior point} (IP), @dfn{majorize and minimize} (MM), @dfn{coordinate descent} (CD), and @dfn{alternating direction method of multipliers algorithms} (ADMM).") (license license:gpl2+))) (define-public r-import (package (name "r-import") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "import" version)) (sha256 (base32 "1h7km8751flxf70112r31wp10vhk4v1jr4avyb969ln317pf8yjq")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/smbache/import") (synopsis "Import mechanism for R") (description "This is an alternative mechanism for importing objects from packages. The syntax allows for importing multiple objects from a package with a single command in an expressive way. The import package bridges some of the gap between using @code{library} (or @code{require}) and direct (single-object) imports. Furthermore the imported objects are not placed in the current environment. It is also possible to import objects from stand-alone @code{.R} files.") (license license:expat))) (define-public r-shinyace (package (name "r-shinyace") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs (list r-shiny r-jsonlite)) (home-page "https://cran.r-project.org/web/packages/shinyAce/") (synopsis "Ace editor bindings for Shiny") (description "This package provides Ace editor bindings to enable a rich text editing environment within Shiny.") (license license:expat))) (define-public r-rafalib (package (name "r-rafalib") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rafalib" version)) (sha256 (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k")))) (properties `((upstream-name . "rafalib"))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer)) (home-page "https://cran.r-project.org/package=rafalib") (synopsis "Convenience functions for routine data exploration") (description "This package provides a series of shortcuts for routine tasks to facilitate data exploration.") (license license:artistic2.0))) (define-public r-randomizr (package (name "r-randomizr") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "randomizr" version)) (sha256 (base32 "0r7yawh4dnxawinnlz09f57kgdwa08rpwxq3y35jam3x2q48qijn")))) (properties `((upstream-name . "randomizr"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://declaredesign.org/r/randomizr/") (synopsis "Tools for common forms of random assignment and sampling") (description "This package provides tools for generating random assignments for common experimental designs and random samples for common sampling designs.") (license license:expat))) (define-public r-roptim (package (name "r-roptim") (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "roptim" version)) (sha256 (base32 "11h6qdi0rsv0bpps6nxkzzapan284q0gldzkmgx3ww5kvnic5w3y")))) (properties `((upstream-name . "roptim"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "https://github.com/ypan1988/roptim/") (synopsis "General purpose optimization in R using C++") (description "This package performs optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms (Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying @code{optim()}.") (license license:gpl2+))) (define-public r-base64url (package (name "r-base64url") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "base64url" version)) (sha256 (base32 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x")))) (build-system r-build-system) (propagated-inputs (list r-backports)) (home-page "https://github.com/mllg/base64url") (synopsis "Fast and URL-safe base64 encoder and decoder") (description "This package provides a URL-safe base64 encoder and decoder. In contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-}, the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the encoder does not fill the string with trailing @code{=}. The resulting encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]} and thus are safe to use in URLs or for file names. The package also comes with a simple base32 encoder/decoder suited for case insensitive file systems.") (license license:gpl3))) (define-public r-baseline (package (name "r-baseline") (version "1.3-5") (source (origin (method url-fetch) (uri (cran-uri "baseline" version)) (sha256 (base32 "0l0llb3pi89ixkpvfg5vbvwwv3gzldf0g98rrd3vkm7q26rqmmd2")))) (properties `((upstream-name . "baseline"))) (build-system r-build-system) (propagated-inputs (list r-gwidgets2tcltk ;for GUI r-limsolve r-sparsem)) (home-page "https://github.com/khliland/baseline/") (synopsis "Baseline correction of spectra") (description "This package is a collection of baseline correction algorithms. Beside those it provides a framework and a Tcl/Tk enabled GUI for optimizing baseline algorithm parameters. Typical use is the removal of the background effects from spectra, which are originating from various types of spectroscopy and spectrometry. Also, there is a possibility of optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.") (license license:gpl2))) (define-public r-radiant-data (package (name "r-radiant-data") (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 "1nwiw5dps0030f893gs0fixis6xigfr8y8rqhi3l505yx2bsrjbj")) (modules '((guix build utils))) (snippet '(delete-file "inst/assets/html2canvas/html2canvas.min.js")))) (properties `((upstream-name . "radiant.data"))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/assets/html2canvas/" (minify (assoc-ref inputs "_") #:target "html2canvas.min.js"))))))) (propagated-inputs (list r-arrow r-base64enc r-broom r-bslib r-car r-curl r-dplyr r-dt r-ggplot2 r-glue r-import r-jsonlite r-knitr r-lubridate r-magrittr r-markdown r-mass r-patchwork r-plotly r-png r-psych r-randomizr r-readr r-readxl r-rlang r-rmarkdown r-rstudioapi r-scales r-shiny r-shinyace r-shinyfiles r-stringi r-tibble r-tidyr r-writexl)) (native-inputs (list esbuild (origin (method url-fetch) (uri "https://web.archive.org/web/20230428182027id_/\ https://html2canvas.hertzen.com/dist/html2canvas.js") (sha256 (base32 "0svkfnzzsydbsrwi7ky91rjqj97x5rfic69hbr9pwhm0zxlb9i81"))))) (home-page "https://github.com/radiant-rstats/radiant.data") (synopsis "Data menu for Radiant: business analytics using R and Shiny") (description "The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.") (license license:agpl3))) (define-public r-algdesign (package (name "r-algdesign") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "AlgDesign" version)) (sha256 (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar")))) (properties `((upstream-name . "AlgDesign"))) (build-system r-build-system) (home-page "https://github.com/jvbraun/AlgDesign") (synopsis "Algorithmic experimental design") (description "This package provides tools to calculate exact and approximate theory experimental designs for D, A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.") (license license:gpl2+))) (define-public r-alluvial (package (name "r-alluvial") (version "0.1-2") (source (origin (method url-fetch) (uri (cran-uri "alluvial" version)) (sha256 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp")))) (properties `((upstream-name . "alluvial"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/mbojan/alluvial") (synopsis "Create parallel sets plots (Alluvial Diagrams)") (description "This package creates alluvial diagrams (also known as parallel sets plots) for multivariate and time series-like data.") (license license:expat))) (define-public r-signal (package (name "r-signal") (version "1.8-0") (source (origin (method url-fetch) (uri (cran-uri "signal" version)) (sha256 (base32 "1126p631zm0wc4h9ghqai5yb9vklpz676fygb0d0aavs2raaijw9")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/signal/") (synopsis "Signal processing") (description "This package provides a set of signal processing functions originally written for Matlab and GNU Octave. It includes filter generation utilities, filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.") (license license:gpl2))) (define-public r-simplermarkdown (package (name "r-simplermarkdown") (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "simplermarkdown" version)) (sha256 (base32 "0lffwsrhsdqcqhklh24v0y0x6w4vq9jch93m330kfdv2amab1l06")))) (properties `((upstream-name . "simplermarkdown"))) (build-system r-build-system) (propagated-inputs ;; We cannot patch references to pandoc because the patched files are ;; compiled to an opaque rdb/rdx pair. "guix gc" would not be able to ;; find the patched references in those files. (list pandoc r-rjson)) (home-page "https://github.com/djvanderlaan/simplermarkdown") (synopsis "Simple engine for generating reports using R") (description "This package runs R-code present in a pandoc markdown file and includes the resulting output in the resulting markdown file. This file can then be converted into any of the output formats supported by pandoc. The package can also be used as an engine for writing package vignettes.") (license license:gpl3+))) (define-public r-sitar (package (name "r-sitar") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "sitar" version)) (sha256 (base32 "14qc5qy21qyj4gml0gwfn8izbsmzwy30ddc7mazhszi487jrcrp0")))) (properties `((upstream-name . "sitar"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-forcats r-ggplot2 r-glue r-magrittr r-nlme r-purrr r-rlang r-rsample r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/statist7/sitar") (synopsis "Super imposition by translation and rotation growth curve analysis") (description "This package provides functions for fitting and plotting @acronym{SITAR, Super Imposition by Translation And Rotation} growth curve models. SITAR is a shape- invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.") (license license:gpl2+))) (define-public r-gsubfn (package (name "r-gsubfn") (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "gsubfn" version)) (sha256 (base32 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) (build-system r-build-system) (propagated-inputs (list r-proto)) (home-page "https://code.google.com/archive/p/gsubfn/") (synopsis "Utilities for strings and function arguments") (description "This package provides @code{gsubfn} which is like @code{gsub} but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. @code{gsubfn} can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions.") (license license:gpl2+))) (define-public r-sqldf (package (name "r-sqldf") (version "0.4-11") (source (origin (method url-fetch) (uri (cran-uri "sqldf" version)) (sha256 (base32 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff")))) (build-system r-build-system) (propagated-inputs (list r-chron r-dbi r-gsubfn r-proto r-rsqlite)) (home-page "https://github.com/ggrothendieck/sqldf") (synopsis "Manipulate R data frames using SQL") (description "The @code{sqldf} function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. @code{sqldf} transparently sets up a database, imports the data frames into that database, performs the SQL statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be used to read filtered files into R even if the original files are larger than R itself can handle.") (license license:gpl2))) (define-public r-abind (package (name "r-abind") (version "1.4-5") (source (origin (method url-fetch) (uri (cran-uri "abind" version)) (sha256 (base32 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abind/") (synopsis "Combine multidimensional arrays") (description "This package provides tools to combine multidimensional arrays into a single array. This is a generalization of @code{cbind} and @code{rbind}. It works with vectors, matrices, and higher-dimensional arrays. It also provides the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating, extracting and replacing data in arrays.") (license license:lgpl2.0+))) (define-public r-prroc (package (name "r-prroc") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "PRROC" version)) (sha256 (base32 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7")))) (properties `((upstream-name . "PRROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PRROC/") (synopsis "Precision-Recall and ROC curves for weighted and unweighted data") (description "This package computes the areas under the @dfn{precision-recall} (PR) and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.") (license license:gpl3))) (define-public r-vim (package (name "r-vim") (version "6.2.2") (source (origin (method url-fetch) (uri (cran-uri "VIM" version)) (sha256 (base32 "1r0myxcx8y1a3fkf9ssk882f09snn2j6zilsygpld32hahn4k9xg")))) (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs (list r-car r-colorspace r-data-table r-e1071 r-laeken r-magrittr r-mass r-nnet r-ranger r-rcpp r-robustbase r-sp r-vcd)) (native-inputs (list r-knitr)) (home-page "https://github.com/alexkowa/VIM") (synopsis "Visualization and imputation of missing values") (description "This package provides tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods.") (license license:gpl2+))) (define-public r-fnn (package (name "r-fnn") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 "09zwlblkb7wkyk6azq2iizv3kj2wdqmjhg0r8zjiy1f692ivakfv")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") (synopsis "Fast nearest neighbor search algorithms and applications") (description "This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms. Related applications including KNN classification, regression and information measures are implemented.") ;; The DESCRIPTION file erroneously states that GPL version 2.1 or ;; later can be used. (license license:gpl2+))) (define-public r-smoother (package (name "r-smoother") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "smoother" version)) (sha256 (base32 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci")))) (build-system r-build-system) (propagated-inputs (list r-ttr)) (home-page "https://cran.r-project.org/web/packages/smoother") (synopsis "Functions relating to the smoothing of numerical data") (description "This package provides a collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.") (license license:gpl2))) (define-public r-riverplot (package (name "r-riverplot") (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "riverplot" version)) (sha256 (base32 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://logfc.wordpress.com") (synopsis "Sankey or ribbon plots") (description "Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For example, they can be used to compare different clusterings. This package provides an implementation of Sankey plots for R.") (license license:gpl2+))) (define-public r-dyn (package (name "r-dyn") (version "0.2-9.6") (source (origin (method url-fetch) (uri (cran-uri "dyn" version)) (sha256 (base32 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/dyn") (synopsis "Time series regression") (description "This package provides the dyn class interfaces @code{ts}, @code{irts}, @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm}, @code{loess}, @code{quantreg::rq}, @code{MASS::rlm}, @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()}, @code{randomForest::randomForest()} and other regression functions, allowing those functions to be used with time series including specifications that may contain lags, diffs and missing values.") ;; Any GPL version. (license license:gpl2+))) (define-public r-dynutils (package (name "r-dynutils") (version "1.0.11") (source (origin (method url-fetch) (uri (cran-uri "dynutils" version)) (sha256 (base32 "06an2bm1d131v28m240vii2wisbz3zs32wbamm2w7r8rl3yrxkh9")))) (properties `((upstream-name . "dynutils"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-crayon r-desc r-dplyr r-magrittr r-matrix r-proxyc r-purrr r-rcpp r-remotes r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/dynverse/dynutils") (synopsis "Common functionality for the dynverse packages") (description "This package provides common functionality for the @url{https://dynverse.org,dynverse} packages. dynverse is created to support the development, execution, and benchmarking of trajectory inference methods.") (license license:expat))) (define-public r-catdap (package (name "r-catdap") (version "1.3.7") (source (origin (method url-fetch) (uri (cran-uri "catdap" version)) (sha256 (base32 "0z84bx808hy70bkzdda9l42ljh9i9pz07isxq756axi7nr0ky6p9")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/catdap/") (synopsis "Tools for categorical data analysis") (description "This package provides functions for analyzing multivariate data. Dependencies of the distribution of the specified variable (response variable) to other variables (explanatory variables) are derived and evaluated by the @dfn{Akaike Information Criterion} (AIC).") (license license:gpl2+))) (define-public r-catdata (package (name "r-catdata") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "catdata" version)) (sha256 (base32 "1d4zndlq2ngjhhqg9d6xi84ddfx262pl63gfw8qhq9m3w7z2dklx")))) (properties `((upstream-name . "catdata"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/package=catdata") (synopsis "Datasets and examples used in the book @emph{Regression for Categorical Data}") (description "This R package contains examples from the book @emph{Regression for Categorical Data}, Tutz 2012, Cambridge University Press. The names of the examples refer to the chapter and the data set that is used.") (license license:gpl2))) (define-public r-arules (package (name "r-arules") (version "1.7-7") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 "183isw4sy5gv5fxajiy4pm5p3nfd1pffa4h8sisl2nrw2rig9na2")))) (build-system r-build-system) (propagated-inputs (list r-generics r-matrix)) (home-page "https://github.com/mhahsler/arules") (synopsis "Mining association rules and frequent itemsets") (description "This package provides an infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). It also provides C implementations of the association mining algorithms Apriori and Eclat.") (license license:gpl3))) (define-public r-parsedate (package (name "r-parsedate") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "parsedate" version)) (sha256 (base32 "1cfinqlbchmkhkgmdwiy3mnxb17lp02jfk2gpw56hq9vh6wimhqz")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/parsedate") (synopsis "Recognize and parse dates in various formats") (description "This package provides three functions for dealing with dates: @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and time formats, @code{parse_date} parses dates in unspecified formats, and @code{format_iso_8601} formats a date in ISO 8601 format.") (license license:gpl2))) (define-public r-abc-data (package (name "r-abc-data") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "abc.data" version)) (sha256 (base32 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj")))) (properties `((upstream-name . "abc.data"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abc.data/") (synopsis "Data for Approximate Bayesian Computation (ABC) package") (description "This package contains data which are used by functions of the abc package which implements several @dfn{Approximate Bayesian Computation} (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit.") (license license:gpl3+))) (define-public r-abc (package (name "r-abc") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "abc" version)) (sha256 (base32 "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv")))) (build-system r-build-system) (propagated-inputs (list r-abc-data r-locfit r-mass r-nnet r-quantreg)) (home-page "https://cran.r-project.org/web/packages/abc/") (synopsis "Tools for Approximate Bayesian Computation (ABC)") (description "This package implements several @dfn{Approximate Bayesian Computation} (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.") (license license:gpl3+))) (define-public r-zip (package (name "r-zip") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 "0hs5yz324jpiy2h0jkrlcb2h9ks65mcc2vpf68briy9aj92aisrk")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") (description "This package provides a cross-platform Zip compression library for R. It is a replacement for the @code{zip} function, that does not require any additional external tools on any platform.") (license license:cc0))) (define-public r-openai (package (name "r-openai") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "openai" version)) (sha256 (base32 "1fi1nc9c7kfnig6b5ifpb1v9r3gxszk984rwyq7i1lb6s5jv0b9z")))) (properties `((upstream-name . "openai"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-glue r-httr r-jsonlite r-lifecycle r-magrittr)) (home-page "https://github.com/irudnyts/openai") (synopsis "R Wrapper for OpenAI API") (description "This package provides an R wrapper of OpenAI API endpoints (see @url{https://platform.openai.com/docs/introduction} for details). This package covers Models, Completions, Chat, Edits, Images, Embeddings, Audio, Files, Fine-tunes, Moderations, and legacy Engines endpoints.") (license license:expat))) (define-public r-operator-tools (package (name "r-operator-tools") (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "operator.tools" version)) (sha256 (base32 "1v4dg7xhz24dnp0zxn815x1405ig64ibii6y40la1gvmzcc41dz5")))) (properties `((upstream-name . "operator.tools"))) (build-system r-build-system) (home-page "https://github.com/decisionpatterns/operator.tools") (synopsis "Utilities for working with R's operators") (description "This package provides a collection of utilities that allow programming with R's operators. Routines allow classifying operators, translating to and from an operator and its underlying function, and inverting some operators (e.g. comparison operators), etc. All methods can be extended to custom infix operators.") (license license:gpl2))) (define-public r-openxlsx (package (name "r-openxlsx") (version "4.2.5.2") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 "0rwvzhk2brhbf1cdpg5jmwiwx5jhr9ybzvnhw0pg4bl3wpkqjw7f")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-stringi r-zip)) (native-inputs (list r-knitr)) (home-page "https://github.com/awalker89/openxlsx") (synopsis "Read, write and edit XLSX files") (description "This package simplifies the creation of Excel @code{.xlsx} files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the @code{xlsx} and @code{XLConnect} packages with the added benefit of removing the dependency on Java.") (license license:gpl3))) (define-public r-rio (package (name "r-rio") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 "1vkvajlmp8kgmkadamy0xm885whfkwacq2jxcrshz1w8amy16k3m")))) (build-system r-build-system) (propagated-inputs (list r-curl r-data-table r-foreign r-haven r-lifecycle r-r-utils r-readxl r-stringi r-tibble r-writexl)) (native-inputs (list r-knitr)) (home-page "https://github.com/leeper/rio") (synopsis "Swiss-army knife for data I/O") (description "This package provides streamlined data import and export infrastructure by making assumptions that the user is probably willing to make: @code{import} and @code{export} determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., @code{stringsAsFactors=FALSE}), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate. An additional convenience function, @code{convert}, provides a simple method for converting between file types.") (license license:gpl2))) (define-public r-maptools (package (name "r-maptools") (version "1.1-8") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 "1xz0cqg629vz7mawwxx650mgmvh3wzn25rnxy4sij5jrypipk1ay")))) (build-system r-build-system) (propagated-inputs (list r-foreign r-lattice r-sp)) (home-page "https://r-forge.r-project.org/projects/maptools/") (synopsis "Tools for reading and handling spatial objects") (description "This package provides a set of tools for manipulating and reading geographic data, in particular ESRI Shapefiles. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with other R packages.") ;; The C source files from shapelib are released under the Expat license. ;; The R code is released under GPL version 2 or later. (license (list license:gpl2+ license:expat)))) (define-public r-maptree (package (name "r-maptree") (version "1.4-8") (source (origin (method url-fetch) (uri (cran-uri "maptree" version)) (sha256 (base32 "1x35nk4fi2b62krcvcv187n5sbqrgvw4pbm7r19ps3jlanpi5ksm")))) (properties `((upstream-name . "maptree"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-rpart)) (home-page "https://cran.r-project.org/package=maptree") (synopsis "Mapping, pruning, and graphing tree models") (description "This package provides a set of functions with example data for graphing, pruning, and mapping models. These models are from hierarchical clustering, and classification and regression trees.") ;; Unlimited distribution; see ;; https://cran.r-project.org/web/packages/maptree/index.html (license (license:non-copyleft "file://DESCRIPTION")))) (define-public r-later (package (name "r-later") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 "07jn5gp4237va5pcq8lvqzyblgij7k2wj9k5wl93q3fd6cyhgxaj")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/later") (synopsis "Utilities for delaying function execution") (description "This package provides tools to execute arbitrary R or C functions some time after the current time, after the R execution stack has emptied.") (license license:gpl2+))) (define-public r-promises (package (name "r-promises") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "promises" version)) (sha256 (base32 "1gp55inqbbj0ifm4n0j5h8854a9v109xpikyhwv7b8lyydns5q1w")))) (build-system r-build-system) (propagated-inputs (list r-fastmap r-later r-magrittr r-r6 r-rcpp r-rlang)) (native-inputs (list r-knitr)) (home-page "https://rstudio.github.io/promises") (synopsis "Abstractions for promise-based asynchronous programming") (description "This package provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to JavaScript promises, but with a syntax that is idiomatic R.") (license license:expat))) (define-public r-dosnow (package (name "r-dosnow") (version "1.0.20") (source (origin (method url-fetch) (uri (cran-uri "doSNOW" version)) (sha256 (base32 "1f5v0k2w0b2478p6iqa3hn2lwd1x3rzc348n57nd38ka2vnsnz4i")))) (properties `((upstream-name . "doSNOW"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators r-snow)) (home-page "https://cran.r-project.org/web/packages/doSNOW") (synopsis "Foreach parallel adaptor for the snow package") (description "This package provides a parallel backend for the @code{%dopar%} function using the @code{snow} package.") (license license:gpl2))) (define-public r-fsa (package (name "r-fsa") (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "FSA" version)) (sha256 (base32 "0b9gf1sh7igd6i14cgl6j8ns2zqvpph3830n7b4q9vw4dfcb53g0")))) (properties `((upstream-name . "FSA"))) (build-system r-build-system) (propagated-inputs (list r-car r-dunn-test r-lmtest r-plotrix r-withr)) (home-page "https://fishr-core-team.github.io/FSA/") (synopsis "Simple fisheries stock assessment methods") (description "This package provides a variety of simple fish stock assessment methods.") (license license:gpl2+))) (define-public r-fstcore (package (name "r-fstcore") (version "0.9.18") (source (origin (method url-fetch) (uri (cran-uri "fstcore" version)) (sha256 (base32 "00wzpr2i7s9pc3alvn4b8f1wgmfqplpwdif9rh9x8qqnylbixiqq")))) (properties `((upstream-name . "fstcore"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (inputs (list zlib)) (native-inputs (list pkg-config)) (home-page "https://www.fstpackage.org/fstcore/") (synopsis "R bindings to the fstlib library") (description "The fstlib library provides multithreaded serialization of compressed data frames using the fst format. The fst format allows for random access of stored data and compression with the LZ4 and ZSTD compressors.") (license license:mpl2.0))) (define-public r-fst (package (name "r-fst") (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "fst" version)) (sha256 (base32 "0r96inwrr960m7wmc80603bw2vvvwab225bh9dq3lalwhy4yiis4")))) (properties `((upstream-name . "fst"))) (build-system r-build-system) (propagated-inputs (list r-fstcore r-rcpp)) (home-page "https://www.fstpackage.org") (synopsis "Fast serialization of data frames") (description "The fst package for R provides a fast, easy and flexible way to serialize data frames. With access speeds of multiple GB/s, fst is specifically designed to unlock the potential of high speed solid state disks. Data frames stored in the fst format have full random access, both in column and rows. The fst format allows for random access of stored data and compression with the LZ4 and ZSTD compressors.") (license license:agpl3))) (define-public r-snftool (package (name "r-snftool") (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "SNFtool" version)) (sha256 (base32 "05hz230aq5wbzhknxzr4iqv3nqjhbpf66n6bp1rc5h2jgz2yfbwq")))) (properties `((upstream-name . "SNFtool"))) (build-system r-build-system) (propagated-inputs (list r-alluvial r-exposition)) (home-page "https://cran.r-project.org/package=SNFtool") (synopsis "Similarity network fusion") (description "Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-snowfall (package (name "r-snowfall") (version "1.84-6.3") (source (origin (method url-fetch) (uri (cran-uri "snowfall" version)) (sha256 (base32 "0hxip3rzv7slxvif1000avbcid2mjxj1y9mimyvk87h404mr6h96")))) (build-system r-build-system) (propagated-inputs (list r-snow)) (home-page "https://cran.r-project.org/web/packages/snowfall/") (synopsis "Easier cluster computing") (description "This package is a usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. The package is also designed as connector to the cluster management tool @code{sfCluster}, but can also used without it.") (license license:gpl2+))) (define-public r-rgexf (package (name "r-rgexf") (version "0.16.2") (source (origin (method url-fetch) (uri (cran-uri "rgexf" version)) (sha256 (base32 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f")) ;; Delete minified JavaScript files (snippet '(for-each delete-file '("inst/gexf-js/js/jquery-2.0.2.min.js" "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js" "inst/gexf-js/js/jquery.mousewheel.min.js"))))) (properties `((upstream-name . "rgexf"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui")) (with-directory-excursion "inst/gexf-js/js/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-jquery") "jquery-2.0.2.min.js") ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js" "jquery-ui-1.10.3.custom.min.js") (,(assoc-ref inputs "js-jquery-mousewheel") "jquery.mousewheel.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-igraph r-servr r-xml)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ("unzip" ,unzip) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-2.0.2.js") (sha256 (base32 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj")))) ("js-jquery-ui" ,(origin (method url-fetch) (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip") (sha256 (base32 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx")))) ("js-jquery-mousewheel" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\ 3.0.6/jquery.mousewheel.js") (sha256 (base32 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v")))))) (home-page "https://gvegayon.github.io/rgexf") (synopsis "Build, import and export GEXF graph files") (description "Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others). It allows the user to easily build/read graph files including attributes, GEXF visual attributes (such as color, size, and position), network dynamics (for both edges and nodes) and edge weighting. Users can build/handle graphs element-by-element or massively through data-frames, visualize the graph on a web browser through gexf-js (a JavaScript library) and interact with the igraph package.") (license license:expat))) (define-public r-data-tree (package (name "r-data-tree") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "data.tree" version)) (sha256 (base32 "0qxd1g159phc6f18iddjljdg96sh09w63xqawjwbwyhg4blm9ddh")))) (properties `((upstream-name . "data.tree"))) (build-system r-build-system) (propagated-inputs (list r-r6 r-stringi)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/gluc/data.tree") (synopsis "General purpose hierarchical data structure") (description "Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. This is useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.") (license license:gpl2+))) (define-public r-dtplyr (package (name "r-dtplyr") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "dtplyr" version)) (sha256 (base32 "1rfnr1f3dzzivzmw9jjaclckkany6c625bqr8lkx32qbcjd6iad5")))) (properties `((upstream-name . "dtplyr"))) (build-system r-build-system) (propagated-inputs (list r-cli r-data-table r-dplyr r-glue r-lifecycle r-rlang r-tibble r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidyverse/dtplyr") (synopsis "Data Table back-end for dplyr") (description "This package provides a @code{data.table} backend for @code{dplyr}. The goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is automatically translated to the equivalent, but usually much faster, @code{data.table} code.") (license license:expat))) (define-public r-collapsibletree (package (name "r-collapsibletree") (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "collapsibleTree" version)) (sha256 (base32 "1i5nmw5w7m8xdgxzim8z8n4w321f42isxbvvajl8ii59pg7drilq")) (snippet '(begin ;; Delete minified JavaScript file (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js") #true)))) (properties `((upstream-name . "collapsibleTree"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/" (let ((source (assoc-ref inputs "d3.v4.js")) (target "d3.min.js")) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs (list r-data-tree r-htmlwidgets)) (native-inputs `(("esbuild" ,esbuild) ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) (home-page "https://github.com/AdeelK93/collapsibleTree") (synopsis "Interactive collapsible tree diagrams using D3.js") (description "This is a package for interactive Reingold-Tilford tree diagrams created using D3.js, where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame.") (license license:gpl3+))) (define-public r-rapiclient (package (name "r-rapiclient") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "rapiclient" version)) (sha256 (base32 "1pm4kdga2nz1cpmchdb0ad8gr3bqfm84b1kl32cyc0x3x5rr2syz")))) (properties `((upstream-name . "rapiclient"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-yaml)) (home-page "https://github.com/bergant/rapiclient") (synopsis "Dynamic OpenAPI/Swagger client") (description "This package lets you access services specified in OpenAPI (formerly Swagger) format. It is not a code generator. The client is generated dynamically as a list of R functions.") (license license:expat))) (define-public r-rappdirs (package (name "r-rappdirs") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "rappdirs" version)) (sha256 (base32 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rappdirs/") (synopsis "Determine where to save data, caches, and logs") (description "This package provides an easy way to determine which directories on the user's computer should be used to save data, caches and logs. It is a port of Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (license license:expat))) (define-public r-rastervis (package (name "r-rastervis") (version "0.51.6") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 "12cl201gwah0bn14ji4nbygayd77w5fck9zkcikhrda5s0chvgb1")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs (list r-hexbin r-lattice r-latticeextra r-raster r-rcolorbrewer r-sp r-terra r-viridislite r-zoo)) (home-page "https://oscarperpinan.github.io/rastervis/") (synopsis "Visualization methods for raster data") (description "This package provides methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields.") (license license:gpl3))) (define-public r-rentrez (package (name "r-rentrez") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "rentrez" version)) (sha256 (base32 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv")))) (properties `((upstream-name . "rentrez"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-xml)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/rentrez/") (synopsis "Entrez in R") (description "This package provides an R interface to the NCBI's EUtils API, allowing users to search databases like GenBank PubMed, process the results of those searches and pull data into their R sessions.") (license license:expat))) (define-public r-renv (package (name "r-renv") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 "1d2y1yks34dg862zcxx03dak1h2gikis6mabmws2srja2hr18nlq")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://rstudio.github.io/renv") (synopsis "Project environments") (description "This package provides a dependency management toolkit for R. Using renv, you can create and manage project-local R libraries, save the state of these libraries to a lockfile, and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.") (license license:expat))) ;; TODO: esbuild (define-public r-learnr (package (name "r-learnr") (version "0.11.5") (source (origin (method url-fetch) (uri (cran-uri "learnr" version)) (sha256 (base32 "01xig6ijsjnkwdjh03zdp86mqm5pjlqp9br34pn644rf98qg8k2y")))) (build-system r-build-system) (native-inputs (list esbuild r-knitr)) (propagated-inputs (list r-checkmate r-digest r-ellipsis r-evaluate r-htmltools r-htmlwidgets r-jsonlite r-knitr r-lifecycle r-markdown r-promises r-rappdirs r-renv r-rlang r-rmarkdown r-rprojroot r-shiny r-withr)) (home-page "https://rstudio.github.io/learnr/") (synopsis "Interactive tutorials for R") (description "This package provides tools to create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.") (license license:asl2.0))) (define-public r-analytics (package (name "r-analytics") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "analytics" version)) (sha256 (base32 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) (build-system r-build-system) (propagated-inputs (list r-car r-cluster r-fractal r-lmtest r-mass r-np r-powerplus r-robust r-trend r-tsa r-urca r-vim)) (home-page "https://cran.r-project.org/web/packages/analytics/") (synopsis "Collection of data analysis tools") (description "This package is a collection of data analysis tools. It includes tools for regression outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.") (license license:gpl2))) (define-public r-here (package (name "r-here") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "here" version)) (sha256 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88")))) (properties `((upstream-name . "here"))) (build-system r-build-system) (propagated-inputs (list r-rprojroot)) (native-inputs (list r-knitr)) (home-page "https://here.r-lib.org/") (synopsis "Simpler way to find files") (description "This package lets you construct paths to your project's files. Use the @code{here} function as a drop-in replacement for @code{file.path}, it will always locate the files relative to your project root.") (license license:expat))) (define-public r-reticulate (package (name "r-reticulate") (version "1.34.0") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 "01j2dr93r5a18irwbm6hlh2v0s2rc5bl6dcmds1m64c1rli8j3cd")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'build-reproducibly (lambda _ (setenv "PYTHONHASHSEED" "0") (setenv "PYTHONDONTWRITEBYTECODE" "1")))))) (inputs (list python)) (propagated-inputs (list r-here r-jsonlite r-matrix r-png r-rappdirs r-rcpp r-rcpptoml r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/reticulate") (synopsis "R interface to Python") (description "This package provides an interface from R to Python modules, classes, and functions. When calling into Python, R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types.") (license license:asl2.0))) (define-public r-bibtex (package (name "r-bibtex") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 "1l9y945qmpla68rx6dnaxc83vmvkw26cw4zzfgfsvi36wsja1hgk")))) (build-system r-build-system) (propagated-inputs (list r-backports)) (home-page "https://github.com/romainfrancois/bibtex") (synopsis "Bibtex parser") (description "This package provides a utility for R to parse a bibtex file.") (license license:gpl2+))) (define-public r-billboarder (package (name "r-billboarder") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "billboarder" version)) (sha256 (base32 "0byj1ilwnmq9n9gswsnj17r8pzhm4fp6567nbz1xfmlvl3402qkn")) (snippet '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js")))) (properties `((upstream-name . "billboarder"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/billboard/" (let ((source (assoc-ref inputs "js-billboard")) (target "billboard.pkgd.min.js")) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs (list r-ggplot2 r-htmltools r-htmlwidgets r-jsonlite r-magrittr r-rlang r-scales r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ;; It is not ideal to use this concatenated (but not minified) ;; JavaScript file, as the original source is written in TypeScript. ;; However, this can still be considered source code as it is readable ;; and can be modified. ("js-billboard" ,(origin (method url-fetch) (uri "https://unpkg.com/billboard.js@3.6.3/dist/billboard.js") (sha256 (base32 "1lyj4yl95qgh06iygb2y2mdg1zxijzxi5h85z7kp8ngm825z6rpi")))))) (home-page "https://github.com/dreamRs/billboarder") (synopsis "Create interactive charts with the JavaScript Billboard library") (description "This package provides an @code{htmlwidgets} interface to billboard.js, a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in shiny apps.") (license license:expat))) (define-public r-ggseqlogo (package (name "r-ggseqlogo") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "ggseqlogo" version)) (sha256 (base32 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (home-page "https://github.com/omarwagih/ggseqlogo") (synopsis "ggplot2 extension for drawing genetic sequence logos") (description "The range of functions provided by this package makes it possible to draw highly versatile genomic sequence logos. Features include, but are not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other ggplot2 plots.") ;; Unspecified version of the LGPL. (license license:lgpl3+))) (define-public r-ggsci (package (name "r-ggsci") (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggsci" version)) (sha256 (base32 "0ag1cj4ycl5xmll8mqmmikyvq94l8yx96pb8m2i853yp2rjk20c9")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales)) (native-inputs (list r-knitr)) (home-page "https://nanx.me/ggsci/") (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") (description "This package provides a collection of ggplot2 color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.") (license license:gpl3))) (define-public r-ggsignif (package (name "r-ggsignif") (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 "02mjailzyqkdnzky60dgampw2sq6mnn7s66fk0lhy32s8apm280i")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-ggplot2)) (home-page "https://github.com/const-ae/ggsignif") (synopsis "Significance brackets for ggplot2") (description "Enrich your ggplots with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance. The package provides a single layer that takes the groups for comparison and the test as arguments and adds the annotation to the plot.") (license license:gpl3))) (define-public r-rstatix (package (name "r-rstatix") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 "1891a976k2qjrh1vkzfg8icxblxa978wbazg7mqq8pcw3nmzbip0")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs (list r-broom r-car r-corrplot r-dplyr r-generics r-magrittr r-purrr r-rlang r-tibble r-tidyr r-tidyselect)) (home-page "https://rpkgs.datanovia.com/rstatix/") (synopsis "Pipe-friendly framework for basic statistical tests") (description "This package provides a simple and intuitive pipe-friendly framework, coherent with the @code{tidyverse} design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.") (license license:gpl2))) (define-public r-ggpubr (package (name "r-ggpubr") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 "0x7p3lbh0xv5qk0shsrj1fjx382zak7mj8l3z1zd348r2pccavif")))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-dplyr r-ggplot2 r-ggrepel r-ggsci r-ggsignif r-glue r-gridextra r-magrittr r-polynom r-purrr r-rlang r-scales r-rstatix r-tibble r-tidyr)) (home-page "http://www.sthda.com/english/rpkgs/ggpubr") (synopsis "ggplot2-based publication-ready plots") (description "The ggplot2 package is an excellent and flexible package for elegant data visualization in R. However the default generated plots require some formatting before we can send them for publication. The ggpubr package provides some easy-to-use functions for creating and customizing ggplot2-based publication-ready plots.") (license license:gpl2))) (define-public r-ellipse (package (name "r-ellipse") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ellipse" version)) (sha256 (base32 "1wy25kw3055zxzidzzkif6c8bmch73qkv2ri4i1w0b6ffcwmbs6d")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ellipse/") (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") (description "This package contains various routines for drawing ellipses and ellipse-like confidence regions, implementing the plots described in Murdoch and Chow (1996), A graphical display of large correlation matrices, The American Statistician 50, 178-180. There are also routines implementing the profile plots described in Bates and Watts (1988), Nonlinear Regression Analysis and its Applications.") (license license:gpl2+))) (define-public r-flashclust (package (name "r-flashclust") (version "1.01-2") (source (origin (method url-fetch) (uri (cran-uri "flashClust" version)) (sha256 (base32 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) (properties `((upstream-name . "flashClust"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/flashClust/") (synopsis "Implementation of optimal hierarchical clustering") (description "This package provides a fast implementation of hierarchical clustering.") (license license:gpl2+))) (define-public r-factominer (package (name "r-factominer") (version "2.9") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 "0c2j3xid85qffsdjwndqiwihclzw6k1nkbpzcc7whhd6k79rh9l8")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs (list r-car r-cluster r-dt r-ellipse r-emmeans r-flashclust r-ggplot2 r-ggrepel r-lattice r-leaps r-mass r-multcompview r-scatterplot3d)) (native-inputs (list r-knitr)) (home-page "http://factominer.free.fr") (synopsis "Multivariate exploratory data analysis and data mining") (description "This package provides exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis.") (license license:gpl2+))) (define-public r-factoextra (package (name "r-factoextra") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "factoextra" version)) (sha256 (base32 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2")))) (build-system r-build-system) (propagated-inputs (list r-abind r-cluster r-dendextend r-factominer r-ggplot2 r-ggpubr r-ggrepel r-reshape2 r-tidyr)) (home-page "http://www.sthda.com/english/rpkgs/factoextra") (synopsis "Extract and visualize the results of multivariate data analyses") (description "This package provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.") (license license:gpl2))) (define-public r-fancova (package (name "r-fancova") (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "fANCOVA" version)) (sha256 (base32 "04mw0blgpwdk6wdg8llrig43psgc0vb42cbimvzbnym8v503dsn3")))) (properties `((upstream-name . "fANCOVA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fANCOVA") (synopsis "Nonparametric analysis of covariance") (description "This package provides a collection of R functions to perform nonparametric analysis of covariance for regression curves or surfaces. Testing the equality or parallelism of nonparametric curves or surfaces is equivalent to analysis of variance (ANOVA) or analysis of covariance (ANCOVA) for one-sample functional data. Three different testing methods are available in the package, including one based on L-2 distance, one based on an ANOVA statistic, and one based on variance estimators.") (license license:gpl3))) (define-public r-fansi (package (name "r-fansi") (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 "0qqq8gz6sfr5yib4qmvk458qa0ypaz0n7f2ygjnpy2p5vy8cd7ga")))) (build-system r-build-system) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/brodieG/fansi") (synopsis "ANSI control sequence aware string functions") (description "This package provides counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.") (license license:gpl2+))) (define-public r-nbclust (package (name "r-nbclust") (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "NbClust" version)) (sha256 (base32 "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs")))) (properties `((upstream-name . "NbClust"))) (build-system r-build-system) (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package") (synopsis "Determine the best number of clusters in a data set") (description "NbClust provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.") (license license:gpl2))) (define-public r-hdf5r (package (name "r-hdf5r") (version "1.3.9") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 "1av3pafbfff4wanw9s1iqgwkcdmc5f8c8h3z0byqll9i661kz3pg")))) (build-system r-build-system) (inputs (list hdf5 zlib)) (propagated-inputs (list r-bit64 r-r6)) (native-inputs (list r-knitr)) (home-page "https://hhoeflin.github.io/hdf5r") (synopsis "Interface to the HDF5 binary data format") (description "HDF5 is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the HDF5 API using R6 classes. Additionally, functionality is added so that HDF5 objects behave very similar to their corresponding R counterparts.") (license license:asl2.0))) (define-public r-itertools (package (name "r-itertools") (version "0.1-3") (source (origin (method url-fetch) (uri (cran-uri "itertools" version)) (sha256 (base32 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn")))) (build-system r-build-system) (propagated-inputs (list r-iterators)) (home-page "https://cran.r-project.org/web/packages/itertools/") (synopsis "Iterator tools") (description "This package provides various tools for creating iterators, many patterned after functions in the Python @code{itertools} module, and others patterned after functions in the snow package.") (license license:gpl2))) (define-public r-itsadug (package (name "r-itsadug") (version "2.4.1") (source (origin (method url-fetch) (uri (cran-uri "itsadug" version)) (sha256 (base32 "1sdqs279qxr3993hw08xg7b54yq03jw1597cqn6cf24sh9vpw9m1")))) (properties `((upstream-name . "itsadug"))) (build-system r-build-system) (propagated-inputs (list r-mgcv r-plotfunctions)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=itsadug") (synopsis "Interpreting time series and autocorrelated data using GAMMs") (description "@dfn{Generalized Additive Mixed Modeling} (GAMM; Lin & Zhang, 1999) as implemented in the R package @code{mgcv} is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).") (license license:gpl2+))) (define-public r-polynom (package (name "r-polynom") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "polynom" version)) (sha256 (base32 "0y4j07syjwpnq5w6a1d90z6h1hjzijmm42pq0f8jk2vcn5xxn7mw")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/polynom/") (synopsis "Functions for univariate polynomial manipulations") (description "This package provides a collection of functions to implement a class for univariate polynomial manipulations.") (license license:gpl2))) (define-public r-pupillometryr (package (name "r-pupillometryr") (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "PupillometryR" version)) (sha256 (base32 "0jqpx5g0fjdxxp7wlgv4jm5vrhchm6r21qd7i825fi5552c46awv")))) (properties `((upstream-name . "PupillometryR"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-fda r-ggplot2 r-itsadug r-mgcv r-rlang r-signal r-stringr r-tidyr r-zoo)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=PupillometryR") (synopsis "Unified pipeline for pupillometry data") (description "This package provides a unified pipeline to clean, prepare, plot, and run basic analyses on pupillometry experiments.") (license license:expat))) (define-public r-gbrd (package (name "r-gbrd") (version "0.4-11") (source (origin (method url-fetch) (uri (cran-uri "gbRd" version)) (sha256 (base32 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82")))) (properties `((upstream-name . "gbRd"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gbRd/") (synopsis "Utilities for processing Rd objects and files") (description "This package provides utilities for processing Rd objects and files. Extract argument descriptions and other parts of the help pages of functions.") (license license:gpl2+))) (define-public r-rjags (package (name "r-rjags") (version "4-15") (source (origin (method url-fetch) (uri (cran-uri "rjags" version)) (sha256 (base32 "188qxyanny4yb1cq8hrz0y7pjafgvj0vhly0gaw271dam8glrk9m")))) (build-system r-build-system) (propagated-inputs (list r-coda)) (inputs (list jags)) (native-inputs (list pkg-config)) (home-page "https://mcmc-jags.sourceforge.net") (synopsis "Bayesian graphical models using MCMC") (description "This package provides an R interface to the JAGS MCMC library. JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (license license:gpl2))) (define-public r-rbibutils (package (name "r-rbibutils") (version "2.2.16") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 "1brab8vzzf44d9rpp9k3r2ajvrs09cbwf4ak014iffzn8yx0yz4w")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") (synopsis "Convert between bibliography formats") (description "This package converts between a number of bibliography formats, including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils utilities and supports all bibliography formats and character encodings implemented in bibutils.") (license license:gpl2))) (define-public r-rdpack (package (name "r-rdpack") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 "02i21i85pb5aim529byjwhmyyz9jd82mi4j26a3kay0pcn6djxba")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs (list r-rbibutils)) (home-page "https://github.com/GeoBosh/Rdpack") (synopsis "Update and manipulate Rd documentation objects") (description "This package provides functions for manipulation of R documentation objects, including functions @code{reprompt()} and @code{ereprompt()} for updating Rd documentation for functions, methods and classes; it also includes Rd macros for citations and import of references from bibtex files for use in Rd files and roxygen2 comments, as well as many functions for manipulation of references and Rd files.") (license license:gpl2+))) (define-public r-officer (package (name "r-officer") (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 "0z3phawwxj4h1pwzw8lsl6pnypr77b329mg6r2qnzmj0j81585z5")))) (build-system r-build-system) (propagated-inputs (list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip)) (home-page "https://davidgohel.github.io/officer") (synopsis "Manipulation of Word and PowerPoint documents") (description "This package provides tools to access and manipulate Word and PowerPoint documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. When working with PowerPoint presentations, slides can be added or removed; shapes inside slides can also be added or removed. When working with Word documents, a cursor can be used to help insert or delete content at a specific location in the document.") (license license:gpl3))) (define-public r-profilemodel (package (name "r-profilemodel") (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "profileModel" version)) (sha256 (base32 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i")))) (properties `((upstream-name . "profileModel"))) (build-system r-build-system) (home-page "https://github.com/ikosmidis/profileModel") (synopsis "Profiling inference functions for various model classes") (description "This package provides tools that can be used to calculate, evaluate, plot and use for inference the profiles of *arbitrary* inference functions for arbitrary @code{glm}-like fitted models with linear predictors. More information on the methods that are implemented can be found in Kosmidis (2008) @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.") (license license:gpl2+))) (define-public r-brglm (package (name "r-brglm") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "brglm" version)) (sha256 (base32 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an")))) (properties `((upstream-name . "brglm"))) (build-system r-build-system) (propagated-inputs (list r-profilemodel)) (home-page "https://github.com/ikosmidis/brglm") (synopsis "Bias reduction in binomial-response generalized linear models") (description "Fit generalized linear models with binomial responses using either an adjusted-score approach to bias reduction or maximum penalized likelihood where penalization is by Jeffreys invariant prior. These procedures return estimates with improved frequentist properties (bias, mean squared error) that are always finite even in cases where the maximum likelihood estimates are infinite (data separation). Fitting takes place by fitting generalized linear models on iteratively updated pseudo-data. The interface is essentially the same as @code{glm}. More flexibility is provided by the fact that custom pseudo-data representations can be specified and used for model fitting. Functions are provided for the construction of confidence intervals for the reduced-bias estimates.") (license license:gpl2+))) (define-public r-entropy (package (name "r-entropy") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "entropy" version)) (sha256 (base32 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg")))) (properties `((upstream-name . "entropy"))) (build-system r-build-system) (home-page "https://www.strimmerlab.org/software/entropy/") (synopsis "Estimation of entropy, mutual information and related quantities") (description "This package implements various estimators of entropy, such as the shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen estimator. It also offers an R interface to the NSB estimator. Furthermore, it provides functions for estimating Kullback-Leibler divergence, chi-squared, mutual information, and chi-squared statistic of independence. In addition there are functions for discretizing continuous random variables.") (license license:gpl3+))) (define-public r-acd (package (name "r-acd") (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "ACD" version)) (sha256 (base32 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6")))) (properties `((upstream-name . "ACD"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACD/") (synopsis "Categorical data analysis with complete or missing responses") (description "This package provides tools for categorical data analysis with complete or missing responses.") (license license:gpl2+))) (define-public r-acdm (package (name "r-acdm") (version "1.0.4.2") (source (origin (method url-fetch) (uri (cran-uri "ACDm" version)) (sha256 (base32 "00i33b76gqllyc6ywwwrgyjvxfspqb3jf52b9sjaazlfwgn5xyjf")))) (properties `((upstream-name . "ACDm"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo)) (home-page "https://cran.r-project.org/web/packages/ACDm/") (synopsis "Tools for Autoregressive Conditional Duration Models") (description "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. It creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.") (license license:gpl2+))) (define-public r-overlap (package (name "r-overlap") (version "0.3.4.1") (source (origin (method url-fetch) (uri (cran-uri "overlap" version)) (sha256 (base32 "0gr0qaay97js3qs11lpci2d3smwl0jda2gc8fqvbw6lb5fznf4r1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/overlap/") (synopsis "Estimates of coefficient of overlapping for animal activity patterns") (description "This package provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.") (license license:gpl3+))) (define-public r-snakecase (package (name "r-snakecase") (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "snakecase" version)) (sha256 (base32 "0888fng8zwm2zmi7rap9hc2q2x2gnhz8gyr35wwjx93w6f8rfpra")))) (build-system r-build-system) (propagated-inputs (list r-stringi r-stringr)) (native-inputs (list r-knitr)) (home-page "https://github.com/Tazinho/snakecase") (synopsis "Convert strings into any case") (description "This package provides a consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.") (license license:gpl3))) (define-public r-prediction (package (name "r-prediction") (version "0.3.14") (source (origin (method url-fetch) (uri (cran-uri "prediction" version)) (sha256 (base32 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://github.com/leeper/prediction") (synopsis "Tidy, type-safe prediction methods") (description "This package provides the @code{prediction()} function, a type-safe alternative to @code{predict()} that always returns a data frame. The package currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"}) from the @code{stats} package, as well as numerous other model classes from other add-on packages.") (license license:expat))) (define-public r-prettygraphs (package (name "r-prettygraphs") (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "prettyGraphs" version)) (sha256 (base32 "0yjpwxdy9mkj2k33zvd5klyv4ava46i19yls87n0bvf79y90ikpy")))) (properties `((upstream-name . "prettyGraphs"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=prettyGraphs") (synopsis "Publication-quality graphics") (description "This package provides simple and crisp publication-quality graphics for the ExPosition family of packages. See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) .") (license license:gpl2))) (define-public r-insight (package (name "r-insight") (version "0.19.7") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 "01hzwz05zz8kxf8hgmz6i4npxwv12723bkv9jk3hhhghlc9lr9a1")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://easystats.github.io/insight/") (synopsis "Easy access to model information for various model objects") (description "This package provides a tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. The package mainly revolves around two types of functions: Functions that find (the names of) information, starting with @code{find_}, and functions that get the underlying data, starting with @code{get_}. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.") (license license:gpl3))) (define-public r-sjlabelled (package (name "r-sjlabelled") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 "1va86q5wddyvqgdpy8d0an2c7v1qbb4hpn0ai6y1v5v1ff87w73k")))) (build-system r-build-system) (propagated-inputs (list r-datawizard r-insight)) (native-inputs (list r-knitr)) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description "This package provides a collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.") (license license:gpl3))) (define-public r-sjmisc (package (name "r-sjmisc") (version "2.8.9") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-insight r-magrittr r-purrr r-rlang r-sjlabelled r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://github.com/strengejacke/sjmisc") (synopsis "Data and variable transformation functions") (description "This package is a collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a tidyverse workflow.") (license license:gpl3))) (define-public r-nodbi (package (name "r-nodbi") (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "nodbi" version)) (sha256 (base32 "1ypwxy560pgn5zza1fv6ip0wh1y872lrf7a1blk2lvwf1q38dlkr")))) (properties `((upstream-name . "nodbi"))) (build-system r-build-system) (propagated-inputs (list r-dbi r-jqr r-jsonlite r-stringi r-uuid)) (home-page "https://docs.ropensci.org/nodbi/") (synopsis "NoSQL database connector") (description "This is a package for simplified document database access and manipulation, providing a common API across supported NoSQL databases Elasticsearch, CouchDB, MongoDB as well as SQLite/JSON1, PostgreSQL, and DuckDB.") (license license:expat))) (define-public r-nortest (package (name "r-nortest") (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "nortest" version)) (sha256 (base32 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/nortest/") (synopsis "Tests for normality") (description "This package provides five omnibus tests for testing the composite hypothesis of normality.") (license license:gpl2+))) (define-public r-moonbook (package (name "r-moonbook") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "moonBook" version)) (sha256 (base32 "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx")))) (properties `((upstream-name . "moonBook"))) (build-system r-build-system) (propagated-inputs (list r-crayon r-magrittr r-nortest r-sjmisc r-stringr r-survival)) (native-inputs (list r-knitr)) (home-page "https://github.com/cardiomoon/moonBook") (synopsis "Functions and datasets for the book by Keon-Woong Moon") (description "This package provides several analysis-related functions for the book entitled \"R statistics and graph for medical articles\" (written in Korean), version 1, by Keon-Woong Moon with Korean demographic data with several plot functions.") (license license:gpl2))) (define-public r-flextable (package (name "r-flextable") (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 "1dlsag1y3s7d5lp1dh2kxf1qax4r9xvxycpmxl64gkr50dk13bam")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-gdtools r-htmltools r-knitr r-officer r-ragg r-rlang r-rmarkdown r-uuid r-xml2)) (native-inputs (list r-knitr)) (home-page "https://davidgohel.github.io/flextable") (synopsis "Functions for tabular reporting") (description "This package provides tools to create pretty tables for HTML documents and other formats. Functions are provided to let users create tables, modify and format their content. It extends the @code{officer} package and can be used within R markdown documents when rendering to HTML and to Word documents.") (license license:gpl3))) (define-public r-writexl (package (name "r-writexl") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 "09whcadnwqcshicbhv1vnvdai087yimmnz9lvc3rld5nn8z66xcg")))) (build-system r-build-system) (inputs (list zlib)) (home-page "https://github.com/ropensci/writexl") (synopsis "Export data frames to xlsx format") (description "This package provides a data frame to xlsx exporter based on libxlsxwriter.") (license license:bsd-2))) (define-public r-writexls (package (name "r-writexls") (version "6.5.0") (source (origin (method url-fetch) (uri (cran-uri "WriteXLS" version)) (sha256 (base32 "1rkc0r6l7cfz7h83i7gw6g0nlyy347mdh6bj73j0f8mdv3nmwwn4")))) (properties `((upstream-name . "WriteXLS"))) (build-system r-build-system) (inputs (list perl)) (home-page "https://github.com/marcschwartz/WriteXLS") (synopsis "Create Excel 2003 (XLS) and Excel 2007 (XLSX) files") (description "This package provides a cross-platform Perl-based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX) files from one or more data frames. Each data frame will be written to a separate named worksheet in the Excel spreadsheet. The worksheet name will be the name of the data frame it contains or can be specified by the user.") (license license:gpl2+))) (define-public r-wrs2 (package (name "r-wrs2") (version "1.1-5") (source (origin (method url-fetch) (uri (cran-uri "WRS2" version)) (sha256 (base32 "028xs424m879siaf3rrhzl1dacp9j7wcl5fpikyx2n0cc7anq4vq")))) (properties `((upstream-name . "WRS2"))) (build-system r-build-system) (propagated-inputs (list r-mass r-plyr r-reshape)) (native-inputs (list r-knitr)) (home-page "https://r-forge.r-project.org/projects/psychor/") (synopsis "Collection of robust statistical methods") (description "R-wrs2 offers a range of strong stats methods from Wilcox WRS functions. It implements robust t-tests, both independent and dependent, robust ANOVA, including designs with between-within subjects, quantile ANOVA, robust correlation, robust mediation, and nonparametric ANCOVA models using robust location measures.") (license license:gpl3))) (define-public r-biasedurn (package (name "r-biasedurn") (version "2.0.11") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 "0dvmkrdmhfh4swilyxf10y856kx0zf9sj1gc0g62bm6r5jhz35b2")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") (synopsis "Biased Urn model distributions") (description "This package provides statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution).") (license license:gpl3))) (define-public r-golem (package (name "r-golem") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "golem" version)) (sha256 (base32 "0pcvp2rmwzvl0wi73fp9pmjq1rrknq2h45sfvbjhmbz8ilvr8zpa")))) (properties `((upstream-name . "golem"))) (build-system r-build-system) (propagated-inputs (list r-attempt r-config r-here r-htmltools r-rlang r-shiny r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ThinkR-open/golem") (synopsis "Framework for robust Shiny applications") (description "This package implements an opinionated framework for building a production- ready Shiny application. Golem contains a series of tools like dependency management, version management, easy installation and deployment or documentation management.") (license license:expat))) (define-public r-goplot (package (name "r-goplot") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "GOplot" version)) (sha256 (base32 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix")))) (properties `((upstream-name . "GOplot"))) (build-system r-build-system) (propagated-inputs (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer)) (home-page "https://github.com/wencke/wencke.github.io") (synopsis "Visualization of functional analysis data") (description "This package provides an implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).") (license license:gpl2))) (define-public r-getopt (package (name "r-getopt") (version "1.20.4") (source (origin (method url-fetch) (uri (cran-uri "getopt" version)) (sha256 (base32 "12qy48adnibfi9rpv5qd8k3hipbc4q85514dsz0xnhdsdnz6rlw7")))) (build-system r-build-system) (home-page "https://github.com/trevorld/getopt") (synopsis "Command-line option processor for R") (description "This package is designed to be used with Rscript to write shebang scripts that accept short and long options. Many users will prefer to use the packages @code{optparse} or @code{argparse} which add extra features like automatically generated help options and usage texts, support for default values, positional argument support, etc.") (license license:gpl2+))) (define-public r-findpython (package (name "r-findpython") (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 "1dydchid5mc79253v5b86bnbg3rm78w0hs586c1rr56lmz5r12hg")))) (build-system r-build-system) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") (description "This package was designed to find an acceptable Python binary that matches version and feature constraints.") (license license:expat))) ;; This in not the same as "r-argparser" (define-public r-argparse (package (name "r-argparse") (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 "0vc59854fxnznjcrzy5kdmnbyk602ml92jk15rxgndfawvsrnb5n")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs (list r-findpython r-jsonlite r-r6)) (native-inputs (list r-knitr)) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description "This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.") (license license:gpl2+))) (define-public r-hash (package (name "r-hash") (version "2.2.6.3") (source (origin (method url-fetch) (uri (cran-uri "hash" version)) (sha256 (base32 "044ifii4gpinzi9vbv5aw0da956ccslxg34xmx24njf6x5dhn0wa")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/hash/") (synopsis "Implementation of hash/associated arrays/dictionaries") (description "This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.") (license license:gpl2+))) (define-public r-orddom (package (name "r-orddom") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "orddom" version)) (sha256 (base32 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) (build-system r-build-system) (propagated-inputs (list r-psych)) (home-page "https://cran.r-project.org/web/packages/orddom/") (synopsis "Ordinal dominance statistics") (description "This package provides tools to compute ordinal, statistics and effect sizes as an alternative to mean comparison: Cliff's delta or success rate difference (SRD), Vargha and Delaney's A or the Area Under a Receiver Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's Common Language Effect Size (CLES) or Grissom & Kim's Probability of Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover, comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of Group (Non-)Overlap considerations.") (license license:gpl2))) (define-public r-deriv (package (name "r-deriv") (version "4.1.3") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") (synopsis "Symbolic differentiation") (description "This package provides an R-based solution for symbolic differentiation. It admits user-defined functions as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.") (license license:gpl3+))) (define-public r-doby (package (name "r-doby") (version "4.6.20") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 "08nsl9xzyi2k7xkwa9mn91fn77ji0z9z5lm388pfdmydbfmpy2ks")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs (list r-broom r-deriv r-dplyr r-ggplot2 r-magrittr r-mass r-matrix r-microbenchmark r-pbkrtest r-tibble)) (native-inputs (list r-knitr)) (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") (description "This package contains: @itemize @item facilities for working with grouped data: @code{do} something to data stratified @code{by} some variables. @item implementations of least-squares means, general linear contrasts, and @item miscellaneous other utilities. @end itemize\n") (license license:gpl2+))) (define-public r-refgenome (package (name "r-refgenome") (version "1.7.7") (source (origin (method url-fetch) (uri (cran-uri "refGenome" version)) (sha256 (base32 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5")))) (properties `((upstream-name . "refGenome"))) (build-system r-build-system) (propagated-inputs (list r-dbi r-doby r-rsqlite)) (home-page "https://cran.r-project.org/web/packages/refGenome/") (synopsis "Gene and splice site annotation using annotation data from Ensembl and UCSC") (description "This package contains functionality for importing and managing of downloaded genome annotation data from the Ensembl genome browser (European Bioinformatics Institute) and from the UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.") (license license:gpl2))) (define-public r-basix (package (name "r-basix") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "BASIX" version)) (sha256 (base32 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id")))) (properties `((upstream-name . "BASIX"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BASIX/") (synopsis "Efficient C/C++ toolset for R") (description "BASIX provides some efficient C/C++ implementations of native R procedures to speed up calculations in R.") (license license:gpl2))) (define-public r-blockfest (package (name "r-blockfest") (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs (list r-basix)) (home-page "https://cran.r-project.org/web/packages/BlockFeST/") (synopsis "Bayesian calculation of region-specific fixation index") (description "This package provides an R implementation of an extension of the BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.") (license license:gpl2))) (define-public r-proc (package (name "r-proc") (version "1.18.5") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 "129cnh3kh9sr42nc7n9f14kr9svi3501834x40njynnzlr0wi4sm")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs (list r-plyr r-rcpp)) (home-page "https://web.expasy.org/pROC/") (synopsis "Display and analyze ROC curves") (description "This package provides tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). The area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (license license:gpl3+))) (define-public r-rootsolve (package (name "r-rootsolve") (version "1.8.2.4") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 "0p9qmn82bg0ks9hmh2dkygnzhxcnp5z8z8b8aq52w6clliz32sp1")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/rootSolve/") (synopsis "Tools for the analysis of ordinary differential equations") (description "This package provides routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of @dfn{ordinary differential equations} (ODE). It includes routines that: @enumerate @item generate gradient and jacobian matrices (full and banded), @item find roots of non-linear equations by the Newton-Raphson method, @item estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running, @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). @end enumerate\n") (license license:gpl2+))) (define-public r-abcanalysis (package (name "r-abcanalysis") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ABCanalysis" version)) (sha256 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) (properties `((upstream-name . "ABCanalysis"))) (build-system r-build-system) (propagated-inputs (list r-plotrix)) (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") (synopsis "Computed ABC Analysis") (description "Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to the perception of losing information from a data set. This package provides tools to calculate these limits on the basis of the mathematical properties of the distribution of the analyzed items.") (license license:gpl3))) (define-public r-slam (package (name "r-slam") (version "0.1-50") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") (description "This package contains data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.") (license license:gpl2))) (define-public r-manipulatewidget (package (name "r-manipulatewidget") (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-codetools r-htmltools r-htmlwidgets r-knitr r-miniui r-shiny r-shinyjs r-webshot)) (native-inputs (list r-knitr)) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description "This package lets you create in just a few lines of R code a nice user interface to modify the data or the graphical parameters of one or multiple interactive charts. It is useful to quickly explore visually some data or for package developers to generate user interfaces easy to maintain.") (license license:gpl2+))) (define-public r-a3 (package (name "r-a3") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "A3" version)) (sha256 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) (properties `((upstream-name . "A3"))) (build-system r-build-system) (propagated-inputs (list r-pbapply r-xtable)) (home-page "https://cran.r-project.org/web/packages/A3/") (synopsis "Error metrics for predictive models") (description "This package supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward.") (license license:gpl2+))) (define-public r-infotheo (package (name "r-infotheo") (version "1.2.0.1") (source (origin (method url-fetch) (uri (cran-uri "infotheo" version)) (sha256 (base32 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0")))) (build-system r-build-system) (home-page "http://homepage.meyerp.com/software") (synopsis "Information-theoretic measures") (description "This package implements various measures of information theory based on several entropy estimators.") (license license:gpl3+))) (define-public r-nsprcomp (package (name "r-nsprcomp") (version "0.5.1-2") (source (origin (method url-fetch) (uri (cran-uri "nsprcomp" version)) (sha256 (base32 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f")))) (properties `((upstream-name . "nsprcomp"))) (build-system r-build-system) (home-page "https://sigg-iten.ch/research/") (synopsis "Non-negative and sparse PCA") (description "This package implements two methods for performing a constrained principal component analysis (PCA), where non-negativity and/or sparsity constraints are enforced on the principal axes (PAs). The function @code{nsprcomp} computes one principal component (PC) after the other. Each PA is optimized such that the corresponding PC has maximum additional variance not explained by the previous components. In contrast, the function @code{nscumcomp} jointly computes all PCs such that the cumulative variance is maximal. Both functions have the same interface as the @code{prcomp} function from the @code{stats} package (plus some extra parameters).") (license license:gpl2+))) (define-public r-cmplot (package (name "r-cmplot") (version "4.5.0") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 "1gg3pq55shh9khw5bsrdhk0yqgyr9xhdzqhaqksihka64wsqmhd3")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") (synopsis "Circle Manhattan plot") (description "Circle Manhattan Plot is an R package that can lay out genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.") (license license:gpl2+))) (define-public r-precrec (package (name "r-precrec") (version "0.14.4") (source (origin (method url-fetch) (uri (cran-uri "precrec" version)) (sha256 (base32 "03hvp5h7fz4v2aswxim0mqgj9rdrhnk5xqz212161kpcrw6m67z8")))) (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-data-table r-ggplot2 r-gridextra r-rcpp r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://evalclass.github.io/precrec/") (synopsis "Calculate accurate precision-recall and ROC curves") (description "This package provides tools for accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.") (license license:gpl3))) (define-public r-netrep (package (name "r-netrep") (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "NetRep" version)) (sha256 (base32 "02ss45giv30pi31b5rysa36bn5c4fs5x58g4vb0arz9cnicznv97")))) (properties `((upstream-name . "NetRep"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bh r-foreach r-rcolorbrewer r-rcpp r-rcpparmadillo r-rhpcblasctl r-statmod)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=NetRep") (synopsis "Permutation testing network module preservation across datasets") (description "This package provides functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing.") (license license:gpl2))) (define-public r-intergraph (package (name "r-intergraph") (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "intergraph" version)) (sha256 (base32 "1s578six6chn98ifgc8kdi2kxgim0mgw5di9sbk8c4aamjl40iim")))) (properties `((upstream-name . "intergraph"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-network)) (native-inputs (list r-knitr)) (home-page "https://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description "Functions implemented in this package allow coercing (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages @code{network} and @code{igraph}.") (license license:gpl3))) (define-public r-interp (package (name "r-interp") (version "1.1-5") (source (origin (method url-fetch) (uri (cran-uri "interp" version)) (sha256 (base32 "082b1sx7m62csqig582syki8ny9vwxk311rh8hp1cmh1l5qhjlhc")))) (properties `((upstream-name . "interp"))) (build-system r-build-system) (propagated-inputs (list r-deldir r-rcpp r-rcppeigen)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=interp") (synopsis "Interpolation methods") (description "Bivariate data interpolation on regular and irregular grids, either linear or using splines are the main part of this package. It is intended to provide replacement functions for the ACM licensed @code{akima::interp} and @code{tripack::tri.mesh} functions.") (license license:gpl2+))) (define-public r-abcoptim (package (name "r-abcoptim") (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "ABCoptim" version)) (sha256 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) (properties `((upstream-name . "ABCoptim"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/gvegayon/ABCoptim/") (synopsis "Optimization of Artificial Bee Colony algorithm") (description "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms, and uses only common control parameters such as colony size and maximum cycle number. The @code{r-abcoptim} implements the Artificial bee colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. This version is a work-in-progress and is written in R code.") (license license:expat))) (define-public r-abcp2 (package (name "r-abcp2") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "ABCp2" version)) (sha256 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) (properties `((upstream-name . "ABCp2"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ABCp2/") (synopsis "Approximate Bayesian Computational Model for Estimating P2") (description "This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.") (license license:gpl2))) (define-public r-abcrf (package (name "r-abcrf") (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "abcrf" version)) (sha256 (base32 "08mh1a6gxp0mfx6qnp1qzcrfx7xp64qj9kad4ziyswfx22ykdsxi")))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-mass r-matrixstats r-ranger r-rcpp r-rcpparmadillo r-readr r-stringr)) (home-page "https://cran.r-project.org/web/packages/abcrf/") (synopsis "Approximate bayesian computation via random forests") (description "This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.") (license license:gpl2+))) (define-public r-abctools (package (name "r-abctools") (version "1.1.7") (source (origin (method url-fetch) (uri (cran-uri "abctools" version)) (sha256 (base32 "16gn5hk25glbjml7bclxqkybi90gqjijz6hl6ak8aig5wm08pgx2")))) (build-system r-build-system) (propagated-inputs (list r-abc r-abind r-hmisc r-plyr)) (home-page "https://github.com/dennisprangle/abctools/") (synopsis "Tools for ABC analyses") (description "This @code{r-abctools} package provides tools for approximate Bayesian computation including summary statistic selection and assessing coverage. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods to tune the choice of threshold.") (license license:gpl2+))) (define-public r-ggstance (package (name "r-ggstance") (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "ggstance" version)) (sha256 (base32 "0wk3gbi5365sndi02gwd4c33vcrj5p8cfwakwjg010y5hgxx96nd")))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-plyr r-rlang r-withr)) (home-page "https://cran.r-project.org/web/packages/ggstance/") (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") (description "This package is a @code{r-ggplot2} extension that provides flipped components: @enumerate @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms; @item vertical versions of @code{r-ggplot2} positions. @end enumerate") (license license:gpl3))) (define-public r-ggnetwork (package (name "r-ggnetwork") (version "0.5.12") (source (origin (method url-fetch) (uri (cran-uri "ggnetwork" version)) (sha256 (base32 "1kg9354f39asq5baryh3zzzdl54g75mn1pxdr3pws9d2q5i8cdkl")))) (properties `((upstream-name . "ggnetwork"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggrepel r-igraph r-network r-sna)) (native-inputs (list r-knitr)) (home-page "https://github.com/briatte/ggnetwork") (synopsis "Geometries to plot networks with ggplot2") (description "This package provides geometries to plot network objects with the ggplot2 package.") (license license:gpl3))) (define-public r-cvauc (package (name "r-cvauc") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "cvAUC" version)) (sha256 (base32 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28")))) (properties `((upstream-name . "cvAUC"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-rocr)) (home-page "https://github.com/ledell/cvAUC") (synopsis "Cross-validated area under the ROC curve confidence intervals") (description "This package contains various tools for working with and evaluating cross-validated area under the ROC curve (AUC) estimators. The primary functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which report cross-validated AUC and compute confidence intervals for cross-validated AUC estimates based on influence curves for i.i.d. and pooled repeated measures data, respectively.") (license license:asl2.0))) (define-public r-gam (package (name "r-gam") (version "1.22-3") (source (origin (method url-fetch) (uri (cran-uri "gam" version)) (sha256 (base32 "153ig136i3dpy87f8v9f5055x94sl74fnrf5ivpa9fc67f76ikb6")))) (properties `((upstream-name . "gam"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=gam") (synopsis "Generalized additive models") (description "This package provides functions for fitting and working with generalized additive models, as described in chapter 7 of \"Statistical Models in S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive Models\" (Hastie and Tibshirani, 1990).") (license license:gpl2))) (define-public r-superlearner (package (name "r-superlearner") (version "2.0-28.1") (source (origin (method url-fetch) (uri (cran-uri "SuperLearner" version)) (sha256 (base32 "19kb4shfhj5aigjm1ljmlvr0jmgcbd6yl4gl3wfddy0nk2wi2bvm")))) (properties `((upstream-name . "SuperLearner"))) (build-system r-build-system) (propagated-inputs (list r-cvauc r-gam r-nnls)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/ecpolley/SuperLearner") (synopsis "Super learner prediction") (description "This package implements the super learner prediction method and contains a library of prediction algorithms to be used in the super learner.") (license license:gpl3))) (define-public r-drtmle (package (name "r-drtmle") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "drtmle" version)) (sha256 (base32 "0qvdxzvpi7a66gx61v6fj31zy4y5cid18g4qgv5lir7qc74rbbx0")))) (properties `((upstream-name . "drtmle"))) (build-system r-build-system) (propagated-inputs (list r-future-apply r-np r-superlearner)) (native-inputs (list r-knitr)) (home-page "https://github.com/benkeser/drtmle") (synopsis "Doubly-robust nonparametric estimation and inference") (description "This package implements targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality.") (license license:expat))) (define-public r-dofuture (package (name "r-dofuture") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "doFuture" version)) (sha256 (base32 "1avv5kv1c43gmvbh5iwxlwk7yl6prndpcgy0blkwarl3nsgcq4cm")))) (properties `((upstream-name . "doFuture"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-foreach r-future r-future-apply r-globals r-iterators)) (native-inputs (list r-markdown ;check phase requires markdown package r-r-rsp)) ;vignette builder (home-page "https://github.com/HenrikBengtsson/doFuture") (synopsis "Foreach parallel adapter using the future API") (description "This package provides a @code{%dopar%} adapter such that any type of futures can be used as backends for the @code{foreach} framework.") (license license:lgpl2.1+))) (define-public r-superheat (package (name "r-superheat") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "superheat" version)) (sha256 (base32 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83")))) (properties `((upstream-name . "superheat"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggdendro r-ggplot2 r-gtable r-magrittr r-plyr r-scales)) (home-page "https://cran.r-project.org/package=superheat") (synopsis "Graphical tool for exploring complex datasets using heatmaps") (description "This package provides a system for generating extendable and customizable heatmaps for exploring complex datasets, including big data and data with multiple data types.") (license license:cc0))) (define-public r-qualv (package (name "r-qualv") (version "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "qualV" version)) (sha256 (base32 "09qqfx94f46x585iipr9wii8ji6ih31xymbw4p5v3qixmfpja276")))) (properties `((upstream-name . "qualV"))) (build-system r-build-system) (propagated-inputs (list r-kernsmooth)) (home-page "https://qualV.R-Forge.R-Project.org/") (synopsis "Qualitative Validation Methods") (description "This package provides qualitative methods for the validation of dynamic models. It contains @enumerate @item an orthogonal set of deviance measures for absolute, relative and ordinal scale and @item approaches accounting for time shifts. @end enumerate The first approach transforms time to take time delays and speed differences into account. The second divides the time series into interval units according to their main features and finds the @dfn{longest common subsequence} (LCS) using a dynamic programming algorithm.") (license license:gpl2+))) (define-public r-mosaiccore (package (name "r-mosaiccore") (version "0.9.4.0") (source (origin (method url-fetch) (uri (cran-uri "mosaicCore" version)) (sha256 (base32 "0v3xhv6yfk1hc6a40jjgp6vvq102qa1l4n787pfywx6jhzbhamp2")))) (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-mass r-rlang r-tidyr)) (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") (synopsis "Common utilities for mosaic family packages") (description "Common utilities used in other Mosaic family packages are collected here.") (license license:gpl2+))) (define-public r-labelled (package (name "r-labelled") (version "2.12.0") (source (origin (method url-fetch) (uri (cran-uri "labelled" version)) (sha256 (base32 "1f6jh1mrbwb3v1kc49pb65sf5ffqs0h9vizpig4r5rhhv4n3q17y")))) (properties `((upstream-name . "labelled"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-haven r-lifecycle r-rlang r-stringr r-tidyr r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://larmarange.github.io/labelled/") (synopsis "Manipulating labelled data") (description "This package provides useful functions to deal with the @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the haven package.") (license license:gpl3))) (define-public r-ggformula (package (name "r-ggformula") (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "ggformula" version)) (sha256 (base32 "0vbpivyxms46px3wqkbl1wq199mqdxq94gsiplv4i7lz0lzghsfm")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggridges r-labelled r-mosaiccore r-rlang r-scales r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/ProjectMOSAIC/ggformula/") (synopsis "Formula interface for the @code{r-ggplot2}") (description "The @code{r-ggformula} introduces a family of graphics functions, gf_point(), gf_density(), and so on, bring the formula interface to ggplot(). This captures and extends the excellent simplicity of the lattice-graphics formula interface, while providing the intuitive capabilities of @code{r-ggplot2}.") (license license:expat))) (define-public r-mosaicdata (package (name "r-mosaicdata") (version "0.20.4") (source (origin (method url-fetch) (uri (cran-uri "mosaicData" version)) (sha256 (base32 "0y6ii234paknak0p8cm5wcjia4s4wh7iixjbbvdgp0w17c05dckh")))) (properties `((upstream-name . "mosaicData"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mosaicData/") (synopsis "Data sets for project Mosaic") (description "This package provides data sets from project Mosaic @url{http://mosaic-web.org} used to teach mathematics, statistics, computation and modeling.") (license license:gpl2+))) (define-public r-raster (package (name "r-raster") (version "3.6-26") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 "14jmpm6rlhya192ckyjlwhais6fgc16gb600wycsdba6b8i7fmy6")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) (home-page "https://www.rspatial.org/") (synopsis "Geographic data analysis and modeling") (description "The package implements basic and high-level functions for reading, writing, manipulating, analyzing and modeling of gridded spatial data. Processing of very large files is supported.") (license license:gpl3+))) (define-public r-mosaic (package (name "r-mosaic") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "mosaic" version)) (sha256 (base32 "1dydqawljv5l9lmhdrhmr7wh3q1c2mnc61gc99jr0jbb1bmls327")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggformula r-ggplot2 r-lattice r-mass r-matrix r-mosaiccore r-mosaicdata r-purrr r-rlang r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/ProjectMOSAIC/mosaic/") (synopsis "Mathematics, statistics, and computation teaching utilities") (description "This package contain data sets and utilities from @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics, statistics, computation and modeling. Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.") (license license:gpl2+))) (define-public r-abd (package (name "r-abd") (version "0.2-8") (source (origin (method url-fetch) (uri (cran-uri "abd" version)) (sha256 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mosaic r-nlme)) (home-page "https://cran.r-project.org/web/packages/abd/") (synopsis "Analysis of biological data") (description "The @code{r-abd} package contains data sets and sample code for the Analysis of biological data by Michael Whitlock and Dolph Schluter.") (license license:gpl2))) (define-public r-svgui (package (name "r-svgui") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "svGUI" version)) (sha256 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979")))) (properties `((upstream-name . "svGUI"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/SciViews/svGUI/") (synopsis "Functions for managing GUI clients in R") (description "The SciViews @code{svGUI} package eases the management of Graphical User Interfaces (GUI) in R. It is independent from any particular GUI widgets. It centralizes info about GUI elements currently used, and it dispatches GUI calls to the particular toolkits in use in function of the context.") (license license:gpl2))) (define-public r-svdialogs (package (name "r-svdialogs") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "svDialogs" version)) (sha256 (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif")))) (properties `((upstream-name . "svDialogs"))) (build-system r-build-system) (inputs (list yad zenity)) (propagated-inputs (list r-rstudioapi r-svgui)) (native-inputs (list r-knitr)) (home-page "https://github.com/SciViews/svDialogs/") (synopsis "Portable dialog boxes") (description "This package helps to construct standard dialog boxes for your GUI, including message boxes, input boxes, list, file or directory selection, and others. In case R cannot display GUI dialog boxes, a simpler command line version of these interactive elements is also provided as a fallback solution.") (license license:gpl2))) (define-public r-abe (package (name "r-abe") (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "abe" version)) (sha256 (base32 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abe/") (synopsis "Augmented backward elimination") (description "This package performs augmented backward elimination and checks the stability of the obtained model. Augmented backward elimination combines significance or information based criteria with the change in estimate to either select the optimal model for prediction purposes or to serve as a tool to obtain a practically sound, highly interpretable model.") (license license:gpl2+))) (define-public r-abf2 (package (name "r-abf2") (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "abf2" version)) (sha256 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abf2/") (synopsis "Load gap-free axon @code{r-abf2} files") (description "This package loads electrophysiology data from ABF2 files, as created by Axon Instruments/Molecular Devices software. Only files recorded in gap-free mode are currently supported.") (license license:artistic2.0))) (define-public r-abhgenotyper (package (name "r-abhgenotyper") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ABHgenotypeR" version)) (sha256 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l")))) (properties `((upstream-name . "ABHgenotypeR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) (home-page "https://github.com/StefanReuscher/ABHgenotypeR/") (synopsis "Visualize and manipulate ABH genotypes") (description "The @code{r-abhgenotyper} package provides simple imputation, error-correction and plotting capacities for genotype data. The package is supposed to serve as an intermediate but independent analysis tool between the TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities not found in either TASSEL or @code{r-qtl} in addition to visualization of genotypes as \"graphical genotypes\".") (license license:gpl3))) (define-public r-furrr (package (name "r-furrr") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 "12z4q0fn7asxis17hisi82bvfabl5if1338lmfqmkrwv5rg7748d")))) (build-system r-build-system) (propagated-inputs (list r-future r-globals r-lifecycle r-purrr r-rlang r-vctrs)) (home-page "https://github.com/DavisVaughan/furrr") (synopsis "Apply mapping functions in parallel using futures") (description "This package provides implementations of the family of @code{map()} functions from the @code{purrr} package that can be resolved using any @code{future}-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.") (license license:lgpl2.1+))) (define-public r-abjutils (package (name "r-abjutils") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "abjutils" version)) (sha256 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-purrr r-rlang r-rstudioapi r-stringi r-stringr r-tidyr)) (home-page "https://github.com/abjur/abjutils/") (synopsis "Collection of tools for jurimetrical analysis") (description "This package implements general purpose tools, such as functions for sampling and basic manipulation of Brazilian lawsuits identification number. It also implements functions for text cleaning, such as accentuation removal.") (license license:expat))) (define-public r-abnormality (package (name "r-abnormality") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "abnormality" version)) (sha256 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/abnormality/") (synopsis "Measure a subject's abnormality with respect to a reference population") (description "This package contains functions to implement the methodology and considerations laid out by Marks et al. in the article \"Measuring abnormality in high dimensional spaces: applications in biomechanical gait analysis\". Using high-dimensional datasets to measure a subject's overall level of abnormality as compared to a reference population is often needed in outcomes research.") (license license:expat))) (define-public r-abodoutlier (package (name "r-abodoutlier") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "abodOutlier" version)) (sha256 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj")))) (properties `((upstream-name . "abodOutlier"))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/abodOutlier/") (synopsis "Angle-based outlier detection") (description "This package performs angle-based outlier detection on a given data frame. It offers three methods to process data: @enumerate @item full but slow implementation using all the data that has cubic complexity; @item a fully randomized method; @item a method using k-nearest neighbours. @end enumerate These algorithms are well suited for high dimensional data outlier detection.") (license license:expat))) (define-public r-abps (package (name "r-abps") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ABPS" version)) (sha256 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) (properties `((upstream-name . "ABPS"))) (build-system r-build-system) (propagated-inputs (list r-kernlab)) (home-page "https://cran.r-project.org/web/packages/ABPS/") (synopsis "Abnormal blood profile score to detect blood doping") (description "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS). The ABPS is a part of the Athlete biological passport program of the World anti-doping agency, which combines several blood parameters into a single score in order to detect blood doping. The package also contains functions to calculate other scores used in anti-doping programs, such as the ratio of hemoglobin to reticulocytes (OFF-score), as well as example data.") (license license:gpl2+))) (define-public r-parmigene (package (name "r-parmigene") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "parmigene" version)) (sha256 (base32 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/parmigene/") (synopsis "Mutual information estimation for gene network reconstruction") (description "This package provides a parallel estimation of the mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks.") (license license:agpl3+))) (define-public r-partr2 (package (name "r-partr2") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "partR2" version)) (sha256 (base32 "06ky0hhrq0mcsn9rwrzvwn0rrjj0l8rxs0hqp10668gdq5hjk8bn")))) (properties `((upstream-name . "partR2"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-lme4 r-magrittr r-pbapply r-purrr r-rlang r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mastoffel/partR2") (synopsis "Partitioning R2 in generalized linear mixed models") (description "This package provides an R tool for estimating and partitioning R2 in @dfn{generalized linear mixed models} (GLMMs) based on predictor variance.") (license license:gpl2+))) (define-public r-pscl (package (name "r-pscl") (version "1.5.5.1") (source (origin (method url-fetch) (uri (cran-uri "pscl" version)) (sha256 (base32 "0nwdwyxmy4baiwjjvrypdclzhpbsipik1rkrvgag4y2csg1nf4v1")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://github.com/atahk/pscl/") (synopsis "Political science computational laboratory") (description "The @code{pscl} is an R package providing classes and methods for: @enumerate @item Bayesian analysis of roll call data (item-response models); @item elementary Bayesian statistics; @item maximum likelihood estimation of zero-inflated and hurdle models for count data; @item utility functions. @end enumerate") (license license:gpl2))) (define-public r-accelmissing (package (name "r-accelmissing") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "accelmissing" version)) (sha256 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) (build-system r-build-system) (propagated-inputs (list r-mice r-pscl)) (home-page "https://cran.r-project.org/web/packages/accelmissing/") (synopsis "Missing value imputation for accelerometer data") (description "This package provides a statistical method to impute the missing values in accelerometer data. The methodology includes both parametric and semi-parametric multiple imputations under the zero-inflated Poisson lognormal model. It also provides multiple functions to preprocess the accelerometer data previous to the missing data imputation. These include detecting the wearing and the non-wearing time, selecting valid days and subjects, and creating plots.") (license license:gpl2+))) (define-public r-mhsmm (package (name "r-mhsmm") (version "0.4.21") (source (origin (method url-fetch) (uri (cran-uri "mhsmm" version)) (sha256 (base32 "1fibgpl65bl3rwlf9dhlams3gxbjqgwcd26gb0flp4wln6pl8d99")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://github.com/jaredo/mhsmm/") (synopsis "Inference for hidden Markov and semi-Markov models") (description "The @code{r-mhsmm} package implements estimation and prediction methods for hidden Markov and semi-Markov models for multiple observation sequences. Such techniques are of interest when observed data is thought to be dependent on some unobserved (or hidden) state. Also, this package is suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.") (license license:gpl2+))) (define-public r-nleqslv (package (name "r-nleqslv") (version "3.3.5") (source (origin (method url-fetch) (uri (cran-uri "nleqslv" version)) (sha256 (base32 "0fjby0qva2lp2i7x752wva0z15xqys9fgrrcfimqszg65wnig60j")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nleqslv/") (synopsis "Solve systems of nonlinear equations") (description "The @code{r-nleqslv} package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.") (license license:gpl2+))) (define-public r-phyclust (package (name "r-phyclust") (version "0.1-34") (source (origin (method url-fetch) (uri (cran-uri "phyclust" version)) (sha256 (base32 "1wzmd02ng7zphn97xdra3hgivrxqpizqcy5kpg45sk7jx4q7016j")))) (properties `((upstream-name . "phyclust"))) (build-system r-build-system) (propagated-inputs (list r-ape)) (home-page "https://snoweye.github.io/phyclust/") (synopsis "Studying phyloclustering and exploring DNA sequence data") (description "@dfn{Phylogenetic clustering} (phyloclustering) is an evolutionary continuous time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package @code{phyclust} provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in @code{C} for performance and interfaced with @code{R} for visualization.") (license license:gpl2+))) (define-public r-physicalactivity (package (name "r-physicalactivity") (version "0.2-4") (source (origin (method url-fetch) (uri (cran-uri "PhysicalActivity" version)) (sha256 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40")))) (properties `((upstream-name . "PhysicalActivity"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") (synopsis "Processing accelerometer data for physical activity measurement") (description "This @code{r-physicalactivity} package provides a function @code{wearingMarking} for classification of monitored wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plots of accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. The revised package version 0.2-1 improved the functions regarding speed, robustness and add better support for time zones and daylight saving. In addition, several functions were added: @enumerate @item the @code{markDelivery} can classify days for ActiGraph delivery by mail; @item the @code{markPAI} can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. @end enumerate It also supports importing ActiGraph (AGD) files with @code{readActigraph} and @code{queryActigraph} functions.") (license license:gpl3+))) (define-public r-acc (package (name "r-acc") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "acc" version)) (sha256 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-dbi r-ggplot2 r-iterators r-mhsmm r-nleqslv r-physicalactivity r-plyr r-r-utils r-rcpp r-rcpparmadillo r-rsqlite r-zoo)) (home-page "https://cran.r-project.org/web/packages/acc/") (synopsis "Exploring accelerometer data") (description "This package processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also, includes functions to plot, analyze, and simulate accelerometer data.") (license license:gpl2+))) (define-public r-rbenchmark (package (name "r-rbenchmark") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rbenchmark" version)) (sha256 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rbenchmark/") (synopsis "Benchmarking routine for R") (description "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.") (license license:gpl2+))) (define-public r-mitools (package (name "r-mitools") (version "2.4") (source (origin (method url-fetch) (uri (cran-uri "mitools" version)) (sha256 (base32 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j")))) (build-system r-build-system) (propagated-inputs (list r-dbi)) (home-page "https://cran.r-project.org/web/packages/mitools/") (synopsis "Tools for multiple imputation of missing data") (description "This package provides tools to perform analyses and combine results from multiple-imputation datasets.") (license license:gpl2))) (define-public r-mixsqp (package (name "r-mixsqp") (version "0.3-54") (source (origin (method url-fetch) (uri (cran-uri "mixsqp" version)) (sha256 (base32 "13pv3mmz514kl4svxqwyk5b241dy1q52khwdc6rmh712ia8xxl7p")))) (properties `((upstream-name . "mixsqp"))) (build-system r-build-system) (propagated-inputs (list r-irlba r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/stephenslab/mixsqp") (synopsis "Sequential quadratic programming for maximum-likelihood estimation") (description "This package provides an optimization method based on sequential quadratic programming for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithm is expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver, and they are expected to arrive at solutions more quickly when the number of samples is large and the number of mixture components is not too large.") (license license:expat))) (define-public r-magick (package (name "r-magick") (version "2.8.2") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 "15ja7f46f77a67wmzqfaxvhmvvzgb9yj92p2if5di7i61vlmnid1")))) (properties '((updater-extra-inputs . ("imagemagick")))) (build-system r-build-system) (inputs (list imagemagick pcre2 zlib)) (propagated-inputs (list r-curl r-magrittr r-rcpp)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/ropensci/magick") (synopsis "Advanced graphics and image-processing in R") (description "This package provides bindings to ImageMagick, a comprehensive image processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio, images are automatically previewed when printed to the console, resulting in an interactive editing environment.") (license license:expat))) (define-public r-survey (package (name "r-survey") (version "4.2-1") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 "0l7iml53k2blmcgvbvplln08fn2s6da856m5izcvw87v6bhn2g6c")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-matrix r-minqa r-mitools r-numderiv r-survival)) (home-page "https://r-survey.r-forge.r-project.org/survey/") (synopsis "Analysis of complex survey samples") (description "This package provides tools for the analysis of complex survey samples. The provided features include: summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples; variances by Taylor series linearisation or replicate weights; post-stratification, calibration, and raking; two-phase subsampling designs; graphics; PPS sampling without replacement; principal components, and factor analysis.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-gee (package (name "r-gee") (version "4.13-26") (source (origin (method url-fetch) (uri (cran-uri "gee" version)) (sha256 (base32 "1323qv2hiinixmwcb8rfvf5qmkffnnq9f1g8kj9amwsimfsm71cs")))) (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/gee/") (synopsis "Generalized estimation equation solver") (description "This package provides a solver for generalized estimation equations.") (license license:gpl2))) (define-public r-tab (package (name "r-tab") (version "5.1.1") (source (origin (method url-fetch) (uri (cran-uri "tab" version)) (sha256 (base32 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv")))) (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-kableextra r-knitr r-mass r-survey)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tab/") (synopsis "Create summary tables for statistical reports") (description "This package contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards models. Functions are available to handle data from simple random samples as well as complex surveys.") (license license:gpl3+))) (define-public r-tarchetypes (package (name "r-tarchetypes") (version "0.7.11") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 "1iqrz27n8ndazx97ngqbz5yz5ppyimpbxam30zgdwnnzf963s5ym")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) (propagated-inputs (list r-digest r-dplyr r-fs r-rlang r-targets r-tibble r-tidyselect r-vctrs r-withr)) (home-page "https://docs.ropensci.org/tarchetypes/") (synopsis "Archetypes for Targets") (description "Function-oriented Make-like declarative pipelines for statistics and data science are supported in the targets R package. As an extension to targets, the tarchetypes package provides convenient user-side functions to make targets easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the drake R package by Will Landau (2018) .") (license license:expat))) (define-public r-targets (package (name "r-targets") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 "0kax8nj66jbcp8sbv7zl68hzf4clz5m50fibrcypnzvpamhafw1q")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url r-callr r-cli r-codetools r-data-table r-digest r-igraph r-knitr r-r6 r-rlang r-tibble r-tidyselect r-vctrs r-yaml)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/targets/") (synopsis "Dynamic function-oriented Make-like declarative pipelines") (description "This package provides a pipeline toolkit for statistics and data science in R; the @code{targets} package brings function-oriented programming to Make-like declarative pipelines. It orchestrates a pipeline as a graph of dependencies, skips steps that are already up to date, runs the necessary computation with optional parallel workers, abstracts files as R objects, and provides tangible evidence that the results are reproducible given the underlying code and data. The methodology in this package borrows from GNU Make (2015, ISBN:978-9881443519) and drake (2018, ).") (license license:expat))) (define-public r-tidygeocoder (package (name "r-tidygeocoder") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "tidygeocoder" version)) (sha256 (base32 "1ffj8ka5miv3jnds7fdrkcqdc3m2w1ab724z9m10biky213skqka")))) (properties `((upstream-name . "tidygeocoder"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-httr r-jsonlite r-lifecycle r-progress r-tibble)) (native-inputs (list r-knitr)) (home-page "https://jessecambon.github.io/tidygeocoder/") (synopsis "Intuitive interface for getting data from geocoding services") (description "Tidygeocoder makes getting data from geocoding services easy. A unified high-level interface is provided for a selection of supported geocoding services and results are returned in tibble format.") (license license:expat))) (define-public r-dvmisc (package (name "r-dvmisc") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dvmisc" version)) (sha256 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs (list r-cubature r-data-table r-dplyr r-ggplot2 r-mass r-mvtnorm r-pracma r-rbenchmark r-rcpp r-survey r-tab)) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description "This package implements faster versions of base R functions (e.g. mean, standard deviation, covariance, weighted mean), mostly written in C++, along with miscellaneous functions for various purposes (e.g. create the histogram with fitted probability density function or probability mass function curve, create the body mass index groups, assess the linearity assumption in logistic regression).") (license license:gpl2))) (define-public r-accelerometry (package (name "r-accelerometry") (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "accelerometry" version)) (sha256 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) (build-system r-build-system) (propagated-inputs (list r-dvmisc r-rcpp)) (home-page "https://cran.r-project.org/web/packages/accelerometry/") (synopsis "Functions for processing accelerometer data") (description "This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented.") (license license:gpl3))) (define-public r-absim (package (name "r-absim") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "AbSim" version)) (sha256 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) (properties `((upstream-name . "AbSim"))) (build-system r-build-system) (propagated-inputs (list r-ape r-powerlaw)) (home-page "https://cran.r-project.org/web/packages/AbSim/") (synopsis "Time resolved simulations of antibody repertoires") (description "This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins with an initial V-D-J recombination event, starting the first phylogenetic tree. Upon completion, the main loop of the algorithm begins, with each iteration representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.") (license license:gpl2))) (define-public r-quic (package (name "r-quic") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "QUIC" version)) (sha256 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) (properties `((upstream-name . "QUIC"))) (build-system r-build-system) (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") (synopsis "Regularized sparse inverse covariance matrix estimation") (description "This package implements the regularized Gaussian maximum likelihood estimation of the inverse of a covariance matrix. It uses Newton's method and coordinate descent to solve the regularized inverse covariance matrix estimation problem.") ;; The project home page states that the release is under GPLv3 or later. ;; The CRAN page only says GPL-3. (license license:gpl3+))) (define-public r-quickjsr (package (name "r-quickjsr") (version "1.0.9") (source (origin (method url-fetch) (uri (cran-uri "QuickJSR" version)) (sha256 (base32 "12a0m57kwn2k9j5k6vl8hb10081rydpz9rczc9hccdj9ky9wiv0k")))) (properties `((upstream-name . "QuickJSR"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-r6 r-rcpp)) (home-page "https://cran.r-project.org/package=QuickJSR") (synopsis "Interface for the QuickJS lightweight JavaScript engine") (description "This package provides an R interface to the @code{QuickJS} portable @code{JavaScript} engine. The engine is bundled entirely within the package, requiring no external system dependencies beyond a C compiler.") (license license:expat))) (define-public r-abundant (package (name "r-abundant") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "abundant" version)) (sha256 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd")))) (build-system r-build-system) (propagated-inputs (list r-glasso)) (home-page "https://cran.r-project.org/web/packages/abundant/") (synopsis "Abundant regression and high-dimensional principal fitted components") (description "This package provides tools to fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) @url{doi:10.1214/11-AOS962}.") ;; The DESCRIPTION file states GPL-2, but since it directly depends on a ;; GPLv3+ package (QUIC) this likely means GPLv2+. (license license:gpl2+))) (define-public r-ac3net (package (name "r-ac3net") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "Ac3net" version)) (sha256 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) (properties `((upstream-name . "Ac3net"))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/Ac3net/") (synopsis "Inferring directional conservative causal core gene networks") (description "This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.") (license license:gpl3+))) (define-public r-aca (package (name "r-aca") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "ACA" version)) (sha256 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) (properties `((upstream-name . "ACA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACA/") (synopsis "Abrupt change-point or aberration detection in point series") (description "This package offers an interactive function for the detection of breakpoints in series.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-acceptancesampling (package (name "r-acceptancesampling") (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 (base32 "1sbv2yrvnn0zgdmqvjlmz2vllsg6r9nlmxdgadhymhm9s51gfx65")))) (properties `((upstream-name . "AcceptanceSampling"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") (synopsis "Creation and evaluation of acceptance sampling plans") (description "This @code{r-acceptancesampling} provides functionality for creating and evaluating acceptance sampling plans. Acceptance sampling is a methodology commonly used in quality control and improvement. International standards of acceptance sampling provide sampling plans for specific circumstances. The aim of this package is to provide an easy-to-use interface to visualize single, double or multiple sampling plans. In addition, methods have been provided to enable the user to assess sampling plans against pre-specified levels of performance, as measured by the probability of acceptance for a given level of quality in the lot.") (license license:gpl3+))) (define-public r-acclma (package (name "r-acclma") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ACCLMA" version)) (sha256 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) (properties `((upstream-name . "ACCLMA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACCLMA/") (synopsis "ACC & LMA graph plotting") (description "This package contains a function that imports data from a @acronym{CSV, Comma-Separated Values} file, or uses manually entered data from the format (x, y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration Curve} vs @acronym{LOI, Line of Independence} graph and @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main function is @code{plotLMA} (source file, header) that takes a data set and plots the appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a string) was passed, a manual data entry window is opened. The header parameter indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has a header row or not. The dataset should contain only one independent variable (x) and one dependent variable (y) and can contain a weight for each observation.") (license license:gpl2))) (define-public r-aspi (package (name "r-aspi") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "aspi" version)) (sha256 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/aspi/") (synopsis "Analysis of symmetry of parasitic infections") (description "This package provides tools for the analysis and visualization of bilateral asymmetry in parasitic infections.") (license license:gpl3+))) (define-public r-sandwich (package (name "r-sandwich") (version "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 "1yi3l2q63j0vlaqqh1x3bxb0i7v6lrmmbsc6s8gilfahxq2y3c4n")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/doc" ;; These files are generated from Rnw files. (for-each delete-file (list "sandwich-OOP.pdf" "sandwich-OOP.R" "sandwich-OOP.Rnw" "sandwich-CL.R" "sandwich-CL.Rnw" "sandwich-CL.pdf" "sim-CL.rda" "sim-CL.R" "sandwich.pdf" "sandwich.R")))))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/sandwich/") (synopsis "Robust Covariance Matrix Estimators") (description "This package provides model-robust standard error estimators for cross-sectional, time series, clustered, panel, and longitudinal data.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-th-data (package (name "r-th-data") (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 "0wyyvm6l6yvqvfnd1c4l9ff5445zaq9lr0ihz8pg9kkggfslxya7")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs (list r-mass r-survival)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TH.data/") (synopsis "Shared data sets") (description "This package contains supporting data sets that are used in other packages maintained by Torsten Hothorn.") (license license:gpl3))) (define-public r-multcomp (package (name "r-multcomp") (version "1.4-25") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 "10njzzxdi3jw5f419s7chcynxkzyqmmvzf7jk7ybdrwrlqhpiylx")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) (home-page "https://cran.r-project.org/web/packages/multcomp/") (synopsis "Simultaneous inference in general parametric models") (description "Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, Hothorn, Westfall, 2010, CRC Press).") (license license:gpl2))) (define-public r-multcompview (package (name "r-multcompview") (version "0.1-9") (source (origin (method url-fetch) (uri (cran-uri "multcompView" version)) (sha256 (base32 "15vki166n2k4ng72hy62c2mzz18s10h6l6w839qplg0zsplr6f8z")))) (properties `((upstream-name . "multcompView"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=multcompView") (synopsis "Visualizations of paired comparisons") (description "Convert a logical vector or a vector of p-values or a correlation, difference, or distance matrix into a display identifying the pairs for which the differences were not significantly different.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-emmeans (package (name "r-emmeans") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 "18gib8ly7kfzdbi3srczrdqvjghf7swp127ksfs1fvs9dzgkkg96")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") (synopsis "Estimated marginal means, aka least-squares means") (description "This package provides tools to obtain @dfn{estimated marginal means} (EMMs) for many linear, generalized linear, and mixed models. It can be used to compute contrasts or linear functions of EMMs, trends, and comparisons of slopes.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-pwr (package (name "r-pwr") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "pwr" version)) (sha256 (base32 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/heliosdrm/pwr") (synopsis "Basic functions for power analysis") (description "This package provides power analysis functions along the lines of Cohen (1988).") (license license:gpl3+))) (define-public r-libcoin (package (name "r-libcoin") (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 (base32 "1bvysrq2s3951vr5ab1jzbz4hyx5j04yzh04vxdpd287bm4y08rh")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/libcoin") (synopsis "Linear test statistics for permutation inference") (description "This package provides basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999).") (license license:gpl2))) (define-public r-coin (package (name "r-coin") (version "1.4-3") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 "0x5rh002w4xgczbvnh7qfv3qv4iv7p6vdrwwyvchqmzgygdh4qwa")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; This test fails because the file has an invalid encoding (add-after 'unpack 'remove-test-file-with-latin-encoding (lambda _ (delete-file "tests/regtest_size.R")))))) (propagated-inputs (list r-libcoin r-matrixstats r-modeltools r-multcomp r-mvtnorm r-survival)) (home-page "https://coin.r-forge.r-project.org") (synopsis "Conditional inference procedures in a permutation test framework") (description "This package provides conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.") (license license:gpl2))) (define-public r-bayesplot (package (name "r-bayesplot") (version "1.10.0") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 "1zqka7lg7a6ccli1yzhk1n13vbrlp8m0kjxmykjqmkz438mvjk5v")))) (build-system r-build-system) (inputs (list pandoc)) (native-inputs (list r-knitr)) (propagated-inputs (list r-dplyr r-ggplot2 r-ggridges r-glue r-posterior r-reshape2 r-rlang r-tibble r-tidyselect)) (home-page "https://mc-stan.org/bayesplot") (synopsis "Plotting for Bayesian models") (description "This package provides plotting functions for posterior analysis, model checking, and MCMC diagnostics. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling.") (license license:gpl3+))) (define-public r-tmb (package (name "r-tmb") (version "1.9.10") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 "1cc34zxn2x88fbh4clgbzia36800i30pdlywbkwc26zm50nsxpwi")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcppeigen)) (home-page "http://tmb-project.org") (synopsis "Template model builder: a general random effect tool") (description "With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through BLAS and parallel user templates.") (license license:gpl2))) (define-public r-sjstats (package (name "r-sjstats") (version "0.18.2") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 "0a1y6bqyvgs0avzasr8g6vwcxcnj4d9g0rfz2qiznwadpjzqw66h")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-broom r-datawizard r-dplyr r-effectsize r-emmeans r-insight r-lme4 r-magrittr r-mass r-modelr r-parameters r-performance r-purrr r-rlang r-sjlabelled r-sjmisc r-tidyr)) (home-page "https://github.com/strengejacke/sjstats") (synopsis "Functions for common statistical computations") (description "This package provides a collection of convenient functions for common statistical computations, which are not directly provided by R's @code{base} or @code{stats} packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort. Second, these shortcut functions are generic, and can be applied not only to vectors, but also to other objects as well. The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models, mixed effects models and Bayesian models.") (license license:gpl3))) (define-public r-glmmtmb (package (name "r-glmmtmb") (version "1.1.8") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 "055xi424cd1glhbv8a8v9cm79zq9skb7230nq0xm90iggb1zcj22")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-matrix r-mgcv r-nlme r-numderiv r-rcppeigen r-tmb)) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description "Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via the Template Model Builder. Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.") (license license:agpl3+))) (define-public r-bayestestr (package (name "r-bayestestr") (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 "0mmnifi3j29qlsj917wbdqpgpk05x3cc7111k842gsv7y34h4ir7")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs (list r-datawizard r-insight)) (native-inputs (list r-knitr)) (home-page "https://github.com/easystats/bayestestR") (synopsis "Describe Bayesian models and posterior distributions") (description "This package provides utilities to understand and describe posterior distributions and Bayesian models. It includes point-estimates such as @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest Density Interval} (HDI), and indices used for null-hypothesis testing (such as ROPE percentage and pd).") (license license:gpl3))) (define-public r-performance (package (name "r-performance") (version "0.10.8") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 "0zvj0bzbqcy35jcg1s6b1wqbz7rbajzvjm74aks4j6iq4grh4d2j")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) (home-page "https://easystats.github.io/performance/") (synopsis "Assessment of regression models performance") (description "This package provides utilities for computing measures to assess model quality, which are not directly provided by R's @code{base} or @code{stats} packages. These include e.g. measures like r-squared, intraclass correlation coefficient, root mean squared error or functions to check models for overdispersion, singularity or zero-inflation and more. Functions apply to a large variety of regression models, including generalized linear models, mixed effects models and Bayesian models.") (license license:gpl3))) (define-public r-ggeffects (package (name "r-ggeffects") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 "0hxcal1rldi3295hy5n1nzad092gis1cxnjsbbhfrbj3z35aacbs")))) (build-system r-build-system) (propagated-inputs (list r-insight)) (native-inputs (list r-knitr)) (home-page "https://github.com/strengejacke/ggeffects") (synopsis "Create tidy data frames of marginal effects for ggplot") (description "This package provides tools to compute marginal effects from statistical models and return the result as tidy data frames. These data frames are ready to use with the @code{ggplot2} package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are @code{ggpredict()} and @code{ggeffect()}. There is a generic @code{plot()} method to plot the results using @code{ggplot2}.") (license license:gpl3))) (define-public r-effectsize (package (name "r-effectsize") (version "0.8.6") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 "0gdk6f2713k2vhv7qa6dgxl6kgc6r6yb12hb27k4bbibj5njvvni")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight r-parameters r-performance)) (native-inputs (list r-knitr)) (home-page "https://github.com/easystats/effectsize") (synopsis "Indices of effect size and standardized parameters") (description "This package provides utilities to work with indices of effect size and standardized parameters for a wide variety of models, allowing computation and conversion of indices such as Cohen's d, r, odds, etc.") (license license:gpl3))) (define-public r-effsize (package (name "r-effsize") (version "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "effsize" version)) (sha256 (base32 "1m5ch2g77f4ldbxhzp2ls1pga8hq7ggkz1xs8a90h0s09rj0gd7w")))) (properties `((upstream-name . "effsize"))) (build-system r-build-system) (home-page "https://github.com/mtorchiano/effsize/") (synopsis "Efficient effect size computation") (description "This package provides a collection of functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.") (license license:gpl2))) (define-public r-sjplot (package (name "r-sjplot") (version "2.8.15") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 "10lvn8dnckpjjpapmf0d2zwjkzjvs4iiswd3rmijzviz4ichhxjs")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-dplyr r-ggeffects r-ggplot2 r-insight r-knitr r-mass r-parameters r-performance r-purrr r-rlang r-scales r-sjlabelled r-sjmisc r-sjstats r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://strengejacke.github.io/sjPlot/") (synopsis "Data visualization for statistics in social science") (description "This package represents a collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.") (license license:gpl3))) (define-public r-ini (package (name "r-ini") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "ini" version)) (sha256 (base32 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) (build-system r-build-system) (home-page "https://github.com/dvdscripter/ini") (synopsis "Read and write configuration files") (description "This package provides tools to parse simple @code{.ini} configuration files to an structured list. Users can manipulate this resulting list with @code{lapply()} functions. This same structured list can be used to write back to file after modifications.") (license license:gpl3))) (define-public r-gillespiessa2 (package (name "r-gillespiessa2") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "GillespieSSA2" version)) (sha256 (base32 "0wjz0fh9cwvaw6n7hs2lkh818jzbjl11ps5gxnjqizz8gfp9fr10")))) (properties `((upstream-name . "GillespieSSA2"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-dplyr r-dynutils r-matrix r-purrr r-rcpp r-rcppxptrutils r-readr r-rlang r-stringr r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/rcannood/GillespieSSA2") (synopsis "Gillespie's stochastic simulation algorithm") (description "This package provides a fast, scalable, and versatile framework for simulating large systems with Gillespie's @dfn{Stochastic Simulation Algorithm} (SSA). This package is the spiritual successor to the GillespieSSA package. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended.") (license license:gpl3+))) (define-public r-gitcreds (package (name "r-gitcreds") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "gitcreds" version)) (sha256 (base32 "0pf70g4a2kxjcid5rc4ppmgcl3kpjhkszdgz4fqn4l33lp6apij1")))) (properties `((upstream-name . "gitcreds"))) (build-system r-build-system) (inputs (list git-minimal)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/gitcreds") (synopsis "Query git credentials from R") (description "Query, set, and delete credentials from the git credential store. Manage GitHub tokens and other git credentials. This package is to be used by other packages that need to authenticate to GitHub and/or other git repositories.") (license license:expat))) (define-public r-gh (package (name "r-gh") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 "0wcbnnws472v1i6q012pbdxjpsd4clj6a2cscf73g6s2336rzik8")))) (build-system r-build-system) (propagated-inputs (list r-cli r-gitcreds r-httr2 r-ini r-jsonlite r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/gh#readme") (synopsis "Access the GitHub API via R") (description "This package provides a minimal R client to access the GitHub API.") (license license:expat))) (define-public r-fs (package (name "r-fs") (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 "0wgrq0vgaf9czjyzlxdmpy7swxcyd4mryks0gr5xk96pa0g0d0ps")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://fs.r-lib.org") (synopsis "Cross-platform file system operations based on libuv") (description "This package provides a cross-platform interface to file system operations, built on top of the libuv C library.") (license license:gpl3))) (define-public r-clisymbols (package (name "r-clisymbols") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "clisymbols" version)) (sha256 (base32 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/clisymbols") (synopsis "Unicode symbols at the R prompt") (description "This package provides a small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode.") (license license:expat))) (define-public r-credentials (package (name "r-credentials") (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "credentials" version)) (sha256 (base32 "12rm7hjrbl3vfcbvdqc1hx3a6b91gf83xm455cn9myjapm2zqz1c")))) (properties `((upstream-name . "credentials"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'setenv-HOME (lambda _ ;; This is necessary because git looks for $HOME/.gitconfig (setenv "HOME" "/tmp")))))) (inputs (list git-minimal)) (propagated-inputs (list r-askpass r-curl r-jsonlite r-openssl r-sys)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/credentials/") (synopsis "Tools for managing SSH and Git credentials") (description "This package assists you in setting up and retrieving of HTTPS and SSH credentials for use with git and other services. For HTTPS remotes the package interfaces the @command{git-credential} utility which @command{git} uses to store HTTP usernames and passwords. For SSH remotes this package provides convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.") (license license:expat))) (define-public r-gert (package (name "r-gert") (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 "14nh7j0xz1s4ngsd5n3hixr534z843a38y57grwqkkh9g21q9mqf")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs (list libgit2 openssh openssl zlib)) (propagated-inputs (list r-askpass r-credentials r-openssl r-rstudioapi r-sys r-zip)) (native-inputs (list pkg-config r-knitr)) (home-page "https://docs.ropensci.org/gert/") (synopsis "Simple Git client for R") (description "This package provides a simple git client for R based on libgit2 with support for SSH and HTTPS remotes. All functions in gert use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line git through the @code{git-credential} store and SSH keys stored on disk or ssh-agent.") (license license:expat))) (define-public r-usethis (package (name "r-usethis") (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 "0imy9izchr9xzc5wrr91ydfr4jifv8lsqx712zkx0vxfi6kw3n6r")))) (build-system r-build-system) (propagated-inputs (list r-cli r-clipr r-crayon r-curl r-desc r-fs r-gert r-gh r-glue r-jsonlite r-lifecycle r-purrr r-rappdirs r-rlang r-rprojroot r-rstudioapi r-whisker r-withr r-yaml)) (home-page "https://github.com/r-lib/usethis") (synopsis "Automate R package and project setup") (description "This package helps you to automate R package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, GitHub integration, licenses, Rcpp, RStudio projects, and more.") (license license:gpl3))) (define-public r-sessioninfo (package (name "r-sessioninfo") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "sessioninfo" version)) (sha256 (base32 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm")))) (build-system r-build-system) (propagated-inputs (list r-cli)) (home-page "https://github.com/r-lib/sessioninfo#readme") (synopsis "R session information") (description "This package provides tools to query and print information about the current R session. It is similar to @code{utils::sessionInfo()}, but includes more information about packages, and where they were installed from.") (license license:gpl2))) (define-public r-remotes (package (name "r-remotes") (version "2.4.2.1") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 "1790q52z4fy4zb1hnpn066q9fph53syl7gaxlbgbqq1dcndcma3v")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") (description "Download and install R packages stored in GitHub, BitBucket, or plain subversion or git repositories. This package is a lightweight replacement of the @code{install_*} functions in the @code{devtools} package. Indeed most of the code was copied over from @code{devtools}.") (license license:gpl2+))) (define-public r-xopen (package (name "r-xopen") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "xopen" version)) (sha256 (base32 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) (build-system r-build-system) (propagated-inputs (list r-processx)) (home-page "https://github.com/r-lib/xopen#readme") (synopsis "Open system files, URLs, anything") (description "This package provides a cross-platform solution to open files, directories or URLs with their associated programs.") (license license:expat))) (define-public r-rcmdcheck (package (name "r-rcmdcheck") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v")))) (build-system r-build-system) (propagated-inputs (list r-callr r-cli r-curl r-desc r-digest r-pkgbuild r-prettyunits r-r6 r-rprojroot r-sessioninfo r-withr r-xopen)) (home-page "https://github.com/r-Lib/rcmdcheck#readme") (synopsis "Run R CMD check from R and capture results") (description "Run @code{R CMD check} from R programmatically, and capture the results of the individual checks.") (license license:expat))) (define-public r-rapportools (package (name "r-rapportools") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "rapportools" version)) (sha256 (base32 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm")))) (build-system r-build-system) (propagated-inputs (list r-mass r-pander r-plyr r-reshape2)) (home-page "https://cran.r-project.org/web/packages/rapportools/") (synopsis "Miscellaneous helper functions with sane defaults for reporting") (description "This package provides helper functions that act as wrappers to more advanced statistical methods with the advantage of having sane defaults for quick reporting.") (license license:agpl3+))) (define-public r-pander (package (name "r-pander") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "pander" version)) (sha256 (base32 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a")))) (build-system r-build-system) (propagated-inputs (list r-digest r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://rapporter.github.io/pander") (synopsis "Render R objects into Pandoc's markdown") (description "The main aim of the pander R package is to provide a minimal and easy tool for rendering R objects into Pandoc's markdown. The package is also capable of exporting/converting complex Pandoc documents (reports) in various ways.") ;; This package is licensed under either the AGPLv3+ or the very rarely ;; used OSL 3.0. (license license:agpl3+))) (define-public r-summarytools (package (name "r-summarytools") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-checkmate r-dplyr r-htmltools r-lubridate r-magick r-matrixstats r-pander r-pryr r-rapportools r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/dcomtois/summarytools") (synopsis "Tools to quickly and neatly summarize data") (description "This package provides tools for data frame summaries, cross-tabulations, weight-enabled frequency tables and common univariate statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.") (license license:gpl2))) (define-public r-lsei (package (name "r-lsei") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "lsei" version)) (sha256 (base32 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Solve regression problems under equality/inequality constraints") (description "It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving quadratic programming problems are also available, which transform such problems into least squares ones first.") (license license:gpl2+))) (define-public r-npsurv (package (name "r-npsurv") (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "npsurv" version)) (sha256 (base32 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw")))) (build-system r-build-system) (propagated-inputs (list r-lsei)) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Nonparametric survival analysis") (description "This package contains functions for non-parametric survival analysis of exact and interval-censored observations.") (license license:gpl2+))) (define-public r-clustercrit (package (name "r-clustercrit") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "clusterCrit" version)) (sha256 (base32 "0raxlyvr3kr8c8bzjgs7hb9n76m314vzvfiz7c74v6cqpkmh6dkx")))) (properties `((upstream-name . "clusterCrit"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.r-project.org/") (synopsis "Computing clustering validation indices") (description "The @code{clusterCrit} package provides an implementation of the following indices: Czekanowski-Dice, Folkes-Mallows, Hubert Γ, Jaccard, McNemar, Kulczynski, Phi, Rand, Rogers-Tanimoto, Russel-Rao or Sokal-Sneath. ClusterCrit defines several functions which compute internal quality indices or external comparison indices. The partitions are specified as an integer vector giving the index of the cluster each observation belongs to.") (license license:gpl2+))) (define-public r-clusteval (package (name "r-clusteval") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "clusteval" version)) (sha256 (base32 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm r-rcpp)) (home-page "https://cran.r-project.org/web/packages/clusteval/") (synopsis "Evaluation of clustering algorithms") (description "This R package provides a suite of tools to evaluate clustering algorithms, clusterings, and individual clusters.") (license license:expat))) (define-public r-clustergeneration (package (name "r-clustergeneration") (version "1.3.8") (source (origin (method url-fetch) (uri (cran-uri "clusterGeneration" version)) (sha256 (base32 "0w1sywv9cgl78wrsamh1zrig67r3grnyl27f036ipd1ab1b2510g")))) (properties `((upstream-name . "clusterGeneration"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/package=clusterGeneration") (synopsis "Random cluster generation (with specified degree of separation)") (description "The clusterGeneration package provides functions for generating random clusters, generating random covariance/correlation matrices, calculating a separation index (data and population version) for pairs of clusters or cluster distributions, and 1-D and 2-D projection plots to visualize clusters. The package also contains a function to generate random clusters based on factorial designs with factors such as degree of separation, number of clusters, number of variables, number of noisy variables.") (license license:gpl2+))) (define-public r-tweedie (package (name "r-tweedie") (version "2.3.5") (source (origin (method url-fetch) (uri (cran-uri "tweedie" version)) (sha256 (base32 "0ghwggdx6d391m7nay9n5li2xjqh3kmw416xx130sy2sxrgp8g4q")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tweedie/") (synopsis "Evaluation of Tweedie exponential family models") (description "Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; ) and the Fourier inversion (Dunn and Smyth, 2008; ), and related methods.") (license license:gpl2+))) (define-public r-rcppgsl (package (name "r-rcppgsl") (version "0.3.13") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 (base32 "1rwkin79ppkdz1y9pghxx29vlyvs84bylvqblkhj8r4w26y76ppy")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs (list r-rcpp gsl)) (home-page "https://cran.r-project.org/web/packages/RcppGSL/") (synopsis "Rcpp integration for GSL vectors and matrices") (description "The GNU Scientific Library (or GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp which is itself a package that eases the interfaces between R and C++.") (license license:gpl2+))) (define-public r-mvabund (package (name "r-mvabund") (version "4.2.1") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 "01kss9dx4an1ir5zs46jypvhj8sdc8wcs00i1223ai09av4lcsgd")))) (build-system r-build-system) (propagated-inputs (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie)) (home-page "https://cran.r-project.org/web/packages/mvabund/") (synopsis "Statistical methods for analysing multivariate abundance data") (description "This package provides a set of tools for displaying, modeling and analysing multivariate abundance data in community ecology.") (license license:lgpl2.1+))) (define-public r-afex (package (name "r-afex") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 "0cqr3vv4aapg8ckhrkwqhs5qvzl8zla147fvhd5wb2020yhpdqpq")))) (build-system r-build-system) ;; This is needed for the vignette builder (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2)) (native-inputs (list r-knitr r-r-rsp)) ;vignette builder (home-page "https://afex.singmann.science/") (synopsis "Analysis of factorial experiments") (description "This package provides convenience functions for analyzing factorial experiments using ANOVA or mixed models.") (license license:gpl2+))) (define-public r-lmertest (package (name "r-lmertest") (version "3.1-3") (source (origin (method url-fetch) (uri (cran-uri "lmerTest" version)) (sha256 (base32 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim")))) (properties `((upstream-name . "lmerTest"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-lme4 r-mass r-numderiv)) (home-page "https://github.com/runehaubo/lmerTestR") (synopsis "Tests in linear mixed effects models") (description "This package provides p-values in type I, II or III anova and summary tables for @code{lmer} model fits via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the @code{pbkrtest} package. Model selection methods include step, drop1 and anova-like tables for random effects (ranova). Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed effects are also available.") (license license:gpl2+))) (define-public r-r2glmm (package (name "r-r2glmm") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "r2glmm" version)) (sha256 (base32 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) (build-system r-build-system) (propagated-inputs (list r-afex r-data-table r-dplyr r-ggplot2 r-gridextra r-lmertest r-mass r-matrix r-mgcv r-pbkrtest)) (home-page "https://github.com/bcjaeger/r2glmm") (synopsis "Compute R squared for mixed (multilevel) models") (description "This package computes model and semi partial R squared with confidence limits for the linear and generalized linear mixed model (LMM and GLMM). The R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et al. (2016)).") (license license:gpl2))) (define-public r-cmdfun (package (name "r-cmdfun") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "cmdfun" version)) (sha256 (base32 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j")))) (properties `((upstream-name . "cmdfun"))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-purrr r-r-utils r-rlang r-testthat r-usethis)) (native-inputs (list r-knitr)) (home-page "https://snystrom.github.io/cmdfun/") (synopsis "Framework for building interfaces to shell commands") (description "Writing interfaces to command line software is cumbersome. The cmdfun package provides a framework for building function calls to seamlessly interface with shell commands by allowing lazy evaluation of command line arguments. It also provides methods for handling user-specific paths to tool installs or secrets like API keys. Its focus is to equally serve package builders who wish to wrap command line software, and to help analysts stay inside R when they might usually leave to execute non-R software.") (license license:expat))) (define-public r-rslurm (package (name "r-rslurm") (version "0.6.2") (source (origin (method url-fetch) (uri (cran-uri "rslurm" version)) (sha256 (base32 "0z5lyrkvfh2201sc772gzbz3hc1mc04pxww611iwjf6qwzn5h0al")))) (properties `((upstream-name . "rslurm"))) (build-system r-build-system) (propagated-inputs (list r-whisker)) (native-inputs (list r-knitr)) (home-page "http://cyberhelp.sesync.org/rslurm/") (synopsis "Submit R calculations to a Slurm cluster") (description "This package provides functions that simplify submitting R scripts to a Slurm workload manager, in part by automating the division of embarrassingly parallel calculations across cluster nodes.") (license license:gpl3))) (define-public r-chk (package (name "r-chk") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "chk" version)) (sha256 (base32 "19q5ylkgrkdmnzg2df1lnrp2arbfzwfz4rbrr16j9ih2237kvd7r")))) (properties `((upstream-name . "chk"))) (build-system r-build-system) (propagated-inputs (list r-lifecycle r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/poissonconsulting/chk") (synopsis "Check user-supplied function arguments") (description "This is a package for developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.") (license license:expat))) (define-public r-weights (package (name "r-weights") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "weights" version)) (sha256 (base32 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg")))) (build-system r-build-system) (propagated-inputs (list r-gdata r-hmisc r-lme4 r-mice)) (home-page "https://cran.r-project.org/web/packages/weights/") (synopsis "Weighting and weighted statistics") (description "This package Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial correlations, Chi-Squared statistics, histograms, and t-tests. Also now includes some software for quickly recoding survey data and plotting point estimates from interaction terms in regressions (and multiply imputed regressions). NOTE: Weighted partial correlation calculations pulled to address a bug.") (license license:gpl2+))) (define-public r-rcppalgos (package (name "r-rcppalgos") (version "2.8.3") (source (origin (method url-fetch) (uri (cran-uri "RcppAlgos" version)) (sha256 (base32 "0ppix426yg8rnh07z2clv634ynvvwmjlsjnsxh3srss6xa8yfrb0")))) (properties `((upstream-name . "RcppAlgos"))) (build-system r-build-system) (inputs (list gmp)) (propagated-inputs (list r-cpp11 r-gmp)) (native-inputs (list r-knitr)) (home-page "https://github.com/jwood000/RcppAlgos") (synopsis "High performance tools for combinatorics and computational mathematics") (description "This package provides optimized functions and flexible combinatorial iterators implemented in C++ for solving problems in combinatorics and computational mathematics. It utilizes the @code{RMatrix} class from @code{RcppParallel} for thread safety. There are combination/permutation functions with constraint parameters that allow for generation of all results of a vector meeting specific criteria. It is capable of generating specific combinations/permutations which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large. Additionally, there are several high performance number theoretic functions that are useful for problems common in computational mathematics.") (license license:gpl2+))) (define-public r-rcppannoy (package (name "r-rcppannoy") (version "0.0.21") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 "1xzhax5hmn79h6kmz7inrlaya5mdpzqj6j7n5ridyzc4vcrs412q")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") (description "Annoy is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from and save to disk. This package provides an R interface.") ;; Annoy is released under ASL 2.0, but this wrapper is released under ;; GPLv2+. (license (list license:gpl2+ license:asl2.0)))) (define-public r-rcpphnsw (package (name "r-rcpphnsw") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "RcppHNSW" version)) (sha256 (base32 "0sb9g41lk2f7fj0hpg9qvyp6gbvwlcjpi9gxs3lh3xxfzrnap5w9")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") (description "Hnswlib is a C++ library for approximate nearest neighbors. This package provides a minimal R interface by relying on the Rcpp package.") ;; hnswlib is released under Version 2.0 of the Apache License. (license (list license:gpl3 license:asl2.0)))) (define-public r-rcppparallel (package (name "r-rcppparallel") (version "5.1.7") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 "175j0plh9gzy45sxsck0wdqfkjwdsbb17m9511czrgqsrswhxhzr")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/tbb/")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'use-system-tbb (lambda* (#:key inputs #:allow-other-keys) (setenv "TBB_ROOT" (assoc-ref inputs "tbb"))))))) (inputs (list tbb-2020)) (home-page "https://rcppcore.github.io/RcppParallel/") (synopsis "Parallel programming tools for Rcpp") (description "This package provides high level functions for parallel programming with Rcpp. For example, the @code{parallelFor()} function can be used to convert the work of a standard serial @code{for} loop into a parallel one and the @code{parallelReduce()} function can be used for accumulating aggregates or other values.") (license license:gpl2))) (define-public r-ncdf4 (package (name "r-ncdf4") (version "1.22") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 "040jpcgsb98s6knch0z3f3f5fpmlwks1grpvb9k8s02c9w0a5adr")))) (build-system r-build-system) (inputs (list netcdf zlib)) (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") (synopsis "R interface to Unidata netCDF format data files") (description "This package provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files.") (license license:gpl3+))) (define-public r-ncmisc (package (name "r-ncmisc") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "NCmisc" version)) (sha256 (base32 "10wzznqa26fxyj6bl979qmq29p3dkr8yap4s70l3mwhhk33zpz16")))) (properties `((upstream-name . "NCmisc"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=NCmisc") (synopsis "Functions for creating adaptive functions and scripts") (description "This package provides a set of handy functions. It includes a versatile one line progress bar, one line function timer with detailed output, time delay function, text histogram, object preview, CRAN package search, simpler package installer, Linux command install check, a flexible Mode function, top function, simulation of correlated data, and more.") (license license:gpl2+))) (define-public r-biocmanager (package (name "r-biocmanager") (version "1.30.22") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 (base32 "0dg86nbh9h77ypaarsd79df24j0vnlm2df4zcmbhfasnsv0ck2ak")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/BiocManager/") (synopsis "Access the Bioconductor project package repository") (description "This package provides a convenient tool to install and update Bioconductor packages.") (license license:artistic2.0))) ;; TODO: one more minified JavaScript files is included that should be built ;; from the included .src.js files, but it is not entirely clear how. The ;; file is inst/htmlwidgets/lib/rglClass/rglClass.min.js. (define-public r-rgl (package (name "r-rgl") (version "1.2.8") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 "1x0p2yldg2mjf64xd5dd0bidzgy7b39w7zn18ghan2rdf0wffdg5")) (snippet '(delete-file "inst/htmlwidgets/lib/CanvasMatrix/CanvasMatrix.min.js")))) ;; For OpenGL and X11 support (properties '((updater-extra-inputs . ("glu" "libx11")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (let ((source "CanvasMatrix/CanvasMatrix.src.js") (target "CanvasMatrix/CanvasMatrix.min.js")) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (native-inputs (list esbuild pkg-config r-knitr r-rmarkdown)) ;for vignettes (inputs (list freetype libpng glu libx11 pandoc zlib)) (propagated-inputs (list r-base64enc r-htmltools r-htmlwidgets r-jsonlite r-knitr r-magrittr r-mime r-r6)) (home-page "https://r-forge.r-project.org/projects/rgl/") (synopsis "3D visualization using OpenGL") (description "This package provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (@code{plot3d()}, etc.) as well as functions for constructing representations of geometric objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-multicool (package (name "r-multicool") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "multicool" version)) (sha256 (base32 "0gcic5w3z5yibq75j7jzjv3lmy04rfmxswmw60vxba4xsnbqxc2g")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/multicool/") (synopsis "Permutations of multisets in cool-lex order") (description "This package provides a set of tools to permute multisets without loops or hash tables and to generate integer partitions. Cool-lex order is similar to colexicographical order.") (license license:gpl2))) (define-public r-multidplyr (package (name "r-multidplyr") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "multidplyr" version)) (sha256 (base32 "18yl24s1g8wf3xi6f0k7jhs99ka4dslxf5p9ax9m5l1rbva5xdwj")))) (properties `((upstream-name . "multidplyr"))) (build-system r-build-system) (propagated-inputs (list r-callr r-cli r-crayon r-dplyr r-magrittr r-qs r-r6 r-rlang r-tibble r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://multidplyr.tidyverse.org") (synopsis "Multi-process dplyr backend") (description "Partition a data frame across multiple worker processes to provide simple multicore parallelism.") (license license:expat))) (define-public r-misc3d (package (name "r-misc3d") (version "0.9-1") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/misc3d/") (synopsis "Miscellaneous 3D Plots") (description "This package provides a collection of miscellaneous 3d plots, including isosurfaces.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-missforest (package (name "r-missforest") (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "missForest" version)) (sha256 (base32 "13c38hpl60ca1kwyv61cxsla6ccmsj4qzp0vrxcq7b827fh5aw21")))) (properties `((upstream-name . "missForest"))) (build-system r-build-system) (propagated-inputs (list r-dorng r-foreach r-iterators r-itertools r-randomforest)) (home-page "https://github.com/stekhoven/missForest") (synopsis "Nonparametric missing value imputation using Random Forest") (description "The function @code{missForest} in this package is used to impute missing values, particularly in the case of mixed-type data. It uses a random forest trained on the observed values of a data matrix to predict the missing values. It can be used to impute continuous and/or categorical data, including complex interactions and non-linear relations. It yields an @acronym{OOB, out-of-bag} imputation error estimate without the need of a test set or elaborate cross- validation. It can be run in parallel to save computation time.") (license license:gpl2+))) (define-public r-ks (package (name "r-ks") (version "1.14.2") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 (base32 "1jrzh1syq6jdqpp5xmb25hqsk07bpbn6caqhp9mw5zpsdi3k14gi")))) (build-system r-build-system) (propagated-inputs (list r-fnn r-kernlab r-kernsmooth r-matrix r-mclust r-mgcv r-multicool r-mvtnorm r-pracma)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description "This package provides kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-feature (package (name "r-feature") (version "1.2.15") (source (origin (method url-fetch) (uri (cran-uri "feature" version)) (sha256 (base32 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y")))) (build-system r-build-system) (propagated-inputs (list r-ks r-plot3d)) (native-inputs (list r-knitr)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Inferential feature significance for kernel density estimation") (description "The feature package contains functions to display and compute kernel density estimates, significant gradient and significant curvature regions. Significant gradient and/or curvature regions often correspond to significant features (e.g. local modes).") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-arm (package (name "r-arm") (version "1.13-1") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 "0dz9dnsky77da2mc198dr3600kz9vk75z1iihjarnsdrq68a4bf0")))) (build-system r-build-system) (propagated-inputs (list r-abind r-coda r-lme4 r-mass r-matrix r-nlme)) (home-page "https://cran.r-project.org/web/packages/arm/") (synopsis "Data analysis using regression and multilevel/hierarchical models") (description "This package provides functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.") (license license:gpl3+))) (define-public r-circular (package (name "r-circular") (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 "14kvkbmvdfzh8j4hgw93qkjkg86xlpw69sp7g8d5smcyw9fxmx2b")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mvtnorm)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/circular/") (synopsis "Circular statistics") (description "This package provides tools for circular statistics, from \"Topics in circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.") (license license:gpl2+))) (define-public r-activity (package (name "r-activity") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 "10gp2yvqxz5ysmh5z8qvrpli8kc2kn2z3nd2llfabpyh21476in2")))) (build-system r-build-system) (propagated-inputs (list r-pbapply)) (home-page "https://cran.r-project.org/web/packages/activity/") (synopsis "Animal activity statistics") (description "This package provides functions to fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; and evaluate variation in linear variables with time (or other circular variables).") (license license:gpl3))) (define-public r-ouch (package (name "r-ouch") (version "2.19") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 "15ryd76max77zwjlbijj4v7h42mscr4zqg8b01cq3gsr51l8bwkf")))) (build-system r-build-system) (propagated-inputs (list r-subplex)) (home-page "https://kingaa.github.io/ouch/") (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") (description "This package provides tools to fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.") (license license:gpl2+))) (define-public r-fmri (package (name "r-fmri") (version "1.9.12") (source (origin (method url-fetch) (uri (cran-uri "fmri" version)) (sha256 (base32 "1cv5mxcdpyf05n5pcjdawl59j7f4k40386r4m38qf15vcy45zdfq")))) (properties `((upstream-name . "fmri"))) (build-system r-build-system) (propagated-inputs (list r-aws r-metafor r-nlme r-oro-nifti)) (native-inputs (list gfortran)) (home-page "http://www.wias-berlin.de/software/imaging/") (synopsis "Analysis of fMRI experiments") (description "This package contains R-functions to perform an fMRI analysis as described in Polzehl and Tabelow (2019) , Tabelow et al. (2006) , Polzehl et al. (2010) , Tabelow and Polzehl (2011) .") (license license:gpl2+))) (define-public r-fmsb (package (name "r-fmsb") (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 "082qj08kzyzwvjacwq0sl3xxdx6iz5hgx6q24jv1mnvx7z5xn5ry")))) (build-system r-build-system) (home-page "https://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") (description "This package provides several utility functions for the book entitled \"Practices of Medical and Health Data Analysis using R\" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.") (license license:gpl2+))) (define-public r-stabledist (package (name "r-stabledist") (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "stabledist" version)) (sha256 (base32 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86")))) (build-system r-build-system) (home-page "https://www.rmetrics.org") (synopsis "Stable distribution functions") (description "This package provides density, probability and quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.") (license license:gpl2+))) (define-public r-gsl (package (name "r-gsl") (version "2.1-8") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 "159d782nz7fqhgcj3fa79hlmkdrqnkd0ypgzcl71kgas92zhjdpk")))) (build-system r-build-system) (inputs (list gsl)) (home-page "https://cran.r-project.org/web/packages/gsl") (synopsis "Wrapper for the GNU Scientific Library") (description "This package provides an R wrapper for the special functions and quasi random number generators of the GNU Scientific Library.") (license license:gpl2+))) (define-public r-adgoftest (package (name "r-adgoftest") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ADGofTest" version)) (sha256 (base32 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) (properties `((upstream-name . "ADGofTest"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ADGofTest") (synopsis "Anderson-Darling GoF test") (description "This package provides an implementation of the Anderson-Darling GoF test with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the Anderson-Darling Distribution\".") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-adimpro (package (name "r-adimpro") (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "adimpro" version)) (sha256 (base32 "0d5viz9ayywpp1pas1yzmhllzn9rjrl8a3k7bj7h46f95l5x1586")))) (properties `((upstream-name . "adimpro"))) (build-system r-build-system) (propagated-inputs (list r-awsmethods imagemagick)) (native-inputs (list gfortran)) (home-page "https://www.wias-berlin.de/software/imaging/") (synopsis "Adaptive smoothing of digital images") (description "This package implements tools for manipulation of digital images and the Propagation Separation approach by Polzehl and Spokoiny (2006) for smoothing digital images, see Polzehl and Tabelow (2007) .") (license license:gpl2+))) (define-public r-admisc (package (name "r-admisc") (version "0.34") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 (base32 "1psvi8hb7j65abw8g4ya9r43r5kd9mcv478pg2d09za0cig8gkzx")))) (properties `((upstream-name . "admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") (synopsis "Adrian Dusa's miscellaneous") (description "This package contains miscellaneous functions used to interpret and translate, factorize and negate Sum of Products expressions, for both binary and multi-value crisp sets, and to extract information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly flexible recoding routine and a more flexible alternative to the base function @code{with()}.") (license license:gpl3+))) (define-public r-oro-nifti (package (name "r-oro-nifti") (version "0.11.4") (source (origin (method url-fetch) (uri (cran-uri "oro.nifti" version)) (sha256 (base32 "01mn90qxb7i15zr83xrl2cn4akayfzpm83r5x71zczz3qb9gbr7g")))) (properties `((upstream-name . "oro.nifti"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bitops r-rnifti)) (home-page "https://rigorousanalytics.blogspot.com") (synopsis "Vizualization of medical imaging data") (description "This package provides functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle.") (license license:bsd-3))) (define-public r-mritc (package (name "r-mritc") (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "mritc" version)) (sha256 (base32 "1bpnm2qzq67dgjxsa4wxn51f4a4cxal5r6abgs3m7p5a9a16jmjp")))) (properties `((upstream-name . "mritc"))) (build-system r-build-system) (propagated-inputs (list r-lattice r-misc3d r-oro-nifti)) (home-page "https://cran.r-project.org/package=mritc") (synopsis "MRI tissue classification") (description "This package provides various methods for MRI tissue classification.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-sodium (package (name "r-sodium") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "sodium" version)) (sha256 (base32 "0cbj7mgchi42ri6h1fc24asj7lkcn9n3l0zbabrx89s9zi4im0gx")))) (properties `((upstream-name . "sodium"))) (build-system r-build-system) (inputs (list libsodium)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/sodium") (synopsis "R bindings to the libsodium crypto library") (description "This package provides bindings to libsodium: a library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.") (license license:expat))) (define-public r-softimpute (package (name "r-softimpute") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "softImpute" version)) (sha256 (base32 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a")))) (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran r-knitr)) (home-page "https://cran.r-project.org/web/packages/softImpute") (synopsis "Matrix completion via iterative soft-thresholded SVD") (description "This package provides iterative methods for matrix completion that use nuclear-norm regularization. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank @dfn{single value decompositions} (SVDs) on large sparse centered matrices (i.e. principal components).") (license license:gpl2))) (define-public r-som (package (name "r-som") (version "0.3-5.1") (source (origin (method url-fetch) (uri (cran-uri "som" version)) (sha256 (base32 "1fbza1jxvwrkf5x3inkj36vshhkn7mz0ajqlxalbfmk6ngjw1x56")))) (properties `((upstream-name . "som"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=som") (synopsis "Self-organizing map") (description "This package implements a self-organizing map which has application in gene clustering. It provides functions like: @itemize @item filtering data by certain floor, ceiling, max/min ratio, and max - min difference; @item normalization of the data; @item get the average distortion measure; @item train a self-organizing map; @item summarize a som object; @item yeast cell cycle. @end itemize") (license license:gpl3+))) (define-public r-fftwtools (package (name "r-fftwtools") (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "fftwtools" version)) (sha256 (base32 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i")))) (build-system r-build-system) (inputs (list fftw)) (native-inputs (list pkg-config)) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description "This package provides a wrapper for several FFTW functions. It provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using the FFTW3 library. The package includes the functions @code{fftw()} and @code{mvfftw()} which are designed to mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. The FFT functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.") (license license:gpl2+))) (define-public r-tiff (package (name "r-tiff") (version "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 "0p41irri0nxg9mm06g8jp5zqssv80g5zg0iifrr7ancjkxqww46z")))) (build-system r-build-system) (inputs (list libtiff libjpeg-turbo zlib)) (native-inputs (list pkg-config)) (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description "This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.") ;; Either of these two license versions. (license (list license:gpl2 license:gpl3)))) (define-public r-nlp (package (name "r-nlp") (version "0.2-1") (source (origin (method url-fetch) (uri (cran-uri "NLP" version)) (sha256 (base32 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5")))) (properties `((upstream-name . "NLP"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/NLP/") (synopsis "Natural language processing infrastructure") (description "This package provides basic classes and methods for Natural Language Processing.") (license license:gpl3))) (define-public r-tm (package (name "r-tm") (version "0.7-11") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 "0hp7xamjmifd56qwsin5m0xng592wwxsbfxdz37n4k6zjf28paws")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs (list r-bh r-nlp r-rcpp r-slam r-xml2)) (home-page "https://tm.r-forge.r-project.org/") (synopsis "Text mining package") (description "This package provides a framework for text mining applications within R.") (license license:gpl3))) (define-public r-waffle (package (name "r-waffle") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "waffle" version)) (sha256 (base32 "17z05mlnp2k9dywr0bbqz633sq1xs8q9879bl2na1in39qxq0l76")))) (properties `((upstream-name . "waffle"))) (build-system r-build-system) (propagated-inputs (list r-curl r-dt r-extrafont r-ggplot2 r-gridextra r-gtable r-htmlwidgets r-plyr r-rcolorbrewer r-rlang r-stringr)) (home-page "https://github.com/hrbrmstr/waffle/tree/cran") (synopsis "Creating waffle chart visualizations in R") (description "This package creates square pie charts also known as waffle charts. These can be used to communicate parts of a whole for categorical quantities. To emulate the percentage view of a pie chart, a 10x10 grid should be used. In this way each square is representing 1% of the total. Waffle provides tools to create charts as well as stitch them together. Isotype pictograms can be made by using glyphs.") (license license:gpl2+))) (define-public r-waveslim (package (name "r-waveslim") (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "waveslim" version)) (sha256 (base32 "1510xpkgrhdw394m5anxccdczjikcxazyd09ix2z73i15akyx3j0")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://waveslim.blogspot.com") (synopsis "Basic wavelet routines for signal processing") (description "This package provides basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).") (license license:bsd-3))) (define-public r-word2vec (package (name "r-word2vec") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "word2vec" version)) (sha256 (base32 "14ba0cj430d02bd6fay3nl4ldwqyj77iwjm4gzgdc0f6sx597iiq")))) (properties `((upstream-name . "word2vec"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppprogress)) (home-page "https://github.com/bnosac/word2vec") (synopsis "Distributed representations of words") (description "Learn vector representations of words by continuous bag of words and skip-gram implementations of the word2vec algorithm. The techniques are detailed in the paper \"Distributed Representations of Words and Phrases and their Compositionality\" by Mikolov et al. (2013), available at .") (license license:asl2.0))) (define-public r-wordcloud (package (name "r-wordcloud") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "wordcloud" version)) (sha256 (base32 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-rcpp ;; The "tm" package is only "suggested" according to CRAN, but the ;; wordcloud package cannot be loaded without it. r-tm)) (home-page "https://cran.r-project.org/web/packages/wordcloud") (synopsis "Word clouds") (description "This package provides functionality to create pretty word clouds, visualize differences and similarity between documents, and avoid over-plotting in scatter plots with text.") (license license:lgpl2.1))) (define-public r-colorramps (package (name "r-colorramps") (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "colorRamps" version)) (sha256 (base32 "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1")))) (properties `((upstream-name . "colorRamps"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/colorRamps") (synopsis "Build color tables") (description "This package provides features to build gradient color maps.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-tidytree (package (name "r-tidytree") (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 (base32 "14i2v6ryqw4cd74n8kz4qwwx730wzx4f0rssg5vgm0vjfsx0kafv")))) (build-system r-build-system) (propagated-inputs (list r-ape r-cli r-dplyr r-lazyeval r-magrittr r-pillar r-rlang r-tibble r-tidyr r-tidyselect r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/GuangchuangYu/tidytree") (synopsis "Tidy tool for phylogenetic tree data manipulation") (description "Phylogenetic trees generally contain multiple components including nodes, edges, branches and associated data. This package provides an approach to convert tree objects to tidy data frames. It also provides tidy interfaces to manipulate tree data.") (license license:artistic2.0))) (define-public r-rvcheck (package (name "r-rvcheck") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a")))) (build-system r-build-system) (propagated-inputs (list r-biocmanager r-yulab-utils)) (home-page "https://cran.r-project.org/web/packages/rvcheck") (synopsis "R package version check") (description "This package provides tools to check the latest release version of R and R packages (on CRAN, Bioconductor or Github).") (license license:artistic2.0))) (define-public r-doc2vec (package (name "r-doc2vec") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "doc2vec" version)) (sha256 (base32 "0249hm0103kxxsi4gks4h20wf6p00gbrk9jf8c148mbja1l56f6v")))) (properties `((upstream-name . "doc2vec"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/bnosac/doc2vec") (synopsis "Distributed representations of sentences, documents and topics") (description "Learn vector representations of sentences, paragraphs or documents by using the Paragraph Vector algorithms, namely the distributed bag of words (PV-DBOW) and the distributed memory (PV-DM) model. Top2vec finds clusters in text documents by combining techniques to embed documents and words and density-based clustering. It does this by embedding documents in the semantic space as defined by the doc2vec algorithm. Next it maps these document embeddings to a lower-dimensional space using the Uniform Manifold Approximation and Projection (UMAP) clustering algorithm and finds dense areas in that space using a Hierarchical Density-Based Clustering technique (HDBSCAN). These dense areas are the topic clusters which can be represented by the corresponding topic vector which is an aggregate of the document embeddings of the documents which are part of that topic cluster. In the same semantic space similar words can be found which are representative of the topic.") (license license:expat))) (define-public r-docopt (package (name "r-docopt") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "docopt" version)) (sha256 (base32 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz")))) (build-system r-build-system) (home-page "https://github.com/docopt/docopt.R") (synopsis "Command-line interface specification language") (description "This package enables you to define a command-line interface by just giving it a description in the specific format.") (license license:expat))) (define-public r-sparsesvd (package (name "r-sparsesvd") (version "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "sparsesvd" version)) (sha256 (base32 "0dnqjqypjwac8aqdqsqdgcd70lyrfv6idz8q2kzjiv1sxrlwqh5v")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") (synopsis "Sparse truncated singular value decomposition") (description "This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported.") ;; SVDLIBC is released under BSD-2. The R interface is released under ;; BSD-3. (license (list license:bsd-3 license:bsd-2)))) (define-public r-speedglm (package (name "r-speedglm") (version "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "speedglm" version)) (sha256 (base32 "0jxvh9gbhip1hj7hzjs5fj8iw6ibvl6hc0llcg2j9wqgq5vkcrpq")))) (build-system r-build-system) (propagated-inputs (list r-biglm r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/speedglm") (synopsis "Fit linear and generalized linear models to large data sets") (description "This package provides tools for fitting linear models and generalized linear models to large data sets by updating algorithms.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-densityclust (package (name "r-densityclust") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "densityClust" version)) (sha256 (base32 "05x2fi1zdnkrg2nimf8k904j3lpyw0f7nmk6ax5p7x7a98wb2iqs")))) (properties `((upstream-name . "densityClust"))) (build-system r-build-system) (propagated-inputs (list r-fnn r-ggplot2 r-ggrepel r-gridextra r-rcolorbrewer r-rcpp r-rtsne)) (home-page "https://cran.r-project.org/web/packages/densityClust") (synopsis "Clustering by fast search and find of density peaks") (description "This package provides an improved implementation (based on k-nearest neighbors) of the density peak clustering algorithm, originally described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle large datasets (> 100,000 samples) very efficiently.") (license license:gpl2+))) (define-public r-combinat (package (name "r-combinat") (version "0.0-8") (source (origin (method url-fetch) (uri (cran-uri "combinat" version)) (sha256 (base32 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/combinat") (synopsis "Combinatorics utilities") (description "This package provides assorted routines for combinatorics.") (license license:gpl2))) (define-public r-qlcmatrix (package (name "r-qlcmatrix") (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "qlcMatrix" version)) (sha256 (base32 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) (properties `((upstream-name . "qlcMatrix"))) (build-system r-build-system) (propagated-inputs (list r-docopt r-matrix r-slam r-sparsesvd)) (home-page "https://cran.r-project.org/web/packages/qlcMatrix") (synopsis "Sparse matrix functions for quantitative language comparison") (description "This package provides an extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for the special data format used for @dfn{quantitative language comparison} (QLC).") (license license:gpl3))) (define-public r-qmri (package (name "r-qmri") (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "qMRI" version)) (sha256 (base32 "0jiwvnhmm4zwqydqkzsygwkm23nc0zzjz5w7yckwdfc5zafch4hk")))) (properties `((upstream-name . "qMRI"))) (build-system r-build-system) (propagated-inputs (list r-adimpro r-aws r-awsmethods r-oro-nifti r-stringr)) (native-inputs (list gfortran r-knitr)) (home-page "http://www.wias-berlin.de/research/ats/imaging/") (synopsis "Methods for quantitative magnetic resonance imaging (qMRI)") (description "This package provides implementation of methods for estimation of quantitative maps from @dfn{Multi-Parameter Mapping} (MPM) acquisitions including adaptive smoothing methods in the framework of the ESTATICS model. The smoothing method is described in Mohammadi et al. (2017). . Usage of the package is also described in Polzehl and Tabelow (2019), Magnetic Resonance Brain Imaging, Chapter 6, Springer, Use R! Series. .") (license license:gpl2+))) (define-public r-ddrtree (package (name "r-ddrtree") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "DDRTree" version)) (sha256 (base32 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) (properties `((upstream-name . "DDRTree"))) (build-system r-build-system) (propagated-inputs (list r-bh r-irlba r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/DDRTree") (synopsis "Learning principal graphs with DDRTree") (description "This package provides an implementation of the framework of @dfn{reversed graph embedding} (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of the data simultaneously. DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the ordering as well as the intrinsic structure of single cell genomics data. In general, it could be used to reconstruct the temporal progression as well as the bifurcation structure of any data type.") (license license:asl2.0))) (define-public r-corpcor (package (name "r-corpcor") (version "1.6.10") (source (origin (method url-fetch) (uri (cran-uri "corpcor" version)) (sha256 (base32 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i")))) (build-system r-build-system) (home-page "https://strimmerlab.org/software/corpcor/") (synopsis "Efficient estimation of covariance and (partial) correlation") (description "This package implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.") (license license:gpl3+))) (define-public r-rspectra (package (name "r-rspectra") (version "0.16-1") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) (native-inputs (list r-knitr)) (home-page "https://github.com/yixuan/RSpectra") (synopsis "Solvers for large-scale Eigenvalue and SVD problems") (description "This package provides an R interface to the Spectra library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than @code{eigen()} if k << n.") ;; MPL 2 or later. (license license:mpl2.0))) (define-public r-vbsr (package (name "r-vbsr") (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "vbsr" version)) (sha256 (base32 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/vbsr") (synopsis "Variational Bayes spike regression regularized linear models") (description "This package provides an efficient algorithm for solving ultra-sparse regularized regression models using a variational Bayes algorithm with a spike prior. The algorithm is solved on a path, with coordinate updates, and is capable of generating very sparse models. Very general model diagnostics for controlling type-1 errors are also provided.") (license license:gpl2))) (define-public r-flare (package (name "r-flare") (version "1.7.0.1") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-lattice r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/flare") (synopsis "Family of Lasso regression implementations") (description "This package provides implementations of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear models.") (license license:gpl2))) (define-public r-lassopv (package (name "r-lassopv") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "lassopv" version)) (sha256 (base32 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) (build-system r-build-system) (propagated-inputs (list r-lars)) (home-page "https://github.com/lingfeiwang/lassopv") (synopsis "Non-parametric p-value estimation for predictors in Lasso") (description "This package enables you to estimate the p-values for predictors x against target variable y in Lasso regression, using the regularization strength when each predictor enters the active set of regularization path for the first time as the statistic.") (license license:gpl3))) (define-public r-splitstackshape (package (name "r-splitstackshape") (version "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "splitstackshape" version)) (sha256 (base32 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://github.com/mrdwab/splitstackshape") (synopsis "Stack and reshape datasets after splitting concatenated values") (description "Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The @code{concat.split} (cSplit) family of functions provided by this package splits such data into separate cells. This package also includes functions to stack groups of columns and to reshape wide data, even when the data are \"unbalanced\"---something which @code{reshape} (from base R) does not handle, and which @code{melt} and @code{dcast} from @code{reshape2} do not easily handle.") (license license:gpl3))) (define-public r-tfmpvalue (package (name "r-tfmpvalue") (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "TFMPvalue" version)) (sha256 (base32 "1rsxqvq1nkyhwmhm7mf7rd02rvh7xinnhqbqic6q9vicbvkmdnxr")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/ge11232002/TFMPvalue") (synopsis "P-value computation for position weight matrices") (description "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match scores. TFMPvalue provides the accurate calculation of a p-value with a score threshold for position weight matrices, or the score with a given p-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) (define-public r-rnaturalearth (package (name "r-rnaturalearth") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "rnaturalearth" version)) (sha256 (base32 "1vfkn4bf77mr2n7dhmnl55ma4cvwy2nazhizmdqd98w2ydl13z3p")))) (properties `((upstream-name . "rnaturalearth"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-sf r-terra)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=rnaturalearth") (synopsis "World map data from Natural Earth") (description "This package facilitates mapping by making natural earth map data from @url{https://www.naturalearthdata.com/} more easily available to R users.") (license license:expat))) (define-public r-rnaturalearthdata (package (name "r-rnaturalearthdata") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "rnaturalearthdata" version)) (sha256 (base32 "1z32j5lz2lb8xgpkr73majw22k0b49iazj6jjc7j4w9k4zxxa102")))) (properties `((upstream-name . "rnaturalearthdata"))) (build-system r-build-system) (propagated-inputs (list r-sp)) (home-page "https://github.com/ropenscilabs/rnaturalearthdata") (synopsis "World vector map data from Natural Earth") (description "This package provides vector map data from @url{https://www.naturalearthdata.com/}. Access functions are provided in the accompanying package @code{rnaturalearth}.") (license license:cc0))) (define-public r-rncl (package (name "r-rncl") (version "0.8.7") (source (origin (method url-fetch) (uri (cran-uri "rncl" version)) (sha256 (base32 "0flrqz7pansy11ds23qv06bcmh6vxqljq0517v6292ibbx7nx1qx")))) (build-system r-build-system) (propagated-inputs (list r-progress r-rcpp)) (home-page "https://github.com/fmichonneau/rncl") (synopsis "Interface to the Nexus class library") (description "This package provides an interface to the Nexus class library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s @code{phylo4(d)}. This functionality is demonstrated with @code{read_newick_phylo()} and @code{read_nexus_phylo()}.") (license license:bsd-2))) (define-public r-phylobase (package (name "r-phylobase") (version "0.8.10") (source (origin (method url-fetch) (uri (cran-uri "phylobase" version)) (sha256 (base32 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-rcpp r-rncl r-rnexml)) (native-inputs (list r-knitr)) (home-page "https://github.com/fmichonneau/phylobase") (synopsis "Base package for phylogenetic structures and comparative data") (description "This package provides a base @code{S4} class for comparative methods, incorporating one or more trees and trait data.") (license license:gpl2+))) (define-public r-phylotools (package (name "r-phylotools") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "phylotools" version)) (sha256 (base32 "1dhk1ncp5zi4zl1xfnjz64v983dm7bq7iimfjin80j0bdcpps44w")))) (properties `((upstream-name . "phylotools"))) (build-system r-build-system) (propagated-inputs (list r-ape)) (home-page "https://github.com/helixcn/phylotools") (synopsis "Phylogenetic tools for eco-phylogenetics") (description "This package provides a collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.") (license license:gpl2))) (define-public r-rnexml (package (name "r-rnexml") (version "2.4.11") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 "0ipxdhfzccpqmnfrqdy8bizm80k2chhdlzg3p0dl05p8n35i6s94")))) (build-system r-build-system) (propagated-inputs (list r-ape r-dplyr r-httr r-plyr r-reshape2 r-rlang r-stringi r-stringr r-tidyr r-uuid r-xml r-xml2)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/RNeXML/") (synopsis "Semantically rich I/O for the NeXML Format") (description "This package provides access to phyloinformatic data in NeXML format. The package should add new functionality to R such as the possibility to manipulate NeXML objects in more various and refined way and compatibility with @code{ape} objects.") (license license:bsd-3))) (define-public r-rnifti (package (name "r-rnifti") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 "0rbym1svldahd4rlbcfb5s62rigws2w1fa1f1chp504gn340b555")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/jonclayden/RNifti") (synopsis "Fast R and C++ access to NIfTI images") (description "This package provides very fast read and write access to images stored in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. It also provides a C/C++ API that can be used by other packages.") (license license:gpl2))) (define-public r-shades (package (name "r-shades") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "shades" version)) (sha256 (base32 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/shades") (synopsis "Simple color manipulation") (description "This package provides functions for easily manipulating colors, creating color scales and calculating color distances.") (license license:bsd-3))) (define-public r-ore (package (name "r-ore") (version "1.7.4.1") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 (base32 "01ayvjyjbarmi7l2jwp7bp4m0k42zy8bvf9rbwynfwmm8mv6vx0j")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") (description "This package provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.") (license license:bsd-3))) (define-public r-reportr (package (name "r-reportr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "reportr" version)) (sha256 (base32 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) (build-system r-build-system) (propagated-inputs (list r-ore)) (home-page "https://github.com/jonclayden/reportr") (synopsis "General message and error reporting system") (description "This package provides a system for reporting messages, which offers certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current \"output level\".") (license license:gpl2))) (define-public r-tractor-base (package (name "r-tractor-base") (version "3.3.5.1") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 "0fxbzbhpi6l55m14nmww8y3kdxgchzj4mw1yf4xkm2y6s68phvgc")))) (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs (list r-ore r-reportr r-rnifti r-shades)) (home-page "https://www.tractor-mri.org.uk") (synopsis "Read, manipulate and visualize magnetic resonance images") (description "This package provides functions for working with magnetic resonance images. It supports reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualization; flexible image manipulation; metadata and sparse image handling.") (license license:gpl2))) (define-public r-gridpattern (package (name "r-gridpattern") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "gridpattern" version)) (sha256 (base32 "1v7xfgbnrr4v3arr7nm0663aywn47xb89sd0rn9s9dcz7r50aa2i")))) (properties `((upstream-name . "gridpattern"))) (build-system r-build-system) (propagated-inputs (list r-glue r-memoise r-png r-rlang r-sf)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://trevorldavis.com/R/gridpattern/") (synopsis "Grid pattern grobs") (description "This package provides grid grobs that fill in a user-defined area with various patterns. It includes enhanced versions of the geometric and image-based patterns originally contained in the ggpattern package as well as original @code{pch}, @code{polygon_tiling}, @code{regular_polygon}, @code{rose}, @code{text}, @code{wave}, and @code{weave} patterns plus support for custom user-defined patterns.") (license license:expat))) (define-public r-gridsvg (package (name "r-gridsvg") (version "1.7-5") (source (origin (method url-fetch) (uri (cran-uri "gridSVG" version)) (sha256 (base32 "1p8qnx9q96bni39x44l40rgcdi9r440zbipdfvkbs2paysx6mkr5")))) (properties `((upstream-name . "gridSVG"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-xml)) (home-page "https://cran.r-project.org/package=gridSVG") (synopsis "Export grid gaphics as SVG") (description "This package provides functions to export graphics drawn with package grid to SVG format. Extra functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.") ;; Any version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-grimport (package (name "r-grimport") (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 "196h7i4y1gzkwlybml9iz78p5xsx7y22nk5pmzibryn5amdbdy05")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs (list ghostscript)) (propagated-inputs (list r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport") (synopsis "Convert, import, and draw PostScript pictures") (description "This package provides functions for converting, importing, and drawing PostScript pictures in R plots.") (license license:gpl2+))) (define-public r-grimport2 (package (name "r-grimport2") (version "0.3-1") (source (origin (method url-fetch) (uri (cran-uri "grImport2" version)) (sha256 (base32 "1lj58z6yc2p6ns27fkgh11ac90bcihi65hf62gxpsylcn5dilsi1")))) (properties `((upstream-name . "grImport2"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-jpeg r-png r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport2/") (synopsis "Import SVG graphics") (description "This package provides functions for importing external vector images and drawing them as part of R plots. This package is different from the @code{grImport} package because, where that package imports PostScript format images, this package imports SVG format images. Furthermore, this package imports a specific subset of SVG, so external images must be preprocessed using a package like @code{rsvg} to produce SVG that this package can import. SVG features that are not supported by R graphics, such as gradient fills, can be imported and then exported via the @code{gridSVG} package.") (license license:gpl2+))) (define-public r-kohonen (package (name "r-kohonen") (version "3.0.12") (source (origin (method url-fetch) (uri (cran-uri "kohonen" version)) (sha256 (base32 "188cxw2fvpfr3dyi8g52igcyc8d5jffyn6rhc84dja52da8lp520")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/kohonen") (synopsis "Supervised and unsupervised self-organising maps") (description "This package provides functions to train @dfn{self-organising maps} (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.") (license license:gpl2+))) (define-public r-nnls (package (name "r-nnls") (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 "0lilga63p7k5mkkfcf5p3swx76vwysl979jxszm6svzqhsrgww6d")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nnls") (synopsis "Lawson-Hanson algorithm for non-negative least squares") (description "This package provides an R interface to the Lawson-Hanson implementation of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows the combination of non-negative and non-positive constraints.") (license license:gpl2+))) (define-public r-iso (package (name "r-iso") (version "0.0-21") (source (origin (method url-fetch) (uri (cran-uri "Iso" version)) (sha256 (base32 "19lgwbfbca30mh3hhnarzab5cvnrwnr0pxam6fvfnadnqzhjm15n")))) (properties `((upstream-name . "Iso"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~rolf/") (synopsis "Functions to perform isotonic regression") (description "This package provides support for linear order and unimodal order (univariate) isotonic regression and bivariate isotonic regression with linear order on both variables.") (license license:gpl2+))) (define-public r-chemometrics (package (name "r-chemometrics") (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "chemometrics" version)) (sha256 (base32 "10d8g8sgck6v2cgkv988yiawv9vrziyqsrhagmkzf7rjpqgdn3px")))) (properties `((upstream-name . "chemometrics"))) (build-system r-build-system) (propagated-inputs (list r-class r-e1071 r-lars r-mass r-mclust r-nnet r-pcapp r-pls r-robustbase r-rpart r-som)) (home-page "http://www.statistik.tuwien.ac.at/public/filz/") (synopsis "Multivariate statistical analysis in Chemometrics") (description "Multivariate data analysis is the simultaneous observation of more than one characteristic. In contrast to the analysis of univariate data, in this approach not only a single variable or the relation between two variables can be investigated, but the relations between many attributes can be considered. For the statistical analysis of chemical data one has to take into account the special structure of this type of data. This package contains about 30 functions, mostly for regression, classification and model evaluation and includes some data sets used in the R help examples. It was designed as a R companion to the book \"Introduction to Multivariate Statistical Analysis in Chemometrics\" written by K. Varmuza and P. Filzmoser (2009).") (license license:gpl3+))) (define-public r-chemometricswithr (package (name "r-chemometricswithr") (version "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "ChemometricsWithR" version)) (sha256 (base32 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) (properties `((upstream-name . "ChemometricsWithR"))) (build-system r-build-system) (propagated-inputs (list r-devtools r-kohonen r-mass r-pls)) (home-page "https://github.com/rwehrens/CWR") (synopsis "Chemometrics with R") (description "This package provides functions and scripts used in the book \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences\" by Ron Wehrens, Springer (2011).") (license license:gpl2+))) (define-public r-als (package (name "r-als") (version "0.0.7") (source (origin (method url-fetch) (uri (cran-uri "ALS" version)) (sha256 (base32 "184d6xr4mgs78jvi7xa4njrq6p625i9sx69wak6mdn53qpl9b8ap")))) (properties `((upstream-name . "ALS"))) (build-system r-build-system) (propagated-inputs (list r-iso r-nnls)) (home-page "https://cran.r-project.org/web/packages/ALS") (synopsis "Multivariate curve resolution alternating least squares") (description "Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. This package provides an implementation of @dfn{multivariate curve resolution alternating least squares} (MCR-ALS). Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.") (license license:gpl2+))) (define-public r-strucchange (package (name "r-strucchange") (version "1.5-3") (source (origin (method url-fetch) (uri (cran-uri "strucchange" version)) (sha256 (base32 "11hgz64snlwhfqsmqajmkciflwkz1wficxr340wqvk38iw1b9ina")))) (build-system r-build-system) (propagated-inputs (list r-sandwich r-zoo)) (home-page "https://cran.r-project.org/web/packages/strucchange") (synopsis "Testing, monitoring, and dating structural changes") (description "This package provides tools for testing, monitoring and dating structural changes in (linear) regression models. It features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F statistics, respectively. It is possible to monitor incoming data online using fluctuation processes. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data.") ;; Either of these two GPL versions (license (list license:gpl2 license:gpl3)))) (define-public r-pixmap (package (name "r-pixmap") (version "0.4-12") (source (origin (method url-fetch) (uri (cran-uri "pixmap" version)) (sha256 (base32 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pixmap") (synopsis "Tools for bitmap images") (description "This package provides functions for importing, exporting, plotting and other manipulations of bitmapped images.") (license license:gpl2))) (define-public r-rapidjsonr (package (name "r-rapidjsonr") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "rapidjsonr" version)) (sha256 (base32 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rapidjsonr") (synopsis "JSON parser") (description "This package provides JSON parsing capability through the Rapidjson library.") (license license:expat))) (define-public r-ontologyindex (package (name "r-ontologyindex") (version "2.11") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 "17ndvqvb74b980gpb3hpg9bd68bb5f52k9s1i2kd1f9cdrdjvw97")))) (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ontologyIndex") (synopsis "Functions for processing ontologies in R") (description "This package provides functions for reading ontologies into R as lists and manipulating sets of ontological terms.") (license license:gpl2+))) (define-public r-gargle (package (name "r-gargle") (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 "00ch0ddysva3dbs6wsybgy76j3f2ib6iypdg9f5ic2mmdq2fnnsa")))) (build-system r-build-system) (propagated-inputs (list r-cli r-fs r-glue r-httr r-jsonlite r-lifecycle r-openssl r-rappdirs r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://gargle.r-lib.org") (synopsis "Utilities for working with Google APIs") (description "This package provides utilities for working with Google APIs. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.") (license license:expat))) (define-public r-bigrquery (package (name "r-bigrquery") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "bigrquery" version)) (sha256 (base32 "1rw0w4bmqs1v8xjg787n6dsk5dmizgvjg9wrky38s7a7zsvlryri")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-bit64 r-brio r-cli r-curl r-dbi r-gargle r-glue r-httr r-jsonlite r-lifecycle r-prettyunits r-progress r-rapidjsonr r-rcpp r-rlang r-tibble r-withr)) (home-page "https://github.com/rstats-db/bigrquery") (synopsis "R interface to Google's BigQuery API") (description "This package provides an R interface to Google's BigQuery database.") (license license:gpl3))) (define-public r-gmp (package (name "r-gmp") (version "0.7-4") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 "069r0m0jwhwaknnd1vmp3pxcbxrnfgsbhw2ivc8rqqfjfw7v9mm7")))) (properties '((updater-extra-inputs . ("gmp")))) (build-system r-build-system) (inputs (list gmp)) (home-page "https://cran.r-project.org/web/packages/gmp") (synopsis "Multiple precision arithmetic") (description "This package supports multiple precision arithmetic (big integers and rationals, prime number tests, matrix computation), \"arithmetic without limitations\" using the GNU Multiple Precision library.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-rmpfr (package (name "r-rmpfr") (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 "1fx8l42bbipzlaaljp7iwdkgbmb0rcw07vh4py8fycb3dvs9iiyf")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs (list gmp mpfr)) (propagated-inputs (list r-gmp)) (native-inputs (list pkg-config)) (home-page "https://rmpfr.r-forge.r-project.org/") (synopsis "R bindings to the MPFR library") (description "This package supports arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental functions. To this end, the package interfaces with the @dfn{Multiple Precision Floating-Point Reliable} (MPFR) library.") (license license:gpl2+))) (define-public r-rmutil (package (name "r-rmutil") (version "1.1.10") (source (origin (method url-fetch) (uri (cran-uri "rmutil" version)) (sha256 (base32 "1yd5gkg4jg3rvqrfl8c5r07lcr37n1p9h1a7b6s45iswd77dg7w1")))) (properties `((upstream-name . "rmutil"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.commanster.eu/rcode.html") (synopsis "Utilities for nonlinear regression and repeated measurements models") (description "This package provides a toolkit of functions for nonlinear regression and repeated measurements. It was designated to be imported by other packages such as @code{gnlm}, @code{stable}, @code{growth}, @code{repeated}, and @code{event}.") (license license:gpl2+))) (define-public r-assertive-base (package (name "r-assertive-base") (version "0.0-9") (source (origin (method url-fetch) (uri (cran-uri "assertive.base" version)) (sha256 (base32 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b")))) (properties `((upstream-name . "assertive.base"))) (build-system r-build-system) (home-page "https://bitbucket.org/richierocks/assertive.base") (synopsis "Core of the assertive package") (description "This package provides a minimal set of predicates and assertions used by the assertive package. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-properties (package (name "r-assertive-properties") (version "0.0-5") (source (origin (method url-fetch) (uri (cran-uri "assertive.properties" version)) (sha256 (base32 "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn")))) (properties `((upstream-name . "assertive.properties"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.properties") (synopsis "Assertions to check properties of variables") (description "This package provides a set of predicates and assertions for checking the properties of variables, such as length, names and attributes. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-numbers (package (name "r-assertive-numbers") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.numbers" version)) (sha256 (base32 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds")))) (properties `((upstream-name . "assertive.numbers"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.numbers") (synopsis "Assertions to check properties of numbers") (description "This package provides a set of predicates and assertions for checking the properties of numbers. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-sets (package (name "r-assertive-sets") (version "0.0-3") (source (origin (method url-fetch) (uri (cran-uri "assertive.sets" version)) (sha256 (base32 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7")))) (properties `((upstream-name . "assertive.sets"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.sets") (synopsis "Assertions to check properties of sets") (description "This package provides a set of predicates and assertions for checking the properties of sets. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-matrices (package (name "r-assertive-matrices") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.matrices" version)) (sha256 (base32 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil")))) (properties `((upstream-name . "assertive.matrices"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.matrices") (synopsis "Assertions to check properties of matrices") (description "This package provides a set of predicates and assertions for checking the properties of matrices. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-models (package (name "r-assertive-models") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.models" version)) (sha256 (base32 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr")))) (properties `((upstream-name . "assertive.models"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.models") (synopsis "Assertions to check properties of models") (description "This package provides a set of predicates and assertions for checking the properties of models. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-reflection (package (name "r-assertive-reflection") (version "0.0-5") (source (origin (method url-fetch) (uri (cran-uri "assertive.reflection" version)) (sha256 (base32 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2")))) (properties `((upstream-name . "assertive.reflection"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.reflection") (synopsis "Assertions for checking the state of R") (description "This package provides a set of predicates and assertions for checking the state and capabilities of R, the operating system it is running on, and the IDE being used. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-types (package (name "r-assertive-types") (version "0.0-3") (source (origin (method url-fetch) (uri (cran-uri "assertive.types" version)) (sha256 (base32 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb")))) (properties `((upstream-name . "assertive.types"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-properties r-codetools)) (home-page "https://bitbucket.org/richierocks/assertive.types") (synopsis "Assertions to check types of variables") (description "This package provides a set of predicates and assertions for checking the types of variables. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-files (package (name "r-assertive-files") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.files" version)) (sha256 (base32 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy")))) (properties `((upstream-name . "assertive.files"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-numbers)) (home-page "https://bitbucket.org/richierocks/assertive.files") (synopsis "Assertions to check properties of files") (description "This package provides a set of predicates and assertions for checking the properties of files and connections. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-code (package (name "r-assertive-code") (version "0.0-4") (source (origin (method url-fetch) (uri (cran-uri "assertive.code" version)) (sha256 (base32 "11qkhbjyxw0njzhcszyc2452518yrn3jr5l4n9jnzq10xms090ig")))) (properties `((upstream-name . "assertive.code"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-properties r-assertive-types)) (home-page "https://bitbucket.org/richierocks/assertive.code") (synopsis "Assertions to check properties of code") (description "This package provides a set of predicates and assertions for checking the properties of code. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-datetimes (package (name "r-assertive-datetimes") (version "0.0-3") (source (origin (method url-fetch) (uri (cran-uri "assertive.datetimes" version)) (sha256 (base32 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1")))) (properties `((upstream-name . "assertive.datetimes"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-types)) (home-page "https://bitbucket.org/richierocks/assertive.datetimes") (synopsis "Assertions to check properties of dates and times") (description "This package provides a set of predicates and assertions for checking the properties of dates and times. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-strings (package (name "r-assertive-strings") (version "0.0-3") (source (origin (method url-fetch) (uri (cran-uri "assertive.strings" version)) (sha256 (base32 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm")))) (properties `((upstream-name . "assertive.strings"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-types r-stringi)) (home-page "https://bitbucket.org/richierocks/assertive.strings") (synopsis "Assertions to check properties of strings") (description "This package provides a set of predicates and assertions for checking the properties of strings. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-data-us (package (name "r-assertive-data-us") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.data.us" version)) (sha256 (base32 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq")))) (properties `((upstream-name . "assertive.data.us"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data.us") (synopsis "Assertions to check properties of strings") (description "This package provides a set of predicates and assertions for checking the properties of US-specific complex data types. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-data-uk (package (name "r-assertive-data-uk") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.data.uk" version)) (sha256 (base32 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b")))) (properties `((upstream-name . "assertive.data.uk"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data.uk") (synopsis "Assertions to check properties of strings") (description "This package provides a set of predicates and assertions for checking the properties of UK-specific complex data types. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-data (package (name "r-assertive-data") (version "0.0-3") (source (origin (method url-fetch) (uri (cran-uri "assertive.data" version)) (sha256 (base32 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s")))) (properties `((upstream-name . "assertive.data"))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data") (synopsis "Assertions to check properties of data") (description "This package provides a set of predicates and assertions for checking the properties of (country independent) complex data types. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive (package (name "r-assertive") (version "0.3-6") (source (origin (method url-fetch) (uri (cran-uri "assertive" version)) (sha256 (base32 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4")))) (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-code r-assertive-data r-assertive-data-uk r-assertive-data-us r-assertive-datetimes r-assertive-files r-assertive-matrices r-assertive-models r-assertive-numbers r-assertive-properties r-assertive-reflection r-assertive-sets r-assertive-strings r-assertive-types r-knitr)) (native-inputs (list r-knitr)) (home-page "https://bitbucket.org/richierocks/assertive") (synopsis "Readable check functions to ensure code integrity") (description "This package provides lots of predicates (@code{is_*} functions) to check the state of your variables, and assertions (@code{assert_*} functions) to throw errors if they aren't in the right form.") (license license:gpl3+))) (define-public r-dotcall64 (package (name "r-dotcall64") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 "06y9y9m5prjvqlprqpanbamgr6jkw27wj7nnha5ayyn08zbxgf11")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") (synopsis "Enhanced foreign function interface supporting long vectors") (description "This package provides @code{.C64()}, an enhanced version of @code{.C()} and @code{.Fortran()} from the R foreign function interface. @code{.C64()} supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.") (license license:gpl2+))) (define-public r-spam (package (name "r-spam") (version "2.10-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 (base32 "0ydc513jg7phzdqg8jp7210ayrrmxq91jafqzx8z1v0172i8d73i")))) (build-system r-build-system) (propagated-inputs (list r-dotcall64 r-rcpp)) (native-inputs (list gfortran r-knitr r-r-rsp)) (home-page "https://www.math.uzh.ch/pages/spam/") (synopsis "Sparse matrix algebra") (description "This package provides a set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: @enumerate @item it only supports (essentially) one sparse matrix format; @item it is based on transparent and simple structure(s); @item it is tailored for MCMC calculations within G(M)RF; @item and it is fast and scalable (with the extension package @code{spam64}). @end enumerate\n") ;; Either of these licenses (license (list license:bsd-3 license:lgpl2.0)))) (define-public r-fields (package (name "r-fields") (version "15.2") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 (base32 "0gdddigzbzlhrbp6h2ma5b05m68pmggrkcd80hzgjbjj64ihy9qz")))) (build-system r-build-system) (propagated-inputs (list r-maps r-spam r-viridislite)) (native-inputs (list gfortran)) (home-page "https://www.image.ucar.edu/fields") (synopsis "Tools for spatial data") (description "This is a package for curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets.") (license license:gpl2+))) (define-public r-spatialextremes (package (name "r-spatialextremes") (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "SpatialExtremes" version)) (sha256 (base32 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3")))) (properties `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) (propagated-inputs (list r-fields r-maps)) (home-page "https://spatialextremes.r-forge.r-project.org/") (synopsis "Modelling spatial extremes") (description "This package provides tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction.") (license license:gpl2+))) (define-public r-drc (package (name "r-drc") (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "drc" version)) (sha256 (base32 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) (build-system r-build-system) (propagated-inputs (list r-car r-gtools r-mass r-multcomp r-plotrix r-scales)) (home-page "https://cran.r-project.org/web/packages/drc") (synopsis "Analysis of dose-response curves") (description "This package provides a suite of flexible and versatile model fitting and after-fitting functions for the analysis of dose-response data.") (license license:gpl2+))) (define-public r-rmeta (package (name "r-rmeta") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "rmeta" version)) (sha256 (base32 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rmeta") (synopsis "Tools for meta-analysis") (description "This package provides functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. It draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.") (license license:gpl2))) (define-public r-bootstrap (package (name "r-bootstrap") (version "2019.6") (source (origin (method url-fetch) (uri (cran-uri "bootstrap" version)) (sha256 (base32 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/bootstrap") (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") (description "This package provides software and data for the book \"An Introduction to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. This package is primarily provided for projects already based on it, and for support of the book. New projects should preferentially use the recommended package \"boot\".") (license license:bsd-3))) (define-public r-survivalroc (package (name "r-survivalroc") (version "1.0.3.1") (source (origin (method url-fetch) (uri (cran-uri "survivalROC" version)) (sha256 (base32 "0p6irjs8a9xxgxwax0y9fzapcib237if3iy8g6lzv793mzmsyx41")))) (properties `((upstream-name . "survivalROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/survivalROC") (synopsis "Time-dependent ROC curve estimation from censored survival data") (description "Compute time-dependent ROC curve from censored survival data using Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") (license license:gpl2+))) (define-public r-locfdr (package (name "r-locfdr") (version "1.1-8") (source (origin (method url-fetch) (uri (cran-uri "locfdr" version)) (sha256 (base32 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/locfdr/") (synopsis "Computes local false discovery rates") (description "This package can be used to compute local false discovery rates.") (license license:gpl2))) (define-public r-logging (package (name "r-logging") (version "0.10-108") (source (origin (method url-fetch) (uri (cran-uri "logging" version)) (sha256 (base32 "13gd40ygx586vs6xcp6clg69a92aj8zxlk1rn3xzkx8klfjimjc5")))) (properties `((upstream-name . "logging"))) (build-system r-build-system) (home-page "https://github.com/WLOGSolutions/r-logging") (synopsis "R logging implementation of log4j") (description "This package implements the R version of the @code{log4j} package. It offers hierarchic loggers, multiple handlers per logger, level based filtering, space handling in messages and custom formatting.") (license license:gpl3))) (define-public r-logistf (package (name "r-logistf") (version "1.26.0") (source (origin (method url-fetch) (uri (cran-uri "logistf" version)) (sha256 (base32 "02qrh07c13khlpz3z3f6qq827h37j91i88n7jn3c8ky6r1lfa5pr")))) (properties `((upstream-name . "logistf"))) (build-system r-build-system) (propagated-inputs (list r-formula-tools r-matrix r-mgcv r-mice)) (home-page "https://cemsiis.meduniwien.ac.at/en/kb/science-research\ /software/statistical-software/firth-correction/") (synopsis "Firth's bias-reduced logistic regression") (description "Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal solution to the problem of separation in logistic regression, see Heinze and Schemper (2002) . If needed, the bias reduction can be turned off such that ordinary maximum likelihood logistic regression is obtained. Two new modifications of Firth's method, FLIC and FLAC, lead to unbiased predictions and are now available in the package as well, see Puhr et al (2017) .") ;; Any version of the GPL (license license:gpl3+))) (define-public r-longdat (package (name "r-longdat") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "LongDat" version)) (sha256 (base32 "1rzkb7byd32jqvhf75zyvy0dlkq79aicz8j0x7lk821qiq4dfv6l")))) (properties `((upstream-name . "LongDat"))) (build-system r-build-system) (propagated-inputs (list r-bestnormalize r-car r-dplyr r-effsize r-emmeans r-ggplot2 r-glmmtmb r-lme4 r-magrittr r-mass r-patchwork r-reshape2 r-rlang r-rstatix r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/CCY-dev/LongDat") (synopsis "Tool for covariate-sensitive longitudinal analysis on omics data") (description "This tool takes longitudinal dataset as input and analyzes if there is significant change of the features over time (a proxy for treatments), while detects and controls for covariates simultaneously. LongDat is able to take in several data types as input, including count, proportion, binary, ordinal and continuous data. The output table contains p values, effect sizes and covariates of each feature, making the downstream analysis easy.") (license license:gpl2))) (define-public r-longitudinal (package (name "r-longitudinal") (version "1.1.13") (source (origin (method url-fetch) (uri (cran-uri "longitudinal" version)) (sha256 (base32 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p")))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) (home-page "https://strimmerlab.org/software/longitudinal/") (synopsis "Analysis of multiple time course data") (description "This package contains general data structures and functions for longitudinal data with multiple variables, repeated measurements, and irregularly spaced time points. It also implements a shrinkage estimator of dynamical correlation and dynamical covariance.") (license license:gpl3+))) (define-public r-genenet (package (name "r-genenet") (version "1.2.16") (source (origin (method url-fetch) (uri (cran-uri "GeneNet" version)) (sha256 (base32 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1")))) (properties `((upstream-name . "GeneNet"))) (build-system r-build-system) (propagated-inputs (list r-corpcor r-fdrtool r-longitudinal)) (home-page "https://strimmerlab.org/software/genenet/") (synopsis "Modeling and inferring gene networks") (description "This package analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).") (license license:gpl3+))) (define-public r-rbamtools (package (name "r-rbamtools") (version "2.16.17") (source (origin (method url-fetch) (uri (cran-uri "rbamtools" version)) (sha256 (base32 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc")))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-refgenome)) (home-page "https://cran.r-project.org/web/packages/rbamtools") (synopsis "Read and write BAM (binary alignment) files") (description "This package provides an R interface to functions of the SAMtools library.") (license license:artistic2.0))) (define-public r-profvis (package (name "r-profvis") (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "profvis" version)) (sha256 (base32 "1cmlcp91q8v0550iay9vsw5wllb6w2ldy6k99rb76ylhr5dwf0pc")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib" (for-each delete-file (list "highlight/highlight.js" ;from rmarkdown "jquery/jquery.min.js" ;version 1.12.4 "d3/d3.min.js")))))) ;version 3.5.6 (properties `((upstream-name . "profvis"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (copy-file (search-input-file inputs "/site-library/rmarkdown/rmd/h/highlightjs/highlight.js") "highlight/highlight.js") (let ((mapping `((,(assoc-ref inputs "js-jquery") . "jquery/jquery.min.js") (,(assoc-ref inputs "js-d3") . "d3/d3.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (native-inputs `(("esbuild" ,esbuild) ("r-rmarkdown" ,r-rmarkdown) ("js-d3" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/d3/d3/v3.5.6/d3.js") (sha256 (base32 "17qlbwn7vgx335gciq6zp2ib6zg1r9lfa6p1bd9g0ds0xbcsbvgd")))) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.12.4.js") (sha256 (base32 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))))) (propagated-inputs (list r-htmlwidgets r-purrr r-rlang r-stringr r-vctrs)) (home-page "https://rstudio.github.io/profvis/") (synopsis "Interactive visualizations for profiling R code") (description "This package provides interactive visualizations for profiling R code.") (license license:gpl3))) (define-public r-prospectr (package (name "r-prospectr") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "prospectr" version)) (sha256 (base32 "1p53hcgcs2p09zhc2n7byjzrgvcgz6w7q00mlsn4kmnz7l4p7rrm")))) (properties `((upstream-name . "prospectr"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators r-lifecycle r-mathjaxr r-rcpp r-rcpparmadillo)) (home-page "https://github.com/l-ramirez-lopez/prospectr") (synopsis "Functions for processing and sample selection of spectroscopic data") (description "@code{prospectr} provides miscellaneous functions to preprocess spectroscopic data and conduct representative sample selection, or calibration sampling.") (license license:expat))) (define-public r-protviz (package (name "r-protviz") (version "0.7.9") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 "1wsjr4asjsknv8fkfv15xqnl67zfv8d2xmvw1i2l0wflxbps3af7")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/protViz/protViz/") (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") (description "This package helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich, where it is used mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.") (license license:gpl3))) (define-public r-cmprsk (package (name "r-cmprsk") (version "2.2-11") (source (origin (method url-fetch) (uri (cran-uri "cmprsk" version)) (sha256 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44")))) (build-system r-build-system) (propagated-inputs (list r-survival)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/cmprsk") (synopsis "Subdistribution analysis of competing risks") (description "This package provides tool for estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), A proportional hazards model for the subdistribution of a competing risk, JASA, 94:496-509.") (license license:gpl2+))) (define-public r-etm (package (name "r-etm") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "etm" version)) (sha256 (base32 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/etm") (synopsis "Empirical transition matrix") (description "The @dfn{empirical transition matrix} (etm) package estimates the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator.") (license license:expat))) (define-public r-epi (package (name "r-epi") (version "2.47.1") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 "1a4h6hfpwcy3lb49y949h86vr4sdnjfbqqnr4jgc45mc64fhafp1")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs (list r-cmprsk r-data-table r-dplyr r-etm r-magrittr r-mass r-matrix r-mgcv r-numderiv r-plyr r-survival r-zoo)) (home-page "https://BendixCarstensen.com/Epi/") (synopsis "Statistical analysis in epidemiology") (description "This package provides functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation, manipulation and simulation of multistate data - the Lexis suite of functions, which includes interfaces to the @code{mstate}, @code{etm} and @code{cmprsk} packages. It also contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.") (license license:gpl2))) (define-public r-ppls (package (name "r-ppls") (version "1.6-1.1") (source (origin (method url-fetch) (uri (cran-uri "ppls" version)) (sha256 (base32 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ppls") (synopsis "Penalized partial least squares") (description "This package contains linear and nonlinear regression methods based on partial least squares and penalization techniques. Model parameters are selected via cross-validation, and confidence intervals ans tests for the regression coefficients can be conducted via jackknifing.") (license license:gpl2+))) (define-public r-huge (package (name "r-huge") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "huge" version)) (sha256 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/huge") (synopsis "High-dimensional undirected graph estimation") (description "This package provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline.") (license license:gpl2))) (define-public r-parcor (package (name "r-parcor") (version "0.2-6") (source (origin (method url-fetch) (uri (cran-uri "parcor" version)) (sha256 (base32 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) (build-system r-build-system) (propagated-inputs (list r-epi r-genenet r-glmnet r-mass r-ppls)) (home-page "https://cran.r-project.org/web/packages/parcor") (synopsis "Regularized estimation of partial correlation matrices") (description "This package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso and Ridge regression based on cross-validation.") (license license:gpl2+))) (define-public r-mcmc (package (name "r-mcmc") (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "mcmc" version)) (sha256 (base32 "19vfh868lr4a491gc2x2b2xs83gldw294zbl4bqsgs2q9c6l81ka")))) (build-system r-build-system) (home-page "https://www.stat.umn.edu/geyer/mcmc/") (synopsis "Markov chain Monte Carlo") (description "This package simulates continuous distributions of random vectors using @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are random walk Metropolis algorithm (function @code{metrop}), simulated tempering (function @code{temper}), and morphometric random walk Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity by change of variable.") (license license:expat))) (define-public r-listenv (package (name "r-listenv") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 "11s8cy259al6x98xcz93jw6p87si01gcgzccnxhx69879zh42a1m")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/listenv") (synopsis "Environments behaving (almost) as lists") (description "This package implements list environments. List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting.") (license license:lgpl2.1+))) (define-public r-globals (package (name "r-globals") (version "0.16.2") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 "02kpdlrx1bannaixz03c0f7bii9g36iy2nw779mfgi56byljcb38")))) (build-system r-build-system) (propagated-inputs (list r-codetools)) (home-page "https://github.com/HenrikBengtsson/globals") (synopsis "Identify global objects in R expressions") (description "This package provides tools to identify global (\"unknown\" or \"free\") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.") (license license:lgpl2.1+))) (define-public r-parallelly (package (name "r-parallelly") (version "1.36.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 "123w89hmd7fn7lmdsl044npidvf7472h1ascvf7swjllan8s5h5r")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") (synopsis "Enhancements of the parallel package") (description "This package provides utility functions that enhance the @code{parallel} package and support the built-in parallel backends of the @code{future} package. For example, @code{availableCores} gives the number of CPU cores available to your R process as given by R options and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to @code{parallel::detectCores}. Another example is @code{makeClusterPSOCK}, which is backward compatible with @code{parallel::makePSOCKcluster} while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.") (license license:lgpl2.1+))) (define-public r-future (package (name "r-future") (version "1.33.1") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 "1xvb7rhwnsi7l735jfrh7ij0l6q6hazwcb2620hvfjwl2kkpk00r")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-digest r-globals r-listenv r-parallelly)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future") (synopsis "Unified parallel and distributed processing in R") (description "The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify any code in order to switch from sequential on the local machine to, say, distributed processing on a remote compute cluster.") (license license:lgpl2.1+))) (define-public r-future-apply (package (name "r-future-apply") (version "1.11.1") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 "0zf22vip8w50pywc47xjghca9wkvcsvvfaa2yfaydwwzc3ss3bh2")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-future r-globals)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future.apply") (synopsis "Apply function to elements in parallel using futures") (description "This package provides implementations of @code{apply()}, @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()}, @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.") (license license:gpl2+))) (define-public r-future-callr (package (name "r-future-callr") (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "future.callr" version)) (sha256 (base32 "14hq53cam65ff25l6y17zv37448ls90sa0w51f13199m1kffaaqb")))) (properties '((upstream-name . "future.callr") (updater-extra-native-inputs . ("r-markdown")))) (build-system r-build-system) ;; This is needed for the vignette builder R.rsp. (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-callr r-future)) (native-inputs (list r-markdown r-r-rsp)) (home-page "https://future.callr.futureverse.org") (synopsis "Future API for Parallel Processing using 'callr'") (description "This is an implementation of the Future API on top of the callr package. This allows you to process futures, as defined by the future package, in parallel out of the box, on your local machine. Contrary to backends relying on the parallel package (e.g. @code{future::multisession}) and socket connections, the callr backend provided here can run more than 125 parallel R processes.") (license license:lgpl2.1+))) (define-public r-rsvd (package (name "r-rsvd") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "rsvd" version)) (sha256 (base32 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "https://github.com/erichson/rSVD") (synopsis "Randomized singular value decomposition") (description "Low-rank matrix decompositions are fundamental tools and widely used for data analysis, dimension reduction, and data compression. Classically, highly accurate deterministic matrix algorithms are used for this task. However, the emergence of large-scale data has severely challenged our computational ability to analyze big data. The concept of randomness has been demonstrated as an effective strategy to quickly produce approximate answers to familiar problems such as the @dfn{singular value decomposition} (SVD). This package provides several randomized matrix algorithms such as the randomized singular value decomposition (@code{rsvd}), randomized principal component analysis (@code{rpca}), randomized robust principal component analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}), and the randomized CUR decomposition (@code{rcur}). In addition several plot functions are provided.") (license license:gpl3+))) (define-public r-sloop (package (name "r-sloop") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "sloop" version)) (sha256 (base32 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-crayon r-purrr r-rlang r-tibble)) (home-page "https://github.com/r-lib/sloop") (synopsis "Helpers for object-oriented programming in R") (description "This package provides a collection of helper functions designed to help you to better understand object oriented programming in R, particularly using @code{S3}.") (license license:gpl3))) (define-public r-capushe (package (name "r-capushe") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "capushe" version)) (sha256 (base32 "1mazsfdiqmhy0ywahqw49qql899ph0l6jllriz2spyp1bs98q9b7")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/capushe/index.html") (synopsis "Calibrating penalties using slope heuristics") (description "This package provides tools for the calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics.") (license license:gpl2+))) (define-public r-dorng (package (name "r-dorng") (version "1.8.6") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 "1qkxa3jxpnn5anhqycqcbk18kw87m9pl5m78q8d89ygihghascjh")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators r-rngtools)) (native-inputs (list r-knitr)) (home-page "https://renozao.github.io/doRNG/") (synopsis "Generic reproducible parallel backend for foreach loops") (description "This package provides functions to perform reproducible parallel @code{foreach} loops, using independent random streams as generated by L'Ecuyer's combined multiple-recursive generator. It enables to easily convert standard @code{%dopar%} loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.") (license license:gpl2+))) (define-public r-blockmodeling (package (name "r-blockmodeling") (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "blockmodeling" version)) (sha256 (base32 "00qmpf0jdc8vl76rzfg12z2mdr215q8qd9p3a4b816y2g0092vrv")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/blockmodeling") (synopsis "Generalized and classical blockmodeling of valued networks") (description "This package is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted.") (license license:gpl2+))) (define-public r-upsetr (package (name "r-upsetr") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "UpSetR" version)) (sha256 (base32 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im")))) (properties `((upstream-name . "UpSetR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-plyr r-scales)) (home-page "https://github.com/hms-dbmi/UpSetR") (synopsis "Visualize intersecting sets") (description "This package provides a more scalable alternative to Venn and Euler diagrams for visualizing intersecting sets. Create visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.") (license license:expat))) (define-public r-shinycustomloader (package (name "r-shinycustomloader") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "shinycustomloader" version)) (sha256 (base32 "1klx71vr26g0gjf6hbiia1qidqii5d467i1sdjvlrg1hxdcggqff")))) (properties `((upstream-name . "shinycustomloader"))) (build-system r-build-system) (propagated-inputs (list r-glue r-shiny)) (home-page "https://cran.r-project.org/package=shinycustomloader") (synopsis "Custom loader for Shiny outputs") (description "This package provides a custom @code{CSS/HTML} or @code{GIF/image} file for the loading screen in R @code{Shiny}. It also can use the marquee to have a custom text loading screen.") (license license:gpl3))) ;; This package includes a JavaScript file, which is not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinybs (package (name "r-shinybs") (version "0.61.1") (source (origin (method url-fetch) (uri (cran-uri "shinyBS" version)) (sha256 (base32 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a")))) (properties `((upstream-name . "shinyBS"))) (build-system r-build-system) ;; The tests spawn Shiny browser apps. They cannot be run ;; non-interactively. (arguments '(#:tests? #f)) (propagated-inputs (list r-htmltools r-shiny)) (home-page "https://ebailey78.github.io/shinyBS/") (synopsis "Twitter Bootstrap components for Shiny") (description "This package adds additional Twitter Bootstrap components to Shiny.") (license license:gpl3))) (define-public r-shinyjqui (package (name "r-shinyjqui") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "shinyjqui" version)) (sha256 (base32 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1")) (snippet '(for-each delete-file (list "inst/www/shinyjqui.min.js" "inst/www/jquery.ui.touch-punch.min.js"))))) (properties `((upstream-name . "shinyjqui"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www" (let ((mapping `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch") "/jquery.ui.touch-punch.js") . "jquery.ui.touch-punch.min.js") ("shinyjqui.js" . "shinyjqui.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (propagated-inputs (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ("js-jquery.ui.touch-punch" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/furf/jquery-ui-touch-punch") (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5"))) (sha256 (base32 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q")))))) (home-page "https://github.com/yang-tang/shinyjqui") (synopsis "jQuery UI interactions and effects for Shiny") (description "This is an extension to Shiny that brings interactions and animation effects from the jQuery UI library.") (license license:expat))) (define-public r-shinymanager (package (name "r-shinymanager") (version "1.0.410") (source (origin (method url-fetch) (uri (cran-uri "shinymanager" version)) (sha256 (base32 "0nl672dgwj34wm4i3pxk28lv6qw9xsgg3hm0h78q3zdgk8a33kdn")))) (properties `((upstream-name . "shinymanager"))) (build-system r-build-system) (propagated-inputs (list r-billboarder r-dbi r-dt r-htmltools r-openssl r-r-utils r-r6 r-rsqlite r-scrypt r-shiny)) (native-inputs (list r-knitr)) (home-page "https://github.com/datastorm-open/shinymanager") (synopsis "Authentication management for Shiny applications") (description "This package provides simple and secure authentication mechanism for single Shiny applications. Credentials are stored in an encrypted SQLite database.") (license license:gpl3))) (define-public r-outliers (package (name "r-outliers") (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "outliers" version)) (sha256 (base32 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/outliers/index.html") (synopsis "Tests for outliers") (description "This package provides a collection of some tests commonly used for identifying outliers.") (license license:gpl2+))) (define-public r-bayesm (package (name "r-bayesm") (version "3.1-6") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 (base32 "1d9wp7yr5hadyv48f51xqa5yzfnhh01n813sivwla209vjf2pmqp")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://www.perossi.org/home/bsm-1") (synopsis "Bayesian inference for marketing/micro-econometrics") (description "This package covers many important models used in marketing and micro-econometrics applications, including Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mixtures of Normals (including clustering), Dirichlet Process Prior Density Estimation with normal base, Hierarchical Linear Models with normal prior and covariates, Hierarchical Linear Models with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates, Hierarchical Negative Binomial Regression Models, Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random Coefficient Logit Models.") (license license:gpl2+))) (define-public r-tensora (package (name "r-tensora") (version "0.36.2.1") (source (origin (method url-fetch) (uri (cran-uri "tensorA" version)) (sha256 (base32 "1dvxc4d5c8k3mqkx6bjgfmnb98rrdd1rsazyva76mzvxzrhq4n06")))) (properties `((upstream-name . "tensorA"))) (build-system r-build-system) (home-page "http://www.stat.boogaart.de/tensorA") (synopsis "Advanced tensor arithmetic with named indices") (description "This package provides convenience functions for advanced linear algebra with tensors and computation with datasets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, and parallel computations on sequences of tensors.") (license license:gpl2+))) (define-public r-rarpack (package (name "r-rarpack") (version "0.11-0") (source (origin (method url-fetch) (uri (cran-uri "rARPACK" version)) (sha256 (base32 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) (properties `((upstream-name . "rARPACK"))) (build-system r-build-system) (propagated-inputs (list r-rspectra)) (home-page "https://github.com/yixuan/rARPACK") (synopsis "Solvers for large scale eigenvalue and SVD problems") (description "This package was previously an R wrapper of the ARPACK library, and now a shell of the R package RSpectra, an R interface to the Spectra library for solving large scale eigenvalue/vector problems. The current version of rARPACK simply imports and exports the functions provided by RSpectra. New users of rARPACK are advised to switch to the RSpectra package.") (license license:bsd-3))) (define-public r-compositions (package (name "r-compositions") (version "2.0-7") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 "1j1qa0lkb7ywh0q79dklhw4gvkxgvk3qhw3rx9srrlrc7jv22hml")))) (build-system r-build-system) (propagated-inputs (list r-bayesm r-mass r-robustbase r-tensora)) (native-inputs (list r-knitr)) (home-page "http://www.stat.boogaart.de/compositions") (synopsis "Compositional data analysis") (description "This package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations).") (license license:gpl2+))) (define-public r-cobs (package (name "r-cobs") (version "1.3-5") (source (origin (method url-fetch) (uri (cran-uri "cobs" version)) (sha256 (base32 "04f6a6gp11p93j2k35mbrfqgjx5qsgi3dj1085a5v5s0z6l7vbkz")))) (build-system r-build-system) (propagated-inputs (list r-quantreg r-sparsem)) (home-page "https://cran.r-project.org/web/packages/cobs") (synopsis "Constrained B-Splines (sparse matrix based)") (description "This package provides qualitatively constrained (regression) smoothing splines via linear programming and sparse matrices.") (license license:gpl2+))) (define-public r-drimpute (package (name "r-drimpute") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "DrImpute" version)) (sha256 (base32 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b")))) (properties `((upstream-name . "DrImpute"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "https://github.com/ikwak2/DrImpute") (synopsis "Imputing dropout events in single-cell RNA-Seq data") (description "This is an R package for imputing dropout events. Many statistical methods in cell type identification, visualization and lineage reconstruction do not account for dropout events. DrImpute can improve the performance of such software by imputing dropout events.") (license license:gpl3))) (define-public r-gamlss-dist (package (name "r-gamlss-dist") (version "6.1-1") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 (base32 "0sch2bh1mchl7kfdy4wcmwzzgx7cldswn65a2br2x73rb1v3mnyj")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "http://www.gamlss.org/") (synopsis "Distributions for Generalized Additive Models for location scale and shape") (description "This package provides a set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} transformation, respectively.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) ;; This package includes JavaScript files, which are not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinyjs (package (name "r-shinyjs") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjs" version)) (sha256 (base32 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky")))) (build-system r-build-system) (propagated-inputs (list r-digest r-jsonlite r-shiny)) (native-inputs (list r-knitr)) (home-page "https://deanattali.com/shinyjs") (synopsis "Improve the user experience of your Shiny apps") (description "Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. Examples include: hiding an element, disabling an input, resetting an input back to its original value, delaying code execution by a few seconds, and many more useful functions for both the end user and the developer. Shinyjs can also be used to easily call your own custom JavaScript functions from R.") (license license:agpl3+))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-colourpicker (package (name "r-colourpicker") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "colourpicker" version)) (sha256 (base32 "0415238r7a8xrp3kvq8lczzxz534irj2q1zfbb0pl7xfs6663wn7")) (snippet '(for-each delete-file (list "inst/examples/colourInput/www/salvattore.min.js" "inst/htmlwidgets/lib/jquery/jquery.min.js" "inst/www/shared/colourpicker/js/colourpicker.min.js"))))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" (let ((mapping `((,(assoc-ref inputs "js-salvattore") . "examples/colourInput/www/salvattore.min.js") (,(assoc-ref inputs "js-jquery") . "htmlwidgets/lib/jquery/jquery.min.js") ("www/shared/colourpicker/js/colourpicker.js" . "www/shared/colourpicker/js/colourpicker.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (propagated-inputs (list r-ggplot2 r-htmltools r-htmlwidgets r-jsonlite r-miniui r-shiny r-shinyjs)) (native-inputs `(("esbuild" ,esbuild) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.6.1.js") (sha256 (base32 "1lm4zcpvqdi7qi2s7bgci2z74wazq0z0bdvjmlrqbhmfrpk42ffz")))) ("js-salvattore" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js") (sha256 (base32 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5")))))) (home-page "https://github.com/daattali/colourpicker") (synopsis "Color picker tool for Shiny and for selecting colors in plots") (description "This package provides a color picker that can be used as an input in Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, custom color palettes, and many more options. A plot color helper tool is available as an RStudio Addin, which helps you pick colors to use in your plots. A more generic color picker RStudio Addin is also provided to let you select colors to use in your R code.") (license license:expat))) (define-public r-ggextra (package (name "r-ggextra") (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "ggExtra" version)) (sha256 (base32 "0b78bnkhjlfa2h3f5iib0hqas8r289vqglfbk71a419rivzfsyb8")))) (properties `((upstream-name . "ggExtra"))) (build-system r-build-system) (propagated-inputs (list r-colourpicker r-ggplot2 r-gtable r-miniui r-r6 r-scales r-shiny r-shinyjs)) (native-inputs (list r-knitr)) (home-page "https://github.com/daattali/ggExtra") (synopsis "Marginal histograms for ggplot2 and other enhancements") (description "This package is a collection of functions and layers to enhance ggplot2. The flagship function is @code{ggMarginal()}, which can be used to add marginal histograms/boxplots/density plots to ggplot2 scatterplots.") (license license:expat))) (define-public r-ggpattern (package (name "r-ggpattern") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ggpattern" version)) (sha256 (base32 "1b9bfxlg64gr39bz58fp6jmg4nziwk8rk94rzpjsqhfhpwi2lrgr")))) (properties `((upstream-name . "ggpattern"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-glue r-gridpattern r-rlang r-scales)) (native-inputs (list r-knitr r-ragg r-rmarkdown)) (home-page "https://github.com/coolbutuseless/ggpattern") (synopsis "Ggplot2 pattern geoms") (description "This package provides ggplot2 geoms filled with various patterns. It includes a patterned version of every ggplot2 geom that has a region that can be filled with a pattern. It provides a suite of ggplot2 aesthetics and scales for controlling pattern appearances. It supports over a dozen builtin patterns (every pattern implemented by gridpattern) as well as allowing custom user-defined patterns.") (license license:expat))) (define-public r-minpack-lm (package (name "r-minpack-lm") (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 "0cg7arnmb7x6v5x487gkc2k4i5gchgdwblrrd0k0vw1w6pza83z3")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/minpack.lm") (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") (description "The @code{nls.lm} function provides an R interface to @code{lmder} and @code{lmdif} from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via @code{nls}-like calls using the @code{nlsLM} function.") (license license:gpl3))) (define-public r-moments (package (name "r-moments") (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "moments" version)) (sha256 (base32 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/moments") (synopsis "Moments, cumulants, skewness, kurtosis and related tests") (description "This package provides functions to calculate: moments, Pearson's kurtosis, Geary's kurtosis and skewness; it also includes tests related to them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") (license license:gpl2+))) (define-public r-msir (package (name "r-msir") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "msir" version)) (sha256 (base32 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84")))) (build-system r-build-system) (propagated-inputs (list r-mclust)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/msir") (synopsis "Model-based sliced inverse regression") (description "This is an R package for dimension reduction based on finite Gaussian mixture modeling of inverse regression.") (license license:gpl2+))) (define-public r-pbivnorm (package (name "r-pbivnorm") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "pbivnorm" version)) (sha256 (base32 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://github.com/brentonk/pbivnorm") (synopsis "Vectorized bivariate normal CDF") (description "This package provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF.") (license license:gpl2+))) (define-public r-lavaan (package (name "r-lavaan") (version "0.6-17") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 "1bppbv17b35h48vfci6zplix9zb5isi210za52cs9yyc68g2acwj")))) (build-system r-build-system) (propagated-inputs (list r-mass r-mnormt r-numderiv r-pbivnorm r-quadprog)) (home-page "https://lavaan.ugent.be") (synopsis "Latent variable analysis") (description "This package provides tools to fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.") (license license:gpl2+))) (define-public r-nonnest2 (package (name "r-nonnest2") (version "0.5-6") (source (origin (method url-fetch) (uri (cran-uri "nonnest2" version)) (sha256 (base32 "1s31a03c148azvc20ihmz8vhzgs7a3r0nxzf806zsr5j1zsl94dm")))) (build-system r-build-system) (propagated-inputs (list r-compquadform r-lavaan r-mvtnorm r-sandwich)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/nonnest2/") (synopsis "Tests of non-nested models") (description "This package allows for testing of non-nested models. It includes tests of model distinguishability and of model fit that can be applied to both nested and non-nested models. The package also includes functionality to obtain confidence intervals associated with AIC and BIC.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-penalized (package (name "r-penalized") (version "0.9-52") (source (origin (method url-fetch) (uri (cran-uri "penalized" version)) (sha256 (base32 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/penalized/") (synopsis "Penalized estimation in GLMs and in the Cox model") (description "This package provides tools for fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.") (license license:gpl2+))) (define-public r-zim (package (name "r-zim") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "ZIM" version)) (sha256 (base32 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) (properties `((upstream-name . "ZIM"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://github.com/biostatstudio/ZIM") (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") (description "Analyze count time series with excess zeros. Two types of statistical models are supported: Markov regression and state-space models. They are also known as observation-driven and parameter-driven models respectively in the time series literature. The functions used for Markov regression or observation-driven models can also be used to fit ordinary regression models with independent data under the zero-inflated Poisson (ZIP) or zero-inflated negative binomial (ZINB) assumption. The package also contains miscellaneous functions to compute density, distribution, quantile, and generate random numbers from ZIP and ZINB distributions.") (license license:gpl3))) (define-public r-nor1mix (package (name "r-nor1mix") (version "1.3-2") (source (origin (method url-fetch) (uri (cran-uri "nor1mix" version)) (sha256 (base32 "0252kqhdsp374isc59pm1c6dmsb16jibpnsp1bpyh4k5mg73cdj6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/nor1mix/") (synopsis "Normal (1-d) mixture models") (description "This package provides S3 classes and methods for one-dimensional normal mixture models, for, e.g., density estimation or clustering algorithms research and teaching; it provides the widely used Marron-Wand densities. It also provides tools for efficient random number generation and graphics.") (license license:gpl2+))) (define-public r-beanplot (package (name "r-beanplot") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "beanplot" version)) (sha256 (base32 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/beanplot/") (synopsis "Visualization via beanplots") (description "This package provides beanplots, an alternative to boxplot/stripchart/violin plots. It can be used to plot univariate comparison graphs.") (license license:gpl2))) (define-public r-pbdzmq (package (name "r-pbdzmq") (version "0.3-10") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 "14fi1bcvc77k5qjh0vb5r44p9rzlzrbzbw2c99psnzq2wic018ir")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs (list zeromq zlib)) (native-inputs (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "R interface to ZeroMQ") (description "ZeroMQ is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize ZeroMQ. The main focus is on interactive client/server programming frameworks. A few wrapper functions compatible with @code{rzmq} are also provided.") (license license:gpl3))) (define-public r-repr (package (name "r-repr") (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 "0gv72qydk4r070q3jcqakvfcm4r0n9zzzpl82s0w87iw6sdnqbix")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-htmltools r-jsonlite r-pillar)) (home-page "https://cran.r-project.org/web/packages/repr/") (synopsis "Serializable representations") (description "This package provides string and binary representations of objects for several formats and MIME types.") (license license:gpl3))) (define-public r-irdisplay (package (name "r-irdisplay") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "IRdisplay" version)) (sha256 (base32 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3")))) (properties `((upstream-name . "IRdisplay"))) (build-system r-build-system) (propagated-inputs (list r-repr)) (home-page "https://cran.r-project.org/web/packages/IRdisplay/") (synopsis "Jupyter display machinery") (description "This package provides an interface to the rich display capabilities of Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a running IRkernel session.") (license license:expat))) (define-public r-irkernel (package (name "r-irkernel") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 "19i4wj5cb62n6j83nxgv500dcdzrf6rzwdy5v6fh7r93vjyxiip1")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'install 'install-kernelspec (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (setenv "HOME" "/tmp") (invoke "jupyter" "kernelspec" "install" "--name" "ir" "--prefix" out (string-append out "/site-library/IRkernel/kernelspec")) ;; Record the absolute file name of the 'R' executable in ;; 'kernel.json'. (substitute* (string-append out "/share/jupyter" "/kernels/ir/kernel.json") (("\\[\"R\",") (string-append "[\"" (which "R") "\","))) #t)))))) (inputs (list jupyter)) (propagated-inputs (list r-crayon r-digest r-evaluate r-irdisplay r-jsonlite ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) r-minimal r-pbdzmq r-repr r-uuid)) (home-page "https://cran.r-project.org/web/packages/IRkernel/") (synopsis "Native R kernel for Jupyter") (description "The R kernel for the Jupyter environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.") (license license:expat))) (define-public r-gmodels (package (name "r-gmodels") (version "2.18.1.1") (source (origin (method url-fetch) (uri (cran-uri "gmodels" version)) (sha256 (base32 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs")))) (build-system r-build-system) (propagated-inputs (list r-gdata r-mass)) (home-page "https://cran.r-project.org/web/packages/gmodels/") (synopsis "Various R programming tools for model fitting") (description "This package provides various R programming tools for model fitting.") (license license:gpl2))) (define-public r-apcluster (package (name "r-apcluster") (version "1.4.11") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 "0crk7skivcmlvr0njsbd8dksj5wa6qlvdp99ay5b2b40cs3xm5s4")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/apcluster/") (synopsis "Affinity propagation clustering") (description "This package implements affinity propagation clustering introduced by Frey and Dueck (2007). The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.") (license license:gpl2+))) (define-public r-remacor (package (name "r-remacor") (version "0.0.16") (source (origin (method url-fetch) (uri (cran-uri "remaCor" version)) (sha256 (base32 "1xznj2y3qszw8s1fgbs8fiadg7c0gl3ml1blxmwixb32kr2cv5vq")))) (properties `((upstream-name . "remaCor"))) (build-system r-build-system) (propagated-inputs (list r-envstats r-ggplot2 r-mvtnorm r-rcpp r-rcpparmadillo r-rdpack r-reshape2)) (native-inputs (list r-knitr)) (home-page "https://diseaseneurogenomics.github.io/remaCor/") (synopsis "Random effects meta-analysis for correlated test statistics") (description "Meta-analysis is widely used to summarize estimated effects sizes across multiple statistical tests. Standard fixed and random effect meta-analysis methods assume that the estimated of the effect sizes are statistically independent. Here we relax this assumption and enable meta-analysis when the correlation matrix between effect size estimates is known.") (license license:artistic2.0))) (define-public r-rematch2 (package (name "r-rematch2") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "rematch2" version)) (sha256 (base32 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y")))) (build-system r-build-system) (propagated-inputs (list r-tibble)) (home-page "https://github.com/r-lib/rematch2") (synopsis "Tidy output from regular expression matching") (description "This package provides wrappers on @code{regexpr} and @code{gregexpr} to return the match results in tidy data frames.") (license license:expat))) (define-public r-picante (package (name "r-picante") (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "picante" version)) (sha256 (base32 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn")))) (build-system r-build-system) (propagated-inputs (list r-ape r-nlme r-vegan)) (home-page "https://cran.r-project.org/web/packages/picante/") (synopsis "Integrating phylogenies and ecology") (description "This package provides functions for phylocom integration, community analyses, null-models, traits and evolution. It implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010).") (license license:gpl2))) (define-public r-reinforcelearn (package (name "r-reinforcelearn") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "reinforcelearn" version)) (sha256 (base32 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-nnet r-purrr r-r6)) (home-page "https://markusdumke.github.io/reinforcelearn") (synopsis "Reinforcement learning") (description "This package implements reinforcement learning environments and algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm can be used with function approximation, eligibility traces (Singh & Sutton, 1996) and experience replay (Mnih et al., 2013).") (license license:expat))) (define-public r-lemon (package (name "r-lemon") (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 "1r33n7bkfhjpyi23j7gsi387qvyazcy9b912dsd3vg2yqir8s26p")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-gtable r-knitr r-lattice r-plyr r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/stefanedwards/lemon") (synopsis "Freshen up your ggplot2 plots") (description "This package provides functions for working with legends and axis lines of ggplot2, facets that repeat axis lines on all panels, and some knitr extensions.") (license license:gpl3))) (define-public r-wgaim (package (name "r-wgaim") (version "2.0-1") (source (origin (method url-fetch) (uri (cran-uri "wgaim" version)) (sha256 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-qtl)) (home-page "https://cran.r-project.org/web/packages/wgaim") (synopsis "Whole genome average interval mapping for QTL detection") (description "This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.") (license license:gpl2+))) (define-public r-bedr (package (name "r-bedr") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "bedr" version)) (sha256 (base32 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-r-utils r-testthat r-venndiagram r-yaml bedops bedtools htslib)) ; for tabix (native-inputs (list r-knitr)) ; for vignettes (home-page "https://cran.r-project.org/web/packages/bedr") (synopsis "Genomic region processing") (description "This package is for genomic regions processing using command line tools such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. The bedr package's API enhances access to these tools as well as offers additional utilities for genomic regions processing.") (license license:gpl2))) (define-public r-setrng (package (name "r-setrng") (version "2022.4-1") (source (origin (method url-fetch) (uri (cran-uri "setRNG" version)) (sha256 (base32 "09089vr5x8snwxh38kdhgpjl3jl7zrk056f6f9a2jg5lsrmnxh31")))) (properties `((upstream-name . "setRNG"))) (build-system r-build-system) (home-page "https://distr.r-forge.r-project.org/") (synopsis "Set (normal) random number generator and seed") (description "This package provides utilities to help set and record the setting of the seed and the uniform and normal generators used when a random experiment is run. The utilities can be used in other functions that do random experiments to simplify recording and/or setting all the necessary information for reproducibility. See the vignette and reference manual for examples.") (license license:gpl2))) (define-public r-sets (package (name "r-sets") (version "1.0-25") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 "1x14q29jjmrs5ldbjc7pxp5pr52j3dw6zr9k5qvz4ycniwhnk92w")))) (properties `((upstream-name . "sets"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sets") (synopsis "Sets, generalized sets, customizable sets and intervals") (description "This package provides data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.") (license license:gpl2))) (define-public r-partitions (package (name "r-partitions") (version "1.10-7") (source (origin (method url-fetch) (uri (cran-uri "partitions" version)) (sha256 (base32 "1kxiy1wl7dr39kyfg2y9hd67s32knd83r2jsb7j9p3vg8iqq7yqb")))) (build-system r-build-system) (propagated-inputs (list r-gmp r-mathjaxr r-polynom r-rdpack r-sets)) (home-page "https://cran.r-project.org/web/packages/partitions") (synopsis "Additive partitions of integers") (description "This package provides tools to enumerates the partitions, unequal partitions, and restricted partitions of an integer; the three corresponding partition functions are also given.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-brobdingnag (package (name "r-brobdingnag") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "Brobdingnag" version)) (sha256 (base32 "07p9416rdzfyiigbglxjpbcg7pfly9nw19yn2mwg98621cjjs0gr")))) (properties `((upstream-name . "Brobdingnag"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "https://github.com/RobinHankin/Brobdingnag.git") (synopsis "Very large numbers in R") (description "This package handles very large numbers in R. Real numbers are held using their natural logarithms, plus a logical flag indicating sign. The package includes a vignette that gives a step-by-step introduction to using S4 methods.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-unglue (package (name "r-unglue") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "unglue" version)) (sha256 (base32 "0w8ld4xllx0lj1jz8i2sj92f8136hlwri1d8ldpg1ymxj7aw93vg")))) (properties `((upstream-name . "unglue"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=unglue") (synopsis "Extract matched substrings using a pattern") (description "This package lets you use syntax inspired by the package @code{glue} to extract matched substrings in a more intuitive and compact way than by using standard regular expressions.") (license license:gpl3))) (define-public r-untb (package (name "r-untb") (version "1.7-7") (source (origin (method url-fetch) (uri (cran-uri "untb" version)) (sha256 (base32 "0sd9vapgzy3ifpyl08hm5l7d5g1yvyccqf3n9dyc9x5gmqkvhri1")))) (build-system r-build-system) (propagated-inputs (list r-brobdingnag r-partitions r-polynom)) (home-page "https://github.com/RobinHankin/untb.git") (synopsis "Ecological drift under the UNTB") (description "This package provides numerical simulations, and visualizations, of Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).") (license license:gpl2+))) (define-public r-stepwise (package (name "r-stepwise") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "stepwise" version)) (sha256 (base32 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2")))) (build-system r-build-system) (home-page "https://stat.sfu.ca/statgen/research/stepwise.html") (synopsis "Stepwise detection of recombination breakpoints") (description "This package provides a stepwise approach to identifying recombination breakpoints in a genomic sequence alignment.") (license license:gpl2+))) (define-public r-snpmaxsel (package (name "r-snpmaxsel") (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "SNPmaxsel" version)) (sha256 (base32 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z")))) (properties `((upstream-name . "SNPmaxsel"))) (build-system r-build-system) (propagated-inputs (list r-combinat r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") (synopsis "Maximally selected statistics for SNP data") (description "This package implements asymptotic methods related to maximally selected statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP) data.") (license license:gpl2+))) (define-public r-acsnminer (package (name "r-acsnminer") (version "0.16.8.25") (source (origin (method url-fetch) (uri (cran-uri "ACSNMineR" version)) (sha256 (base32 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) (properties `((upstream-name . "ACSNMineR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra)) (home-page "https://cran.r-project.org/web/packages/ACSNMineR") (synopsis "Gene enrichment analysis") (description "This package provides tools to compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the @dfn{Atlas of Cancer Signalling Networks} (ACSN) or user imported maps. The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections. Visualization of data can be done either by barplots or heatmaps.") (license license:gpl2+))) (define-public r-seqinr (package (name "r-seqinr") (version "4.2-36") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 "09dj2k5mi6xylsihnwbmdd8f4qg855gyh7yvz9gamam7j6h646lk")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-segmented)) (inputs (list zlib)) (home-page "https://seqinr.r-forge.r-project.org/") (synopsis "Biological sequences retrieval and analysis") (description "This package provides tools for exploratory data analysis and data visualization of biological sequence (DNA and protein) data. It also includes utilities for sequence data management under the ACNUC system.") (license license:gpl2+))) (define-public r-units (package (name "r-units") (version "0.8-5") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 "1c836qazrs8z9p1xkcfl9gl882i8q7qf2g73l483w18bfspq0pnr")))) (build-system r-build-system) (inputs (list udunits)) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-quantities/units/") (synopsis "Measurement Units for R Vectors") (description "This package provides support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. It is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} classes.") (license license:gpl2))) (define-public r-udunits2 (package (name "r-udunits2") (version "0.13.2.1") (source (origin (method url-fetch) (uri (cran-uri "udunits2" version)) (sha256 (base32 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z")))) (properties `((upstream-name . "udunits2"))) (build-system r-build-system) (inputs (list udunits)) (home-page "https://cran.r-project.org/package=udunits2") (synopsis "Udunits-2 bindings for R") (description "This package provides simple bindings to Unidata's udunits library.") (license license:gpl2))) (define-public r-classint (package (name "r-classint") (version "0.4-10") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 "12rbwh7g0a6abvy423xjiv53gx1f9lg4y78r80lc0fj9pjpiwmn3")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs (list r-class r-e1071 r-kernsmooth)) (native-inputs (list gfortran r-knitr)) (home-page "https://github.com/r-spatial/classInt/") (synopsis "Choose univariate class intervals") (description "This package provides selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.") (license license:gpl2+))) (define-public r-spdata (package (name "r-spdata") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 "12w4chk71vqy1chij79928ppxdg2cz03hx9bgs5cgwj9f1ciyb2b")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs (list r-sp)) (home-page "https://github.com/Nowosad/spData") (synopsis "Datasets for spatial analysis") (description "This a package containing diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some of the datasets are designed to illustrate specific analysis techniques. @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to illustrate point pattern analysis techniques.") (license license:cc0))) (define-public r-learnbayes (package (name "r-learnbayes") (version "2.15.1") (source (origin (method url-fetch) (uri (cran-uri "LearnBayes" version)) (sha256 (base32 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv")))) (properties `((upstream-name . "LearnBayes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/LearnBayes") (synopsis "Functions for learning Bayesian inference") (description "This package provides a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.") (license license:gpl2+))) (define-public r-deldir (package (name "r-deldir") (version "2.0-2") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 "1qzfq47fs3pr0946m53z6cq93pbpkgwwhqkcdgfahxsq1izpigz9")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/deldir") (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") (description "This package provides tools for calculating the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. It plots triangulations and tessellations in various ways, clips tessellations to sub-windows, calculates perimeters of tessellations, and summarizes information about the tiles of the tessellation.") (license license:gpl2+))) (define-public r-wk (package (name "r-wk") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 "0yxzyb09by9winspdn0585xhjmdcablb07wx6pf7ahg0q18sz85p")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) (home-page "https://paleolimbot.github.io/wk/") (synopsis "Lightweight well-known geometry parsing") (description "This package provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are only useful in R if the information they contain can be accessed in R, for which high-performance functions are provided here.") (license license:expat))) (define-public r-s2 (package (name "r-s2") (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "s2" version)) (sha256 (base32 "0rm0jd5k5w725v1bnn6ix8vic40grdh61y6qdy8jy4lhg1mjx78x")))) (properties `((upstream-name . "s2"))) (build-system r-build-system) (arguments (list #:phases `(modify-phases %standard-phases ;; We don't want to convert -lssl to -l:libssl.so.1.1; there is only ;; one libssl.so anyway and the -l:* thing breaks linking. (add-after 'unpack 'undo-library-versioning (lambda _ (substitute* "configure" (("PKG_LIBS_VERSIONED=.*") "PKG_LIBS_VERSIONED=\"${PKG_LIBS}\"\n"))))))) (propagated-inputs (list r-rcpp r-wk)) (inputs (list openssl)) (native-inputs (list pkg-config)) (home-page "https://r-spatial.github.io/s2/") (synopsis "Spherical geometry operators using the S2 geometry library") (description "This package provides R bindings for Google's s2 library for geometric calculations on the sphere. High-performance constructors and exporters provide high compatibility with existing spatial packages, transformers construct new geometries from existing geometries, predicates provide a means to select geometries based on spatial relationships, and accessors extract information about geometries.") (license license:asl2.0))) (define-public r-sf (package (name "r-sf") (version "1.0-15") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 "0b9whfi709gjkzslkrkm8ki1yz5az6vrv5b1l2w712sjqy8r47f8")))) (build-system r-build-system) (inputs (list curl gdal geos openssh openssl pcre2 proj sqlite zlib)) (propagated-inputs (list r-classint r-dbi r-magrittr r-rcpp r-s2 r-units)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-spatial/sf/") (synopsis "Simple features for R") (description "This package provides support for simple features, a standardized way to encode spatial vector data. It binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum transformations.") ;; Either of these licenses (license (list license:gpl2 license:expat)))) (define-public r-sftime (package (name "r-sftime") (version "0.2-0") (source (origin (method url-fetch) (uri (cran-uri "sftime" version)) (sha256 (base32 "1ymi60ag8kqb3293bdcvb83zwsgrz000ylifjvlpzzmh1xsisanq")))) (properties `((upstream-name . "sftime"))) (build-system r-build-system) (propagated-inputs (list r-sf)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=sftime") (synopsis "Simple feature objects that have a time column") (description "This package provides classes and methods for spatial objects that have a registered time column, in particular for irregular spatiotemporal data. The @code{time} column can be of any type, but needs to be ordinal. Regularly laid out spatiotemporal data (vector or raster data cubes) are handled by package stars'.") (license license:asl2.0))) (define-public r-spdep (package (name "r-spdep") (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 "15jkx3f4c1255kidsqdq4gyi28r4jk3h46fm7jj114ag176jq1in")) (snippet '(for-each delete-file '("inst/doc/CO69.html" "inst/doc/CO69.R" "inst/doc/nb.html" "inst/doc/nb.R" "inst/doc/nb_sf.html" "inst/doc/nb_sf.R" "inst/doc/nb_sf.Rmd" "inst/doc/sids.html" "inst/doc/sids.R"))))) (build-system r-build-system) (propagated-inputs (list r-boot r-deldir r-e1071 r-s2 r-sf r-sp r-spdata r-units)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-spatial/spdep/") (synopsis "Spatial dependence: weighting schemes, statistics and models") (description "This package provides a collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.") (license license:gpl2+))) (define-public r-adegenet (package (name "r-adegenet") (version "2.1.10") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 "0qxig2jyj1q0a8pwpv5f5v5b4x4af8s9p1p0yc0msmyxq457hqmb")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-boot r-dplyr r-ggplot2 r-igraph r-mass r-reshape2 r-seqinr r-shiny r-vegan)) (home-page "https://github.com/thibautjombart/adegenet") (synopsis "Exploratory analysis of genetic and genomic data") (description "This package provides a toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure (@code{genind} class), alleles counts by populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.") (license license:gpl2+))) (define-public r-pegas (package (name "r-pegas") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 (base32 "1j1xrnwi80ycwziwcsb48sfdm2ifdzgsn8clh0ai7rvhknrb4ghh")))) (build-system r-build-system) (propagated-inputs (list r-ape)) (home-page "http://ape-package.ird.fr/pegas.html") (synopsis "Population and evolutionary genetics analysis system") (description "This package provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.") (license license:gpl2+))) (define-public r-genetics (package (name "r-genetics") (version "1.3.8.1.3") (source (origin (method url-fetch) (uri (cran-uri "genetics" version)) (sha256 (base32 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy")))) (build-system r-build-system) (propagated-inputs (list r-combinat r-gdata r-gtools r-mass r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/genetics/") (synopsis "Population genetics") (description "This package provides classes and methods for handling genetic data. It includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...") ;; Any GPL version. (license license:gpl2+))) (define-public r-snp-plotter (package (name "r-snp-plotter") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "snp.plotter" version)) (sha256 (base32 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) (properties `((upstream-name . "snp.plotter"))) (build-system r-build-system) (propagated-inputs (list r-genetics)) (home-page "https://cran.r-project.org/web/packages/snp.plotter/") (synopsis "Plot p-values using single SNP and/or haplotype data") (description "This package helps you create plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple datasets simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either PDF/EPS files.") (license license:gpl2+))) (define-public r-polspline (package (name "r-polspline") (version "1.1.24") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 (base32 "0mal78f79jl6cj02xabv9vqf88m4iiadmgiv3qliv117cxkc6hb6")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") (synopsis "Polynomial spline routines") (description "This package provides routines for the polynomial spline fitting routines hazard regression, hazard estimation with flexible tails, logspline, lspec, polyclass, and polymars.") (license license:gpl2+))) (define-public r-rms (package (name "r-rms") (version "6.7-1") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 (base32 "199xb98zxsbd8wa9g33bgrvbcpq79glnfmq060ic8f9vjw96r0qz")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-colorspace r-digest r-ggplot2 r-hmisc r-htmltable r-htmltools r-knitr r-mass r-multcomp r-nlme r-polspline r-quantreg r-rpart r-sparsem r-survival)) (native-inputs (list gfortran)) (home-page "http://biostat.mc.vanderbilt.edu/rms") (synopsis "Regression modeling strategies") (description "This is a package for regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. The rms package is a collection of functions that assist with and streamline modeling. It also contains functions for binary and ordinal logistic regression models, ordinal models for continuous Y with a variety of distribution families, and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. The package works with almost any regression model, but it was especially written to work with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.") (license license:gpl2+))) (define-public r-arsenal (package (name "r-arsenal") (version "3.6.3") (source (origin (method url-fetch) (uri (cran-uri "arsenal" version)) (sha256 (base32 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms")))) (properties `((upstream-name . "arsenal"))) (build-system r-build-system) (propagated-inputs (list r-knitr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mayoverse/arsenal") (synopsis "Functions for large-scale statistical summaries") (description "This package provides an arsenal of R functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in R and RStudio and which use formulas and versatile summary statistics for summary tables and models. The primary functions include @enumerate @item @code{tableby}, a Table-1-like summary of multiple variable types by the levels of one or more categorical variables; @item @code{paired}, a Table-1-like summary of multiple variable types paired across two time points; @item @code{modelsum}, which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); @item @code{freqlist}, a powerful frequency table across many categorical variables; @item @code{comparedf}, a function for comparing @code{data.frames}; and @item @code{write2}, a function to output tables to a document. @end enumerate ") (license license:gpl2+))) (define-public r-haplo-stats (package (name "r-haplo-stats") (version "1.9.5") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 "17h7nxpc5ggxwpc4j4cxf7n0qglc93vhwd4ljwa8ic33x3yab673")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs (list r-arsenal r-rms)) (native-inputs (list r-r-rsp)) ; for vignettes (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") (synopsis "Analysis of haplotypes when linkage phase is ambiguous") (description "This package provides routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()}, @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed examples in the vignette.") (license license:gpl2+))) (define-public r-bqtl (package (name "r-bqtl") (version "1.0-35") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 "107yq7mk4gdr1wm20i751682jlj172bzbdjgqwviwgjxzbd0c2xa")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") (synopsis "Bayesian QTL mapping toolkit") (description "This is a QTL mapping toolkit for inbred crosses and recombinant inbred lines. It includes maximum likelihood and Bayesian tools.") (license license:gpl2+))) (define-public r-ibdreg (package (name "r-ibdreg") (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "ibdreg" version)) (sha256 (base32 "0c4svyfd7xjx9k6pl40l7y9rc67zschs0nz1l386xi1m7arsp44n")))) (build-system r-build-system) (home-page "https://www.mayo.edu/research/labs/\ statistical-genetics-genetic-epidemiology/software") (synopsis "Regression methods for IBD linkage with covariates") (description "This package provides a method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree.") (license license:gpl2+))) (define-public r-dlmap (package (name "r-dlmap") (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "dlmap" version)) (sha256 (base32 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) (build-system r-build-system) (propagated-inputs (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim)) (home-page "https://cran.r-project.org/web/packages/dlmap/") (synopsis "Detection localization mapping for QTL") (description "This is package for QTL mapping in a mixed model framework with separate detection and localization stages. The first stage detects the number of QTL on each chromosome based on the genetic variation due to grouped markers on the chromosome; the second stage uses this information to determine the most likely QTL positions. The mixed model can accommodate general fixed and random effects, including spatial effects in field trials and pedigree effects. It is applicable to backcrosses, doubled haploids, recombinant inbred lines, F2 intercrosses, and association mapping populations.") (license license:gpl2))) (define-public r-hwde (package (name "r-hwde") (version "0.67-3") (source (origin (method url-fetch) (uri (cran-uri "hwde" version)) (sha256 (base32 "0kj3vf4pmcvxy95hx1d0q6c626y8d0ljj3r76y5hd90a6v75b5xa")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/hwde/") (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium") (description "This package fits models for genotypic disequilibria, as described in Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast terms are available that account for first order interactions between loci. It also implements, for a single locus in a single population, a conditional exact test for Hardy-Weinberg equilibrium.") (license license:gpl2+))) (define-public r-tdthap (package (name "r-tdthap") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "tdthap" version)) (sha256 (base32 "05yj7jwwd0q2yk8gpp44fhh3sknvw3g6p9glj6z6rz46p9xf31kr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tdthap/") (synopsis "TDT tests for extended haplotypes") (description "Functions and examples are provided for transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) \"Transmission/disequilibrium tests for extended marker haplotypes\".") (license license:artistic2.0))) (define-public r-sparql (package (name "r-sparql") (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "SPARQL" version)) (sha256 (base32 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) (properties `((upstream-name . "SPARQL"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-xml)) (home-page "https://cran.r-project.org/web/packages/SPARQL") (synopsis "SPARQL client for R") (description "This package provides an interface to use SPARQL to pose SELECT or UPDATE queries to an end-point.") ;; The only license indication is found in the DESCRIPTION file, ;; which states GPL-3. So we cannot assume GPLv3+. (license license:gpl3))) (define-public r-bookdown (package (name "r-bookdown") (version "0.37") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 "18j8ylaq5wnw1c0lif9a002kbymv04pd0i43ahmqkskkv1b13hdk")) ;; TODO: there is one more file to replace: ;; inst/resources/gitbook/js/app.min.js (snippet '(for-each delete-file '("inst/resources/gitbook/js/clipboard.min.js" "inst/resources/gitbook/js/lunr.js" "inst/resources/mathquill/mathquill.min.js"))))) (properties `((upstream-name . "bookdown") ;; We cannot add knitr because this package depends on xfun, which is ;; an input to knitr. (updater-ignored-native-inputs . ("r-knitr")))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/resources" (invoke "tar" "-xf" (assoc-ref inputs "js-mathquill") "-C" "/tmp" "--strip-components=2") (for-each (match-lambda ((source . target) (minify source #:target target))) `((,(search-input-file inputs "/dist/clipboard.js") . "gitbook/js/clipboard.min.js") (,(search-input-file inputs "/lunr.js") . "gitbook/js/lunr.js") ("/tmp/mathquill.js" . "mathquill/mathquill.min.js"))))))))) (propagated-inputs (list r-htmltools r-jquerylib r-knitr r-rmarkdown r-tinytex r-xfun r-yaml pandoc)) (native-inputs `(("esbuild" ,esbuild) ("js-clipboard" ,(let ((version "2.0.4")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/zenorocha/clipboard.js") (commit (string-append "v" version)))) (file-name (git-file-name "clipboard.js" version)) (sha256 (base32 "02zzirnddf4kcqdiqb2i7a7yki3rwgscca388qhy3namkw793x4z"))))) ("js-lunarjs" ,(let ((version "0.5.12")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/olivernn/lunr.js") (commit (string-append "v" version)))) (file-name (git-file-name "lunr.js" version)) (sha256 (base32 "1xwdymcnc75b22bb95hq7ijcf7agf47g2fnqzzj09aihx2c5r430"))))) ("js-mathquill" ,(origin (method url-fetch) (uri "https://github.com/mathquill/mathquill/\ releases/download/v0.10.1/mathquill-0.10.1.tgz") (sha256 (base32 "1159l2fi7k3wyclp0pksc0qng291glb8qpa67bvcxwyb9dfiwav7")))))) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for authoring books and technical documents with R Markdown.") (license license:gpl3))) (define-public r-optparse (package (name "r-optparse") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 "1v87db7fm494dwxvdsnl1m2kj84nplq7pkh0g41najhx0npy31v2")))) (build-system r-build-system) (propagated-inputs (list r-getopt)) (native-inputs (list r-knitr)) (home-page "https://github.com/trevorld/optparse") (synopsis "Command line option parser") (description "This package provides a command line parser inspired by Python's @code{optparse} library to be used with Rscript to write shebang scripts that accept short and long options.") (license license:gpl2+))) (define-public r-osqp (package (name "r-osqp") (version "0.6.3.2") (source (origin (method url-fetch) (uri (cran-uri "osqp" version)) (sha256 (base32 "0i1jh3fr8d45b7inq9s6iyqszhh18hps8jpzkm0hzgj2k8r3nm0q")))) (properties `((upstream-name . "osqp"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-r6 r-rcpp)) (home-page "https://osqp.org") (synopsis "Quadratic Programming Solver using the OSQP Library") (description "This package provides bindings to the OSQP solver. The OSQP solver is a numerical optimization package or solving convex quadratic programs written in C and based on the alternating direction method of multipliers. See for details.") (license (list license:asl2.0)))) (define-public r-kernlab (package (name "r-kernlab") (version "0.9-32") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 "1p3gbn9qgc6yqx9irkl8c23khvkx77jl96hk9hn4vsrx6i7g6kk5")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/kernlab") (synopsis "Kernel-based machine learning tools") (description "This package provides kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods @code{kernlab} includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.") (license license:gpl2))) (define-public r-hierfstat (package (name "r-hierfstat") (version "0.5-11") (source (origin (method url-fetch) (uri (cran-uri "hierfstat" version)) (sha256 (base32 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-adegenet r-gaston r-gtools)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/hierfstat/") (synopsis "Estimation and tests of hierarchical F-statistics") (description "This package allows the estimation of hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions are also given to test via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G.") (license license:gpl2+))) (define-public r-hapassoc (package (name "r-hapassoc") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "hapassoc" version)) (sha256 (base32 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6")))) (build-system r-build-system) (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html") (synopsis "Inference of trait associations with SNP haplotypes") (description "Hapassoc performs likelihood inference of trait associations with haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.") (license license:gpl2))) (define-public r-sampling (package (name "r-sampling") (version "2.10") (source (origin (method url-fetch) (uri (cran-uri "sampling" version)) (sha256 (base32 "0x976wblv663aidqmcif1rjv72nbxf4nzms901lmryxbq1p9gv7x")))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-mass)) (home-page "https://cran.r-project.org/web/packages/sampling/") (synopsis "Survey sampling") (description "This package provides functions for drawing and calibrating samples.") (license license:gpl2+))) (define-public r-r2html (package (name "r-r2html") (version "2.3.3") (source (origin (method url-fetch) (uri (cran-uri "R2HTML" version)) (sha256 (base32 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja")))) (properties `((upstream-name . "R2HTML"))) (build-system r-build-system) (home-page "https://github.com/nalimilan/R2HTML") (synopsis "HTML export for R objects") (description "This package includes HTML functions and methods to write in an HTML file. Thus, making HTML reports is easy. It includes a function that allows redirection on the fly, which appears to be very useful for teaching purposes, as the student can keep a copy of the produced output to keep all that they did during the course. The package comes with a vignette describing how to write HTML reports for statistical analysis. Finally, a driver for Sweave parses HTML flat files containing R code and to automatically write the corresponding outputs (tables and graphs).") (license license:gpl2+))) (define-public r-rjava (package (name "r-rjava") (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 "0srrjfqrcp7b6k62qv3d18r97k6kbcz0g4pn2y0rv0f5wlc6i0mm")) (snippet '(for-each delete-file (list "inst/javadoc/jquery/jquery-ui.min.js" "inst/javadoc/jquery/jszip/dist/jszip.min.js" "inst/javadoc/jquery/jszip-utils/dist/jszip-utils-ie.min.js" "inst/javadoc/jquery/jszip-utils/dist/jszip-utils.min.js"))))) (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'set-JAVA_HOME (lambda* (#:key inputs #:allow-other-keys) (let ((jdk (assoc-ref inputs "jdk"))) (setenv "JAVA_HOME" jdk) (setenv "JAVA" (which "java")) (setenv "JAR" (which "jar")) (setenv "JAVAC" (which "javac")) (setenv "JAVAH" (which "javah")) (setenv "JAVA_CPPFLAGS" (string-append "-I" jdk "/include " "-I" jdk "/include/linux")) (setenv "JAVA_LIBS" (search-input-file inputs "/lib/libjvm.so"))))) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda _ (with-directory-excursion "inst/javadoc" (for-each (match-lambda ((source . target) (minify source #:target target))) `(("jquery/jquery-ui.js" . "jquery/jquery-ui.min.js") ("jquery/jszip/dist/jszip.js" . "jquery/jszip/dist/jszip.min.js") ("jquery/jszip-utils/dist/jszip-utils-ie.js" . "jquery/jszip-utils/dist/jszip-utils-ie.min.js") ("jquery/jszip-utils/dist/jszip-utils.js" . "jquery/jszip-utils/dist/jszip-utils.min.js"))))))))) (inputs `(("icu4c" ,icu4c) ("jdk" ,openjdk11 "jdk") ("zlib" ,zlib))) (native-inputs (list esbuild)) (home-page "https://www.rforge.net/rJava/") (synopsis "Low-Level R to Java interface") (description "This package provides a low-level interface to the Java VM very much like .C/.Call and friends. It allows the creation of objects, calling methods and accessing fields.") (license license:gpl2))) (define-public r-svmisc (package (name "r-svmisc") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "svMisc" version)) (sha256 (base32 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d")))) (properties `((upstream-name . "svMisc"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/SciViews/svMisc") (synopsis "Miscellaneous functions for SciViews") (description "This package provides miscellaneous functions for SciViews or general use, including tools to manage a temporary environment attached to the search path for temporary variables you do not want to @code{save()} or @code{load()}; test the current platform; showing progress bars, etc.") (license license:gpl2))) (define-public r-xyz (package (name "r-xyz") (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "xyz" version)) (sha256 (base32 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/xyz/") (synopsis "Algorithm for fast interaction search in high-dimensional data") (description "High dimensional interaction search by brute force requires a quadratic computational cost in the number of variables. The xyz algorithm provably finds strong interactions in almost linear time. For details of the algorithm see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast interaction search in high-dimensional data.") ;; Any version of the GPL. (license license:gpl2+))) (define-public r-rttf2pt1 (package (name "r-rttf2pt1") (version "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "Rttf2pt1" version)) (sha256 (base32 "10x580dnzddm9z045gya5ya01d10s9mpp0fy8ilrldlh74q7ljqb")))) (properties `((upstream-name . "Rttf2pt1"))) (build-system r-build-system) (home-page "https://github.com/wch/Rttf2pt1") (synopsis "Font conversion utility") (description "This package contains the program @code{ttf2pt1}, for use with the @code{extrafont} package.") ;; Most of the files are covered under the Expat license. Some files are ;; covered under BSD-3. Deviations for individual files are recorded in ;; the LICENSE file. (license (list license:bsd-3 license:expat (license:non-copyleft "file://LICENSE"))))) (define-public r-extrafontdb (package (name "r-extrafontdb") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "extrafontdb" version)) (sha256 (base32 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs")))) (build-system r-build-system) (home-page "https://github.com/wch/extrafontdb") (synopsis "Database for the extrafont package") (description "This package holds the database for the @code{extrafont} package.") (license license:gpl2))) (define-public r-extrafont (package (name "r-extrafont") (version "0.19") (source (origin (method url-fetch) (uri (cran-uri "extrafont" version)) (sha256 (base32 "13dbrlf54nbyfz3z2snz7x4m6rfnnhk2l8kkwpgcagzi5lar13sf")))) (build-system r-build-system) (propagated-inputs (list r-extrafontdb r-rttf2pt1)) (home-page "https://github.com/wch/extrafont") (synopsis "Tools for using fonts in R") (description "The extrafont package makes it easier to use fonts other than the basic PostScript fonts that R uses. Fonts that are imported into extrafont can be used with PDF or PostScript output files. There are two hurdles for using fonts in PDF (or Postscript) output files: @enumerate @item Making R aware of the font and the dimensions of the characters. @item Embedding the fonts in the PDF file so that the PDF can be displayed properly on a device that doesn't have the font. This is usually needed if you want to print the PDF file or share it with others. @end enumerate The extrafont package makes both of these things easier.") (license license:gpl2))) (define-public r-xkcd (package (name "r-xkcd") (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "xkcd" version)) (sha256 (base32 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) (build-system r-build-system) (propagated-inputs (list r-extrafont r-ggplot2 r-hmisc)) (home-page "https://cran.r-project.org/web/packages/xkcd/") (synopsis "Plot ggplot2 graphics in the XKCD style") (description "This package provides the means to plot ggplot2 graphs in the style of the XKCD web comic.") (license license:gpl3))) (define-public r-babelgene (package (name "r-babelgene") (version "22.9") (source (origin (method url-fetch) (uri (cran-uri "babelgene" version)) (sha256 (base32 "1ql5r1chl5ajzy9ppcnk755ia3m2a8n08m837dnm2ll3nzf02rnf")))) (properties `((upstream-name . "babelgene"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-rlang)) (native-inputs (list r-knitr)) (home-page "https://igordot.github.io/babelgene/") (synopsis "Gene orthologs for model organisms in a Tidy data format") (description "Genomic analysis of model organisms often requires the use of databases based on human data or making comparisons to patient-derived resources. This requires converting genes between human and non-human analogues. The babelgene R package provides predicted gene orthologs/homologs for frequently studied model organisms in an R-friendly tidy/long format. The package integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP).") (license license:expat))) (define-public r-msigdbr (package (name "r-msigdbr") (version "7.5.1") (source (origin (method url-fetch) (uri (cran-uri "msigdbr" version)) (sha256 (base32 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w")))) (build-system r-build-system) (propagated-inputs (list r-babelgene r-dplyr r-magrittr r-rlang r-tibble r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://github.com/igordot/msigdbr") (synopsis "MSigDB gene sets for multiple organisms") (description "This package provides the @dfn{Molecular Signatures Database} (MSigDB) gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA) software in a standard R data frame with key-value pairs. Included are the original human gene symbols and Entrez IDs as well as the equivalents for various frequently studied model organisms such as mouse, rat, pig, fly, and yeast.") ;; The package is covered under the Expat license, but the upstream MSigDB ;; files are made available under the Creative Commons Attribution 4.0 ;; International license. (license (list license:expat license:cc-by4.0)))) (define-public r-gridgraphics (package (name "r-gridgraphics") (version "0.5-1") (source (origin (method url-fetch) (uri (cran-uri "gridGraphics" version)) (sha256 (base32 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219")))) (properties `((upstream-name . "gridGraphics"))) (build-system r-build-system) (home-page "https://github.com/pmur002/gridgraphics") (synopsis "Redraw base graphics using @code{grid} graphics") (description "This package provides functions to convert a page of plots drawn with the @code{graphics} package into identical output drawn with the @code{grid} package. The result looks like the original @code{graphics}-based plot, but consists of @code{grid} grobs and viewports that can then be manipulated with @code{grid} functions (e.g., edit grobs and revisit viewports).") (license license:gpl2+))) (define-public r-farver (package (name "r-farver") (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "farver" version)) (sha256 (base32 "1klnr73fhm7n46q85in1v9gi99y6rcdzzg4h4wvnbx23lxndmkqd")))) (build-system r-build-system) (home-page "https://github.com/thomasp85/farver") (synopsis "Vectorized color conversion and comparison") (description "The encoding of color can be handled in many different ways, using different color spaces. As different color spaces have different uses, efficient conversion between these representations are important. This package provides a set of functions that gives access to very fast color space conversion and comparisons implemented in C++, and offers 100-fold speed improvements over the @code{convertColor} function in the @code{grDevices} package.") (license license:expat))) (define-public r-yulab-utils (package (name "r-yulab-utils") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 "0yh29d28i67z3wyif72lr35ki92rqv6rljdjwj28559f7n864yjv")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (propagated-inputs (list r-cli r-digest r-fs r-memoise r-rlang)) (home-page "https://cran.r-project.org/package=yulab.utils") (synopsis "Supporting functions for packages maintained by YuLab-SMU") (description "Miscellaneous functions commonly used by YuLab-SMU, such as @code{install_zip_gh} to install R packages from Github ZIP files.") (license license:artistic2.0))) (define-public r-ggplotify (package (name "r-ggplotify") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 "11qfk4pj0bb013m9964q2fsrj4x39c4kwh84vfyi3qhlkrsybfh1")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridgraphics r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/GuangchuangYu/ggplotify") (synopsis "Convert plots to @code{grob} or @code{ggplot} object") (description "This package provides tools to convert plot function calls (using expression or formula) to @code{grob} or @code{ggplot} objects that are compatible with the @code{grid} and @code{ggplot2} environment. With this package, we are able to e.g. use @code{cowplot} to align plots produced by @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by converting them to @code{ggplot} objects.") (license license:artistic2.0))) (define-public r-triebeard (package (name "r-triebeard") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "triebeard" version)) (sha256 (base32 "1xz0xwq9c986as6g7z2g1ycvw1ryh4g89ygldvakpr21cgpjybqr")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/Ironholds/triebeard/") (synopsis "Radix trees in Rcpp") (description "Radix trees, or tries, are key-value data structures optimized for efficient lookups, similar in purpose to hash tables. This package provides an implementation of radix trees for use in R programming and in developing packages with Rcpp.") (license license:expat))) (define-public r-tweenr (package (name "r-tweenr") (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "tweenr" version)) (sha256 (base32 "1wqzcsxlz1isb1j0v5g6dgvd40q3q9qlahvgcgiq0j4d87nzvfv4")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'build-reproducibly (lambda _ (substitute* "R/aaa.R" (("BASEDATETIME <- Sys.time.*") "BASEDATETIME <- structure(0, class = c(\"POSIXct\", \"POSIXt\"))\n"))))))) (propagated-inputs (list r-cpp11 r-farver r-magrittr r-rlang r-vctrs)) (home-page "https://github.com/thomasp85/tweenr") (synopsis "Interpolate data for smooth animations") (description "In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that can be used as basis for animation. Furthermore it adds a number of vectorized interpolaters for common R data types such as numeric, date and color.") (license license:expat))) (define-public r-polyclip (package (name "r-polyclip") (version "1.10-6") (source (origin (method url-fetch) (uri (cran-uri "polyclip" version)) (sha256 (base32 "0qwb5w1ishbhg1nhdp8985ddvcs7ljdyrbv059hx576xmgni6brw")))) (build-system r-build-system) (native-inputs (list pkg-config)) (home-page "http://www.angusj.com/delphi/clipper.php") (synopsis "Polygon clipping") (description "This package provides an R port of the library Clipper. It performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. It computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. It computes the Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.") (license license:boost1.0))) (define-public r-urlchecker (package (name "r-urlchecker") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "urlchecker" version)) (sha256 (base32 "06034lb94krbzawqg5xklwcksvyyzl3qy355f66baj5pw7dms5k2")))) (properties `((upstream-name . "urlchecker"))) (build-system r-build-system) (propagated-inputs (list r-cli r-curl r-xml2)) (home-page "https://github.com/r-lib/urlchecker") (synopsis "Run CRAN URL checks from older R versions") (description "This package provides the URL checking tools available in R 4.1+ as a package for earlier versions of R. It also uses concurrent requests so can be much faster than the serial versions.") (license license:gpl3))) (define-public r-urltools (package (name "r-urltools") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "urltools" version)) (sha256 (base32 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-triebeard)) (home-page "https://github.com/Ironholds/urltools/") (synopsis "Vectorized tools for URL handling and parsing") (description "This package provides a toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorized. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.") (license license:expat))) (define-public r-ggforce (package (name "r-ggforce") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggforce" version)) (sha256 (base32 "0wqq8l7lq96k4w0vq12jcg7clvgia8s35jjbqq1s0py4cgxijhml")))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-gtable r-lifecycle r-mass r-polyclip r-rcpp r-rcppeigen r-rlang r-scales r-systemfonts r-tidyselect r-tweenr r-vctrs r-withr)) (home-page "https://ggforce.data-imaginist.com") (synopsis "Accelerating ggplot2") (description "The aim of the ggplot2 package is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialized plots. This package aims to be a collection of mainly new statistics and geometries that fills this gap.") (license license:expat))) (define-public r-eulerr (package (name "r-eulerr") (version "7.0.0") (source (origin (method url-fetch) (uri (cran-uri "eulerr" version)) (sha256 (base32 "16a84a2xgv1iqsir0hzn6qclljni4f3prpycb7qpp06vrd0yn8lw")))) (properties `((upstream-name . "eulerr"))) (build-system r-build-system) (propagated-inputs (list r-gensa r-polyclip r-polylabelr r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/jolars/eulerr") (synopsis "Area-proportional Euler and Venn diagrams with ellipses") (description "This package generates area-proportional Euler diagrams using numerical optimization. An Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented. Diagrams may be fit with ellipses and circles via a wide range of inputs and can be visualized in numerous ways.") (license license:gpl3))) (define-public r-europepmc (package (name "r-europepmc") (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "europepmc" version)) (sha256 (base32 "160rvp4yl5myccasyzaq8qhgxwv858y1wdwyrmnrmn3va8s5b515")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-httr r-jsonlite r-plyr r-progress r-purrr r-rlang r-tibble r-tidyr r-urltools r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/europepmc/") (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") (description "This package provides an R Client for the @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web Service}. It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible.") (license license:gpl3))) (define-public r-ggraph (package (name "r-ggraph") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggraph" version)) (sha256 (base32 "07sw4h94dzbs44dcvvj80g8v8252k4iw8pkmzdrk4qagvhidnvv8")))) (build-system r-build-system) (propagated-inputs (list r-cli r-digest r-dplyr r-ggforce r-ggplot2 r-ggrepel r-graphlayouts r-gtable r-igraph r-lifecycle r-mass r-rcpp r-rlang r-scales r-tidygraph r-vctrs r-viridis r-withr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ggraph/") (synopsis "Implementation of grammar of graphics for graphs and networks") (description "The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. The ggraph package is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.") (license license:gpl3))) (define-public r-gkmsvm (package (name "r-gkmsvm") (version "0.83.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 "1bg9jw4ra76j132lkr0p5m2xlr952fdij1hn6f1v7g687l55m0k5")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs (list r-kernlab r-rcpp r-rocr r-seqinr)) (home-page "https://cran.r-project.org/web/packages/gkmSVM") (synopsis "Gapped-kmer support vector machine") (description "This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (license license:gpl2+))) (define-public r-varselrf (package (name "r-varselrf") (version "0.7-8") (source (origin (method url-fetch) (uri (cran-uri "varSelRF" version)) (sha256 (base32 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i")))) (properties `((upstream-name . "varSelRF"))) (build-system r-build-system) (propagated-inputs (list r-randomforest)) (home-page "https://www.ligarto.org/rdiaz/software/software") (synopsis "Variable selection using random forests") (description "This package provides tools for the variable selection from random forests using both backwards variable elimination (for the selection of small sets of non-redundant variables) and selection based on the importance spectrum (somewhat similar to scree plots; for the selection of large, potentially highly-correlated variables). The main applications are in high-dimensional data (e.g., microarray data, and other genomics and proteomics applications).") (license license:gpl2+))) (define-public r-pamr (package (name "r-pamr") (version "1.56.1") (source (origin (method url-fetch) (uri (cran-uri "pamr" version)) (sha256 (base32 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-survival)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pamr/") (synopsis "Prediction Analysis for Microarrays") (description "This package provides some functions for sample classification in microarrays.") (license license:gpl2))) (define-public r-rda (package (name "r-rda") (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "rda" version)) (sha256 (base32 "16mf76hlhii30f2m5xlwa4gv4a5ydnla2kz6ylcka4y9668ql0rp")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rda/") (synopsis "Shrunken centroids regularized discriminant analysis") (description "This package provides tools for shrunken centroids regularized discriminant analysis for the purpose of classifying high dimensional data.") (license license:gpl2+))) (define-public r-ggvis (package (name "r-ggvis") (version "0.4.8") (source (origin (method url-fetch) (uri (cran-uri "ggvis" version)) (sha256 (base32 "0sm28s2zlr3rbp7qzpgin7d9axixn4kgi1apb5mw4mvsp6h80m1x")) (snippet '(for-each delete-file '("inst/www/lib/d3/d3.min.js" "inst/www/lib/jquery-ui/jquery-ui.min.js" "inst/www/lib/jquery/jquery.min.js" "inst/www/lib/lodash/lodash.min.js" "inst/www/lib/vega/vega.min.js"))))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/lib" (call-with-values (lambda () (unzip2 `(("d3/d3.js" "d3/d3.min.js") ("jquery-ui/jquery-ui.js" "jquery-ui/jquery-ui.min.js") ("jquery/jquery.js" "jquery/jquery.min.js") (,(search-input-file inputs "/dist/lodash.js") "lodash/lodash.min.js") ("vega/vega.js" "vega/vega.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-assertthat r-dplyr r-htmltools r-jsonlite r-magrittr r-rlang r-shiny)) (native-inputs `(("esbuild" ,esbuild) ;; Version according to commit ;; https://github.com/rstudio/ggvis/commit/0a197c25b5a1d94724f1868270d5163b27ad2e76 ("js-lodash" ,(let ((version "4.17.21")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/lodash/lodash") (commit version))) (file-name (git-file-name "lodash.js" version)) (sha256 (base32 "0gd1rhp85z0xybii19fkkqkbshcklwrrcvj335z17q2cnbb57v44"))))))) (home-page "https://ggvis.rstudio.com/") (synopsis "Interactive grammar of graphics") (description "This package is a data visualization package for R providing an implementation of an interactive grammar of graphics, taking the best parts of ggplot2, combining them with the reactive framework of Shiny and drawing web graphics using Vega.") (license license:gpl2))) (define-public r-gbm (package (name "r-gbm") (version "2.1.9") (source (origin (method url-fetch) (uri (cran-uri "gbm" version)) (sha256 (base32 "1r5d8mkg4z14l3743h39r35r0qqjx5p40ixdkcc5iyjab0fzm24x")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-survival)) (native-inputs (list r-knitr)) (home-page "https://github.com/gbm-developers/gbm") (synopsis "Generalized boosted regression models") (description "This package is an implementation of extensions to Freund and Schapire's AdaBoost algorithm and Friedman's gradient boosting machine. It includes regression methods for least squares, absolute loss, t-distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures (LambdaMart).") (license license:gpl2+))) (define-public r-threejs (package (name "r-threejs") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "threejs" version)) (sha256 (base32 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn")))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-jquery") "htmlwidgets/lib/jquery/jquery.min.js") (,(assoc-ref inputs "js-threejs-111") "htmlwidgets/lib/threejs-111/three.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs (list r-base64enc r-crosstalk r-htmlwidgets r-igraph)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.12.4.js") (sha256 (base32 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))) ("js-threejs-111" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js") (sha256 (base32 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky")))))) (home-page "https://bwlewis.github.io/rthreejs") (synopsis "Interactive 3D scatter plots, networks and globes") (description "Create interactive 3D scatter plots, network plots, and globes in R using the three.js visualization library.") (license license:expat))) (define-public r-mlbench (package (name "r-mlbench") (version "2.1-3.1") (source (origin (method url-fetch) (uri (cran-uri "mlbench" version)) (sha256 (base32 "1w2w7nkrp69c0di0lss82jf4fbxdpqwxzqa2lrp55av8i7awdzks")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mlbench/") (synopsis "Machine learning benchmark problems") (description "This package provides a collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.") (license license:gpl2))) (define-public r-mpm (package (name "r-mpm") (version "1.0-23") (source (origin (method url-fetch) (uri (cran-uri "mpm" version)) (sha256 (base32 "1jpv2ddmw7aarqbbyfys1yb840arw33319wnny3v2hk84hldmayj")))) (build-system r-build-system) (propagated-inputs (list r-kernsmooth r-mass)) (home-page "https://mpm.r-forge.r-project.org") (synopsis "Multivariate projection methods") (description "This is a package for exploratory graphical analysis of multivariate data, specifically gene expression data with different projection methods: principal component analysis, correspondence analysis, spectral map analysis.") (license license:gpl2+))) (define-public r-png (package (name "r-png") (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "png" version)) (sha256 (base32 "077nca3x0l6mq2g6izknzcn994bqs3nfqk7wscrjbfk2dnxzldjs")))) (build-system r-build-system) (inputs (list libpng zlib)) (home-page "https://www.rforge.net/png/") (synopsis "Read and write PNG images") (description "This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.") ;; Any of these GPL versions. (license (list license:gpl2 license:gpl3)))) (define-public r-ggcorrplot (package (name "r-ggcorrplot") (version "0.1.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggcorrplot" version)) (sha256 (base32 "0yd865lfs4144jqh9ilznqa69rj0183ashnhvmjmis87zw69a45q")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) (home-page "http://www.sthda.com/english/wiki/ggcorrplot") (synopsis "Visualization of a correlation matrix using ggplot2") (description "The ggcorrplot package can be used to visualize easily a correlation matrix using ggplot2. It provides a solution for reordering the correlation matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.") (license license:gpl2))) (define-public r-ggfun (package (name "r-ggfun") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "ggfun" version)) (sha256 (base32 "1jk94qridy587dnw3j97k73wa02vs3vcfrjgrri35kvv7fkjw8w9")))) (properties `((upstream-name . "ggfun"))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-rlang)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ggfun") (synopsis "Miscellaneous functions for ggplot2") (description "This package provides useful functions to edit ggplot object (e.g., setting fonts for theme and layers, adding rounded rectangle as background for each of the legends).") (license license:artistic2.0))) (define-public r-gridtext (package (name "r-gridtext") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "gridtext" version)) (sha256 (base32 "0f7i2qb8fawi8agy2iz2c173kfwj7cbb5ikjix64nmzqc5j7363d")))) (properties `((upstream-name . "gridtext"))) (build-system r-build-system) (propagated-inputs (list r-curl r-jpeg r-markdown r-png r-rcpp r-rlang r-stringr r-xml2)) (home-page "https://wilkelab.org/gridtext/") (synopsis "Improved text rendering support for Grid graphics") (description "This package provides support for rendering of formatted text using Grid graphics. Text can be formatted via a minimal subset of Markdown, HTML, and inline CSS directives, and it can be rendered both with and without word wrap.") (license license:expat))) (define-public r-ggghost (package (name "r-ggghost") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "ggghost" version)) (sha256 (base32 "0kvsjadxxdf6yvzk4a6yqkg02q1ysslvf3m0a369bdim396z4hnv")))) (properties `((upstream-name . "ggghost"))) (build-system r-build-system) (propagated-inputs (list r-animation r-ggplot2)) (home-page "https://github.com/jonocarroll/ggghost") (synopsis "Capture the spirit of your ggplot2 calls") (description "This package lets you create a reproducible @code{ggplot2} object by storing the data and calls.") (license license:gpl3+))) (define-public r-ggtext (package (name "r-ggtext") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "ggtext" version)) (sha256 (base32 "10vrrxviv4yp9lqsanqvwsvbj64vn66hwm1w7860x1g58hf1g0l7")))) (properties `((upstream-name . "ggtext"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridtext r-rlang r-scales)) (native-inputs (list r-knitr)) (home-page "https://wilkelab.org/ggtext/") (synopsis "Improved text rendering support for ggplot2") (description "This package provides a ggplot2 extension that enables the rendering of complex formatted plot labels (titles, subtitles, facet labels, axis labels, etc.). Text boxes with automatic word wrap are also supported.") (license license:gpl2))) (define-public r-ggthemeassist (package (name "r-ggthemeassist") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "ggThemeAssist" version)) (sha256 (base32 "1biw91a8p13h62v4w3yim6ghr98khmyhb3qd0h04asf91vvmpxbv")))) (properties `((upstream-name . "ggThemeAssist"))) (build-system r-build-system) (propagated-inputs (list r-formatr r-ggplot2 r-miniui r-rstudioapi r-shiny)) (home-page "https://github.com/calligross/ggthemeassist") (synopsis "Add-in to customize ggplot2 themes") (description "This package provides an Rstudio add-in that delivers a graphical interface for editing @code{ggplot2} theme elements.") (license license:gpl3))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-flexdashboard (package (name "r-flexdashboard") (version "0.6.2") (source (origin (method url-fetch) (uri (cran-uri "flexdashboard" version)) (sha256 (base32 "0zxyrfp1inv19palaba81pxlq0nz655hcliynvh995a58cvg6c5n")) ;; Delete bundled minified JavaScript files (snippet '(for-each delete-file '("inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js" "inst/www/featherlight/featherlight.min.js" "inst/www/prism/prism.js" "inst/www/sly/sly.min.js" "inst/www/stickytableheaders/jquery.stickytableheaders.min.js"))))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (srfi srfi-26) (ice-9 textual-ports)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" ;; Concatenate all components of prism.js (let ((contents (string-join (map (lambda (name) (call-with-input-file (assoc-ref inputs name) get-string-all)) (list "js-prism" "js-prism-r" "js-prism-line-numbers")) "\n"))) (call-with-output-file "prism-src.js" (cut display contents <>))) (call-with-values (lambda () (unzip2 `(("www/stickytableheaders/jquery.stickytableheaders.js" "www/stickytableheaders/jquery.stickytableheaders.min.js") ("www/sly/sly.js" "www/sly/sly.min.js") ("prism-src.js" "www/prism/prism.js") (,(assoc-ref inputs "js-raphael") "htmlwidgets/lib/raphael/raphael-2.1.4.min.js") (,(assoc-ref inputs "js-featherlight") "www/featherlight/featherlight.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-bslib r-htmltools r-htmlwidgets r-jsonlite r-knitr r-rmarkdown r-sass r-scales r-shiny)) (native-inputs `(("esbuild" ,esbuild) ("js-raphael" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js") (sha256 (base32 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x")))) ;; It actually wants version 1.4.1 according to R/dependencies.R. ("js-prism" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js") (sha256 (base32 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c")))) ("js-prism-r" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js") (sha256 (base32 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki")))) ("js-prism-line-numbers" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js") (sha256 (base32 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991")))) ;; See R/dependencies.R ("js-featherlight" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.5/src/featherlight.js") (sha256 (base32 "0pbxgcipzbyivzlf3hal0lpajjj33p86fggm704c1b5bcq7ljl80")))))) (home-page "https://rmarkdown.rstudio.com/flexdashboard") (synopsis "R Markdown format for flexible dashboards") (description "This package provides an R Markdown format for converting an R Markdown document to a grid-oriented dashboard. The dashboard flexibly adapts the size of its components to the containing web page.") (license license:expat))) (define-public r-preseqr (package (name "r-preseqr") (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "preseqR" version)) (sha256 (base32 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1")))) (properties `((upstream-name . "preseqR"))) (build-system r-build-system) (propagated-inputs (list r-polynom)) (home-page "https://cran.r-project.org/web/packages/preseqR/") (synopsis "Predicting species accumulation curves") (description "This package can be used to predict the r-species accumulation curve (r-SAC), which is the number of species represented at least r times as a function of the sampling effort. When r = 1, the curve is known as the species accumulation curve, or the library complexity curve in high-throughput genomic sequencing. The package includes both parametric and nonparametric methods, as described by Deng C, et al. (2018).") (license license:gpl3))) (define-public r-mapplots (package (name "r-mapplots") (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "mapplots" version)) (sha256 (base32 "064a3jc7p4wh5x8rxmjap6kqkg19zfkq8ac820d9sm35d0fia3pd")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mapplots/") (synopsis "Data visualization on maps") (description "This package helps you create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying fisheries data but most functions can be used for more generic data visualisation.") (license license:gpl2+))) (define-public r-pmcmr (package (name "r-pmcmr") (version "4.4") (source (origin (method url-fetch) (uri (cran-uri "PMCMR" version)) (sha256 (base32 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77")))) (properties `((upstream-name . "PMCMR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PMCMR/") (synopsis "Calculate pairwise multiple comparisons of mean rank sums") (description "This is a deprecated package for calculating pairwise multiple comparisons of mean rank sums. This package is superseded by the novel PMCMRplus package. The PMCMR package is no longer maintained, but kept for compatibility of dependent packages for some time.") (license license:gpl3+))) (define-public r-downloader (package (name "r-downloader") (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "downloader" version)) (sha256 (base32 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q")))) (build-system r-build-system) (propagated-inputs (list r-digest)) (home-page "https://github.com/wch/downloader") (synopsis "Download files over HTTP and HTTPS") (description "This package provides a wrapper for the @code{download.file} function, making it possible to download files over HTTPS across platforms. The @code{RCurl} package provides this functionality (and much more) but has external dependencies. This package has is implemented purely in R.") (license license:gpl2))) (define-public r-aplot (package (name "r-aplot") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "aplot" version)) (sha256 (base32 "094bzrcjybs2dk2plmxf80mbx9dz1hi5m7gp8bbs5qqh03xn7wf7")))) (properties `((upstream-name . "aplot"))) (build-system r-build-system) (propagated-inputs (list r-ggfun r-ggplot2 r-ggplotify r-magrittr r-patchwork)) (home-page "https://github.com/YuLab-SMU/aplot") (synopsis "Decorate a ggplot with associated information") (description "Users may want to align plots with associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. This package provides utilities to align associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.") (license license:artistic2.0))) (define-public r-ggnewscale (package (name "r-ggnewscale") (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "ggnewscale" version)) (sha256 (base32 "1vy0i2gk57k06gzywy8hdhl2k9511c5mhy9dzvkzlagqihp5b8bh")))) (properties `((upstream-name . "ggnewscale"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (home-page "https://cran.r-project.org/package=ggnewscale") (synopsis "Multiple fill and color scales in ggplot2") (description "This package lets you use multiple fill and color scales in ggplot2.") (license license:gpl3))) (define-public r-ggpointdensity (package (name "r-ggpointdensity") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggpointdensity" version)) (sha256 (base32 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy")))) (properties `((upstream-name . "ggpointdensity"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (home-page "https://github.com/LKremer/ggpointdensity") (synopsis "Cross between a 2D density plot and a scatter plot") (description "This package provides a cross between a 2D density plot and a scatter plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are colored by the number of neighboring points. This is useful to visualize the 2D-distribution of points in case of overplotting.") (license license:gpl3))) (define-public r-arrow (package (name "r-arrow") (version "14.0.0.2") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 "1dwap9lap0hac0bhi8ajz06n9ccjdyfr5s153k1lxfgicqnsaf3i")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs (list `(,apache-arrow "lib") zlib)) (propagated-inputs (list r-assertthat r-bit64 r-cpp11 r-glue r-purrr r-r6 r-rlang r-tidyselect r-vctrs)) (native-inputs (list pkg-config)) (home-page "https://github.com/apache/arrow/") (synopsis "R integration to Apache Arrow") (description "Apache Arrow is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an R interface to the Arrow C++ library.") (license license:asl2.0))) (define-public r-rex (package (name "r-rex") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "rex" version)) (sha256 (base32 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg")))) (build-system r-build-system) (propagated-inputs (list r-lazyeval)) (native-inputs (list r-knitr)) (home-page "https://github.com/kevinushey/rex") (synopsis "Friendly regular expressions") (description "This package provides a friendly interface for the construction of regular expressions. Regular expressions are a very powerful feature, however they are often difficult to interpret. Rex allows you to build complex regular expressions from human readable expressions") (license license:expat))) (define-public r-mlapi (package (name "r-mlapi") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "mlapi" version)) (sha256 (base32 "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr")))) (properties `((upstream-name . "mlapi"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-r6)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=mlapi") (synopsis "Abstract classes for building scikit-learn like API") (description "This package provides R6 abstract classes for building machine learning models with a scikit-learn like API. Scikit-learn is a popular module for the Python programming language whose design became a de facto standard in industry for machine learning tasks.") (license license:expat))) (define-public r-float (package (name "r-float") (version "0.3-2") (source (origin (method url-fetch) (uri (cran-uri "float" version)) (sha256 (base32 "149affr0swb1vqnhkzm5lr4knfsh78ygswy123j1qj823zbhsfi3")))) (properties `((upstream-name . "float"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://github.com/wrathematics/float") (synopsis "32-bit floats") (description "R comes with a suite of utilities for linear algebra with \"numeric\" (double precision) vectors/matrices. However, sometimes single precision (or less!) is more than enough for a particular task. This package extends R's linear algebra facilities to include 32-bit float (single precision) data. Float vectors/matrices have half the precision of their \"numeric\"-type counterparts but are generally faster to numerically operate on, for a performance vs accuracy trade-off.") (license license:bsd-2))) (define-public r-rsparse (package (name "r-rsparse") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "rsparse" version)) (sha256 (base32 "15kdllm2lh6xdlv4j0ljyj5pczhx26s9d8cac7953zbb0sd45chz")))) (properties `((upstream-name . "rsparse"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-float r-lgr r-matrix r-matrixextra r-rcpp r-rcpparmadillo r-rhpcblasctl)) (home-page "https://github.com/rexyai/rsparse") (synopsis "Statistical learning on sparse matrices") (description "This package implements many algorithms for statistical learning on sparse matrices: matrix factorizations, matrix completion, elastic net regressions, factorization machines. The rsparse package also enhances the Matrix package by providing methods for multithreaded matrix products and native slicing of the sparse matrices in @dfn{Compressed Sparse Row} (CSR) format.") (license license:gpl2+))) (define-public r-text2vec (package (name "r-text2vec") (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "text2vec" version)) (sha256 (base32 "0sjlvp4zhzwc0ai7626fpw3ws8xv0xhl8gv8mrk24lrpk5nhin2h")))) (properties `((upstream-name . "text2vec"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-digest r-lgr r-matrix r-mlapi r-r6 r-rcpp r-rsparse r-stringi)) (native-inputs (list r-knitr)) (home-page "https://text2vec.org") (synopsis "Text mining framework for R") (description "This package provides fast and memory-friendly tools for text vectorization, topic modeling (LDA, LSA), word embeddings (GloVe), similarities. It provides a source-agnostic streaming API, which allows researchers to perform analysis of collections of documents which are larger than available RAM. All core functions are parallelized to benefit from multicore machines.") (license license:gpl2+))) (define-public r-mcmcpack (package (name "r-mcmcpack") (version "1.6-3") (source (origin (method url-fetch) (uri (cran-uri "MCMCpack" version)) (sha256 (base32 "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b")))) (properties `((upstream-name . "MCMCpack"))) (build-system r-build-system) (propagated-inputs (list r-coda r-lattice r-mass r-mcmc r-quantreg)) (home-page "https://cran.r-project.org/package=MCMCpack") (synopsis "Markov Chain Monte Carlo (MCMC) package") (description "This package contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library. All models return @code{coda} @code{mcmc} objects that can then be summarized using the @code{coda} package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.") (license license:gpl3))) (define-public r-xmlparsedata (package (name "r-xmlparsedata") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "xmlparsedata" version)) (sha256 (base32 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n")))) (properties `((upstream-name . "xmlparsedata"))) (build-system r-build-system) (home-page "https://github.com/r-lib/xmlparsedata#readme") (synopsis "Parse data of @code{R} code as an @code{XML} tree") (description "This package provides tools to convert the output of @code{utils::getParseData()} to an @code{XML} tree, that one can search via @code{XPath}, and is easier to manipulate in general.") (license license:expat))) (define-public r-cyclocomp (package (name "r-cyclocomp") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "cyclocomp" version)) (sha256 (base32 "0kdinnn6cgkfc94japyyp5qr7imjxddajds3qqxf4q5higahdzws")))) (properties `((upstream-name . "cyclocomp"))) (build-system r-build-system) (propagated-inputs (list r-callr r-crayon r-desc r-remotes r-withr)) (home-page "https://github.com/MangoTheCat/cyclocomp") (synopsis "Cyclomatic complexity of R code") (description "Cyclomatic complexity is a software metric, used to indicate the complexity of a program. It is a quantitative measure of the number of linearly independent paths through a program's source code. This package provides tools to compute this metric.") (license license:expat))) (define-public r-lintr (package (name "r-lintr") (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "lintr" version)) (sha256 (base32 "07c7h30nh1529wba8xkyg2sapj6r7jjckrxyzhrg2ssfwzs4dwdw")))) (properties `((upstream-name . "lintr"))) (build-system r-build-system) (propagated-inputs (list r-backports r-codetools r-cyclocomp r-digest r-glue r-knitr r-rex r-xml2 r-xmlparsedata)) (native-inputs (list r-knitr)) (home-page "https://github.com/jimhester/lintr") (synopsis "Linter for R code") (description "This package checks adherence to a given style, syntax errors and possible semantic issues. It supports on the fly checking of R code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (license license:expat))) (define-public r-sccore (package (name "r-sccore") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "sccore" version)) (sha256 (base32 "11l7xl1ylzmda4i2p1b08a43pvciin2i2sas2n3cj1gmamflkji3")))) (properties `((upstream-name . "sccore"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-ggrepel r-igraph r-irlba r-magrittr r-matrix r-pbmcapply r-proc r-rcpp r-rcpparmadillo r-rcppeigen r-rcppprogress r-rlang r-scales r-tibble r-uwot r-withr)) (home-page "https://github.com/kharchenkolab/sccore") (synopsis "Core utilities for single-cell RNA-Seq") (description "This package implements core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with @acronym{DE, differential expression} matrices and count matrices, a collection of functions for manipulating and plotting data via ggplot2, and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP, collapsing vertices of each cluster in the graph, and propagating graph labels.") (license license:gpl3))) (define-public r-scs (package (name "r-scs") (version "3.2.4") (source (origin (method url-fetch) (uri (cran-uri "scs" version)) (sha256 (base32 "13r944b9ip078hqwdpzn3jv21zm47d9l2b1f5y6glcj5pxs9iwy3")))) (properties `((upstream-name . "scs"))) (build-system r-build-system) (home-page "https://github.com/FlorianSchwendinger/scs") (synopsis "Splitting conic solver") (description "This package solves convex cone programs via operator splitting. It can solve: linear programs, second-order cone programs, semidefinite programs, exponential cone programs, and power cone programs, or problems with any combination of those cones. SCS uses AMD (a set of routines for permuting sparse matrices prior to factorization) and LDL (a sparse LDL factorization and solve package) from SuiteSparse.") (license license:gpl3))) (define-public r-sctransform (package (name "r-sctransform") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 "0wgimf7qqgnnmyspn2rpb4a8hl570fv0fwh0r0r4qgjlpvwffssz")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-future r-future-apply r-ggplot2 r-gridextra r-magrittr r-mass r-matrix r-matrixstats r-rcpp r-rcpparmadillo r-reshape2 r-rlang)) (home-page "https://github.com/ChristophH/sctransform") (synopsis "Variance stabilizing transformations for Single Cell UMI Data") (description "This package provides a normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction.") (license license:gpl3))) (define-public r-styler (package (name "r-styler") (version "1.10.2") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 "043v9xwm72jqrrzzmjgrkf34lncjnn69650ks72z7rjb1wqmbh56")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-cli r-magrittr r-purrr r-r-cache r-rlang r-rprojroot r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/styler") (synopsis "Non-invasive pretty printing of R code") (description "This is a package for pretty-printing R code without changing the user's formatting intent.") (license license:gpl3))) (define-public r-scrime (package (name "r-scrime") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "scrime" version)) (sha256 (base32 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/scrime/") (synopsis "Analysis of high-dimensional categorical data such as SNP data") (description "This package provides tools for the analysis of high-dimensional data developed/implemented at the group \"Statistical Complexity Reduction In Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of the functions can also be applied to other types of categorical data.") (license license:gpl2))) (define-public r-pbmcapply (package (name "r-pbmcapply") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "pbmcapply" version)) (sha256 (base32 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z")))) (build-system r-build-system) (home-page "https://github.com/kvnkuang/pbmcapply") (synopsis "Track the progress of apply procedures with a progress bar") (description "This light-weight package helps you track and visualize the progress of parallel versions of vectorized R functions of the @code{mc*apply} family.") (license license:expat))) (define-public r-blme (package (name "r-blme") (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "blme" version)) (sha256 (base32 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7")))) (build-system r-build-system) (propagated-inputs (list r-lme4)) (home-page "https://github.com/vdorie/blme") (synopsis "Bayesian linear mixed-effects models") (description "This package provides tools for maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting. It extends the lme4 package.") (license license:gpl2+))) (define-public r-batchtools (package (name "r-batchtools") (version "0.9.17") (source (origin (method url-fetch) (uri (cran-uri "batchtools" version)) (sha256 (base32 "1rlvfk0279saf930z48g230p9z30dd7qil9aiprjn35px1advqdn")))) (build-system r-build-system) (propagated-inputs (list r-backports r-base64url r-brew r-checkmate r-data-table r-digest r-fs r-progress r-r6 r-rappdirs r-stringi r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mllg/batchtools") (synopsis "Tools for computation on batch systems") (description "As a successor of the packages BatchJobs and BatchExperiments, this package provides a parallel implementation of the Map function for high performance computing systems managed by various schedulers. A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.") (license license:lgpl3))) (define-public r-clue (package (name "r-clue") (version "0.3-65") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 "1y1ycb5yw034ccxz15x41ah699hgjffsfvbn15fwdcdjbz9zvy5x")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") (synopsis "Tools for analyzing cluster ensembles") (description "Cluster ensembles are collections of individual solutions to a given clustering problem which are useful or necessary to consider in a wide range of applications. This R package provides an extensible computational environment for creating and analyzing cluster ensembles, with basic data structures for representing partitions and hierarchies, and facilities for computing on them, including methods for measuring proximity and obtaining consensus and secondary clusterings.") (license license:gpl2))) (define-public r-sitmo (package (name "r-sitmo") (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "sitmo" version)) (sha256 (base32 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/coatless/sitmo/") (synopsis "Parallel pseudo random number generator header files") (description "This package provides two high quality and fast PPRNGs that may be used in an OpenMP parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence.") (license license:expat))) (define-public r-dqrng (package (name "r-dqrng") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "dqrng" version)) (sha256 (base32 "171y7487flla0vqxmzvf9nls7vn046vplcgzvyiva3d418hwl0nd")))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp r-sitmo)) (native-inputs (list r-knitr)) (home-page "https://www.daqana.org/dqrng") (synopsis "Fast pseudo random number generators") (description "Several fast random number generators are provided as C++ header-only libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+. Additionally, fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a ;; whole is distributed under the terms of the AGPL 3. (license license:agpl3))) (define-public r-ingredients (package (name "r-ingredients") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 "0jvxkdhbc28a096hi0y6519cj4im4mnl1vz9s563dvb5g4vb7r7b")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-scales)) (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/ingredients/") (synopsis "Effects and importances of model ingredients") (description "This is a collection of tools for assessment of feature importance and feature effects. Key functions are: @itemize @item @code{feature_importance()} for assessment of global level feature importance, @item @code{ceteris_paribus()} for calculation of the what-if plots, @item @code{partial_dependence()} for partial dependence plots, @item @code{conditional_dependence()} for conditional dependence plots, @item @code{accumulated_dependence()} for accumulated local effects plots, @item @code{aggregate_profiles()} and @code{cluster_profiles()} for aggregation of ceteris paribus profiles, @item generic @code{print()} and @code{plot()} for better usability of selected explainers, @item generic @code{plotD3()} for interactive, D3 based explanations, and @item generic @code{describe()} for explanations in natural language. @end itemize\n") (license license:gpl3))) (define-public r-ibreakdown (package (name "r-ibreakdown") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "iBreakDown" version)) (sha256 (base32 "1qacvfzknchfm27mhl7a357fnb6lzjkj4vh8lch5aljz82sdmdaf")))) (properties `((upstream-name . "iBreakDown"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/iBreakDown/") (synopsis "Model agnostic instance level variable attributions") (description "This package provides a model agnostic tool for decomposition of predictions from black boxes. It supports additive attributions and attributions with interactions. The Break Down Table shows contributions of every variable to a final prediction. The Break Down Plot presents variable contributions in a concise graphical way. This package works for classification and regression models.") (license license:gpl3))) (define-public r-dae (package (name "r-dae") (version "3.2.19") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 "18cvxj2qjfqdp7gxpl93185f9c7q0fcxnc63h9car1y9dgwqsild")))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME ;; Needed for vignette builder (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-ggplot2 r-ggpubr r-plyr)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "http://chris.brien.name") (synopsis "Functions useful in the design and ANOVA of experiments") (description "This package provides functions useful in the design and ANOVA of experiments. The content falls into the following groupings: @enumerate @item data, @item factor manipulation functions, @item design functions, @item ANOVA functions, @item matrix functions, @item projector and canonical efficiency functions, and @item miscellaneous functions. @end enumerate There is a vignette called @code{DesignNotes} describing how to use the design functions for randomizing and assessing designs. The ANOVA functions facilitate the extraction of information when the @code{Error} function has been used in the call to @code{aov}.") (license license:gpl2))) (define-public r-dalex (package (name "r-dalex") (version "2.4.3") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 "08cd5nhgd6vaazcqq985kwivg99v6ily4idhgkpz8l9ffl3lavm0")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ibreakdown r-ingredients)) (home-page "https://pbiecek.github.io/DALEX/") (synopsis "Descriptive machine learning explanations") (description "Machine Learning models are widely used and have various applications in classification or regression. Models created with boosting, bagging, stacking or similar techniques are often used due to their high performance, but such black-box models usually lack interpretability. The DALEX package contains various explainers that help to understand the link between input variables and model output.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-enrichr (package (name "r-enrichr") (version "3.2") (source (origin (method url-fetch) (uri (cran-uri "enrichR" version)) (sha256 (base32 "1g97q6vqwvb2l02y61343sblarqi433gjl3qmlyxjxq2lnjrnak1")))) (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs (list r-curl r-ggplot2 r-httr r-rjson r-writexls)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/enrichR/") (synopsis "R Interface to Enrichr database for analyzing gene sets") (description "This package provides an R interface to all Enrichr databases, a web-based tool for analyzing gene sets and returns any enrichment of common annotated biological functions.") (license license:gpl2+))) (define-public r-plot3d (package (name "r-plot3d") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs (list r-misc3d)) (home-page "https://cran.r-project.org/web/packages/plot3D") (synopsis "Plot multi-dimensional data") (description "This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.") (license license:gpl3+))) (define-public r-plotroc (package (name "r-plotroc") (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "plotROC" version)) (sha256 (base32 "15jvn1dlx8qh5ghnkhqyc49frw6rp58ikpjs3ga8mjxrqyz7wb1g")) (snippet '(delete-file "inst/d3.v3.min.js")))) (properties `((upstream-name . "plotROC"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (let ((source (assoc-ref inputs "d3.v3.js")) (target "inst/d3.v3.min.js")) (invoke "esbuild" source "--minify" (string-append "--outfile=" target)))))))) (propagated-inputs (list r-ggplot2 r-gridsvg r-plyr r-rlang r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ("d3.v3.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v3.js") (sha256 (base32 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))))) (home-page "https://sachsmc.github.io/plotROC/") (synopsis "Generating useful receiver operating characteristic curve charts") (description "This package generates @acronym{ROC, receiver operating characteristic} plots. Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.") (license license:expat))) (define-public r-ggfortify (package (name "r-ggfortify") (version "0.4.16") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 "05h3a4ycain0y621anjpjphsjlhpayb2nnd6n70rlymrbilfw6xv")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-gridextra r-scales r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/sinhrks/ggfortify") (synopsis "Data visualization tools for statistical analysis results") (description "This package provides unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using the @code{ggplot2} package.") (license license:gpl2))) (define-public r-refmanager (package (name "r-refmanager") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "RefManageR" version)) (sha256 (base32 "1kjd66gp2z9fzrnyr1bqfd9p58q0bin3a187z9b56hiqmdjhyc78")))) (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs (list r-bibtex r-httr r-jsonlite r-lubridate r-plyr r-stringr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/RefManageR/") (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") (description "This package provides tools for importing and working with bibliographic references. It greatly enhances the @code{bibentry} class by providing a class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports UTF-8 encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read into R and converted to @code{BibEntry} objects.") ;; Any of these licenses may be picked. (license (list license:gpl2 license:gpl3 license:bsd-3)))) (define-public r-citr (package (name "r-citr") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "citr" version)) (sha256 (base32 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-curl r-httr r-miniui r-refmanager r-rstudioapi r-shiny r-shinyjs r-yaml)) (home-page "https://github.com/crsh/citr") (synopsis "RStudio add-in to insert Markdown citations") (description "This package provides functions and an RStudio add-in that search a BibTeX or BibLaTeX file to create and insert formatted Markdown citations into the current document.") (license license:expat))) (define-public r-xgboost (package (name "r-xgboost") (version "1.7.6.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 "0q1x7ldvjankaf0gqcqiyiy514c5jascggfq6qrfyn3sravdcggj")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/dmlc/xgboost") (synopsis "Extreme gradient boosting") (description "This package provides an R interface to Extreme Gradient Boosting, which is an efficient implementation of the gradient boosting framework from Chen and Guestrin (2016). The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.") (license license:asl2.0))) (define-public r-umap (package (name "r-umap") (version "0.2.10.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 "1abfddi0rq75b7nlx6550fx9nrqa62vb92xyp05ris25jf98ciwd")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra)) (native-inputs (list r-knitr)) (home-page "https://github.com/tkonopka/umap") (synopsis "Uniform manifold approximation and projection") (description "Uniform manifold approximation and projection is a technique for dimension reduction. This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R.") (license license:expat))) (define-public r-uwot (package (name "r-uwot") (version "0.1.16") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 "0j4f7vnb3mwf6p4nhg2limy7i32qrcj2gxbs8wsq9c6xxpcs0qsz")))) (build-system r-build-system) (propagated-inputs (list r-dqrng r-fnn r-irlba r-matrix r-rcpp r-rcppannoy r-rcppprogress)) (home-page "https://github.com/jlmelville/uwot") (synopsis "Uniform manifold approximation and projection") (description "This package provides an implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018). It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) is also provided.") (license license:gpl3))) (define-public r-kableextra (package (name "r-kableextra") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "kableExtra" version)) (sha256 (base32 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9")))) (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs (list r-digest r-glue r-htmltools r-knitr r-magrittr r-rmarkdown r-rstudioapi r-rvest r-scales r-stringr r-svglite r-viridislite r-webshot r-xml2)) (native-inputs (list r-knitr)) (home-page "https://haozhu233.github.io/kableExtra/") (synopsis "Construct complex tables with pipe syntax") (description "Build complex HTML or LaTeX tables using @code{kable()} from @code{knitr} and the piping syntax from @code{magrittr}. The function @code{kable()} is a light weight table generator coming from @code{knitr}. This package simplifies the way to manipulate the HTML or LaTeX codes generated by @code{kable()} and allows users to construct complex tables and customize styles using a readable syntax.") (license license:expat))) (define-public r-glasso (package (name "r-glasso") (version "1.11") (source (origin (method url-fetch) (uri (cran-uri "glasso" version)) (sha256 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/glasso/") (synopsis "Graphical Lasso: estimation of Gaussian graphical models") (description "This is a package for estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.") (license license:gpl2))) (define-public r-gldex (package (name "r-gldex") (version "2.0.0.9.3") (source (origin (method url-fetch) (uri (cran-uri "GLDEX" version)) (sha256 (base32 "0xv9w4kmivmmcnn19a6s6d1ilhi1misdgrp07ks7rbd177zjy5vs")))) (properties `((upstream-name . "GLDEX"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-spacefillr)) (home-page "https://cran.r-project.org/package=GLDEX") (synopsis "Fitting single and mixture of generalised lambda distributions") (description "@code{GLDEX} offers fitting algorithms corresponding to two major objectives. One is to provide a smoothing device to fit distributions to data using the weighted and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, and L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.") (license license:gpl3+))) (define-public r-rhandsontable (package (name "r-rhandsontable") (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "rhandsontable" version)) (sha256 (base32 "07fj6npq65pq836vdwblkhprdaq4i4f13cwdmm9gmxrnk72xj7lh")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib" (for-each delete-file '("chroma/chroma.min.js" "handsontable/all.min.js" "handsontable/handsontable.full.min.js" "jquery/jquery.min.js" "numbro/languages.min.js" "sparkline/jquery.sparkline.min.js")))))) (properties `((upstream-name . "rhandsontable"))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib" ;; Generate languages.js by importing all numbro language ;; files. (with-output-to-file "/tmp/languages.js" (lambda () (for-each (lambda (file) (format (current-output-port) "require(\"~a/~a\")~%" (dirname file) (basename file ".js"))) (find-files (string-append (assoc-ref inputs "js-numbro") "/languages/") "\\.js$")))) ;; Then bundle and minify it. (invoke "esbuild" "/tmp/languages.js" "--bundle" "--minify" "--outfile=numbro/languages.min.js") ;; Minify the other source files. (call-with-values (lambda () (unzip2 `((,(search-input-file inputs "/chroma.js") "chroma/chroma.min.js") (,(search-input-file inputs "/dist/languages/all.js") "handsontable/all.min.js") (,(search-input-file inputs "/dist/handsontable.full.js") "handsontable/handsontable.full.min.js") (,(assoc-ref inputs "js-jquery-sparkline") "sparkline/jquery.sparkline.min.js") (,(assoc-ref inputs "js-jquery") "jquery/jquery.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-htmlwidgets r-jsonlite r-magrittr)) (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) ("js-chroma" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/gka/chroma.js") (commit "v1.3.3"))) (file-name (git-file-name "chroma" "1.3.3")) (sha256 (base32 "091xn40n868pgb76gdl5jpg5gqqqzhykgxsslni230jzgc0hh1vm")))) ("js-handsontable" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/handsontable/handsontable") (commit "6.2.2"))) (file-name (git-file-name "handsontable" "6.2.2")) (sha256 (base32 "1rq4l24m9yz5r4sagdhq78jcjxlyh0ngryp43p5k33q2l77l4cp8")))) ("js-jquery-sparkline" ,(origin (method url-fetch) (uri "https://omnipotent.net/jquery.sparkline/2.1.2/jquery.sparkline.js") (sha256 (base32 "0d28qg5wlv44l02xafla6h6fvl3a71r5w7k0xhadagighh5wnarg")))) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.2.1.js") (sha256 (base32 "08dv528xy8ksrg5qqw73bvpjrzxv66xq41sfidn9ypgskwl2g40d")))) ;; We guessed the version based on ;; 62993ac9be3a1a4188150f7a6502b48b899f075e in ;; https://github.com/jrowen/rhandsontable, which added numbro's ;; languages.min.js. This was committed in Nov 2018, so the most ;; recent release of numbro at that time would have been 2.0.6 from May ;; 2018. ("js-numbro" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/BenjaminVanRyseghem/numbro") (commit "2.0.6"))) (file-name (git-file-name "numbro" "2.0.6")) (sha256 (base32 "1gsswkd482p0id00yx4q67ay0jvvwwidj71v41mq1cws8v2jjywx")))))) (home-page "https://jrowen.github.io/rhandsontable/") (synopsis "Htmlwidget based on the handsontable.js library") (description "Handsontable is a data grid component with an Excel like appearance. Built in JavaScript, it integrates with any data source with peak efficiency. It comes with powerful features like data validation, sorting, grouping, data binding, formula support or column ordering.") (license license:expat))) (define-public r-rhpcblasctl (package (name "r-rhpcblasctl") (version "0.23-42") (source (origin (method url-fetch) (uri (cran-uri "RhpcBLASctl" version)) (sha256 (base32 "05b6jhmxdr1rdpbvf5gwi9dqb57m8z2860qzkw5hcr72d5drv22w")))) (properties `((upstream-name . "RhpcBLASctl"))) (build-system r-build-system) (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/") (synopsis "Control the number of threads on BLAS") (description "This package allows you to control the number of threads the BLAS library uses. It is also possible to control the number of threads in OpenMP.") (license license:agpl3+))) (define-public r-lda (package (name "r-lda") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "lda" version)) (sha256 (base32 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lda/") (synopsis "Collapsed Gibbs sampling methods for topic models") (description "This package implements @dfn{latent Dirichlet allocation} (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is implemented via a fast collapsed Gibbs sampler written in C. Utility functions for reading/writing data typically used in topic models, as well as tools for examining posterior distributions are also included.") ;; Any version of the LGPL (license license:lgpl3+))) (define-public r-rann-l1 (package (name "r-rann-l1") (version "2.5.2") (source (origin (method url-fetch) (uri (cran-uri "RANN.L1" version)) (sha256 (base32 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44")))) (properties `((upstream-name . "RANN.L1"))) (build-system r-build-system) (home-page "https://github.com/jefferis/RANN/tree/master-L1") (synopsis "Fast nearest neighbour search using L1 metric") (description "This package provides tools to find the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. There is support for approximate as well as exact searches, fixed radius searches and @code{bd} as well as @code{kd} trees. The distance is computed using the L1 (Manhattan, taxicab) metric.") (license license:gpl3+))) (define-public r-leiden (package (name "r-leiden") (version "0.4.3.1") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 "1qihzjrwcb09aga27frcdrdv4dp0g295dbrk07fqykbjlb7vpv59")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-reticulate)) (native-inputs (list r-knitr)) (home-page "https://github.com/TomKellyGenetics/leiden") (synopsis "R implementation of Leiden clustering algorithm") (description "This package implements the Python @code{leidenalg} module to be called in R. It enables clustering using the Leiden algorithm for partitioning a graph into communities. See also Traag et al (2018) \"From Louvain to Leiden: guaranteeing well-connected communities.\" .") (license license:gpl3))) (define-public r-leidenalg (package (name "r-leidenalg") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "leidenAlg" version)) (sha256 (base32 "0wqay0rf28pgaf88bsvmrwgggzbma93rv9nqbydhjf1lc96ay1lz")))) (properties `((upstream-name . "leidenAlg") (updater-extra-inputs . ("gmp")))) (build-system r-build-system) (inputs (list glpk gmp libxml2)) (propagated-inputs (list r-igraph r-matrix r-rcpp r-rcpparmadillo r-rcppeigen r-sccore)) (native-inputs (list gfortran)) (home-page "https://github.com/kharchenkolab/leidenAlg") (synopsis "Leiden algorithm via an R interface") (description "This package implements an R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory).") ;; The DESCRIPTION file says GPL-3, but the code was copied from ;; https://github.com/vtraag/leidenalg, which is under GPLv3+. (license license:gpl3+))) (define-public r-patchwork (package (name "r-patchwork") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 "18b83gsv8idi5d062m9dvb46r7kxda97sa72pzllshhcaq9ylcfc")))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-gtable r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/thomasp85/patchwork") (synopsis "Compose ggplot2 plots") (description "The @code{ggplot2} package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. Patchwork is a package that expands the API to allow for arbitrarily complex composition of plots by providing mathematical operators for combining multiple plots.") (license license:expat))) (define-public r-rliger (package (name "r-rliger") (version "0.4.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/MacoskoLab/liger") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx")) (modules '((guix build utils))) (snippet '(delete-file "inst/java/ModularityOptimizer.jar")))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) ((guix build ant-build-system) #:prefix ant:) (guix build utils)) #:imported-modules `((guix build ant-build-system) ,@%r-build-system-modules) #:phases '(modify-phases %standard-phases (add-after 'unpack 'build-java-part (lambda* (#:key inputs #:allow-other-keys) (invoke "unzip" (assoc-ref inputs "optimizer-src")) (for-each (lambda (file) (invoke "javac" file)) (find-files "." "\\.java$")) (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar" (find-files "." "\\.class$")))) (add-after 'install 'strip-jar-timestamps (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))) (propagated-inputs (list r-cowplot r-dosnow r-dplyr r-fnn r-foreach r-ggplot2 r-ggrepel r-hmisc r-ica r-irlba r-matrix r-mclust r-patchwork r-plyr r-rann-l1 r-rcpp r-rcpparmadillo r-riverplot r-rtsne r-snow)) (native-inputs `(("jdk" ,icedtea "jdk") ;; See https://github.com/MacoskoLab/liger/issues/96 ;; The optimizer is released under the Expat license. ("optimizer-src" ,(origin (method url-fetch) (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip") (sha256 (base32 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18")))) ("unzip" ,unzip) ("zip" ,zip) ("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/MacoskoLab/liger") (synopsis "Integrate and analyze multiple single-cell datasets") (description "LIGER is a package for integrating and analyzing multiple single-cell datasets, developed and maintained by the Macosko lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.") (license license:gpl3))) (define-public r-liger (deprecated-package "r-liger" r-rliger)) (define-public r-harmony (package (name "r-harmony") (version "0.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/immunogenomics/harmony") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9")) (modules '((guix build utils))) (snippet '(begin (for-each delete-file '("config.status" "configure")) #t)))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-dplyr r-ggplot2 r-irlba r-matrix r-rcpp r-rcpparmadillo r-rcppprogress r-rlang r-tibble r-tidyr)) (native-inputs (list autoconf)) (home-page "https://github.com/immunogenomics/harmony") (synopsis "Integration of single cell sequencing data") (description "This package provides an implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al @url{doi.org/10.1101/461954}. The package includes a standalone Harmony function and interfaces to external frameworks.") (license license:gpl3))) (define-public r-covr (package (name "r-covr") (version "3.6.4") (source (origin (method url-fetch) (uri (cran-uri "covr" version)) (sha256 (base32 "0al6n4gnnvgxk968skqnajpqpqyl6kpam3fmn782kihhcl1h8qib")) (modules '((guix build utils))) ;; TODO: still need to replace highlight.js/highlight.pack.js (snippet '(with-directory-excursion "inst/www/shared" (for-each delete-file '("bootstrap/js/bootstrap.min.js" "bootstrap/shim/html5shiv.min.js" "bootstrap/shim/respond.min.js")))))) (properties `((upstream-name . "covr"))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/shared" (call-with-values (lambda () (unzip2 `((,(search-input-file inputs "/dist/js/bootstrap.js") "bootstrap/js/bootstrap.min.js") (,(search-input-file inputs "/dist/html5shiv.js") "bootstrap/shim/html5shiv.min.js") (,(search-input-file inputs "/dest/respond.src.js") "bootstrap/shim/respond.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-crayon r-digest r-httr r-jsonlite r-rex r-withr r-yaml)) (native-inputs (list esbuild r-knitr ;for vignettes (let ((version "3.3.5")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/twbs/bootstrap") (commit (string-append "v" version)))) (file-name (git-file-name "js-bootstrap" version)) (sha256 (base32 "1zxrjhnnd594rflnwzqhbx3rx0gjlh6hgx9v2nppgkmrkqb7y1a4")))) (let ((version "3.7.2")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/aFarkas/html5shiv") (commit version))) (file-name (git-file-name "js-html5shiv" version)) (sha256 (base32 "0mw4bbl9a9d1ibywscjgmbky0jkj4081l1yd4x3ss0flwaa3fwsk")))) (let ((version "1.4.2")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/scottjehl/Respond") (commit version))) (file-name (git-file-name "js-respond" version)) (sha256 (base32 "00xid731rirc7sdy1gc8qal3v9g0agr2qx15hm4x97l1lcbylyn2")))))) (home-page "https://github.com/r-lib/covr") (synopsis "Test coverage for R packages") (description "Thisp package enables you to track and report code coverage for your package and (optionally) upload the results to a coverage service. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.") (license license:gpl3))) (define-public r-systemfonts (package (name "r-systemfonts") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 "08sqw5izpwhawcjkcyscvslz914skwfi0s68rdwrqwwkh8fzn3w4")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) (inputs (list fontconfig freetype zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/systemfonts") (synopsis "System native font finding") (description "This package provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries for finding font files that can then be used further by e.g. graphic devices.") (license license:expat))) (define-public r-graphlayouts (package (name "r-graphlayouts") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 "1mg0j9kcjp8dbpd8fy9vr5f35pz41v18vxc7q4pyl986pj859jam")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/schochastics/graphlayouts") (synopsis "Additional layout algorithms for network visualizations") (description "This package provides several layout algorithms to visualize networks which are not part of the igraph library. Most are based on the concept of stress majorization by Gansner et al. (2004) . Some more specific algorithms emphasize hidden group structures in networks or focus on specific nodes.") (license license:expat))) (define-public r-terra (package (name "r-terra") (version "1.7-65") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 "0m9s5am8l6il1q0skab614cx0qjsb1i9xcv6nm0sdzj7p9lrzkfl")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs (list curl gdal geos openssh openssl pcre2 proj sqlite zlib)) (propagated-inputs (list r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://rspatial.org/terra") (synopsis "Spatial data analysis") (description "This package provides methods for spatial data analysis, especially raster data. The included methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction. Processing of very large files is supported.") (license license:gpl3+))) (define-public r-tidygraph (package (name "r-tidygraph") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "tidygraph" version)) (sha256 (base32 "11qlnpn54bdlkh2jcrk807z86vw54jrb6r9za1jkb03x9dqi9cwk")))) (properties `((upstream-name . "tidygraph"))) (build-system r-build-system) (propagated-inputs (list r-cli r-cpp11 r-dplyr r-igraph r-lifecycle r-magrittr r-pillar r-r6 r-rlang r-tibble r-tidyr)) (home-page "https://github.com/thomasp85/tidygraph") (synopsis "Tidy API for graph manipulation") (description "This package provides a graph implementation that can be thought of as two tidy data frames describing node and edge data respectively. It provides an approach to manipulate these two virtual data frames using the API defined in the @code{dplyr} package, and it also provides tidy interfaces to a lot of common graph algorithms.") (license license:expat))) (define-public r-soupx (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8") (revision "1")) (package (name "r-soupx") (version (git-version "0.3.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/constantAmateur/SoupX") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99")))) (properties `((upstream-name . "SoupX"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-matrix r-seurat)) (home-page "https://github.com/constantAmateur/SoupX") (synopsis "Single cell mRNA Soup eXterminator") (description "This package provides a package for quantifying, profiling and removing cell free mRNA contamination (the \"soup\") from droplet based single cell RNA-seq experiments.") (license license:gpl2)))) (define-public r-assertr (package (name "r-assertr") (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "assertr" version)) (sha256 (base32 "0g7h88kkls6v1nfzbar40y56yv3lkqb7vrcy63xqgc99zcf8k4bc")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-mass r-rlang)) (native-inputs (list r-knitr)) ; needed for vignette (home-page "https://github.com/ropensci/assertr") (synopsis "Assertive programming for R analysis pipelines") (description "This package provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. It is similar to @code{stopifnot()} but more powerful, friendly, and easier for use in pipelines.") (license license:expat))) (define-public r-parameters (package (name "r-parameters") (version "0.21.3") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 "091zpyq37v7xjicj4h4r4fqhrrc7d3hicgbdznsjn85sw4d7q595")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/parameters") (synopsis "Processing of model parameters") (description "This package provides utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models, this package implements features like standardization or bootstrapping of parameters and models, feature reduction (feature extraction and variable selection) as well as conversion between indices of effect size.") (license license:gpl3))) (define-public r-rgdal (package (name "r-rgdal") (version "1.6-7") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 (base32 "0cxfmm7niixw3dnbqm7a00603dyqjrphajqx0q5vjpdhmpyysp2m")))) (properties `((upstream-name . "rgdal") (updater-extra-inputs . ("gdal" "proj")) ;; These are only needed for Windows (updater-ignored-inputs . ("curl" "openssl" "openssh" "pcre2")))) (build-system r-build-system) (inputs (list gdal proj zlib)) (propagated-inputs (list r-sp)) (native-inputs (list pkg-config r-knitr)) (home-page "https://rgdal.r-forge.r-project.org") (synopsis "Bindings for the Geospatial Data Abstraction Library") (description "This package provides bindings to the Geospatial Data Abstraction Library (GDAL) and access to projection/transformation operations from the PROJ.4 library.") (license license:gpl2+))) (define-public r-insol (package (name "r-insol") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "insol" version)) (sha256 (base32 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3")))) (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs (list r-raster)) (native-inputs (list gfortran)) (home-page "https://meteoexploration.com/R/insol/index.html") (synopsis "Tools for calculating solar radiation") (description "This package provides functions to compute insolation on tilted surfaces, computes atmospheric transmittance and related parameters such as: Earth radius vector, declination, sunset and sunrise, daylength, equation of time, vector in the direction of the sun, vector normal to surface, and some atmospheric physics.") (license license:gpl2+))) (define-public r-lifecycle (package (name "r-lifecycle") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 "1k4ibf2x90xgmzaq47vf9wrsh6a2fp2lg1l8bq89632bx33x795d")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-rlang)) (properties ;; We can't add this here because via r-stringr this package ends up ;; being an input to r-knitr. '((updater-ignored-native-inputs . ("r-knitr")) (upstream-name . "lifecycle"))) (home-page "https://github.com/r-lib/lifecycle") (synopsis "Manage the life cycle of your package functions") (description "Manage the life cycle of your exported functions with shared conventions, documentation badges, and non-invasive deprecation warnings. The lifecycle package defines four development stages (experimental, maturing, stable, and questioning) and three deprecation stages (soft-deprecated, deprecated, and defunct). It makes it easy to insert badges corresponding to these stages in your documentation. Usage of deprecated functions are signalled with increasing levels of non-invasive verbosity.") (license license:gpl3))) (define-public r-assertable (package (name "r-assertable") (version "0.2.8") (source (origin (method url-fetch) (uri (cran-uri "assertable" version)) (sha256 (base32 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/assertable/") (synopsis "Verbose assertions for tabular data (data.frames and data.tables)") (description "This package provides simple, flexible assertions on data.frame or data.table objects with verbose output for vetting. While other assertion packages apply towards more general use-cases, @code{assertable} is tailored towards tabular data. It includes functions to check variable names and values, whether the dataset contains all combinations of a given set of unique identifiers, and whether it is a certain length. In addition, @code{assertable} includes utility functions to check the existence of target files and to efficiently import multiple tabular data files into one data.table.") (license license:gpl3))) (define-public r-quadprog (package (name "r-quadprog") (version "1.5-8") (source (origin (method url-fetch) (uri (cran-uri "quadprog" version)) (sha256 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/quadprog") (synopsis "Functions to solve quadratic programming problems") (description "This package contains routines and documentation for solving quadratic programming problems.") (license license:gpl3+))) (define-public r-desolve (package (name "r-desolve") (version "1.40") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 (base32 "1vq0yli1pkk3z92x1jgm4z19zwwhnwqdxvj4k2dmcnw7nrmsw2cc")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://desolve.r-forge.r-project.org/") (synopsis "Solvers for initial value problems of differential equations") (description "This package provides functions that solve initial value problems of a system of first-order @dfn{ordinary differential equations} (ODE), of @dfn{partial differential equations} (PDE), of @dfn{differential algebraic equations} (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations that have been converted to ODEs by numerical differencing.") (license license:gpl2+))) (define-public r-pmcmrplus (package (name "r-pmcmrplus") (version "1.9.10") (source (origin (method url-fetch) (uri (cran-uri "PMCMRplus" version)) (sha256 (base32 "0w0zxlq80n673zlrfw46qzidwshc6rxsqka6pahbr816zabzi0yq")))) (properties `((upstream-name . "PMCMRplus"))) (build-system r-build-system) (inputs (list gmp)) (propagated-inputs (list r-bwstest r-gmp r-ksamples r-mass r-multcompview r-mvtnorm r-rmpfr r-suppdists)) (native-inputs (list gfortran r-knitr r-rmarkdown)) (home-page "https://cran.r-project.org/package=PMCMRplus") (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended") (description "This package provides multiple pairwise tests.") (license license:gpl3+))) (define-public r-pracma (package (name "r-pracma") (version "2.4.4") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 (base32 "0zxsqr7f4pcr1nmbbzliihyldv091ykzajv1mbdrkycp46pz6khs")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") (description "This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.") (license license:gpl3+))) (define-public r-subplex (package (name "r-subplex") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "subplex" version)) (sha256 (base32 "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/subplex") (synopsis "Unconstrained optimization using the subplex algorithm") (description "This package implements the Subplex optimization algorithm. It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy or are discontinuous at the solution.") (license license:gpl3+))) (define-public r-txtplot (package (name "r-txtplot") (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "txtplot" version)) (sha256 (base32 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/txtplot/") (synopsis "Text-based plotting") (description "This package provides functions to produce rudimentary ASCII graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.") (license license:lgpl3+))) (define-public r-bio3d (package (name "r-bio3d") (version "2.4-4") (source (origin (method url-fetch) (uri (cran-uri "bio3d" version)) (sha256 (base32 "1scxzmh22ca0nmpkvapsdcmq3n06j2wy74ljz1g27r1k1p0ylm2n")))) (properties `((upstream-name . "bio3d"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "http://thegrantlab.org/bio3d/") (synopsis "Biological structure analysis") (description "This package provides utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data.") (license license:gpl2+))) (define-public r-bios2cor (package (name "r-bios2cor") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "Bios2cor" version)) (sha256 (base32 "0xj7ab9a463p4a67y0hlv6mfd08xf8didkn2mwrfa7gxjqqvix4z")))) (properties `((upstream-name . "Bios2cor"))) (build-system r-build-system) (propagated-inputs (list r-bigmemory r-bio3d r-circular r-igraph)) (home-page "https://cran.r-project.org/web/packages/Bios2cor/") (synopsis "From biological sequences and simulations to correlation analysis") (description "This package provides utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation.") (license license:gpl2+))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-networkd3 (package (name "r-networkd3") (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "networkD3" version)) (sha256 (base32 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k")) (snippet '(begin (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js") #t)))) (properties `((upstream-name . "networkD3"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "d3.v4.js") "d3-4.5.0/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (native-inputs `(("uglifyjs" ,node-uglify-js) ;; NOTE: Make sure that this version of d3 is still valid when ;; upgrading the package. ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) (propagated-inputs (list r-htmlwidgets r-igraph r-magrittr)) (home-page "https://cran.r-project.org/package=networkD3") (synopsis "D3 JavaScript network graphs from R") (description "This package creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.") (license license:gpl3+))) (define-public r-aasea (package (name "r-aasea") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "aaSEA" version)) (sha256 (base32 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h")))) (properties `((upstream-name . "aaSEA"))) (build-system r-build-system) (propagated-inputs (list r-bios2cor r-dt r-hmisc r-magrittr r-networkd3 r-plotly r-seqinr r-shiny r-shinydashboard)) (home-page "https://cran.r-project.org/web/packages/aaSEA/") (synopsis "Amino acid substitution effect analyzer") (description "Given a protein multiple sequence alignment, it is a daunting task to assess the effects of substitutions along sequence length. The aaSEA package is intended to help researchers to rapidly analyze property changes caused by single, multiple and correlated amino acid substitutions in proteins.") (license license:gpl3))) (define-public r-abacus (package (name "r-abacus") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ABACUS" version)) (sha256 (base32 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i")))) (properties `((upstream-name . "ABACUS"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-shiny)) (home-page "https://shiny.abdn.ac.uk/Stats/apps/") (synopsis "Apps-based activities for communicating and understanding statistics") (description "This package provides a set of Shiny apps for effective communication and understanding in statistics. The current version includes properties of normal distribution, properties of sampling distribution, one-sample z and t tests, two samples independent (unpaired) t test and analysis of variance.") (license license:gpl3))) (define-public r-abc-rap (package (name "r-abc-rap") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "ABC.RAP" version)) (sha256 (base32 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk")))) (properties `((upstream-name . "ABC.RAP"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ABC.RAP/") (synopsis "Array-based CpG region analysis pipeline") (description "This package aims to identify candidate genes that are differentially methylated between cases and controls. It applies Student's t-test and delta beta analysis to identify candidate genes containing multiple CpG sites.") (license license:gpl3))) (define-public r-abcadm (package (name "r-abcadm") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "abcADM" version)) (sha256 (base32 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10")))) (properties `((upstream-name . "abcADM"))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp)) (home-page "https://cran.r-project.org/web/packages/abcADM/") (synopsis "Fit accumulated damage models and estimate reliability using ABC") (description "This package provides tools to estimate parameters of accumulated damage (load duration) models based on failure time data under a Bayesian framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess long-term reliability under stochastic load profiles.") (license license:gpl3))) (define-public r-rglpk (package (name "r-rglpk") (version "0.6-5") (source (origin (method url-fetch) (uri (cran-uri "Rglpk" version)) (sha256 (base32 "18bwnpb8645vf233andr411shzp1sm3i7bn848sgxswgb80grvxa")))) (properties `((upstream-name . "Rglpk"))) (build-system r-build-system) (propagated-inputs (list r-slam)) (inputs (list glpk)) (home-page "https://r-forge.r-project.org/projects/rglp/") (synopsis "R interface to the GNU Linear Programming Kit") (description "This package provides an R interface to the GNU Linear Programming Kit, software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed integer linear programming} (MILP) and other related problems.") ;; Either license (license (list license:gpl2 license:gpl3)))) (define-public r-abcdefba (package (name "r-abcdefba") (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "abcdeFBA" version)) (sha256 (base32 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4")))) (properties `((upstream-name . "abcdeFBA"))) (build-system r-build-system) (propagated-inputs (list r-corrplot r-lattice r-rgl r-rglpk)) (home-page "https://cran.r-project.org/web/packages/abcdeFBA/") (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package") (description "This package provides functions for Constraint Based Simulation using Flux Balance Analysis and informative analysis of the data generated during simulation.") (license license:gpl2))) (define-public r-abcrlda (package (name "r-abcrlda") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "abcrlda" version)) (sha256 (base32 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks")))) (properties `((upstream-name . "abcrlda"))) (build-system r-build-system) (home-page "https://ieeexplore.ieee.org/document/8720003/") (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis") (description "This package offers methods to perform @dfn{asymptotically bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for cost-sensitive binary classification. The bias-correction is an estimate of the bias term added to regularized discriminant analysis that minimizes the overall risk.") (license license:gpl3))) (define-public r-abemus (package (name "r-abemus") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "abemus" version)) (sha256 (base32 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb")))) (properties `((upstream-name . "abemus"))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/abemus/") (synopsis "Adaptive base error model in ultra-deep sequencing data") (description "This package provides an implementation of @dfn{Adaptive Base Error Model in Ultra-deep Sequencing data} (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating cell free DNA} (cfDNA).") (license license:gpl3))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-rintrojs (package (name "r-rintrojs") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "rintrojs" version)) (sha256 (base32 "1fy5lz9d9njs4yrnwrrn0n1fn0chccgi1gzn4qz4g6adr3v35rgw")) (snippet '(delete-file "inst/javascript/introjs/intro.min.js")))) (properties `((upstream-name . "rintrojs"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/javascript/introjs/" (let ((source (assoc-ref inputs "intro.js")) (target "intro.min.js")) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (native-inputs `(("esbuild" ,esbuild) ("intro.js" ,(origin (method url-fetch) (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js") (sha256 (base32 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7")))))) (propagated-inputs (list r-jsonlite r-shiny)) (home-page "https://github.com/carlganz/rintrojs") (synopsis "Wrapper for the Intro.js library") (description "This package provides a wrapper for the @url{http://www.introjs.com, Intro.js} library. This package makes it easy to include step-by-step introductions, and clickable hints in a Shiny application. It supports both static introductions in the UI, and programmatic introductions from the server-side.") ;; The intro.js library is licensed under Expat. (license (list license:agpl3+ license:expat)))) (define-public r-sysfonts (package (name "r-sysfonts") (version "0.8.8") (source (origin (method url-fetch) (uri (cran-uri "sysfonts" version)) (sha256 (base32 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn")))) (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs (list freetype libpng zlib)) (native-inputs (list pkg-config)) (home-page "https://github.com/yixuan/sysfonts") (synopsis "Loading fonts into R") (description "This is a package to simplify loading of system fonts and Google Fonts into R, in order to support other packages.") (license license:gpl2))) (define-public r-showtextdb (package (name "r-showtextdb") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "showtextdb" version)) (sha256 (base32 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2")))) (properties `((upstream-name . "showtextdb"))) (build-system r-build-system) (propagated-inputs (list r-sysfonts)) (home-page "https://cran.r-project.org/web/packages/showtextdb/") (synopsis "Font files for the 'showtext' package") (description "This package provides font files that can be used by the @code{showtext} package.") (license license:asl2.0))) (define-public r-showtext (package (name "r-showtext") (version "0.9-6") (source (origin (method url-fetch) (uri (cran-uri "showtext" version)) (sha256 (base32 "0c4cssqk4s27pxfyb7fii97zhy4awzapj7bx9zkbki4va75mkjhf")))) (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs (list freetype libpng zlib)) (propagated-inputs (list r-showtextdb r-sysfonts)) (native-inputs (list pkg-config r-knitr r-rmarkdown)) (home-page "https://github.com/yixuan/showtext") (synopsis "Using fonts more easily in R graphs") (description "This package aims to make it easy to use various types of fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports most output formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted into polygons or raster images, hence after the plot has been created, it no longer relies on the font files. No external software such as Ghostscript is needed to use this package.") (license license:asl2.0))) (define-public r-emoa (package (name "r-emoa") (version "0.5-0.2") (source (origin (method url-fetch) (uri (cran-uri "emoa" version)) (sha256 (base32 "0fr4ia3hkv8c7wkl64a51s6ynldppc812ynwldvbwy25dhlbvs6r")))) (properties `((upstream-name . "emoa"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/emoa/") (synopsis "Evolutionary multiobjective optimization algorithms") (description "This package provides building blocks for the design and analysis of multiobjective optimization algorithms.") (license license:gpl2))) (define-public r-emojifont (package (name "r-emojifont") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "emojifont" version)) (sha256 (base32 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i")))) (properties `((upstream-name . "emojifont"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-proto r-showtext r-sysfonts)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/emojifont") (synopsis "Emoji and Font Awesome in R graphics") (description "This package enables the use of emoji and the Font Awesome glyphs in both base and ggplot2 graphics.") (license license:artistic2.0))) (define-public r-abstractr (package (name "r-abstractr") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "abstractr" version)) (sha256 (base32 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig")))) (properties `((upstream-name . "abstractr"))) (build-system r-build-system) (propagated-inputs (list r-colourpicker r-emojifont r-ggplot2 r-gridextra r-rintrojs r-shiny r-shinythemes)) (home-page "https://matt-kumar.shinyapps.io/portfolio") (synopsis "R-Shiny application for creating visual abstracts") (description "This package provides an R Shiny application to create visual abstracts for original research. A variety of user defined options and formatting are included.") (license license:gpl3))) (define-public r-qgam (package (name "r-qgam") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "qgam" version)) (sha256 (base32 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn")))) (properties `((upstream-name . "qgam"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-mgcv r-plyr r-shiny)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/qgam/") (synopsis "Smooth additive quantile regression models") (description "This package provides smooth additive quantile regression models, fitted using the methods of Fasiolo et al. (2017). Differently from @code{quantreg}, the smoothing parameters are estimated automatically by marginal loss minimization, while the regression coefficients are estimated using either PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian credible intervals of the estimated effects have approximately the correct coverage. The main function is @code{qgam()} which is similar to @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile regression models.") (license license:gpl2+))) (define-public r-abtest (package (name "r-abtest") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "abtest" version)) (sha256 (base32 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg")))) (properties `((upstream-name . "abtest"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-mvtnorm r-plotrix r-qgam r-rcolorbrewer r-rcpp r-sn r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/abtest/") (synopsis "Bayesian A/B testing") (description "This package provides functions for Bayesian A/B testing including prior elicitation options based on Kass and Vaidyanathan (1992) @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.") (license license:gpl2+))) (define-public r-reldist (package (name "r-reldist") (version "1.7-2") (source (origin (method url-fetch) (uri (cran-uri "reldist" version)) (sha256 (base32 "1j99j9a0igb9nwkp7fkqqkmvyz770xmbi1d25pbnaz7d2jy6q26r")))) (properties `((upstream-name . "reldist"))) (build-system r-build-system) (propagated-inputs (list r-densestbayes r-mgcv)) (home-page "http://www.stat.ucla.edu/~handcock/RelDist") (synopsis "Relative distribution methods") (description "This package provides tools for the comparison of distributions. This includes nonparametric estimation of the relative distribution PDF and CDF and numerical summaries as described in \"Relative Distribution Methods in the Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789.") ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for ;; attribution requirements. (license license:gpl3))) (define-public r-accept (package (name "r-accept") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "accept" version)) (sha256 (base32 "0yjihmgi94yfwhnvgw4v235yyr8n6w1ass2qbmvk0ia1hmjis8zq")))) (properties `((upstream-name . "accept"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-reldist)) (home-page "https://cran.r-project.org/web/packages/accept/") (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") (description "This package allows clinicians to predict the rate and severity of future acute exacerbation in @dfn{Chronic Obstructive Pulmonary Disease} (COPD) patients, based on the clinical prediction model published in Adibi et al. (2019) @url{doi:10.1101/651901}.") (license license:gpl3))) (define-public r-smpracticals (package (name "r-smpracticals") (version "1.4-3") (source (origin (method url-fetch) (uri (cran-uri "SMPracticals" version)) (sha256 (base32 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf")))) (properties `((upstream-name . "SMPracticals"))) (build-system r-build-system) (propagated-inputs (list r-ellipse r-mass r-nlme r-survival)) (home-page "http://statwww.epfl.ch/davison/SM/") (synopsis "Practicals for use with Davison (2003) Statistical Models") (description "This package contains the datasets and a few functions for use with the practicals outlined in Appendix A of the book Statistical Models (Davison, 2003, Cambridge University Press). The practicals themselves can be found at @url{http://statwww.epfl.ch/davison/SM/}.") (license license:gpl2+))) (define-public r-fgui (package (name "r-fgui") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "fgui" version)) (sha256 (base32 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv")))) (properties `((upstream-name . "fgui"))) (build-system r-build-system) (home-page "https://sites.google.com/site/thomashoffmannproject/software/fgui") (synopsis "Create GUI for R functions") (description "Rapidly create a GUI for a function you created by automatically creating widgets for arguments of the function. This package automatically parses help routines for context-sensitive help to these arguments. The interface is essentially a wrapper to some Tcl/Tk routines to both simplify and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be incorporated into the interface for greater customization for the more experienced.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-tcltk2 (package (name "r-tcltk2") (version "1.2-11") (source (origin (method url-fetch) (uri (cran-uri "tcltk2" version)) (sha256 (base32 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d")))) (properties `((upstream-name . "tcltk2"))) (build-system r-build-system) (inputs (list tcl tk)) (home-page "https://www.sciviews.org/SciViews-R") (synopsis "Tcl/Tk additions") (description "This package provides a series of additional Tcl commands and Tk widgets with style and various functions to supplement the tcltk package") (license license:lgpl3))) (define-public r-accrual (package (name "r-accrual") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "accrual" version)) (sha256 (base32 "0dygp8xar6dqx822ghjqvi8c597xjb7bqn57475fs4nw5zz709lk")))) (properties `((upstream-name . "accrual"))) (build-system r-build-system) (propagated-inputs (list r-fgui r-smpracticals r-tcltk2)) (home-page "https://cran.r-project.org/web/packages/accrual/") (synopsis "Bayesian accrual prediction") (description "Subject recruitment for medical research is challenging. Slow patient accrual leads to delay in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to manage the accrual rate. This package provides an implementation of a Bayesian method that integrates researcher's experience on previous trials and data from the current study, providing reliable prediction on accrual rate for clinical studies. It provides functions for Bayesian accrual prediction which can be easily used by statisticians and clinical researchers.") (license license:gpl2))) (define-public r-accrued (package (name "r-accrued") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "accrued" version)) (sha256 (base32 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5")))) (properties `((upstream-name . "accrued"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/accrued/") (synopsis "Data quality visualization tools for partially accruing data") (description "This is a package for visualizing data quality of partially accruing data.") (license license:gpl3))) (define-public r-mda (package (name "r-mda") (version "0.5-4") (source (origin (method url-fetch) (uri (cran-uri "mda" version)) (sha256 (base32 "0nd7p3yz7qdzka7jizymv5vhbhzb4v8bjpmmn5wa83vxh0l7ypzj")))) (properties `((upstream-name . "mda"))) (build-system r-build-system) (propagated-inputs (list r-class)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/mda/") (synopsis "Mixture and flexible discriminant analysis") (description "This is a package for mixture and flexible discriminant analysis, @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.") (license license:gpl2))) (define-public r-elasticnet (package (name "r-elasticnet") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "elasticnet" version)) (sha256 (base32 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8")))) (properties `((upstream-name . "elasticnet"))) (build-system r-build-system) (propagated-inputs (list r-lars)) (home-page "http://users.stat.umn.edu/~zouxx019/") (synopsis "Elastic-Net for sparse estimation and sparse PCA") (description "This package provides functions for fitting the entire solution path of the Elastic-Net and also provides functions for estimating sparse Principal Components. The Lasso solution paths can be computed by the same function.") (license license:gpl2+))) (define-public r-sparselda (package (name "r-sparselda") (version "0.1-9") (source (origin (method url-fetch) (uri (cran-uri "sparseLDA" version)) (sha256 (base32 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb")))) (properties `((upstream-name . "sparseLDA"))) (build-system r-build-system) (propagated-inputs (list r-elasticnet r-mass r-mda)) (home-page "https://www.imm.dtu.dk/~lkhc/") (synopsis "Sparse discriminant analysis") (description "This package performs sparse linear discriminant analysis for Gaussians and mixture of Gaussian models.") (license license:gpl2+))) (define-public r-accsda (package (name "r-accsda") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "accSDA" version)) (sha256 (base32 "0jf4x5j9y7a3mvf2ghjp6bxdq1s5jh2sx3x3ar6f3lyzzvrnls4v")))) (properties `((upstream-name . "accSDA"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggthemes r-gridextra r-mass)) (home-page "https://github.com/gumeo/accSDA/wiki") (synopsis "Accelerated sparse discriminant analysis") (description "This package provides an implementation of sparse linear discriminant analysis, which is a supervised classification method for multiple classes. Various novel optimization approaches to this problem are implemented including @dfn{alternating direction method of multipliers} (ADMM), @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG). Functions for performing cross validation are also supplied along with basic prediction and plotting functions. @dfn{Sparse zero variance discriminant} (SZVD) analysis is also included in the package.") (license license:gpl2+))) (define-public r-ace2fastq (package (name "r-ace2fastq") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ace2fastq" version)) (sha256 (base32 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic")))) (properties `((upstream-name . "ace2fastq"))) (build-system r-build-system) (propagated-inputs (list r-stringr)) (home-page "https://github.com/c5sire/ace2fastq") (synopsis "ACE file to FASTQ converter") (description "The ACE file format is used in genomics to store contigs from sequencing machines. This tools converts it into FASTQ format. Both formats contain the sequence characters and their corresponding quality information. Unlike the FASTQ file, the ACE file stores the quality values numerically. The conversion algorithm uses the standard Sanger formula. The package facilitates insertion into pipelines, and content inspection.") (license license:gpl3))) (define-public r-rngwell (package (name "r-rngwell") (version "0.10-9") (source (origin (method url-fetch) (uri (cran-uri "rngWELL" version)) (sha256 (base32 "1jyanz789ylbz9a2agqv5c674zrfqn0k7s9d5dfia63dpq8cqscr")))) (properties `((upstream-name . "rngWELL"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rngWELL/") (synopsis "Toolbox for WELL random number generators") (description "This is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") (license license:bsd-3))) (define-public r-rnmf (package (name "r-rnmf") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "rNMF" version)) (sha256 (base32 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597")))) (build-system r-build-system) (propagated-inputs (list r-knitr r-nnls)) (home-page "https://cran.r-project.org/web/packages/rNMF/") (synopsis "Robust nonnegative matrix factorization") (description "This package provides an implementation of robust nonnegative matrix factorization (rNMF). The rNMF algorithm decomposes a nonnegative high dimension data matrix into the product of two low rank nonnegative matrices, while detecting and trimming outliers. The main function is @code{rnmf()}. The package also includes a visualization tool, @code{see()}, that arranges and prints vectorized images.") (license license:gpl2+))) (define-public r-randtoolbox (package (name "r-randtoolbox") (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 "0jwylffr8zajgd1x24nrv4xxlkic10i8cfd9sy0pkz2g7sai9nll")))) (properties `((upstream-name . "randtoolbox"))) (build-system r-build-system) (propagated-inputs (list r-rngwell)) (home-page "https://cran.r-project.org/web/packages/randtoolbox/") (synopsis "Toolbox for pseudo and quasi random number generation") (description "This package provides @enumerate @item pseudo random generators, such as general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators) @item quasi random generators, such as the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence), and @item some generator tests: the gap test, the serial test, the poker test. @end enumerate See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") (license license:bsd-3))) (define-public r-lhs (package (name "r-lhs") (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "lhs" version)) (sha256 (base32 "0gyjdic714pqvq2jv1v0vh7hl9s83sg2zxx2gdkp38z6xx2cwzz3")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/bertcarnell/lhs") (synopsis "Latin Hypercube Samples") (description "This package provides a number of methods for creating and augmenting Latin Hypercube Samples.") (license license:gpl3))) (define-public r-acebayes (package (name "r-acebayes") (version "1.10") (source (origin (method url-fetch) (uri (cran-uri "acebayes" version)) (sha256 (base32 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73")))) (properties `((upstream-name . "acebayes"))) (build-system r-build-system) (propagated-inputs (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/acebayes/") (synopsis "Optimal Bayesian experimental design using the ACE algorithm") (description "Finding an optimal Bayesian experimental design involves maximizing an objective function given by the expectation of some appropriately chosen utility function with respect to the joint distribution of unknown quantities (including responses). This objective function is usually not available in closed form and the design space can be continuous and of high dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE) to maximise an approximation to the expectation of the utility function.") (license license:gpl2))) (define-public r-acet (package (name "r-acet") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "ACEt" version)) (sha256 (base32 "1071d75sw5bcfw1acjsg6bn81sapb5hkwrxjfrfxlz5r83w6213f")))) (properties `((upstream-name . "ACEt"))) (build-system r-build-system) (propagated-inputs (list r-bh r-mass r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ACEt/") (synopsis "Estimating dynamic heritability and twin model comparison") (description "This package supports twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.") (license license:gpl2+))) (define-public r-acfmperiod (package (name "r-acfmperiod") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "acfMPeriod" version)) (sha256 (base32 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5")))) (properties `((upstream-name . "acfMPeriod"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") (synopsis "Estimation of the ACF from the M-periodogram") (description "This package support non-robust and robust computations of the sample autocovariance (ACOVF) and sample autocorrelation functions (ACF) of univariate and multivariate processes. The methodology consists in reversing the diagonalization procedure involving the periodogram or the cross-periodogram and the Fourier transform vectors, and, thus, obtaining the ACOVF or the ACF as discussed in Fuller (1995) @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting robust M-regressors to obtain the M-periodogram or M-cross-periodogram as discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") (license license:gpl2+))) (define-public r-gamlss-data (package (name "r-gamlss-data") (version "6.0-2") (source (origin (method url-fetch) (uri (cran-uri "gamlss.data" version)) (sha256 (base32 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv")))) (properties `((upstream-name . "gamlss.data"))) (build-system r-build-system) (home-page "http://www.gamlss.org/") (synopsis "GAMLSS data") (description "This package provides data used as examples to demonstrate GAMLSS models.") ;; Either version of the license (license (list license:gpl2 license:gpl3)))) (define-public r-gamlss (package (name "r-gamlss") (version "5.4-20") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 "0wv812xby0i8zn07zw30ic4mmr418gk1ch1lvyh0kybkw4h1w356")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival)) (home-page "http://www.gamlss.org/") (synopsis "Generalized additive models for location scale and shape") (description "This package provides functions for fitting the generalized additive models for location scale and shape introduced by Rigby and Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.") ;; Either version of the license (license (list license:gpl2 license:gpl3)))) (define-public r-acid (package (name "r-acid") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "acid" version)) (sha256 (base32 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd")))) (properties `((upstream-name . "acid"))) (build-system r-build-system) (propagated-inputs (list r-gamlss r-gamlss-dist r-hmisc)) (home-page "https://cran.r-project.org/web/packages/acid/") (synopsis "Analysing conditional income distributions") (description "This package provides functions for the analysis of income distributions for subgroups of the population as defined by a set of variables like age, gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture distribution as well as functions for moments, inequality measures, entropy measures and polarisation measures of income distributions. This package thus aides the analysis of income inequality by offering tools for the exploratory analysis of income distributions at the disaggregated level.") (license license:gpl3))) (define-public r-acm4r (package (name "r-acm4r") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "acm4r" version)) (sha256 (base32 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) (properties `((upstream-name . "acm4r"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acm4r/") (synopsis "Align-and-count method comparisons of RFLP data") (description "This is a package to compare sequence fragment lengths or molecular weights from pairs of lanes. The number of matching bands in the @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using the align-and-count method.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-filelock (package (name "r-filelock") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "filelock" version)) (sha256 (base32 "0dqi0w92zq1f9542ma2nk5gkqzfmd4jlf34vysb4vv7mag20xk9d")))) (properties `((upstream-name . "filelock"))) (build-system r-build-system) (home-page "https://github.com/r-lib/filelock") (synopsis "Portable file locking") (description "This library lets you place an exclusive or shared lock on a file using the appropriate system call provided by the underlying operating system.") (license license:expat))) (define-public r-filematrix (package (name "r-filematrix") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "filematrix" version)) (sha256 (base32 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b")))) (properties `((upstream-name . "filematrix"))) (build-system r-build-system) ;; These inputs are needed for vignettes (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/andreyshabalin/filematrix") (synopsis "File-backed matrix class with convenient read and write access") (description "This package provides an interface for working with large matrices stored in files, not in computer memory. It supports multiple non-character data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 byte real values). Access to parts of the matrix is done by indexing, exactly as with usual R matrices. It supports very large matrices; the package has been tested on multi-terabyte matrices. It allows for more than 2^32 rows or columns, ad allows for quick addition of extra columns to a filematrix.") (license license:lgpl3))) (define-public r-filesstrings (package (name "r-filesstrings") (version "3.2.4") (source (origin (method url-fetch) (uri (cran-uri "filesstrings" version)) (sha256 (base32 "1jl3jhkdjx5x00kllnkpvrlpsmzsvlgd6vhzdavd39zx4jzwjxw3")))) (properties `((upstream-name . "filesstrings"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-magrittr r-purrr r-rlang r-strex r-stringi r-stringr r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/rorynolan/filesstrings") (synopsis "Handy file and string manipulation") (description "This started out as a package for file and string manipulation. Since then, the @code{fs} and @code{strex} packages emerged, offering functionality previously given by this package. Those packages have hence almost pushed filesstrings into extinction. However, it still has a small number of unique, handy file manipulation functions which can be seen in the vignette. One example is a function to remove spaces from all file names in a directory.") (license license:gpl3))) (define-public r-acmeeqtl (package (name "r-acmeeqtl") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "ACMEeqtl" version)) (sha256 (base32 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz")))) (properties `((upstream-name . "ACMEeqtl"))) (build-system r-build-system) (propagated-inputs (list r-filematrix)) (home-page "https://github.com/andreyshabalin/ACMEeqtl") (synopsis "Estimation of interpretable eQTL effect sizes") (description "This package provides a non-linear model, termed ACME, that reflects a parsimonious biological model for allelic contributions of cis-acting eQTLs. With non-linear least-squares algorithm the maximum likelihood parameters can be estimated. The ACME model provides interpretable effect size estimates and p-values with well controlled Type-I error.") (license license:lgpl3))) (define-public r-acmer (package (name "r-acmer") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "acmeR" version)) (sha256 (base32 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) (properties `((upstream-name . "acmeR"))) (build-system r-build-system) (propagated-inputs (list r-foreign)) (home-page "https://cran.r-project.org/web/packages/acmeR/") (synopsis "ACME estimator of bird and bat mortality by wind turbines") (description "This package provides an implementation of the ACME estimator, described in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran Mortality at Wind Turbines. Unlike most other models, this estimator supports decreasing-hazard Weibull model for persistence; decreasing search proficiency as carcasses age; variable bleed-through at successive searches; and interval mortality estimates. The package provides, based on search data, functions for estimating the mortality inflation factor in Frequentist and Bayesian settings.") (license license:expat))) (define-public r-r-huge (package (name "r-r-huge") (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "R.huge" version)) (sha256 (base32 "1wjcssvn76fblpivwkapdwcw08pygbkj7qskcl0wn8mda9w5f72b")))) (properties `((upstream-name . "R.huge"))) (build-system r-build-system) (propagated-inputs (list r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.huge") (synopsis "Methods for accessing huge amounts of data") (description "This is a deprecated package for accessing huge amounts of data. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside the @code{aroma.affymetrix} package.") (license license:lgpl2.1+))) (define-public r-r-filesets (package (name "r-r-filesets") (version "2.15.0") (source (origin (method url-fetch) (uri (cran-uri "R.filesets" version)) (sha256 (base32 "14dngx6ffhfvlaixpvlq890nwgil6zyaw8wy3dlcrv001wynzmms")))) (properties `((upstream-name . "R.filesets"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.filesets") (synopsis "Easy handling of and access to files") (description "This package provides classes and methods to locate, setup, subset, navigate and iterate file sets, i.e. sets of files located in one or more directories on the file system. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files.") (license license:lgpl2.1+))) (define-public r-r-devices (package (name "r-r-devices") (version "2.17.1") (source (origin (method url-fetch) (uri (cran-uri "R.devices" version)) (sha256 (base32 "02cwdhb9m97gxi4pki4kasc5j3a12r7yzsychzzk9h0ijc1mfziv")))) (properties `((upstream-name . "R.devices"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.devices") (synopsis "Unified handling of graphics devices") (description "This package provides functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.") (license license:lgpl2.1+))) (define-public r-acnr (package (name "r-acnr") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "acnr" version)) (sha256 (base32 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym")))) (properties `((upstream-name . "acnr"))) (build-system r-build-system) (home-page "https://github.com/mpierrejean/acnr") (synopsis "Annotated copy-number regions") (description "This package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.") (license license:lgpl2.1+))) (define-public r-acopula (package (name "r-acopula") (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "acopula" version)) (sha256 (base32 "0asxfcjrsr9d7ab59pdajs0zvdjgwfswk9rdlpfdr51535wpjrfy")))) (properties `((upstream-name . "acopula"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/acopula/") (synopsis "Modelling dependence with multivariate Archimax copulas") (description "Archimax copulas are a mixture of Archimedean and EV copulas. This package provides definitions of several parametric families of generator and dependence function, computes CDF and PDF, estimates parameters, tests for goodness of fit, generates random sample and checks copula properties for custom constructs. In the 2-dimensional case explicit formulas for density are used, contrary to higher dimensions when all derivatives are linearly approximated. Several non-archimax families (normal, FGM, Plackett) are provided as well.") (license license:gpl2))) (define-public r-tuner (package (name "r-tuner") (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 "1l270rk1m3967fvgpshrbd71l7ns74wdhivbmavayk68dnsiyi65")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs (list r-signal)) (home-page "https://cran.r-project.org/web/packages/tuneR/") (synopsis "Analysis of music and speech") (description "This is a package for the analysis of music and speech. Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read MP3, read MIDI, perform steps of a transcription, ...") ;; Either of these versions. (license (list license:gpl2 license:gpl3)))) (define-public r-seewave (package (name "r-seewave") (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "seewave" version)) (sha256 (base32 "13c48sn453yp4j0ap8slnnr2gfhlxasz926p2pazkrg817w7m28z")))) (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs (list libsndfile)) (propagated-inputs (list r-tuner)) (home-page "https://rug.mnhn.fr/seewave") (synopsis "Sound analysis and synthesis") (description "This package provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.") (license license:gpl2+))) (define-public r-acousticndlcoder (package (name "r-acousticndlcoder") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "AcousticNDLCodeR" version)) (sha256 (base32 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb")))) (properties `((upstream-name . "AcousticNDLCodeR"))) (build-system r-build-system) (propagated-inputs (list r-seewave r-tuner r-zoo)) (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") (synopsis "Coding sound files for use with NDL") (description "Make acoustic cues to use with the R package @code{ndl}. The package implements functions used in the PLoS ONE paper \"Words from spontaneous conversational speech can be recognized with human-like accuracy by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit.\" @url{doi:10.1371/journal.pone.0174623}") (license license:gpl2+))) (define-public r-acp (package (name "r-acp") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "acp" version)) (sha256 (base32 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn")))) (properties `((upstream-name . "acp"))) (build-system r-build-system) (propagated-inputs (list r-quantmod r-tseries)) (home-page "https://cran.r-project.org/web/packages/acp/") (synopsis "Autoregressive conditional Poisson") (description "This package supports the analysis of count data exhibiting autoregressive properties, using the @dfn{Autoregressive Conditional Poisson} model (ACP(p,q)) proposed by Heinen (2003).") (license license:gpl2))) (define-public r-ada (package (name "r-ada") (version "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "ada" version)) (sha256 (base32 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) (properties `((upstream-name . "ada"))) (build-system r-build-system) (propagated-inputs (list r-rpart)) (home-page "https://cran.r-project.org/web/packages/ada/") (synopsis "Stochastic boosting") (description "This package provides a straightforward, well-documented, and broad boosting routine for classification, ideally suited for small to moderate-sized data sets. It performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-genalg (package (name "r-genalg") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "genalg" version)) (sha256 (base32 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna")))) (properties `((upstream-name . "genalg"))) (build-system r-build-system) (home-page "https://github.com/egonw/genalg") (synopsis "R based genetic algorithm") (description "This package provides an R based genetic algorithm for binary and floating point chromosomes.") (license license:gpl2))) (define-public r-kernelfactory (package (name "r-kernelfactory") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "kernelFactory" version)) (sha256 (base32 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j")))) (properties `((upstream-name . "kernelFactory"))) (build-system r-build-system) (propagated-inputs (list r-auc r-genalg r-kernlab r-randomforest)) (home-page "https://cran.r-project.org/web/packages/kernelFactory/") (synopsis "Ensemble of kernel machines") (description "Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.") (license license:gpl2+))) (define-public r-dummies (package (name "r-dummies") (version "1.5.6") (source (origin (method url-fetch) (uri (cran-uri "dummies" version)) (sha256 (base32 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm")))) (properties `((upstream-name . "dummies"))) (build-system r-build-system) (home-page "https://decisionpatterns.com") (synopsis "Create dummy/indicator variables flexibly and efficiently") (description "This package lets you expand factors, characters and other eligible classes into dummy/indicator variables.") (license license:gpl2+))) (define-public r-dunn-test (package (name "r-dunn-test") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "dunn.test" version)) (sha256 (base32 "0lqwvyl3pyygfc73nf81gzw3zl3w43r7ki0yw2dgrzhkpb2iji4a")))) (properties `((upstream-name . "dunn.test"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=dunn.test") (synopsis "Dunn's test of multiple comparisons using rank sums") (description "Dunn's test computes stochastic dominance & reports pairwise comparisons. This is done following a Kruskal-Wallis test (Kruskal and Wallis, 1952). It employs Dunn's z-test-statistic approximations for rank statistics, conducting k(k-1)/2 comparisons. The null hypothesis assumes that the probability of a randomly selected value from the first group being larger than one from the second group is one half, similar to the Wilcoxon-Mann-Whitney test. Dunn's test serves as a test for median difference and takes into account tied ranks.") (license license:gpl2))) (define-public r-acrm (package (name "r-acrm") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "aCRM" version)) (sha256 (base32 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v")))) (properties `((upstream-name . "aCRM"))) (build-system r-build-system) (propagated-inputs (list r-ada r-dummies r-kernelfactory r-randomforest)) (home-page "https://cran.r-project.org/web/packages/aCRM/") (synopsis "Convenience functions for analytical customer relationship management") (description "This package provides convenience functions for data preparation and modeling often used in @dfn{analytical customer relationship management} (aCRM).") (license license:gpl2+))) (define-public r-tree (package (name "r-tree") (version "1.0-43") (source (origin (method url-fetch) (uri (cran-uri "tree" version)) (sha256 (base32 "11sjkm89ql1576jy0cqbxzjdpx7qs95wbgdxg92lzkiw05nrj2lv")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tree/") (synopsis "Classification and regression trees") (description "This package provides procedures to work with classification and regression trees.") (license license:gpl2+))) (define-public r-treeclust (package (name "r-treeclust") (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "treeClust" version)) (sha256 (base32 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z")))) (properties `((upstream-name . "treeClust"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-rpart)) (home-page "https://cran.r-project.org/web/packages/treeClust/") (synopsis "Cluster distances through trees") (description "This package provides tools to create a measure of inter-point dissimilarity useful for clustering mixed data, and, optionally, perform the clustering.") (license license:gpl2+))) (define-public r-treemap (package (name "r-treemap") (version "2.4-4") (source (origin (method url-fetch) (uri (cran-uri "treemap" version)) (sha256 (base32 "1h3pas3kn8zrpdpvp9vs745q94kixw5lxkbq74l5lh0n3wkqnnn5")))) (properties `((upstream-name . "treemap"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-data-table r-ggplot2 r-gridbase r-igraph r-rcolorbrewer r-shiny)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=treemap") (synopsis "Treemap visualization") (description "A treemap is a space-filling visualization of hierarchical structures. This package offers great flexibility to draw treemaps.") (license license:gpl3+))) (define-public r-acrosstic (package (name "r-acrosstic") (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "AcrossTic" version)) (sha256 (base32 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0")))) (properties `((upstream-name . "AcrossTic"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-treeclust)) (home-page "https://cran.r-project.org/web/packages/AcrossTic/") (synopsis "Cost-minimal regular spanning subgraph with TreeClust") (description "This is a package for constructing minimum-cost regular spanning subgraph as part of a non-parametric two-sample test for equality of distribution.") (license license:gpl2+))) (define-public r-acrt (package (name "r-acrt") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "acrt" version)) (sha256 (base32 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s")))) (properties `((upstream-name . "acrt"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen r-sandwich)) (home-page "https://cran.r-project.org/web/packages/acrt/") (synopsis "Autocorrelation robust testing") (description "This package provides functions for testing affine hypotheses on the regression coefficient vector in regression models with autocorrelated errors.") (license license:gpl2))) (define-public r-acs (package (name "r-acs") (version "2.1.4") (source (origin (method url-fetch) (uri (cran-uri "acs" version)) (sha256 (base32 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5")))) (properties `((upstream-name . "acs"))) (build-system r-build-system) (propagated-inputs (list r-httr r-plyr r-rcpp r-stringr r-xml)) (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn") (synopsis "Work with data from the US Census") (description "This package provides a general toolkit for downloading, managing, analyzing, and presenting data from the @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census}, including SF1 (Decennial short-form), SF3 (Decennial long-form), and the American Community Survey (ACS). Confidence intervals provided with ACS data are converted to standard errors to be bundled with estimates in complex @code{acs} objects. The package provides new methods to conduct standard operations on @code{acs} objects and present/plot data in statistically appropriate ways.") (license license:gpl3))) (define-public r-acss-data (package (name "r-acss-data") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "acss.data" version)) (sha256 (base32 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv")))) (properties `((upstream-name . "acss.data"))) (build-system r-build-system) (home-page "http://complexitycalculator.com/methodology.html") (synopsis "Data for algorithmic complexity of short strings") (description "This is a data only package providing the algorithmic complexity of short strings, computed using the coding theorem method. For a given set of symbols in a string, all possible or a large number of random samples of Turing machines with a given number of states (e.g., 5) and number of symbols corresponding to the number of symbols in the strings were simulated until they reached a halting state or failed to end. This package contains data on 4.5 million strings from length 1 to 12 simulated on Turing machines with 2, 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the distribution of the halting states.") (license license:gpl2+))) (define-public r-acss (package (name "r-acss") (version "0.2-5") (source (origin (method url-fetch) (uri (cran-uri "acss" version)) (sha256 (base32 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk")))) (properties `((upstream-name . "acss"))) (build-system r-build-system) (propagated-inputs (list r-acss-data r-zoo)) (home-page "http://complexitycalculator.com/methodology.html") (synopsis "Algorithmic complexity for short strings") (description "The main purpose of this package is to provide the algorithmic complexity for short strings, an approximation of the Kolmogorov Complexity of a short string using the coding theorem method. While the database containing the complexity is provided in the data only package @code{acss.data}, this package provides functions accessing the data such as @code{prob_random} returning the posterior probability that a given string was produced by a random process. In addition, two traditional (but problematic) measures of complexity are also provided: entropy and change complexity.") (license license:gpl2+))) (define-public r-acswr (package (name "r-acswr") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ACSWR" version)) (sha256 (base32 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n")))) (properties `((upstream-name . "ACSWR"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ACSWR/") (synopsis "Companion package for the book \"A Course in Statistics with R\"") (description "This is a companion package for the book \"A Course in Statistics with R\" (ISBN 978-1-119-15272-9.)") (license license:gpl2))) (define-public r-alabama (package (name "r-alabama") (version "2023.1.0") (source (origin (method url-fetch) (uri (cran-uri "alabama" version)) (sha256 (base32 "075zqyarb970d4zpxsivaxhnmdg916ypfxrp0mqngnww5p3nfpwj")))) (properties `((upstream-name . "alabama"))) (build-system r-build-system) (propagated-inputs (list r-numderiv)) (home-page "https://cran.r-project.org/web/packages/alabama/") (synopsis "Constrained nonlinear optimization") (description "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization Algorithm; it is used for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed.") (license license:gpl2+))) (define-public r-gdina (package (name "r-gdina") (version "2.9.4") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 "10bbwr4q6cp36dnwhddviqg7f00h92gdmvblw0lxn72v4869vhn1")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs (list r-alabama r-ggplot2 r-mass r-nloptr r-numderiv r-rcpp r-rcpparmadillo r-rsolnp r-shiny r-shinydashboard)) (native-inputs (list r-knitr)) (home-page "https://github.com/Wenchao-Ma/GDINA") (synopsis "Generalized DINA model framework") (description "This package provides a set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7} and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.") (license license:gpl3))) (define-public r-actcd (package (name "r-actcd") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "ACTCD" version)) (sha256 (base32 "1a0gsznca5fv7i29xpcns4rkas5q88wv01rxvd4j66n64gw0ri4j")))) (properties `((upstream-name . "ACTCD"))) (build-system r-build-system) (propagated-inputs (list r-gdina r-r-methodss3)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ACTCD/") (synopsis "Asymptotic classification theory for cognitive diagnosis") (description "This is a package supporting cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of sum-scores, cluster analysis techniques can be used to classify examinees into latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.") (license license:gpl2+))) (define-public r-ineq (package (name "r-ineq") (version "0.2-13") (source (origin (method url-fetch) (uri (cran-uri "ineq" version)) (sha256 (base32 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0")))) (properties `((upstream-name . "ineq"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ineq/") (synopsis "Measuring inequality, concentration, and poverty") (description "This package provides tools for measuring inequality, concentration, and poverty measures. It provides both empirical and theoretical Lorenz curves.") ;; Either of these two versions. (license (list license:gpl2 license:gpl3)))) (define-public r-actfrag (package (name "r-actfrag") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "ActFrag" version)) (sha256 (base32 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1")))) (properties `((upstream-name . "ActFrag"))) (build-system r-build-system) (propagated-inputs (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr)) (home-page "https://github.com/junruidi/ActFrag") (synopsis "Activity fragmentation metrics extraction") (description "This package provides functions to extract commonly used fragmentation metrics to quantify time accumulation strategies based on minute level actigraphy-measured activity counts data.") (license license:gpl3))) (define-public r-ash (package (name "r-ash") (version "1.0-15") (source (origin (method url-fetch) (uri (cran-uri "ash" version)) (sha256 (base32 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb")))) (properties `((upstream-name . "ash"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ash/") (synopsis "David Scott's ASH routines") (description "This package provides David Scott's ASH routines ported from S-PLUS to R.") (license license:gpl2+))) (define-public r-hdrcde (package (name "r-hdrcde") (version "3.4") (source (origin (method url-fetch) (uri (cran-uri "hdrcde" version)) (sha256 (base32 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3")))) (properties `((upstream-name . "hdrcde"))) (build-system r-build-system) (propagated-inputs (list r-ash r-ggplot2 r-kernsmooth r-ks r-locfit r-rcolorbrewer)) (native-inputs (list gfortran)) (home-page "https://pkg.robjhyndman.com/hdrcde") (synopsis "Highest density regions and conditional density estimation") (description "This is a package for the computation of highest density regions in one and two dimensions, kernel estimation of univariate density functions conditional on one covariate, and multimodal regression.") (license license:gpl3))) (define-public r-rainbow (package (name "r-rainbow") (version "3.7") (source (origin (method url-fetch) (uri (cran-uri "rainbow" version)) (sha256 (base32 "1cldipi3cb55d434wv03ymwygbisfwgq2b84gwwkgqpfal2xk78m")))) (properties `((upstream-name . "rainbow"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-colorspace r-hdrcde r-ks r-mass r-pcapp)) (home-page "https://cran.r-project.org/web/packages/rainbow/") (synopsis "Bagplots, boxplots and rainbow plots for functional data") (description "This is a package for visualizing functional data and identifying functional outliers with bagplots, boxplots and rainbow plots.") (license license:gpl3))) (define-public r-fds (package (name "r-fds") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "fds" version)) (sha256 (base32 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0")))) (properties `((upstream-name . "fds"))) (build-system r-build-system) (propagated-inputs (list r-rainbow r-rcurl)) (home-page "https://cran.r-project.org/web/packages/fds/") (synopsis "Functional data sets") (description "This package contains a list of functional time series, sliced functional time series, and functional data sets. Functional time series is a special type of functional data observed over time. Sliced functional time series is a special type of functional time series with a time variable observed over time.") (license license:gpl2+))) (define-public r-fda (package (name "r-fda") (version "6.1.4") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 "0595887hv80blx9aq63qnmc9vr022p21zqhgp2wmdjvq1g68x0g2")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs (list r-desolve r-fds)) (native-inputs (list r-knitr)) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description "These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. The package includes data sets and script files working many examples.") (license license:gpl2+))) (define-public r-actigraphy (package (name "r-actigraphy") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "Actigraphy" version)) (sha256 (base32 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20")))) (properties `((upstream-name . "Actigraphy"))) (build-system r-build-system) (propagated-inputs (list r-fda)) (home-page "https://cran.r-project.org/web/packages/Actigraphy/") (synopsis "Actigraphy data analysis") (description "This package provides tools for functional linear modeling and analysis of actigraphy data.") (license license:asl2.0))) (define-public r-activedriver (package (name "r-activedriver") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriver" version)) (sha256 (base32 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa")))) (properties `((upstream-name . "ActiveDriver"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") (synopsis "Tools for finding cancer driver proteins") (description "This package provides a mutation analysis tool that discovers cancer driver genes with frequent mutations in protein signalling sites such as post-translational modifications (phosphorylation, ubiquitination, etc). The Poisson generalized linear regression model identifies genes where cancer mutations in signalling sites are more frequent than expected from the sequence of the entire gene. Integration of mutations with signalling information helps find new driver genes and propose candidate mechanisms to known drivers.") (license license:gpl2+))) (define-public r-activitycounts (package (name "r-activitycounts") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "activityCounts" version)) (sha256 (base32 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz")))) (properties `((upstream-name . "activityCounts"))) (build-system r-build-system) (propagated-inputs (list r-lubridate r-magrittr r-seewave r-signal r-tibble)) (home-page "https://github.com/walkabillylab/activityCounts") (synopsis "Generate ActiLife counts") (description "ActiLife generates activity counts from data collected by Actigraph accelerometers. Actigraph is one of the most common research-grade accelerometers. There is considerable research validating and developing algorithms for human activity using ActiLife counts. Unfortunately, ActiLife counts are proprietary and difficult to implement if researchers use different accelerometer brands. The code creates ActiLife counts from raw acceleration data for different accelerometer brands.") (license license:gpl3))) (define-public r-activityindex (package (name "r-activityindex") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "ActivityIndex" version)) (sha256 (base32 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5")))) (properties `((upstream-name . "ActivityIndex"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-matrixstats r-r-utils)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") (synopsis "Activity Index calculation using raw accelerometry data") (description "This is a package to read raw accelerometry from GT3X+ accelerometry data and plain table data to calculate the Activity Index from Bai et al. (2016) @url{doi:10.1371/journal.pone.0160644}.") (license license:gpl3))) (define-public r-activpal (package (name "r-activpal") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "activPAL" version)) (sha256 (base32 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na")))) (properties `((upstream-name . "activPAL"))) (build-system r-build-system) (propagated-inputs (list r-devtools r-dplyr r-ggplot2 r-lubridate r-magrittr r-tidyr)) (home-page "https://cran.r-project.org/web/packages/activPAL") (synopsis "Processing and chart generation from activPAL events files") (description "This package contains functions to generate pre-defined summary statistics from activPAL events files. The package also contains functions to produce informative graphics that visualize physical activity behaviour and trends. This includes generating graphs that align physical activity behaviour with additional time based observations described by other data sets, such as sleep diaries and continuous glucose monitoring data.") (license license:gpl3))) (define-public r-activpalprocessing (package (name "r-activpalprocessing") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "activpalProcessing" version)) (sha256 (base32 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1")))) (properties `((upstream-name . "activpalProcessing"))) (build-system r-build-system) (propagated-inputs (list r-chron)) (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") (synopsis "Process activPAL events files") (description "This package performs estimation of physical activity and sedentary behavior variables from activPAL events files.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-actogrammr (package (name "r-actogrammr") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "actogrammr" version)) (sha256 (base32 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa")))) (properties `((upstream-name . "actogrammr"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr)) (home-page "https://cran.r-project.org/web/packages/actogrammr/") (synopsis "Read in activity data and plot actograms") (description "Read in activity measurements from standard file formats used by circadian rhythm researchers, currently only ClockLab format, and process and plot the data. The central type of plot is the actogram, as first described in \"Activity and distribution of certain wild mice in relation to biotic communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") (license license:gpl3))) (define-public r-expint (package (name "r-expint") (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "expint" version)) (sha256 (base32 "1cn6c84pqf8bgk109qm4znn186h6s6cpll3d11cw144h0vh4yr8j")))) (properties `((upstream-name . "expint"))) (build-system r-build-system) (home-page "https://gitlab.com/vigou3/expint") (synopsis "Exponential integral and incomplete Gamma function") (description "This package provides the exponential integrals @code{E_1(x)}, @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma function @code{G(a, x)} defined for negative values of its first argument. The package also gives easy access to the underlying C routines through an API; see the package vignette for details.") (license license:gpl2+))) (define-public r-actuar (package (name "r-actuar") (version "3.3-4") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 "06693w4cwcchi0z64vgg7khc4k4209nw6m2x441nwix4x6rk1zjs")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs (list r-expint)) (home-page "https://gitlab.com/vigou3/actuar") (synopsis "Actuarial functions and heavy tailed distributions") (description "This package provides functions and data sets for actuarial science: modeling of loss distributions; risk theory and ruin theory; simulation of compound models, discrete mixtures and compound hierarchical models; credibility theory. It boasts support for many additional probability distributions to model insurance loss amounts and loss frequency: 19 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete distribution; zero-truncated and zero-modified extensions of the standard discrete distributions. It also supports phase-type distributions commonly used to compute ruin probabilities.") (license license:gpl2+))) (define-public r-bmp (package (name "r-bmp") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "bmp" version)) (sha256 (base32 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx")))) (properties `((upstream-name . "bmp"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bmp/") (synopsis "Read Bitmap (BMP) images") (description "This package provides pure R tools to read BMP format images. It is currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") (license license:gpl2+))) (define-public r-readbitmap (package (name "r-readbitmap") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "readbitmap" version)) (sha256 (base32 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk")))) (properties `((upstream-name . "readbitmap"))) (build-system r-build-system) (inputs (list libjpeg-turbo libpng)) (propagated-inputs (list r-bmp r-jpeg r-png r-tiff)) (home-page "https://github.com/jefferis/readbitmap") (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") (description "This package provides tools to identify and read BMP, JPEG, PNG, and TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than the file extension.") (license license:gpl2+))) (define-public r-imager (package (name "r-imager") (version "0.45.2") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 "0mmzp55j1svlaa0lfmmaz8hijlkbk0wkv2craxhc6gyx0g5qp129")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs (list fftw libtiff libx11 zlib)) (propagated-inputs (list r-downloader r-igraph r-jpeg r-magrittr r-png r-purrr r-rcpp r-readbitmap r-stringr)) (native-inputs (list pkg-config r-knitr)) (home-page "https://dahtah.github.io/imager/") (synopsis "Image processing library") (description "This is a package for fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one color dimension). It provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a simple, modern C++ library for image processing.") (license license:lgpl3))) (define-public r-acuityview (package (name "r-acuityview") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "AcuityView" version)) (sha256 (base32 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l")))) (properties `((upstream-name . "AcuityView"))) (build-system r-build-system) (propagated-inputs (list r-fftwtools r-imager r-plotrix)) (home-page "https://cran.r-project.org/web/packages/AcuityView/") (synopsis "Display scenes as seen by an animal with less acute vision") (description "This package provides a simple method for representing a visual scene as it may be seen by an animal with less acute vision.") (license license:gpl2+))) (define-public r-caret (package (name "r-caret") (version "6.0-94") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 "1a191n9qswvf8ri6id8picqgdqx15l6mp996v6f77fv0l8yfh597")))) (build-system r-build-system) (propagated-inputs (list r-e1071 r-foreach r-ggplot2 r-lattice r-modelmetrics r-nlme r-plyr r-proc r-recipes r-reshape2 r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/topepo/caret") (synopsis "Classification and regression training") (description "This package provides miscellaneous functions for training and plotting classification and regression models.") (license license:gpl2+))) (define-public r-caretensemble (package (name "r-caretensemble") (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "caretEnsemble" version)) (sha256 (base32 "14d318czpqpalf18ggd9mx6f4nz3r4zilljvgxzy2a8v450y96ch")))) (properties `((upstream-name . "caretEnsemble"))) (build-system r-build-system) (propagated-inputs (list r-caret r-data-table r-digest r-ggplot2 r-gridextra r-lattice r-pbapply r-plyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/zachmayer/caretEnsemble") (synopsis "Ensembles of caret models") (description "This is a framework for fitting multiple caret models. It uses the same re-sampling strategy as well as creating ensembles of such models. Use @code{caretList} to fit multiple models and then use @code{caretEnsemble} to combine them greedily or @code{caretStack} to combine them using a caret model.") (license license:expat))) (define-public r-adabag (package (name "r-adabag") (version "5.0") (source (origin (method url-fetch) (uri (cran-uri "adabag" version)) (sha256 (base32 "03nnqgia61pavic9l6av0hh81wilxlkrx3g244ypar1fv9ppan7c")))) (properties `((upstream-name . "adabag"))) (build-system r-build-system) (propagated-inputs (list r-caret r-consrank r-doparallel r-dplyr r-foreach r-rpart r-tidyr)) (home-page "https://cran.r-project.org/web/packages/adabag/") (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") (description "This package implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation estimation of the error can be done.") (license license:gpl2+))) (define-public r-adagio (package (name "r-adagio") (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "adagio" version)) (sha256 (base32 "100mqwlzqml154d0hk7spi4sbwx9y3gh06vkls49kca2q1kf99qz")))) (properties `((upstream-name . "adagio"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve)) (home-page "https://cran.r-project.org/web/packages/adagio/") (synopsis "Discrete and global optimization routines") (description "This package provides methods and algorithms for discrete optimization, e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and Hooke-Jeeves minimization, and some (evolutionary) global optimization functions.") (license license:gpl3+))) (define-public r-univoutl (package (name "r-univoutl") (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "univOutl" version)) (sha256 (base32 "1kp014bhs8v02fp7misrj4fpfp2na9lg45p5zqvlfaypnm5imsr9")))) (properties `((upstream-name . "univOutl"))) (build-system r-build-system) (propagated-inputs (list r-hmisc r-robustbase)) (home-page "https://github.com/marcellodo/univOutl") (synopsis "Detection of univariate outliers") (description "This package provides well-known outlier detection techniques in the univariate case. Methods to deal with skewed distribution are included too. The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of historical data is implemented as well. When available, survey weights can be used in outliers detection.") (license license:gpl2+))) (define-public r-tolerance (package (name "r-tolerance") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "tolerance" version)) (sha256 (base32 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd")))) (properties `((upstream-name . "tolerance"))) (build-system r-build-system) (propagated-inputs (list r-mass r-rgl)) (home-page "https://cran.r-project.org/web/packages/tolerance/") (synopsis "Statistical tolerance intervals and regions") (description "This package provides functions for estimating tolerance limits (intervals) for various univariate distributions (binomial, Cauchy, discrete Pareto, exponential, two-parameter exponential, extreme value, hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), Bayesian normal tolerance limits, multivariate normal tolerance regions, nonparametric tolerance intervals, tolerance bands for regression settings (linear regression, nonlinear regression, nonparametric regression, and multivariate regression), and analysis of variance tolerance intervals. Visualizations are also available for most of these settings.") (license license:gpl2+))) ;; Keep this in sync with the liblantern package. (define-public r-torch (package (name "r-torch") (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "torch" version)) (sha256 (base32 "024c8szg3xa2zrl5406jx3bmazbjwp2f07ja7m61ja0dr3z7lvbq")))) (properties `((upstream-name . "torch"))) (build-system r-build-system) (arguments (list #:phases (let ((python-version (version-major+minor (package-version python)))) #~(modify-phases %standard-phases (add-after 'install 'link-libraries (lambda* (#:key inputs #:allow-other-keys) (let ((deps (string-append #$output "/site-library/torch/deps")) (site-packages (string-append "/lib/python" #$python-version "/site-packages"))) (mkdir-p deps) (symlink (search-input-file inputs (string-append site-packages "/torch/lib/libtorch.so")) (string-append deps "/libtorch.so")) (symlink (search-input-file inputs "/lib/liblantern.so") (string-append deps "/liblantern.so"))))))))) (inputs (list python-pytorch-for-r-torch liblantern)) (propagated-inputs (list r-bit64 r-callr r-cli r-coro r-desc r-ellipsis r-glue r-jsonlite r-magrittr r-r6 r-rcpp r-rlang r-safetensors r-withr)) (native-inputs (list r-knitr)) (home-page "https://torch.mlverse.org/docs") (synopsis "Tensors and neural networks with GPU acceleration") (description "This package provides functionality to define and train neural networks similar to PyTorch but written entirely in R using the libtorch library. It also supports low-level tensor operations and GPU acceleration.") (license license:expat))) (define-public r-additivitytests (package (name "r-additivitytests") (version "1.1-4.1") (source (origin (method url-fetch) (uri (cran-uri "additivityTests" version)) (sha256 (base32 "00kzfv86z6kk0gvbz9mg3p6xi5fb8cn74rhslr17rdpd02md0884")))) (properties `((upstream-name . "additivityTests"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/simecek/additivityTests") (synopsis "Additivity tests in the two way Anova with single sub-class numbers") (description "This package provides an implementation of the Tukey, Mandel, Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") (license license:gpl3))) (define-public r-flexclust (package (name "r-flexclust") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "flexclust" version)) (sha256 (base32 "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn")))) (properties `((upstream-name . "flexclust"))) (build-system r-build-system) (propagated-inputs (list r-class r-lattice r-modeltools)) (home-page "https://cran.r-project.org/web/packages/flexclust/") (synopsis "Flexible cluster algorithms") (description "The main function @code{kcca} implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.") (license license:gpl2))) (define-public r-biclust (package (name "r-biclust") (version "2.0.3.1") (source (origin (method url-fetch) (uri (cran-uri "biclust" version)) (sha256 (base32 "11fcb6z5lzz6yl8hsa8ppr53i8yn8k4m19k55ynznhkw780184c7")))) (properties `((upstream-name . "biclust"))) (build-system r-build-system) (propagated-inputs (list r-additivitytests r-colorspace r-flexclust r-ggplot2 r-lattice r-mass r-tidyr)) (home-page "https://cran.r-project.org/web/packages/biclust/") (synopsis "BiCluster algorithms") (description "The main function @code{biclust()} provides several algorithms to find biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax. In addition, the package provides methods for data preprocessing (normalization and discretization), visualization, and validation of bicluster solutions.") (license license:gpl3))) (define-public r-icge (package (name "r-icge") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "ICGE" version)) (sha256 (base32 "13p9v0g5qda8bpj3sj9p277l7idv4jscrsszg2kn080dapp3cppp")))) (properties `((upstream-name . "ICGE"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-fastcluster r-mass)) (home-page "https://cran.r-project.org/web/packages/ICGE/") (synopsis "Cluster estimation and identification of atypical units") (description "ICGE is a package that helps to estimate the number of real clusters in data as well as to identify atypical units. The underlying methods are based on distances rather than on unit x variables.") (license license:gpl2+))) (define-public r-depth (package (name "r-depth") (version "2.1-1.1") (source (origin (method url-fetch) (uri (cran-uri "depth" version)) (sha256 (base32 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m")))) (properties `((upstream-name . "depth"))) (build-system r-build-system) (propagated-inputs (list r-abind r-circular r-rgl)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/depth/") (synopsis "Nonparametric depth functions for multivariate analysis") (description "This package provides tools for depth functions methodology applied to multivariate analysis. Besides allowing calculation of depth values and depth-based location estimators, the package includes functions or drawing contour plots and perspective plots of depth functions. Euclidean and spherical depths are supported.") (license license:gpl2))) (define-public r-archetypes (package (name "r-archetypes") (version "2.2-0.1") (source (origin (method url-fetch) (uri (cran-uri "archetypes" version)) (sha256 (base32 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0")))) (properties `((upstream-name . "archetypes"))) (build-system r-build-system) (propagated-inputs (list r-modeltools r-nnls)) (home-page "https://cran.r-project.org/web/packages/archetypes") (synopsis "Archetypal analysis") (description "The main function @code{archetypes} implements a framework for archetypal analysis supporting arbitrary problem solving mechanisms for the different conceptual parts of the algorithm.") (license license:gpl2+))) (define-public r-shapes (package (name "r-shapes") (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "shapes" version)) (sha256 (base32 "155q6asc9202f85snyjaxhm8qpj7swgzhg95sisjy506gvcb6c8z")))) (properties `((upstream-name . "shapes"))) (build-system r-build-system) (propagated-inputs (list r-mass r-minpack-lm r-rgl r-scatterplot3d)) (home-page "https://www.maths.nottingham.ac.uk/~ild/shapes") (synopsis "Statistical shape analysis") (description "This package provides routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.") (license license:gpl2))) (define-public r-animation (package (name "r-animation") (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "animation" version)) (sha256 (base32 "0sg4sz5lkn85yzpcg22xkr7921cbnh7g74nlp9imjy7c0hdqyhc8")) (snippet '(for-each delete-file '("inst/misc/scianimator/js/jquery.scianimator.min.js" "inst/misc/scianimator/js/jquery-1.4.4.min.js"))))) (properties `((upstream-name . "animation"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/misc/" (symlink (search-input-file inputs "share/javascript/jquery.scianimator.min.js") "scianimator/js/jquery.scianimator.min.js") (invoke "esbuild" (assoc-ref inputs "js-jquery") "--minify" (string-append "--outfile=" "scianimator/js/jquery-1.4.4.min.js")))))))) (propagated-inputs (list r-magick)) (inputs (list js-scianimator)) (native-inputs `(("esbuild" ,esbuild) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.4.4.js") (sha256 (base32 "10nl4smq63vrfb0c3n0fknm1zw7ss8gicy6wc6jb6l3rmyad075k")))))) (home-page "https://yihui.org/animation/") (synopsis "Gallery of animations and utilities to create animations") (description "This package provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. GIF, HTML pages, PDF, and videos. PDF animations can be inserted into Sweave / @code{knitr} easily.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-anthropometry (package (name "r-anthropometry") (version "1.19") (source (origin (method url-fetch) (uri (cran-uri "Anthropometry" version)) (sha256 (base32 "0aj70wm37bd5i4gzajvs6lf3zg0bz3kkf4srrcslg6drqk6n5z5l")))) (properties `((upstream-name . "Anthropometry"))) (build-system r-build-system) (propagated-inputs (list r-archetypes r-biclust r-cluster r-ddalpha r-fnn r-icge r-nnls r-rgl r-shapes)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Anthropometry/") (synopsis "Statistical methods for anthropometric data") (description "This package provides statistical methods especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.") (license license:gpl2+))) (define-public r-anytime (package (name "r-anytime") (version "0.3.9") (source (origin (method url-fetch) (uri (cran-uri "anytime" version)) (sha256 (base32 "0jjpqynai5nd7mfy1smb44356f3d5bmpxhs1i9x9jw5c959c35hh")))) (properties `((upstream-name . "anytime"))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp)) (home-page "https://dirk.eddelbuettel.com/code/anytime.html") (synopsis "Converter of input to POSIXct or Date") (description "The package converts the input in any one of character, integer, numeric, factor, or an ordered type into @code{POSIXct} (or @code{Date}) objects, using one of a number of predefined formats, and relying on Boost facilities for date and time parsing.") (license license:gpl2+))) (define-public r-anndata (package (name "r-anndata") (version "0.7.5.6") (source (origin (method url-fetch) (uri (cran-uri "anndata" version)) (sha256 (base32 "1q1ii43wfj68qdlzhqj9msxqsfzpidhhlfrisax4p943v7yh75mi")))) (properties `((upstream-name . "anndata"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate)) (native-inputs (list r-knitr)) (home-page "https://anndata.dynverse.org") (synopsis "Anndata for R") (description "This package provides a reticulate wrapper for the Python package @code{anndata}. It provides a scalable way of keeping track of data and learned annotations. It is used to read from and write to the h5ad file format.") (license license:expat))) (define-public r-adamethods (package (name "r-adamethods") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "adamethods" version)) (sha256 (base32 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj")))) (properties `((upstream-name . "adamethods"))) (build-system r-build-system) (propagated-inputs (list r-anthropometry r-archetypes r-fnn r-foreach r-nnls r-tolerance r-univoutl)) (home-page "https://cran.r-project.org/web/packages/adamethods/") (synopsis "Archetypoid algorithms and anomaly detection") (description "This package is a collection of several algorithms to obtain archetypoids with small and large databases and with both classical multivariate data and functional data (univariate and multivariate). Some of these algorithms also detect anomalies (outliers).") (license license:gpl2+))) (define-public r-idpmisc (package (name "r-idpmisc") (version "1.1.20") (source (origin (method url-fetch) (uri (cran-uri "IDPmisc" version)) (sha256 (base32 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw")))) (properties `((upstream-name . "IDPmisc"))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/IDPmisc/") (synopsis "Functions for data analyses and visualization") (description "This package provides different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.") (license license:gpl3+))) (define-public r-qqconf (package (name "r-qqconf") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "qqconf" version)) (sha256 (base32 "18wfvljd6gbf9am3hh14fgp06gpa04vw9nhl7q07li7rmlkxc1cl")))) (properties `((upstream-name . "qqconf"))) (build-system r-build-system) (inputs (list fftw)) (propagated-inputs (list r-mass r-rcpp r-robustbase)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/eweine/qqconf") (synopsis "Create simultaneous testing bands for QQ-plots") (description "This package provides functionality for creating Quantile-Quantile (QQ) and Probability-Probability (PP) plots with simultaneous testing bands to asses significance of sample deviation from a reference distribution.") (license license:gpl3))) (define-public r-qqman (package (name "r-qqman") (version "0.1.9") (source (origin (method url-fetch) (uri (cran-uri "qqman" version)) (sha256 (base32 "04xwqp4bnblrn0qijqv9bjdyy7b0vlflf87jg15ifxfkf4br6siz")))) (properties `((upstream-name . "qqman"))) (build-system r-build-system) (propagated-inputs (list r-calibrate)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/qqman/") (synopsis "Q-Q and Manhattan plots for GWAS data") (description "This package allows you to create Q-Q and Manhattan plots for GWAS data from PLINK results.") (license license:gpl3))) (define-public r-gghighlight (package (name "r-gghighlight") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "gghighlight" version)) (sha256 (base32 "1lsvy9ha4d8zs927h8jbdj5r39xqcy1n6g5prw4awiihdvcv9v66")))) (properties `((upstream-name . "gghighlight"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-ggrepel r-lifecycle r-purrr r-rlang r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/yutannihilation/gghighlight/") (synopsis "Highlight lines and points in ggplot2") (description "Suppose we have data that has so many series that it is hard to identify them by their colors as the differences are so subtle. With gghighlight we can highlight those lines that match certain criteria. The result is a usual @code{ggplot} object, so it is fully customizable and can be used with custom themes and facets.") (license license:expat))) (define-public r-ggplot-multistats (package (name "r-ggplot-multistats") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot.multistats" version)) (sha256 (base32 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il")))) (properties `((upstream-name . "ggplot.multistats"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-hexbin r-rlang r-scales)) (home-page "https://github.com/flying-sheep/ggplot.multistats") (synopsis "Multiple summary statistics for binned stats/geometries") (description "This package provides the ggplot binning layer @code{stat_summaries_hex()}, which functions similar to its singular form, but allows the use of multiple statistics per bin. Those statistics can be mapped to multiple bin aesthetics.") (license license:gpl3))) (define-public r-knn-covertree (package (name "r-knn-covertree") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "knn.covertree" version)) (sha256 (base32 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz")))) (properties `((upstream-name . "knn.covertree"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) (home-page "https://github.com/flying-sheep/knn.covertree") (synopsis "Accurate kNN Implementation with multiple distance measures") (description "Similarly to the FNN package, this package allows calculation of the k nearest neighbors (kNN) of a data matrix. The implementation is based on cover trees introduced by Alina Beygelzimer, Sham Kakade, and John Langford (2006) @url{doi:10.1145/1143844.1143857}.") (license license:agpl3+))) (define-public r-poibin (package (name "r-poibin") (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "poibin" version)) (sha256 (base32 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v")))) (properties `((upstream-name . "poibin"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/poibin/") (synopsis "Poisson binomial distribution") (description "This package provides an implementation of both the exact and approximation methods for computing the @dfn{cumulative distribution function} (CDF) of the Poisson binomial distribution. It also provides the @dfn{probability mass function} (PMF), quantile function, and random number generation for the Poisson binomial distribution.") (license license:gpl2))) (define-public r-diagram (package (name "r-diagram") (version "1.6.5") (source (origin (method url-fetch) (uri (cran-uri "diagram" version)) (sha256 (base32 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79")))) (properties `((upstream-name . "diagram"))) (build-system r-build-system) (propagated-inputs (list r-shape)) (home-page "https://cran.r-project.org/web/packages/diagram/") (synopsis "Visualize simple graphs (networks) and plot flow diagrams") (description "This package provides tools to visualize simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualizing webs, electrical networks, etc. It also includes supporting material for the book \"A practical guide to ecological modelling - using R as a simulation platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012).") (license license:gpl2+))) (define-public r-lim (package (name "r-lim") (version "1.4.7") (source (origin (method url-fetch) (uri (cran-uri "LIM" version)) (sha256 (base32 "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj")))) (properties `((upstream-name . "LIM"))) (build-system r-build-system) (propagated-inputs (list r-diagram r-limsolve)) (home-page "https://cran.r-project.org/web/packages/LIM/") (synopsis "Linear inverse model examples and solution methods") (description "This package provides functions that read and solve linear inverse problems (food web problems, linear programming problems).") (license license:gpl2+))) (define-public r-shinycssloaders (package (name "r-shinycssloaders") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "shinycssloaders" version)) (sha256 (base32 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl")))) (properties `((upstream-name . "shinycssloaders"))) (build-system r-build-system) (propagated-inputs (list r-digest r-glue r-shiny)) (home-page "https://github.com/andrewsali/shinycssloaders") (synopsis "Add CSS loading animations to Shiny outputs") (description "This package provides tools to create a lightweight Shiny wrapper for the css-loaders created by Luke Hass @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will automatically show a loader when the output is (re)calculating.") (license license:gpl3))) (define-public r-rsvg (package (name "r-rsvg") (version "2.6.0") (source (origin (method url-fetch) (uri (cran-uri "rsvg" version)) (sha256 (base32 "0w29isj7n33vwacvk5h6ghgm9j3phghnz7a98b1xi60cyk08qi2b")))) (properties `((upstream-name . "rsvg"))) (build-system r-build-system) (inputs (list (librsvg-for-system) pcre2 zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/rsvg#readme") (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays") (description "This package allows you to render vector-based SVG images into high-quality custom-size bitmap arrays using the librsvg2 library. The resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In addition, the package can convert images directly to various formats such as PDF or PostScript.") (license license:expat))) (define-public r-influencer (package (name "r-influencer") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "influenceR" version)) (sha256 (base32 "137m40xs9xfqcm88gi7w86b310rysf3a973wp7x3543n1y1f8r41")))) (properties `((upstream-name . "influenceR"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix)) (home-page "https://github.com/rcc-uchicago/influenceR") (synopsis "Tools to quantify structural importance of nodes in a network") (description "This package provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's algorithm to identify key players, and Valente's bridging metric. The betweenness, Key Players, and bridging implementations are parallelized with OpenMP.") (license license:gpl2))) (define-public r-emplik (package (name "r-emplik") (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "emplik" version)) (sha256 (base32 "1f6v0bg9sl8kn4y8bpgjyc1b18xkmfbs86gbbmbh198v335lgcrb")))) (properties `((upstream-name . "emplik"))) (build-system r-build-system) (propagated-inputs (list r-quantreg)) (home-page "https://www.ms.uky.edu/~mai/EmpLik.html") (synopsis "Empirical likelihood ratio for censored/truncated data") (description "This package provides empirical likelihood ratio tests for means/quantiles/hazards from possibly censored and/or truncated data. It also does regression.") (license license:gpl2+))) (define-public r-imputeyn (package (name "r-imputeyn") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "imputeYn" version)) (sha256 (base32 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs")))) (properties `((upstream-name . "imputeYn"))) (build-system r-build-system) (propagated-inputs (list r-boot r-emplik r-mvtnorm r-quadprog r-survival)) (home-page "https://cran.r-project.org/web/packages/imputeYn/") (synopsis "Impute last largest censored observation under weighted least squares") (description "This package allows for the imputation of the last largest censored observantions. This method brings less bias and more efficient estimates for AFT models.") (license license:gpl2))) (define-public r-adapenetclass (package (name "r-adapenetclass") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "AdapEnetClass" version)) (sha256 (base32 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc")))) (properties `((upstream-name . "AdapEnetClass"))) (build-system r-build-system) (propagated-inputs (list r-glmnet r-imputeyn r-lars r-quadprog)) (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/") (synopsis "Class of adaptive elastic net methods for censored data") (description "This package provides methods for variable selection for AFT models.") (license license:gpl2))) (define-public r-flock (package (name "r-flock") (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "flock" version)) (sha256 (base32 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7")))) (properties `((upstream-name . "flock"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/flock/") (synopsis "Process synchronization using file locks") (description "This package implements synchronization between R processes (spawned by using the @code{parallel} package for instance) using file locks. It supports both exclusive and shared locking.") (license license:asl2.0))) (define-public r-archivist (package (name "r-archivist") (version "2.3.6") (source (origin (method url-fetch) (uri (cran-uri "archivist" version)) (sha256 (base32 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9")))) (properties `((upstream-name . "archivist"))) (build-system r-build-system) (propagated-inputs (list r-dbi r-digest r-flock r-httr r-lubridate r-magrittr r-rcurl r-rsqlite)) (native-inputs (list r-knitr)) (home-page "https://pbiecek.github.io/archivist/") (synopsis "Tools for storing, restoring and searching for R objects") (description "Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. Archivist helps to store and manage artifacts created in R. It allows you to store selected artifacts as binary files together with their metadata and relations. Archivist allows sharing artifacts with others. It can look for already created artifacts by using its class, name, date of the creation or other properties. It also makes it easy to restore such artifacts.") (license license:gpl2))) (define-public r-versions (package (name "r-versions") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "versions" version)) (sha256 (base32 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd")))) (properties `((upstream-name . "versions"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/versions/") (synopsis "Query and install specific versions of CRAN packages") (description "This package allows you to install specified versions of R packages hosted on CRAN and provides functions to list available versions and the versions of currently installed packages.") (license license:bsd-3))) (define-public r-adapr (package (name "r-adapr") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "adapr" version)) (sha256 (base32 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw")))) (properties `((upstream-name . "adapr"))) (build-system r-build-system) (propagated-inputs (list r-archivist r-devtools r-digest r-doparallel r-gdata r-ggplot2 r-git2r r-igraph r-knitr r-plotly r-plyr r-rmarkdown r-shiny r-shinydashboard r-versions)) (home-page "https://cran.r-project.org/web/packages/adapr/") (synopsis "Implementation of an accountable data analysis process") (description "This package tracks reading and writing within R scripts that are organized into a directed acyclic graph. It contains an interactive Shiny application @code{adaprApp()}. It uses Git and file hashes to track version histories of inputs and outputs.") (license license:lgpl2.0))) (define-public r-adapsamp (package (name "r-adapsamp") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "AdapSamp" version)) (sha256 (base32 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis")))) (properties `((upstream-name . "AdapSamp"))) (build-system r-build-system) (propagated-inputs (list r-pracma)) (home-page "https://cran.r-project.org/web/packages/AdapSamp/") (synopsis "Adaptive sampling algorithms") (description "For distributions whose probability density functions are log-concave, the adaptive rejection sampling algorithm can be used to build envelope functions for sampling. For others, the modified adaptive rejection sampling algorithm, the concave-convex adaptive rejection sampling algorithm, and the adaptive slice sampling algorithm can be used. This R package mainly includes these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and @code{rASS()}. These functions can realize sampling based on the algorithms above.") (license license:gpl2))) (define-public r-adaptalint (package (name "r-adaptalint") (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "adaptalint" version)) (sha256 (base32 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf")))) (properties `((upstream-name . "adaptalint"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-lintr r-purrr)) (home-page "https://cran.r-project.org/web/packages/adaptalint/") (synopsis "Check R code style") (description "This package provides tools to infer the code style (which style rules are followed and which ones are not) from one package and use it to check another. This makes it easier to find and correct the most important problems first.") (license license:gpl3))) (define-public r-fracdiff (package (name "r-fracdiff") (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "fracdiff" version)) (sha256 (base32 "0dzl011c92skf7hmx1zvdwsrashmfkxy9p2wig35nzr8609qhpxc")))) (properties `((upstream-name . "fracdiff"))) (build-system r-build-system) (home-page "https://github.com/mmaechler/fracdiff") (synopsis "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models") (description "This package provides tools for the maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (license license:gpl2+))) (define-public r-forecast (package (name "r-forecast") (version "8.21.1") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 "09w1vh96cf9wz071why5f4265cvvwqi2b3wb0khrjvkzgkiaq7l1")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-fracdiff r-generics r-ggplot2 r-lmtest r-magrittr r-nnet r-rcpp r-rcpparmadillo r-timedate r-tseries r-urca r-zoo)) (native-inputs (list r-knitr)) ; needed for vignettes (home-page "https://pkg.robjhyndman.com/forecast/") (synopsis "Forecasting functions for time series and linear models") (description "This package provides methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.") (license license:gpl3))) (define-public r-forestplot (package (name "r-forestplot") (version "3.1.3") (source (origin (method url-fetch) (uri (cran-uri "forestplot" version)) (sha256 (base32 "0jbmhgbf167xi0lxqinf6m4gmh10r582bify1i731k9ywcc7psqk")))) (properties `((upstream-name . "forestplot"))) (build-system r-build-system) (propagated-inputs (list r-abind r-checkmate)) (native-inputs (list r-knitr)) (home-page "https://gforge.se/packages/") (synopsis "Advanced forest plot using @code{grid} graphics") (description "This package provides a forest plot that allows for multiple confidence intervals per row, custom fonts for each text element, custom confidence intervals, text mixed with expressions, and more. The aim is to extend the use of forest plots beyond meta-analyses. This is a more general version of the original @code{rmeta} package's @code{forestplot()} function and relies heavily on the @code{grid} package.") (license license:gpl2))) (define-public r-formattable (package (name "r-formattable") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "formattable" version)) (sha256 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag")))) (properties `((upstream-name . "formattable"))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown)) (native-inputs (list r-knitr)) (home-page "https://github.com/renkun-ken/formattable") (synopsis "Print vectors and data frames with text fromatting") (description "This R package provides functions to create formattable vectors and data frames. @emph{Formattable} vectors are printed with text formatting, and formattable data frames are printed with multiple types of formatting in HTML to improve the readability of data presented in tabular form rendered in web pages.") (license license:expat))) (define-public r-formula-tools (package (name "r-formula-tools") (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "formula.tools" version)) (sha256 (base32 "15d3ikfmsh9zszfgfkrxb3jkipl41inm7n6bhs73kwlnklnygq2g")))) (properties `((upstream-name . "formula.tools"))) (build-system r-build-system) (propagated-inputs (list r-operator-tools)) (home-page "https://github.com/decisionpatterns/formula.tools") (synopsis "Utilities for manipulating formulas, calls, assignments and other R objects") (description "These utilities facilitate the programmatic manipulations of formulas, expressions, calls, assignments and other R language objects. These objects all share the same structure: a left-hand side, operator and right-hand side. This packages provides methods for accessing and modifying this structures as well as extracting and replacing names and symbols from these objects.") (license license:gpl2))) (define-public r-xmisc (package (name "r-xmisc") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "Xmisc" version)) (sha256 (base32 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1")))) (properties `((upstream-name . "Xmisc"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=Xmisc") (synopsis "Xiaobei's miscellaneous classes and functions") (description "This package provides Xiaobei's miscellaneous classes and functions, which are useful when developing R packages for @dfn{object oriented programming} (OOP) using R Reference Class.") (license license:gpl2+))) (define-public r-proxyc (package (name "r-proxyc") (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "proxyC" version)) (sha256 (base32 "1skq5cxd0kh2pccfg4h9bis4wbqb6zm04q4iwfa6dqml6hyiv7gk")))) (properties `((upstream-name . "proxyC"))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel)) (home-page "https://cran.r-project.org/package=proxyC") (synopsis "Compute proximity in large sparse matrices") (description "This package provides efficient tools to compute the proximity between rows or columns of large matrices. Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. Among several built-in similarity/distance measures, computation of correlation, cosine similarity and Euclidean distance is particularly fast.") (license license:gpl3))) (define-public r-isocodes (package (name "r-isocodes") (version "2023.12.07") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 "03nrcv1hh12yyqql03cr94kk3hnpynvrm4kv3plmdli2b3n1yqvk")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") (synopsis "Selected ISO codes") (description "This package provides ISO language, territory, currency, script and character codes. It provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 character codes as well as the UN M.49 area codes.") (license license:gpl2))) (define-public r-stopwords (package (name "r-stopwords") (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "stopwords" version)) (sha256 (base32 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65")))) (properties `((upstream-name . "stopwords"))) (build-system r-build-system) (propagated-inputs (list r-isocodes)) (home-page "https://github.com/quanteda/stopwords") (synopsis "Multilingual stopword lists") (description "This package provides multiple sources of stopwords, for use in text analysis and natural language processing.") (license license:expat))) (define-public r-spacyr (package (name "r-spacyr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "spacyr" version)) (sha256 (base32 "1z4nx8phrc0l73xic2lkff03a54kjw343425h5mm2afz6zidcmf4")))) (properties `((upstream-name . "spacyr"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-reticulate)) (native-inputs (list r-r-rsp)) (home-page "https://spacyr.quanteda.io") (synopsis "R wrapper for the spaCy NLP library") (description "This package provides an R wrapper to the Python @dfn{natural language processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.") (license license:gpl3))) (define-public r-snowballc (package (name "r-snowballc") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "SnowballC" version)) (sha256 (base32 "0d60h5qpk0vahcxm1y6ryqj00s4yrsdz671vq1i1cx8668zz2g3m")))) (properties `((upstream-name . "SnowballC"))) (build-system r-build-system) (home-page "https://r-forge.r-project.org/projects/r-temis/") (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library") (description "This package provides an R interface to the C @code{libstemmer} library that implements Porter's word stemming algorithm for collapsing words to a common root to aid comparison of vocabulary. Currently supported languages are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian, Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (license license:bsd-3))) (define-public r-quanteda (package (name "r-quanteda") (version "3.3.1") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 "0rj13m0fmk0h9akmqwwp7nkwrvym7sj97jgvjr4mvi3sglq451b2")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs (list r-fastmatch r-jsonlite r-magrittr r-matrix r-rcpp r-rcpparmadillo r-rcppparallel r-snowballc r-stopwords r-stringi r-xml2 r-yaml)) (native-inputs (list r-knitr)) (home-page "https://quanteda.io") (synopsis "Quantitative analysis of textual data") (description "This package provides a fast, flexible, and comprehensive framework for quantitative text analysis in R. It provides functionality for corpus management, creating and manipulating tokens and ngrams, exploring keywords in context, forming and manipulating sparse matrices of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and distances, applying content dictionaries, applying supervised and unsupervised machine learning, visually representing text and text analyses, and more.") (license license:gpl3))) (define-public r-topicmodels (package (name "r-topicmodels") (version "0.2-16") (source (origin (method url-fetch) (uri (cran-uri "topicmodels" version)) (sha256 (base32 "01g9avk0ldqnz15n8112vad31c1n7r6rih5dh6x3383vvmjrqp0d")))) (properties '((upstream-name . "topicmodels") (updater-extra-inputs . ("gsl")))) (build-system r-build-system) (inputs (list gsl)) (propagated-inputs (list r-modeltools r-slam r-tm)) (home-page "https://cran.r-project.org/package=topicmodels") (synopsis "Topic models") (description "This package provides an interface to the C code for @dfn{Latent Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by David M. Blei and co-authors and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan and co-authors.") (license license:gpl2))) (define-public r-stm (package (name "r-stm") (version "1.3.7") (source (origin (method url-fetch) (uri (cran-uri "stm" version)) (sha256 (base32 "0cvv6q5r55iqk327rav25dymvnn77rj8chmgkbkwd0c1dpqf4x5q")))) (properties `((upstream-name . "stm"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-glmnet r-lda r-matrix r-matrixstats r-quadprog r-quanteda r-rcpp r-rcpparmadillo r-slam r-stringr)) (home-page "https://www.structuraltopicmodel.com/") (synopsis "Estimation of the Structural Topic Model") (description "The @dfn{Structural Topic Model} (STM) allows researchers to estimate topic models with document-level covariates. The package also includes tools for model selection, visualization, and estimation of topic-covariate regressions.") (license license:expat))) (define-public r-polycor (package (name "r-polycor") (version "0.8-1") (source (origin (method url-fetch) (uri (cran-uri "polycor" version)) (sha256 (base32 "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh")))) (properties `((upstream-name . "polycor"))) (build-system r-build-system) (propagated-inputs (list r-admisc r-matrix r-mvtnorm)) (home-page "https://r-forge.r-project.org/projects/polycor/") (synopsis "Polychoric and polyserial correlations") (description "This package provides tools to compute polychoric and polyserial correlations by quick \"two-step\" methods or ML, optionally with standard errors; tetrachoric and biserial correlations are special cases.") (license license:gpl2+))) (define-public r-msm (package (name "r-msm") (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "msm" version)) (sha256 (base32 "0nvqgx74rwx061vgmhvc872bwq8smccm2n8r51s37vbfjqmphd6i")))) (properties `((upstream-name . "msm"))) (build-system r-build-system) (propagated-inputs (list r-expm r-mvtnorm r-survival)) (home-page "https://github.com/chjackson/msm") (synopsis "Multi-state Markov and hidden Markov models in continuous time") (description "This package provides functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was designed for processes observed at arbitrary times in continuous time (panel data) but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.") (license license:gpl2+))) (define-public r-ltm (package (name "r-ltm") (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "ltm" version)) (sha256 (base32 "0vhgbk6j0z3limsrbjkjkpfn2whiaij5j4jf1gg66mjs9dlylap1")))) (properties `((upstream-name . "ltm"))) (build-system r-build-system) (propagated-inputs (list r-mass r-msm r-polycor)) (home-page "https://github.com/drizopoulos/ltm") (synopsis "Latent trait models under IRT") (description "This is a package supporting the analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded Response, and the Generalized Partial Credit Models.") (license license:gpl2+))) (define-public r-mi (package (name "r-mi") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "mi" version)) (sha256 (base32 "11f75ivnax6p48mp2pasprws488cm2daym87sw2mcrywvf89fyjd")))) (properties `((upstream-name . "mi"))) (build-system r-build-system) (propagated-inputs (list r-arm r-matrix)) (native-inputs (list r-knitr)) (home-page "http://www.stat.columbia.edu/~gelman/") (synopsis "Missing data imputation and model checking") (description "This package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.") (license license:gpl2+))) (define-public r-matrixcalc (package (name "r-matrixcalc") (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "matrixcalc" version)) (sha256 (base32 "09pk0ym6qzribxc6v18cpb6478i4r4kzxpkljjbb3n323zqx5iqb")))) (properties `((upstream-name . "matrixcalc"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/matrixcalc/") (synopsis "Collection of functions for matrix calculations") (description "This package provides a collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics.") (license license:gpl2+))) (define-public r-matrixextra (package (name "r-matrixextra") (version "0.1.14") (source (origin (method url-fetch) (uri (cran-uri "MatrixExtra" version)) (sha256 (base32 "09c6f467sbqa65ny9si9acwkwy4kfvhy532vikr4cd16r89xxr01")))) (properties `((upstream-name . "MatrixExtra"))) (build-system r-build-system) (propagated-inputs (list r-float r-matrix r-rcpp r-rhpcblasctl)) (native-inputs (list r-knitr)) (home-page "https://github.com/david-cortes/MatrixExtra") (synopsis "Extra methods for sparse matrices") (description "This package extends sparse matrix and vector classes from the Matrix package by providing: @enumerate @item Methods and operators that work natively on CSR formats (compressed sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting, assignment, @code{rbind()}, mathematical operators for CSR and COO such as addition or @code{sqrt()}, and methods such as @code{diag()}; @item Multi-threaded matrix multiplication and cross-product for many @code{} types, including the @code{float32} type from @code{float}; @item Coercion methods between pairs of classes which are not present in @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as convenience conversion functions; @item Utility functions for sparse matrices such as sorting the indices or removing zero-valued entries; @item Fast transposes that work by outputting in the opposite storage format; @item Faster replacements for many @code{Matrix} methods for all sparse types, such as slicing and elementwise multiplication. @item Convenience functions for sparse objects, such as @code{mapSparse} or a shorter @code{show} method. @end enumerate ") (license license:gpl2+))) (define-public r-sem (package (name "r-sem") (version "3.1-15") (source (origin (method url-fetch) (uri (cran-uri "sem" version)) (sha256 (base32 "05hk72zxvyv6kkjhk5y6qw253c64108az7030z8j1sz8wq03n0md")))) (properties `((upstream-name . "sem"))) (build-system r-build-system) (propagated-inputs (list r-boot r-mass r-mi)) (home-page "https://cran.r-project.org/package=sem") (synopsis "Structural equation models") (description "This package provides functions for fitting general linear structural equation models (with observed and latent variables) using the RAM approach, and for fitting structural equations in observed-variable models by two-stage least squares.") (license license:gpl2+))) (define-public r-semtools (package (name "r-semtools") (version "0.5-6") (source (origin (method url-fetch) (uri (cran-uri "semTools" version)) (sha256 (base32 "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm")))) (properties `((upstream-name . "semTools"))) (build-system r-build-system) (propagated-inputs (list r-lavaan r-pbivnorm)) (home-page "https://github.com/simsem/semTools/wiki") (synopsis "Useful tools for structural equation modeling") (description "This package provides useful tools for structural equation modeling.") (license license:gpl2+))) (define-public r-regsem (package (name "r-regsem") (version "1.9.5") (source (origin (method url-fetch) (uri (cran-uri "regsem" version)) (sha256 (base32 "0lvsy7byrhiizyhwnwr22v8g36735nb0liyzl1nzk0py9rjbv4kk")))) (properties `((upstream-name . "regsem"))) (build-system r-build-system) (propagated-inputs (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=regsem") (synopsis "Regularized structural equation modeling") (description "This package uses both ridge and lasso penalties (and extensions) to penalize specific parameters in structural equation models. The package offers additional cost functions, cross validation, and other extensions beyond traditional structural equation models. It also contains a function to perform @dfn{exploratory mediation} (XMed).") (license license:gpl2+))) (define-public r-stanheaders (package (name "r-stanheaders") (version "2.32.5") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 "0wqps6xy2xypxsg3p3grdiw67a0xla3vh9x9hcf2ln03yhgkn4jl")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-rcppeigen r-rcppparallel)) (native-inputs (list gfortran r-knitr)) ; for vignettes (home-page "https://mc-stan.org/") (synopsis "C++ header files for Stan") (description "The C++ header files of the Stan project are provided by this package. There is a shared object containing part of the @code{CVODES} library, but it is not accessible from R. @code{r-stanheaders} is only useful for developers who want to utilize the @code{LinkingTo} directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan} package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.") (license license:bsd-3))) (define-public r-rpf (package (name "r-rpf") (version "1.0.14") (source (origin (method url-fetch) (uri (cran-uri "rpf" version)) (sha256 (base32 "15pp6fdqxngsmcibxfzv72g25q3ww3hrazsl4c5fgi0fh450kfz4")))) (properties `((upstream-name . "rpf"))) (build-system r-build-system) (propagated-inputs (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen)) (native-inputs (list r-knitr)) (home-page "https://github.com/jpritikin/rpf") (synopsis "Response probability functions") (description "The purpose of this package is to factor out logic and math common to Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as core support code suitable for more specialized IRT packages to build upon. Complete access to optimized C functions is made available with @code{R_RegisterCCallable()}.") (license license:gpl3+))) (define-public r-openmx (package (name "r-openmx") (version "2.21.11") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 "1k3i82higil43w4pryg1ghpswa8vxmc28dcv60gvkmmjrnwp098m")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs (list r-bh r-digest r-lifecycle r-mass r-matrix r-rcpp r-rcppeigen r-rcppparallel r-rpf r-stanheaders)) (native-inputs (list gfortran r-knitr)) (home-page "http://openmx.ssri.psu.edu") (synopsis "Extended structural equation modelling") (description "This package allows for the estimation of a wide variety of advanced multivariate statistical models. It consists of a library of functions and optimizers that allow you to quickly and flexibly define an SEM model and estimate parameters given observed data.") (license license:asl2.0))) (define-public r-kutils (package (name "r-kutils") (version "1.73") (source (origin (method url-fetch) (uri (cran-uri "kutils" version)) (sha256 (base32 "0xqg1s48afpn2w0mlqfwz3sj1gdjf05cpxq4z9r01k1476lvh6c9")))) (properties `((upstream-name . "kutils"))) (build-system r-build-system) (propagated-inputs (list r-foreign r-openxlsx r-plyr r-runit r-xtable)) (home-page "https://cran.r-project.org/package=kutils") (synopsis "Project management tools") (description "This package provides tools for data importation, recoding, and inspection. There are functions to create new project folders, R code templates, create uniquely named output directories, and to quickly obtain a visual summary for each variable in a data frame. The main feature here is the systematic implementation of the \"variable key\" framework for data importation and recoding.") (license license:gpl2))) (define-public r-rockchalk (package (name "r-rockchalk") (version "1.8.157") (source (origin (method url-fetch) (uri (cran-uri "rockchalk" version)) (sha256 (base32 "13g2rdnxazqfgy653d7vj6w79b2vgnd7bbz0sqn9k4qiig59jh41")))) (properties `((upstream-name . "rockchalk"))) (build-system r-build-system) (propagated-inputs (list r-cardata r-kutils r-lme4 r-mass)) (home-page "https://cran.r-project.org/package=rockchalk") (synopsis "Regression estimation and presentation") (description "This package provides a collection of functions for interpretation and presentation of regression analysis. These functions are used to produce the statistics lectures in @url{http://pj.freefaculty.org/guides}. The package includes regression diagnostics, regression tables, and plots of interactions and \"moderator\" variables. The emphasis is on \"mean-centered\" and \"residual-centered\" predictors. The vignette @code{rockchalk} offers a fairly comprehensive overview.") (license license:gpl3+))) (define-public r-lisreltor (package (name "r-lisreltor") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "lisrelToR" version)) (sha256 (base32 "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk")))) (properties `((upstream-name . "lisrelToR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=lisrelToR") (synopsis "Import output from LISREL into R") (description "This is an unofficial package aimed at automating the import of LISREL output in R.") (license license:gpl2))) (define-public r-bdgraph (package (name "r-bdgraph") (version "2.72") (source (origin (method url-fetch) (uri (cran-uri "BDgraph" version)) (sha256 (base32 "1kc3icd7glivbjlhl9fbmxqza5w2x000w0w8ii8np9gjrhdwrybw")))) (properties `((upstream-name . "BDgraph"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-igraph r-proc)) (native-inputs (list r-knitr)) (home-page "https://www.uva.nl/profile/a.mohammadi") (synopsis "Bayesian structure learning in graphical models") (description "This package provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. It uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based on a continuous-time birth-death process.") (license license:gpl2+))) (define-public r-bundesligr (package (name "r-bundesligr") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "bundesligR" version)) (sha256 (base32 "0dnhbh9jh7dfbk7mfh8msq4ys5kakalr0kwkycycrb2q8rd049vp")))) (properties `((upstream-name . "bundesligR"))) (build-system r-build-system) (home-page "https://github.com/ottlngr/bundesligR") (synopsis "All final tables of the Bundesliga") (description "This package provides all final tables of Germany's highest football league, the Bundesliga. It contains data from 1964 to 2016.") (license license:gpl3))) (define-public r-butcher (package (name "r-butcher") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "butcher" version)) (sha256 (base32 "14zf732rcy0f1n0l7km9jx74i0dwqdf864v2510lwpkfblgnw4s7")))) (properties `((upstream-name . "butcher"))) (build-system r-build-system) (propagated-inputs (list r-cli r-lobstr r-purrr r-rlang r-tibble r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://butcher.tidymodels.org/") (synopsis "Model butcher") (description "This package provides a set of S3 generics to axe components of fitted model objects and help reduce the size of model objects saved to disk.") (license license:expat))) (define-public r-d3network (package (name "r-d3network") (version "0.5.2.1") (source (origin (method url-fetch) (uri (cran-uri "d3Network" version)) (sha256 (base32 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw")))) (properties `((upstream-name . "d3Network"))) (build-system r-build-system) (propagated-inputs (list r-plyr r-rjson r-whisker)) (home-page "https://christophergandrud.github.io/d3Network/") (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs") (description "This package is intended to make it easy to create D3 JavaScript network, tree, dendrogram, and Sankey graphs from R using data frames.") (license license:gpl3+))) (define-public r-qgraph (package (name "r-qgraph") (version "1.9.8") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 "1m019j5nxc0184p0r2zgdn457g555nxsp2s08maa053nydj1va0l")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs (list r-abind r-colorspace r-corpcor r-fdrtool r-ggplot2 r-glasso r-gtools r-hmisc r-igraph r-jpeg r-lavaan r-matrix r-pbapply r-plyr r-png r-psych r-rcpp r-reshape2)) (home-page "http://sachaepskamp.com/qgraph/") (synopsis "Weighted network visualization and analysis") (description "This package implements tools for weighted network visualization and analysis, as well as Gaussian graphical model computation. It contains graph plotting methods, and tools for psychometric data visualization and graphical model estimation. See Epskamp et al. (2012) @url{doi:10.18637/jss.v048.i04}.") (license license:gpl2))) (define-public r-semplot (package (name "r-semplot") (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "semPlot" version)) (sha256 (base32 "0s9bp4pfsllg1k4x8a36yw82fw432dyz0xvmvi8dw9l12q3jkx8i")))) (properties `((upstream-name . "semPlot"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-corpcor r-igraph r-lavaan r-lisreltor r-openmx r-plyr r-qgraph r-rockchalk r-sem r-xml)) (home-page "https://github.com/SachaEpskamp/semPlot") (synopsis "Unified visualizations of structural equation models") (description "Structural equation modeling (SEM) has a long history of representing models graphically as path diagrams. The semPlot package for R fills the gap between advanced, but time-consuming, graphical software and the limited graphics produced automatically by SEM software. In addition, semPlot offers more functionality than drawing path diagrams: it can act as a common ground for importing SEM results into R. Any result usable as input to semPlot can also be represented in any of the three popular SEM frame-works, as well as translated to input syntax for the R packages @code{sem} and @code{lavaan}.") (license license:gpl2))) (define-public r-cdm (package (name "r-cdm") (version "8.2-6") (source (origin (method url-fetch) (uri (cran-uri "CDM" version)) (sha256 (base32 "1lcq3i5rlyqkc12c26kj0x4fm2gh1jsisp6kbf59y3hjdkiqajhl")))) (properties `((upstream-name . "CDM"))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo)) (home-page "https://github.com/alexanderrobitzsch/CDM") (synopsis "Cognitive diagnosis modeling") (description "This package provides functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. It enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the structured latent class model (SLCA), and regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on estimation and the package structure. For tutorials on how to use the CDM package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as well as Ravand and Robitzsch (2015).") (license license:gpl2+))) (define-public r-tam (package (name "r-tam") (version "4.1-4") (source (origin (method url-fetch) (uri (cran-uri "TAM" version)) (sha256 (base32 "0b81d0g4j94yrfzj019jffxrk1aw24iscddp60kjbkrl5p7qy38g")))) (properties `((upstream-name . "TAM"))) (build-system r-build-system) (propagated-inputs (list r-cdm r-rcpp r-rcpparmadillo)) (home-page "https://www.edmeasurementsurveys.com/TAM/Tutorials/") (synopsis "Test analysis modules") (description "This package includes tools for marginal maximum likelihood estimation and joint maximum likelihood estimation for unidimensional and multidimensional item response models. The package functionality covers the Rasch model, 2PL model, 3PL model, generalized partial credit model, multi-faceted Rasch model, nominal item response model, structured latent class model, mixture distribution IRT models, and located latent class models. Latent regression models and plausible value imputation are also supported.") (license license:gpl2+))) (define-public r-erm (package (name "r-erm") (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "eRm" version)) (sha256 (base32 "0rp2lxkwkh09zmv101rzk7x1v1pmscp71qpf8f4chxp3idg6rpid")))) (properties `((upstream-name . "eRm"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-lattice r-mass r-matrix r-psych)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=eRm") (synopsis "Extended Rasch modeling") (description "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear rating scale models} (LRSM), @dfn{partial credit models} (PCM), and @dfn{linear partial credit models} (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, ICC and other plots, automated stepwise item elimination, and a simulation module for various binary data matrices.") (license license:gpl3))) (define-public r-irtoys (package (name "r-irtoys") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "irtoys" version)) (sha256 (base32 "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b")))) (properties `((upstream-name . "irtoys"))) (build-system r-build-system) (propagated-inputs (list r-ltm r-sm)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=irtoys") (synopsis "Collection of functions related to Item Response Theory (IRT)") (description "This package provides a collection of functions useful in learning and practicing @dfn{Item Response Theory} (IRT), which can be combined into larger programs. It provides basic CTT analysis, a simple common interface to the estimation of item parameters in IRT models for binary responses with three different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME, EAP, WLE, plausible values), item and person fit statistics, scaling methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich array of parametric and non-parametric (kernel) plots. It estimates and plots Haberman's interaction model when all items are dichotomously scored.") (license license:gpl2+))) (define-public r-iheatmapr (package (name "r-iheatmapr") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "iheatmapr" version)) (sha256 (base32 "0ym796kf6d8cwd7nmgzy3ga7r8fyywddl3rr2hbn4cfmwhggv02l")) (snippet '(delete-file "inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js")))) (properties `((upstream-name . "iheatmapr"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/plotlyjs/" (invoke "esbuild" (assoc-ref inputs "js-plotly") "--minify" "--outfile=plotly-latest.min.js"))))))) (propagated-inputs (list r-fastcluster r-ggdendro r-htmlwidgets r-jsonlite r-knitr r-magrittr r-rcolorbrewer r-scales)) (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) ("js-plotly" ,(let ((version "2.10.1")) (origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/v" version "/dist/plotly.js")) (sha256 (base32 "1cg2q681yjsrpjmm4nkfia7752wxnszi3c94nq9a91zpnfkm22yb"))))))) (home-page "https://docs.ropensci.org/iheatmapr") (synopsis "Interactive, Complex Heatmaps") (description "iheatmapr is an R package for building complex, interactive heatmaps using modular building blocks. \"Complex\" heatmaps are heatmaps in which subplots along the rows or columns of the main heatmap add more information about each row or column. For example, a one column additional heatmap may indicate what group a particular row or column belongs to. Complex heatmaps may also include multiple side by side heatmaps which show different types of data for the same conditions. Interactivity can improve complex heatmaps by providing tooltips with information about each cell and enabling zooming into interesting features. iheatmapr uses the plotly library for interactivity.") (license license:expat))) (define-public r-packrat (package (name "r-packrat") (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 "1mvj2s78n2r66nlqq5bjrvgdwlwbcqdj81yryc34sv3y4m1mkpv9")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") (synopsis "Dependency management R projects") (description "This package provides a dependency manager for R projects that allows you to manage the R packages your project depends on in an isolated, portable, and reproducible way.") (license license:gpl2))) (define-public r-rsconnect (package (name "r-rsconnect") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 "0g2av3838nnsb51h64ypad0c31gh98zyhib8yf9ffg53ijyqmjs1")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs (list r-cli r-curl r-digest r-jsonlite r-lifecycle r-openssl r-packrat r-renv r-rlang r-rstudioapi r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/rsconnect") (synopsis "Deployment interface for R Markdown documents and Shiny applications") (description "This package provides a programmatic deployment interface for RPubs, shinyapps.io, and RStudio Connect. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.") (license license:gpl2))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-dygraphs (package (name "r-dygraphs") (version "1.1.1.6") (source (origin (method url-fetch) (uri (cran-uri "dygraphs" version)) (sha256 (base32 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3")))) (properties `((upstream-name . "dygraphs"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (call-with-values (lambda () (unzip2 `(("dygraphs/dygraph-combined-dev.js" "dygraph-combined.js") (,(assoc-ref inputs "js-jquery") "jquery/jquery.min.js") (,(assoc-ref inputs "js-fquarter") "fquarter/moment-fquarter.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (native-inputs `(("uglifyjs" ,node-uglify-js) ;; They actually use version 1.11.1, but this more recent version ;; should be just fine. ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.12.4.js") (sha256 (base32 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))) ("js-fquarter" ,(origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/robgallen/" "moment-fquarter/1.0.1/moment-fquarter.js")) (sha256 (base32 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij")))))) (propagated-inputs (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo)) (home-page "https://github.com/rstudio/dygraphs") (synopsis "Interface to Dygraphs interactive time series charting library") (description "This package provides an R interface to the dygraphs JavaScript charting library (a copy of which is included in the package). It provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.") (license license:expat))) (define-public r-shinystan (package (name "r-shinystan") (version "2.6.0") (source (origin (method url-fetch) (uri (cran-uri "shinystan" version)) (sha256 (base32 "0afm703zriyqprz1zvypir80lq2ylfff3qvj5i7p9n365mm8b150")))) (properties `((upstream-name . "shinystan"))) (build-system r-build-system) (propagated-inputs (list r-bayesplot r-colourpicker r-dt r-dygraphs r-ggplot2 r-gridextra r-gtools r-markdown r-reshape2 r-rstan r-shiny r-shinyjs r-shinythemes r-threejs r-xtable r-xts)) (home-page "https://mc-stan.org/") (synopsis "Interactive visual and numerical analysis for Bayesian models") (description "This package provides a graphical user interface for interactive @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful for analyzing a posterior sample. The interface is powered by the Shiny web application framework and works with the output of MCMC programs written in any programming language (and has extended functionality for Stan models fit using the @code{rstan} and @code{rstanarm} packages).") (license license:gpl3+))) (define-public r-rstantools (package (name "r-rstantools") (version "2.3.1.1") (source (origin (method url-fetch) (uri (cran-uri "rstantools" version)) (sha256 (base32 "0bp20jcdbscsm3s4ik86k3hfsdwkj2k6yzj41zwd0q8lq5afwq7j")))) (properties `((upstream-name . "rstantools"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-desc r-rcpp r-rcppparallel)) (native-inputs (list r-knitr)) (home-page "https://mc-stan.org/rstantools/") (synopsis "Tools for developing R packages interfacing with Stan") (description "This package provides various tools for developers of R packages interfacing with @url{https://mc-stan.org, Stan}, including functions to set up the required package structure, S3 generics and default methods to unify function naming across Stan-based R packages, and vignettes with recommendations for developers.") (license license:gpl3+))) (define-public r-loo (package (name "r-loo") (version "2.6.0") (source (origin (method url-fetch) (uri (cran-uri "loo" version)) (sha256 (base32 "040jk0zmpljq3ayd87bjy5vwwfy49im6kylp6z4wnqisypyn1nk6")))) (properties `((upstream-name . "loo"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-checkmate r-matrixstats)) (native-inputs (list r-knitr)) (home-page "https://mc-stan.org/loo/") (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models") (description "This package provides an implementation of efficient approximate @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}. The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new procedure for regularizing importance weights. As a byproduct of the calculations, we also obtain approximate standard errors for estimated predictive errors and for the comparison of predictive errors between models. The package also provides methods for using stacking and other model weighting techniques to average Bayesian predictive distributions.") (license license:gpl3+))) (define-public r-rstan (package (name "r-rstan") (version "2.32.5") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 "0m655pf0lrhqh2mzylximd2vch9wy252k4zwyfqn1sfwmx642dva")))) (properties '((upstream-name . "rstan") (updater-extra-native-inputs . ("tzdata-for-tests")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'set-timezone ;; This package is picky about timezones. (lambda* (#:key inputs #:allow-other-keys) (setenv "TZ" "UTC+1") (setenv "TZDIR" (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs (list r-knitr tzdata-for-tests)) (propagated-inputs (list r-bh r-ggplot2 r-gridextra r-inline r-loo r-pkgbuild r-quickjsr r-rcpp r-rcppeigen r-rcppparallel r-stanheaders)) (home-page "https://discourse.mc-stan.org/") (synopsis "R interface to Stan") (description "User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the StanHeaders package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via 'variational' approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.") (license license:gpl3+))) (define-public r-rstanarm (package (name "r-rstanarm") (version "2.26.1") (source (origin (method url-fetch) (uri (cran-uri "rstanarm" version)) (sha256 (base32 "0i24ah6mcvvb25pkynkacjn1l7dqk3yfnyk42fv32n83dqnpjm2a")))) (properties `((upstream-name . "rstanarm"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-bayesplot r-bh r-ggplot2 r-lme4 r-loo r-matrix r-nlme r-posterior r-rcpp r-rcppeigen r-rcppparallel r-rstan r-rstantools r-shinystan r-stanheaders r-survival)) (native-inputs (list r-knitr)) (home-page "https://mc-stan.org/rstanarm/") (synopsis "Bayesian applied regression modeling via Stan") (description "This package estimates previously compiled regression models using the @code{rstan} package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and @code{data.frame} plus some additional arguments for priors.") (license license:gpl3+))) (define-public r-kendall (package (name "r-kendall") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "Kendall" version)) (sha256 (base32 "1xmk95l4i3kj9jn0xh1chi2rj322k29jq14ra5pa7316gwf9vx2m")))) (properties `((upstream-name . "Kendall"))) (build-system r-build-system) (propagated-inputs (list r-boot)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/Kendall/") (synopsis "Kendall rank correlation and Mann-Kendall trend test") (description "This package computes the Kendall rank correlation and Mann-Kendall trend test.") (license license:gpl2+))) (define-public r-keyring (package (name "r-keyring") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "keyring" version)) (sha256 (base32 "0mps6q7yayx5l78vlq567pndlsjk71izd65znz3lj4dfbh0qq046")))) (properties `((upstream-name . "keyring"))) (build-system r-build-system) (propagated-inputs (list r-askpass r-assertthat r-filelock r-openssl r-r6 r-rappdirs r-sodium r-yaml)) (native-inputs (list pkg-config)) (home-page "https://github.com/r-lib/keyring") (synopsis "Access the system credential store from R") (description "This package provides a platform-independent API to access the operating system's credential store. It currently supports Keychain on macOS, Credential Store on Windows, the Secret Service API on GNU/Linux, and a simple, platform independent store implemented with environment variables. Additional storage back-ends can be added easily.") (license license:expat))) (define-public r-zyp (package (name "r-zyp") (version "0.11-1") (source (origin (method url-fetch) (uri (cran-uri "zyp" version)) (sha256 (base32 "0gqds43ivbsi4770nxj5sf4mp51m410svnap0v1rh8vlk3gkb3l9")))) (properties `((upstream-name . "zyp"))) (build-system r-build-system) (propagated-inputs (list r-kendall)) (home-page "https://cran.r-project.org/web/packages/zyp/") (synopsis "Zhang + Yue-Pilon Trends Package") (description "This package contains an efficient implementation of Sen's slope method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in climate data.") (license license:lgpl2.1))) (define-public r-rlecuyer (package (name "r-rlecuyer") (version "0.3-8") (source (origin (method url-fetch) (uri (cran-uri "rlecuyer" version)) (sha256 (base32 "1jbm5h8zbsx1yw148piw9p0rj9a7cm0ywgidrzi5ylrp6dad7gk6")))) (properties `((upstream-name . "rlecuyer"))) (build-system r-build-system) (home-page "https://www.iro.umontreal.ca/~lecuyer/myftp/papers/streams00.pdf") (synopsis "R interface to RNG with multiple streams") (description "This package provides an interface to the C implementation of the random number generator with multiple independent streams developed by L'Ecuyer et al (2002). The main purpose of this package is to enable the use of this random number generator in parallel R applications.") (license license:gpl2+))) (define-public r-rlinsolve (package (name "r-rlinsolve") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "Rlinsolve" version)) (sha256 (base32 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw")))) (properties `((upstream-name . "Rlinsolve"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcpparmadillo r-rdpack)) (home-page "https://cran.r-project.org/web/packages/Rlinsolve/") (synopsis "Iterative solvers for (sparse) linear system of equations") (description "Solving a system of linear equations is one of the most fundamental computational problems for many fields of mathematical studies, such as regression problems from statistics or numerical partial differential equations. This package provides basic stationary iterative solvers such as Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods. Nonstationary, also known as Krylov subspace methods are also provided. Sparse matrix computation is also supported in that solving large and sparse linear systems can be manageable using the @code{Matrix} package along with @code{RcppArmadillo}.") (license license:gpl3+))) (define-public r-zvcv (package (name "r-zvcv") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "ZVCV" version)) (sha256 (base32 "0ws0v7i6r7skb8lv6j718k29v5qsy1b007jxidv81iv0jcz9zfpy")))) (properties `((upstream-name . "ZVCV"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bh r-dplyr r-glmnet r-magrittr r-mvtnorm r-rcpp r-rcpparmadillo r-rlinsolve)) (home-page "https://cran.r-project.org/web/packages/ZVCV/") (synopsis "Zero-Variance Control Variates") (description "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method to reduce the variance of Monte Carlo estimators of expectations using the derivatives of the log target. Once the derivatives are available, the only additional computational effort is in solving a linear regression problem. This method has been extended to higher dimensions using regularisation. This package can be used to easily perform ZV-CV or regularised ZV-CV when a set of samples, derivatives and function evaluations are available. Additional functions for applying ZV-CV to two estimators for the normalising constant of the posterior distribution in Bayesian statistics are also supplied.") (license license:gpl2+))) (define-public r-ztype (package (name "r-ztype") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "ztype" version)) (sha256 (base32 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx")))) (properties `((upstream-name . "ztype"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-dplyr r-ggplot2 r-lubridate r-magrittr r-rvest r-stringr)) (home-page "https://cran.r-project.org/web/packages/ztype/") (synopsis "Run a Ztype game loaded with R functions") (description "How fast can you type R functions on your keyboard? Find out by running a @code{zty.pe} game: export R functions as instructions to type to destroy opponents' vessels.") (license license:gpl3))) (define-public r-zseq (package (name "r-zseq") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "Zseq" version)) (sha256 (base32 "0xp7qi5kjg8xmci9wrfvmygjmz8gbhq60fl9bvk8rnka6s4ppkrc")))) (properties `((upstream-name . "Zseq"))) (build-system r-build-system) (propagated-inputs (list r-gmp)) (home-page "https://cran.r-project.org/web/packages/Zseq/") (synopsis "Integer sequence generator") (description "This package generates well-known integer sequences. The @code{gmp} package is adopted for computing with arbitrarily large numbers. Every function has a hyperlink to its corresponding item in the @dfn{On-Line Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (license license:gpl3+))) (define-public r-isoband (package (name "r-isoband") (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 "0qfzkkvh4a97qlifhdqjgdnzmnph93qqyqsv5gg8cnxl8crj54vn")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/wilkelab/isoband") (synopsis "Generate isolines and isobands from regularly spaced elevation grids") (description "This package provides a fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.") (license license:expat))) (define-public r-ppcor (package (name "r-ppcor") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "ppcor" version)) (sha256 (base32 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a")))) (properties `((upstream-name . "ppcor"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ppcor/") (synopsis "Partial and semi-partial correlation") (description "This package provides users not only with a function to readily calculate the higher-order partial and semi-partial correlations but also with statistics and p-values of the correlation coefficients.") (license license:gpl2))) (define-public r-hrbrthemes (package (name "r-hrbrthemes") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "hrbrthemes" version)) (sha256 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc")))) (properties `((upstream-name . "hrbrthemes"))) (build-system r-build-system) (propagated-inputs (list r-extrafont r-gdtools r-ggplot2 r-htmltools r-knitr r-magrittr r-rmarkdown r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/hrbrmstr/hrbrthemes/") (synopsis "Additional themes, theme components and utilities for @code{ggplot2}") (description "This package provides a compilation of extra @code{ggplot2} themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography.") (license license:expat))) (define-public r-crochet (package (name "r-crochet") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "crochet" version)) (sha256 (base32 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/agrueneberg/crochet") (synopsis "Implementation Helper for Matrix-Like Types") (description "Functions to help implement the extraction / subsetting / indexing function @code{[} and replacement function @code{[<-} of custom matrix-like types (based on S3, S4, etc.), modeled as closely to the base matrix class as possible (with tests to prove it).") (license license:expat))) (define-public r-boa (package (name "r-boa") (version "1.1.8-2") (source (origin (method url-fetch) (uri (cran-uri "boa" version)) (sha256 (base32 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp")))) (properties `((upstream-name . "boa"))) (build-system r-build-system) (home-page "https://www.jstatsoft.org/v21/i11") (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC") (description "This package provides a menu-driven program and library of functions for carrying out convergence diagnostics and statistical and graphical analysis of @dfn{Markov chain Monte Carlo} (MCMC) sampling output.") (license license:gpl2+))) (define-public r-httpcode (package (name "r-httpcode") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "httpcode" version)) (sha256 (base32 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr")))) (build-system r-build-system) (home-page "https://github.com/sckott/httpcode") (synopsis "HTTP status code helper") (description "@code{httpcode} provides functionality for finding and explaining the meaning of @code{HTTP} status codes. Functions are included for searching for codes by full or partial number, by message, and to get appropriate dog and cat images for many status codes.") (license license:expat))) (define-public r-latex2exp (package (name "r-latex2exp") (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "latex2exp" version)) (sha256 (base32 "1jp0l0hi5kv4yh28qg2yj2z5fj33gnfvdz2g2v4ibn516fj2d636")))) (build-system r-build-system) (propagated-inputs (list r-stringr r-magrittr)) (native-inputs (list r-knitr)) (home-page "https://github.com/stefano-meschiari/latex2exp/") (synopsis "Use LaTeX expressions in plots") (description "@code{latex2exp} parses and converts LaTeX math formulas to R's plotmath expressions, used to enter mathematical formulas and symbols to be rendered as text, axis labels, etc. throughout R's plotting system.") (license license:expat))) (define-public r-oai (package (name "r-oai") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "oai" version)) (sha256 (base32 "0czf8f2qcjl9lh48svicpis09d3iwz9cndfm7hq8wlz5dl3dwh7m")))) (build-system r-build-system) (propagated-inputs (list r-xml2 r-httr r-plyr r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/oai/") (synopsis "General purpose OAI-PMH services client") (description "@code{oai} provides a general purpose client to work with any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH) service. Functions are provided to work with the OAI-PMH verbs: @code{GetRecord}, @code{Identify}, @code{ListIdentifiers}, @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.") (license license:expat))) (define-public r-argon2 (package (name "r-argon2") (version "0.4-0") (source (origin (method url-fetch) (uri (cran-uri "argon2" version)) (sha256 (base32 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw")))) (properties `((upstream-name . "argon2"))) (build-system r-build-system) (home-page "https://github.com/wrathematics/argon2") (synopsis "Secure password hashing based on the argon2 algorithm") (description "This package provides utilities for secure password hashing via the argon2 algorithm.") (license license:bsd-2))) (define-public r-getpass (package (name "r-getpass") (version "0.2-4") (source (origin (method url-fetch) (uri (cran-uri "getPass" version)) (sha256 (base32 "0a0q9v29z49s1iprs5di01wlflxj74sbizwsrzjfc538nkwfpnqm")))) (properties `((upstream-name . "getPass"))) (build-system r-build-system) (propagated-inputs (list r-rstudioapi)) (home-page "https://github.com/wrathematics/getPass") (synopsis "Masked user input") (description "This package provides a micro-package for reading \"passwords\", i.e. reading user input with masking, so that the input is not displayed as it is typed. Currently, RStudio, the command line (every OS), and any platform where tcltk is present are supported.") (license license:bsd-2))) (define-public r-remoter (package (name "r-remoter") (version "0.4-0") (source (origin (method url-fetch) (uri (cran-uri "remoter" version)) (sha256 (base32 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl")))) (properties `((upstream-name . "remoter"))) (build-system r-build-system) (propagated-inputs (list r-argon2 r-getpass r-pbdzmq r-png)) (home-page "https://github.com/RBigData/remoter") (synopsis "Control a remote R session from a local one") (description "This package provides a set of utilities for client/server computing with R, controlling a remote R session (the server) from a local one (the client).") (license license:bsd-2))) (define-public r-asd (package (name "r-asd") (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "asd" version)) (sha256 (base32 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l")))) (properties `((upstream-name . "asd"))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/asd") (synopsis "Simulations for Adaptive Seamless Designs") (description "This package provdes means to run simulations for adaptive seamless designs with and without early outcomes for treatment selection and subpopulation type designs.") (license license:gpl3))) (define-public r-nbconvertr (package (name "r-nbconvertr") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "nbconvertR" version)) (sha256 (base32 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg")))) (properties `((upstream-name . "nbconvertR"))) (build-system r-build-system) (inputs (list python-nbconvert pandoc)) (home-page "https://cran.r-project.org/web/packages/nbconvertR/") (synopsis "Vignette engine wrapping Jupyter notebooks") (description "This package calls the Jupyter script @code{nbconvert} to create vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files containing rich text, code, and its output. Code cells can be edited and evaluated interactively.") (license license:gpl3))) (define-public r-bridgesampling (package (name "r-bridgesampling") (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "bridgesampling" version)) (sha256 (base32 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l")))) (properties `((upstream-name . "bridgesampling"))) (build-system r-build-system) (propagated-inputs (list r-brobdingnag r-coda r-matrix r-mvtnorm r-scales r-stringr)) (native-inputs (list r-knitr)) (home-page "https://github.com/quentingronau/bridgesampling") (synopsis "Bridge sampling for marginal likelihoods and Bayes factors") (description "This package provides functions for estimating marginal likelihoods, Bayes factors, posterior model probabilities, and normalizing constants in general, via different versions of bridge sampling.") (license license:gpl2+))) (define-public r-tea (package (name "r-tea") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "tea" version)) (sha256 (base32 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn")))) (properties `((upstream-name . "tea"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "https://cran.r-project.org/web/packages/tea/") (synopsis "Threshold estimation approaches") (description "This package provides different approaches for selecting the threshold in generalized Pareto distributions. Most of them are based on minimizing the AMSE-criterion or at least by reducing the bias of the assumed GPD-model. Others are heuristically motivated by searching for stable sample paths, i.e. a nearly constant region of the tail index estimator with respect to k, which is the number of data in the tail. The third class is motivated by graphical inspection. In addition, a sequential testing procedure for GPD-GoF-tests is also implemented here.") (license license:gpl3))) (define-public r-awsmethods (package (name "r-awsmethods") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "awsMethods" version)) (sha256 (base32 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh")))) (properties `((upstream-name . "awsMethods"))) (build-system r-build-system) (home-page "http://www.wias-berlin.de/software/imaging/") (synopsis "Class and methods definitions") (description "This package defines the generic method @code{extract} and provides @code{openMP} support as needed in several packages like @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.") (license license:gpl2+))) (define-public r-aws (package (name "r-aws") (version "2.5-3") (source (origin (method url-fetch) (uri (cran-uri "aws" version)) (sha256 (base32 "022igrvxlyi0ckl3c6chcm459kv213jxy5hrvc14m36yhn3xckhm")))) (properties `((upstream-name . "aws"))) (build-system r-build-system) (propagated-inputs (list r-awsmethods r-gsl)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/aws/") (synopsis "Adaptive weights smoothing") (description "This package provides a collection of R-functions implementing adaptive smoothing procedures in 1D, 2D and 3D. This includes the Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting Confidence Intervals} (ICI), variational approaches, and a non-local means filter.") (license license:gpl2+))) (define-public r-sgloptim (package (name "r-sgloptim") (version "1.3.8") (source (origin (method url-fetch) (uri (cran-uri "sglOptim" version)) (sha256 (base32 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr")))) (properties `((upstream-name . "sglOptim"))) (build-system r-build-system) (propagated-inputs (list r-bh r-doparallel r-foreach r-matrix r-rcpp r-rcpparmadillo r-rcppprogress)) (native-inputs (list r-knitr)) (home-page "https://github.com/nielsrhansen/sglOptim") (synopsis "Generic sparse group Lasso solver") (description "This package provides a fast generic solver for sparse group lasso optimization problems. The loss (objective) function must be defined in a C++ module. The optimization problem is solved using a coordinate gradient descent algorithm. Convergence of the algorithm is established and the algorithm is applicable to a broad class of loss functions. Use of parallel computing for cross validation and subsampling is supported through the @code{foreach} and @code{doParallel} packages.") (license license:gpl2+))) (define-public r-grouped (package (name "r-grouped") (version "0.6-0") (source (origin (method url-fetch) (uri (cran-uri "grouped" version)) (sha256 (base32 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976")))) (properties `((upstream-name . "grouped"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/grouped/") (synopsis "Regression analysis of grouped and coarse data") (description "This package provides regression models for grouped and coarse data, under the coarsened at random assumption.") (license license:gpl2+))) (define-public r-stam (package (name "r-stam") (version "0.0-1") (source (origin (method url-fetch) (uri (cran-uri "stam" version)) (sha256 (base32 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv")))) (properties `((upstream-name . "stam"))) (build-system r-build-system) (propagated-inputs (list r-np r-sp)) (home-page "https://cran.r-project.org/web/packages/stam") (synopsis "Spatio-temporal analysis and modelling") (description "This package provides various methods to conduct Spatio-Temporal Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and Inferred Spatio-Temporal Modelling.") (license license:gpl2+))) (define-public r-dcv (package (name "r-dcv") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "dcv" version)) (sha256 (base32 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj")))) (properties `((upstream-name . "dcv"))) (build-system r-build-system) (propagated-inputs (list r-lmtest)) (home-page "https://cran.r-project.org/web/packages/dcv/") (synopsis "Conventional cross-validation statistics for climate-growth model") (description "This package performs several conventional cross-validation statistical methods for climate-growth model in the climate reconstruction from tree rings, including Sign Test statistic, Reduction of Error statistic, Product Mean Test, Durbin-Watson statistic etc.") (license license:gpl2))) (define-public r-rcdd (package (name "r-rcdd") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "rcdd" version)) (sha256 (base32 "0xfvfcjd9gpp6qaalkfkx2f11lyj4sm6n6b763lnk0rrmn6cv2lz")))) (properties `((upstream-name . "rcdd"))) (build-system r-build-system) (inputs (list gmp)) (home-page "https://www.stat.umn.edu/geyer/rcdd/") (synopsis "Computational geometry") (description "This package converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination. All functions can use exact infinite-precision rational arithmetic.") (license license:gpl2))) (define-public r-rxnat (package (name "r-rxnat") (version "1.0.15") (source (origin (method url-fetch) (uri (cran-uri "Rxnat" version)) (sha256 (base32 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2")))) (properties `((upstream-name . "Rxnat"))) (build-system r-build-system) (propagated-inputs (list r-httr r-rcurl r-tibble)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Rxnat/") (synopsis "Queries and extracts images from neuroimaging datasets") (description "This package allows communication with the Extensible Neuroimaging Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and download images.") (license license:gpl2))) (define-public r-rserve (package (name "r-rserve") (version "1.8-6") (source (origin (method url-fetch) (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_" version ".tar.gz")) (sha256 (base32 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'install-server-binary ;; Makevars tries to install to R's store directory. (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin"))) (substitute* "src/Makevars.in" (("\\$\\(R_HOME\\)") out)) (mkdir-p bin))))))) (propagated-inputs (list r-checkmate r-mime r-jsonlite r-knitr r-r6 r-rcpp r-uuid)) (inputs (list openssl zlib)) (home-page "https://github.com/s-u/Rserve") (synopsis "Server providing access to R from many languages and systems") (description "Rserve acts as a socket server (TCP/IP or local sockets) which allows binary requests to be sent to R. Every connection has a separate workspace and working directory. Client-side implementations are available for popular languages such as C/C++ and Java, allowing any application to use facilities of R without the need of linking to R code. Rserve supports remote connection, user authentication and file transfer. A simple R client is included in this package as well.") (license license:gpl2))) (define-public r-gamm4 (package (name "r-gamm4") (version "0.2-6") (source (origin (method url-fetch) (uri (cran-uri "gamm4" version)) (sha256 (base32 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap")))) (properties `((upstream-name . "gamm4"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-matrix r-mgcv)) (home-page "https://cran.r-project.org/web/packages/gamm4/") (synopsis "Generalized additive mixed models using mgcv and lme4") (description "Estimate generalized additive mixed models via a version of function @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor estimation.") (license license:gpl2+))) (define-public r-optimx (package (name "r-optimx") (version "2023-10.21") (source (origin (method url-fetch) (uri (cran-uri "optimx" version)) (sha256 (base32 "1da4daxgk4kbq1n2mn72482c3j96wba0xf4mzffgasn20ib2swqd")))) (properties `((upstream-name . "optimx"))) (build-system r-build-system) (propagated-inputs (list r-nloptr r-numderiv r-pracma)) (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/web/packages/optimx/") (synopsis "Expanded replacement and extension of the optim function") (description "This package provides a replacement and extension of the @code{optim} function to call to several function minimization codes in R in a single statement. These methods handle smooth, possibly box constrained functions of several or many parameters. Note that the function @code{optimr} was prepared to simplify the incorporation of minimization codes going forward. This package also implements some utility codes and some extra solvers, including safeguarded Newton methods. Many methods previously separate are now included here.") (license license:gpl2))) (define-public r-projpred (package (name "r-projpred") (version "2.8.0") (source (origin (method url-fetch) (uri (cran-uri "projpred" version)) (sha256 (base32 "1xm1444qv0pkxdf2nacxnb2apx5lar1f3qz4jrxp6xd2xk2xv0xk")))) (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs (list r-abind r-gamm4 r-ggplot2 r-gtools r-lme4 r-loo r-mass r-mclogit r-mgcv r-mvtnorm r-nnet r-ordinal r-rcpp r-rcpparmadillo r-rstantools r-scales)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://mc-stan.org/projpred/") (synopsis "Projection predictive feature selection") (description "This package performs projection predictive feature selection for generalized linear models and generalized linear and additive multilevel models. The package is compatible with the @code{rstanarm} and @code{brms} packages, but other reference models can also be used. See the package vignette for more information and examples.") (license license:gpl3))) (define-public r-distributional (package (name "r-distributional") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "distributional" version)) (sha256 (base32 "1y08s301mxz7c54lxa1j0zzbsrgphxv5hsyam3jswcw274rxd0y8")))) (properties `((upstream-name . "distributional"))) (build-system r-build-system) (propagated-inputs (list r-digest r-farver r-generics r-ggplot2 r-lifecycle r-numderiv r-rlang r-scales r-vctrs)) (home-page "https://pkg.mitchelloharawild.com/distributional/") (synopsis "Vectorized probability distributions") (description "This package provides vectorized distribution objects with tools for manipulating, visualizing, and using probability distributions. It was designed to allow model prediction outputs to return distributions rather than their parameters, allowing users to directly interact with predictive distributions in a data-oriented workflow. In addition to providing generic replacements for p/d/q/r functions, other useful statistics can be computed including means, variances, intervals, and highest density regions.") (license license:gpl3))) (define-public r-posterior (package (name "r-posterior") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "posterior" version)) (sha256 (base32 "1pp233ddrs116w1rmp3khhmibjf6l021b1x79k6z48g3r9zk042a")))) (properties `((upstream-name . "posterior"))) (build-system r-build-system) (propagated-inputs (list r-abind r-checkmate r-distributional r-matrixstats r-pillar r-rlang r-tensora r-tibble r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://mc-stan.org/posterior/") (synopsis "Tools for working with posterior distributions") (description "This package provides useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to: @enumerate @item Efficiently convert between many different useful formats of draws (samples) from posterior or prior distributions. @item Provide consistent methods for operations commonly performed on draws, for example, subsetting, binding, or mutating draws. @item Provide various summaries of draws in convenient formats. @item Provide lightweight implementations of state of the art posterior inference diagnostics. @end enumerate ") (license license:bsd-3))) (define-public r-brms (package (name "r-brms") (version "2.20.4") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 "0bq76birbaqi2387d4qv2m8vvjcki9nkc2jychz6nkhcd7mg79h0")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs (list r-abind r-backports r-bayesplot r-bridgesampling r-coda r-future r-ggplot2 r-glue r-loo r-matrix r-matrixstats r-mgcv r-nleqslv r-nlme r-posterior r-rcpp r-rlang r-rstan r-rstantools r-shinystan)) (native-inputs (list r-knitr r-r-rsp)) (home-page "https://github.com/paul-buerkner/brms") (synopsis "Bayesian Regression Models using 'Stan'") (description "Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation.") (license license:gpl2))) (define-public r-mstate (package (name "r-mstate") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "mstate" version)) (sha256 (base32 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw")))) (properties `((upstream-name . "mstate"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-lattice r-rcolorbrewer r-rlang r-survival r-viridislite)) (native-inputs (list r-knitr)) (home-page "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/") (synopsis "Data Preparation, Estimation and Prediction in Multi-State Models") (description "Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models.") (license license:gpl2+))) (define-public r-scatterpie (package (name "r-scatterpie") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "scatterpie" version)) (sha256 (base32 "0wfrckyvy4zw34qdvgg1gwqfdi1xhs63v3gfwa4akm7ifd1canlb")))) (properties `((upstream-name . "scatterpie"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/scatterpie/") (synopsis "Scatter pie plot") (description "This package creates scatterpie plots, especially useful for plotting pies on a map.") (license license:artistic2.0))) (define-public r-scrypt (package (name "r-scrypt") (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "scrypt" version)) (sha256 (base32 "11ncpv01a5lgbxl46g07a43ncjp7jdhrrciasxvxc1d56cz26jh1")))) (properties `((upstream-name . "scrypt"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/rstudio/rscrypt") (synopsis "Key derivation functions for R based on Scrypt") (description "This package provides functions for working with the scrypt key derivation functions. Scrypt is a password-based key derivation function created by Colin Percival. The algorithm was specifically designed to make it costly to perform large-scale custom hardware attacks by requiring large amounts of memory.") (license license:bsd-2))) (define-public r-boruta (package (name "r-boruta") (version "8.0.0") (source (origin (method url-fetch) (uri (cran-uri "Boruta" version)) (sha256 (base32 "1irx7qg1sw69ggsk4jgxfd3pp741kd944fipnda1qbcbphg5prrq")))) (properties `((upstream-name . "Boruta"))) (build-system r-build-system) (propagated-inputs (list r-ranger)) (home-page "https://gitlab.com/mbq/Boruta/") (synopsis "Wrapper algorithm for all relevant feature selection") (description "This package provides an all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).") (license license:gpl2+))) (define-public r-directlabels (package (name "r-directlabels") (version "2023.8.25") (source (origin (method url-fetch) (uri (cran-uri "directlabels" version)) (sha256 (base32 "0p7as0yvvywbdqjpng70sdiy0xyczac4qbv534cwqxiqyx81vp8j")))) (build-system r-build-system) (propagated-inputs (list r-quadprog)) (native-inputs (list r-knitr)) (home-page "https://directlabels.r-forge.r-project.org/") (synopsis "Direct labels for multicolor plots") (description "This package provides an extensible framework for automatically placing direct labels onto multicolor plots. Label positions are described using positioning methods that can be re-used across several different plots. There are heuristics for examining @code{trellis} and @code{ggplot} objects and inferring an appropriate positioning method.") (license license:gpl3))) (define-public r-lsd (package (name "r-lsd") (version "4.1-0") (source (origin (method url-fetch) (uri (cran-uri "LSD" version)) (sha256 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm")))) (properties `((upstream-name . "LSD"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/LSD/") (synopsis "Lots of superior depictions tool creates colorful plots") (description "This package creates lots of colorful plots in a multitude of variations. Try a demo of the LSD by running @code{demotour()}.") ;; Either version (license (list license:gpl2 license:gpl3)))) (define-public r-phylogram (package (name "r-phylogram") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "phylogram" version)) (sha256 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v")))) (properties `((upstream-name . "phylogram"))) (build-system r-build-system) (propagated-inputs (list r-ape)) (home-page "https://github.com/ropensci/phylogram/") (synopsis "Dendrograms for evolutionary analysis") (description "The @code{r-phylogram} package is a tool for for developing phylogenetic trees as deeply-nested lists known as \"dendrogram\" objects. It provides functions for conversion between \"dendrogram\" and \"phylo\" class objects, as well as several tools for command-line tree manipulation and import/export via Newick parenthetic text. This improves accessibility to the comprehensive range of object-specific analytical and tree-visualization functions found across a wide array of bioinformatic R packages.") (license license:gpl3))) (define-public r-kmer (package (name "r-kmer") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "kmer" version)) (sha256 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww")))) (properties `((upstream-name . "kmer"))) (build-system r-build-system) (propagated-inputs (list r-openssl r-phylogram r-rcpp)) (home-page "https://github.com/shaunpwilkinson/kmer/") (synopsis "Fast K-Mer counting and clustering for biological sequence analysis") (description "@code{r-kmer} is an R package for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning.") (license license:gpl3))) (define-public r-hardhat (package (name "r-hardhat") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "hardhat" version)) (sha256 (base32 "0bp83yw7j34iwir2f73ainic11cdz0q18m5v1kbx8vdsw84z17zy")))) (properties `((upstream-name . "hardhat"))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-rlang r-tibble r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/hardhat") (synopsis "Construct modeling packages") (description "Building modeling packages is hard. A large amount of effort generally goes into providing an implementation for a new method that is efficient, fast, and correct, but often less emphasis is put on the user interface. A good interface requires specialized knowledge about S3 methods and formulas, which the average package developer might not have. The goal of @code{hardhat} is to reduce the burden around building new modeling packages by providing functionality for preprocessing, predicting, and validating input.") (license license:expat))) (define-public r-lightgbm (package (name "r-lightgbm") (version "4.2.0") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 "0c0q597agzdaimy0q1mssdpm0pw4yvqq9w6n8syvgz1g5q0mcwqi")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-matrix r-r6)) (native-inputs (list r-knitr)) (home-page "https://github.com/Microsoft/LightGBM") (synopsis "Light gradient boosting machine") (description "Tree based algorithms can be improved by introducing boosting frameworks. LightGBM is one such framework, based on Ke, Guolin et al. (2017). This package offers an R interface to work with it. It is designed to be distributed and efficient with the following goals: @enumerate @item Faster training speed and higher efficiency; @item lower memory usage; @item better accuracy; @item parallel learning supported; and @item capable of handling large-scale data. @end enumerate ") (license license:expat))) (define-public r-shapforxgboost (package (name "r-shapforxgboost") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "SHAPforxgboost" version)) (sha256 (base32 "0b3h6py80a0dmb8f8j4h7a7d0k6ld8l0qr24r8pxxy7dbqbyxh5x")))) (properties `((upstream-name . "SHAPforxgboost"))) (build-system r-build-system) (propagated-inputs (list r-bbmisc r-data-table r-ggextra r-ggforce r-ggplot2 r-ggpubr r-rcolorbrewer r-xgboost)) (native-inputs (list r-knitr)) (home-page "https://github.com/liuyanguu/SHAPforxgboost") (synopsis "SHAP Plots for XGBoost") (description "The aim of @code{SHAPforxgboost} is to aid in visual data investigations using @dfn{SHAP} (Shapley additive explanation) visualization plots for @code{XGBoost}. It provides summary plot, dependence plot, interaction plot, and force plot. It relies on the @code{XGBoost} package to produce SHAP values.") (license license:expat))) (define-public r-rismed (package (name "r-rismed") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "RISmed" version)) (sha256 (base32 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b")))) (properties `((upstream-name . "RISmed"))) (build-system r-build-system) (propagated-inputs (list r-httr r-xml2)) (home-page "https://cran.r-project.org/web/packages/RISmed") (synopsis "Download content from NCBI databases") (description "This package provides a set of tools to extract bibliographic content from the National Center for Biotechnology Information (NCBI) databases, including PubMed. The name RISmed is a portmanteau of RIS (for Research Information Systems, a common tag format for bibliographic data) and PubMed.") (license license:gpl2+))) (define-public r-semver (package (name "r-semver") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "semver" version)) (sha256 (base32 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy")))) (properties `((upstream-name . "semver"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/johndharrison/semver") (synopsis "Parser for Semantic Versioning 2.0.0") (description "This package provides tools and functions for parsing, rendering and operating on semantic version strings. Semantic versioning is a simple set of rules and requirements that dictate how version numbers are assigned and incremented as outlined at @url{http://semver.org}.") (license license:expat))) (define-public r-binman (package (name "r-binman") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "binman" version)) (sha256 (base32 "1xz9ky3axidm0fp518rj80ma6q14ybyvashil79hhkk3iqmx0lhw")))) (properties `((upstream-name . "binman"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-httr r-jsonlite r-rappdirs r-semver r-xml2 r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/binman") (synopsis "Binary download manager") (description "This package provides tools and functions for managing the download of binary files. Binary repositories are defined in the YAML format. Defining new pre-download, download and post-download templates allow additional repositories to be added.") (license license:expat))) (define-public r-wdman (package (name "r-wdman") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "wdman" version)) (sha256 (base32 "0n0wwb9ip6qc8qzdxn4dsqfbc8b3f607n8l6jigryd7g83ibnbp6")))) (properties `((upstream-name . "wdman"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-binman r-processx r-semver r-yaml)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/wdman/") (synopsis "Webdriver/Selenium binary manager") (description "There are a number of binary files associated with the Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/}, @url{https://sites.google.com/a/chromium.org/chromedriver/}, @url{https://github.com/mozilla/geckodriver}, @url{http://phantomjs.org/download.html}, and @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for more information). This package provides functions to download these binaries and to manage processes involving them.") (license license:expat))) (define-public r-rselenium (package (name "r-rselenium") (version "1.7.9") (source (origin (method url-fetch) (uri (cran-uri "RSelenium" version)) (sha256 (base32 "18hd0gfpblg9ij99ik7ccc60q9dxha89n5rrwrrzx498c5sscjg2")))) (properties `((upstream-name . "RSelenium"))) (build-system r-build-system) (propagated-inputs (list r-catools r-httr r-wdman)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/RSelenium/") (synopsis "R bindings for Selenium WebDriver") (description "This package provides a set of R bindings for the Selenium 2.0 WebDriver (see @url{https://selenium.dev/documentation/en/} for more information) using the @code{JsonWireProtocol} (see @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more information). Selenium 2.0 WebDriver allows driving a web browser natively as a user would either locally or on a remote machine using the Selenium server it marks a leap forward in terms of web browser automation. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.") (license license:agpl3+))) (define-public r-conquer (package (name "r-conquer") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "conquer" version)) (sha256 (base32 "1fnyjym21i9hw2d1c9da0wvjzbi9abn46n0lg6if5w2asxg1bim2")))) (properties `((upstream-name . "conquer"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) (home-page "https://github.com/XiaoouPan/conquer") (synopsis "Convolution-type smoothed quantile regression") (description "This package provides fast and accurate convolution-type smoothed quantile regression, implemented using Barzilai-Borwein gradient descent with a Huber regression warm start. Confidence intervals for regression coefficients are constructed using multiplier bootstrap.") (license license:gpl3))) (define-public r-consrank (package (name "r-consrank") (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "ConsRank" version)) (sha256 (base32 "0v1dr7zj2fpgncymakv5qszdrlqzvc5zxfyc3yrsj09gbm0gvyby")))) (properties `((upstream-name . "ConsRank"))) (build-system r-build-system) (propagated-inputs (list r-gtools r-proxy r-rgl r-rlist r-tidyr)) (home-page "https://www.r-project.org/") (synopsis "Compute median rankings according to Kemeny's axiomatic approach") (description "This package lets you compute the median ranking according to Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete. The package contains both branch-and-bound algorithms and heuristic solutions recently proposed. The searching space of the solution can either be restricted to the universe of the permutations or unrestricted to all possible ties. The package also provides some useful utilities for deal with preference rankings, including both element-weight Kemeny distance and correlation coefficient.") (license license:gpl3))) (define-public r-fastshap (package (name "r-fastshap") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "fastshap" version)) (sha256 (base32 "112hc585aryzc5pgvr3qaa7arlx2h2sj9jlq9xha3nncyzqkh7c6")))) (properties `((upstream-name . "fastshap"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/bgreenwell/fastshap") (synopsis "Fast approximate Shapley values") (description "This package computes fast (relative to other implementations) approximate Shapley values for any supervised learning model. Shapley values help to explain the predictions from any black box model using ideas from game theory; see @url{Strumbel and Kononenko (2014), doi.org/10.1007/s10115-013-0679-x} for details.") (license license:gpl2+))) (define-public r-memisc (package (name "r-memisc") (version "0.99.31.7") (source (origin (method url-fetch) (uri (cran-uri "memisc" version)) (sha256 (base32 "0drn923y8bwwwk2csa7l9b3fd06zfrfgi3b0pn7b23aja1c1h0xl")))) (properties `((upstream-name . "memisc"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-lattice r-mass r-yaml)) (native-inputs (list r-knitr)) (home-page "https://www.elff.eu/software/memisc/") (synopsis "Management of survey data and presentation of analysis results") (description "This package provides infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) SPSS and Stata files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to LaTeX and HTML.") ;; Either of these two version. (license (list license:gpl2 license:gpl3)))) (define-public r-memuse (package (name "r-memuse") (version "4.2-3") (source (origin (method url-fetch) (uri (cran-uri "memuse" version)) (sha256 (base32 "0816s6airiqmn8faprpwmchxaay6llri4673ivlx1bp2cpvdyvwh")))) (properties `((upstream-name . "memuse"))) (build-system r-build-system) (home-page "https://github.com/shinra-dev/memuse") (synopsis "Memory Estimation Utilities") (description "This package provides procedures to answer the following questions: How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How much ram do you even have?") (license license:bsd-2))) (define-public r-metrics (package (name "r-metrics") (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "Metrics" version)) (sha256 (base32 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk")))) (properties `((upstream-name . "Metrics"))) (build-system r-build-system) (home-page "https://github.com/mfrasco/Metrics") (synopsis "Evaluation metrics for machine learning") (description "This package provides an implementation of evaluation metrics in R that are commonly used in supervised machine learning. It implements metrics for regression, time series, binary classification, classification, and information retrieval problems. It has zero dependencies and a consistent, simple interface for all functions.") (license license:bsd-3))) (define-public r-iml (package (name "r-iml") (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "iml" version)) (sha256 (base32 "0fi37lv9czaxcc123f6r57607shqhs83ks96n2n0b93dl1qs0j52")))) (properties `((upstream-name . "iml"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-formula r-future r-future-apply r-ggplot2 r-metrics r-prediction r-r6)) (native-inputs (list r-knitr)) (home-page "https://github.com/christophM/iml") (synopsis "Interpretable machine learning") (description "This package provides interpretability methods to analyze the behavior and predictions of any machine learning model. Implemented methods are: @itemize @item Feature importance described by Fisher et al. (2018), @item accumulated local effects plots described by Apley (2018), @item partial dependence plots described by Friedman (2001), @item individual conditional expectation ('ice') plots described by Goldstein et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095}, @item local models (variant of 'lime') described by Ribeiro et. al (2016), @item the Shapley Value described by Strumbelj et. al (2014) @url{https://doi.org/10.1007/s10115-013-0679-x}, @item feature interactions described by Friedman et. al @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models. @end itemize ") (license license:expat))) (define-public r-goftest (package (name "r-goftest") (version "1.2-3") (source (origin (method url-fetch) (uri (cran-uri "goftest" version)) (sha256 (base32 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs")))) (properties `((upstream-name . "goftest"))) (build-system r-build-system) (home-page "https://github.com/baddstats/goftest") (synopsis "Classical Goodness-of-Fit tests for univariate distributions") (description "This package provides Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for continuous univariate distributions, using efficient algorithms.") (license license:gpl2+))) (define-public r-tensor (package (name "r-tensor") (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "tensor" version)) (sha256 (base32 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1")))) (properties `((upstream-name . "tensor"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tensor/") (synopsis "Tensor product of arrays") (description "The tensor product of two arrays is notionally an outer product of the arrays collapsed in specific extents by summing along the appropriate diagonals. This package allows you to compute the tensor product of arrays.") (license license:gpl2+))) (define-public r-spatstat-explore (package (name "r-spatstat-explore") (version "3.2-5") (source (origin (method url-fetch) (uri (cran-uri "spatstat.explore" version)) (sha256 (base32 "053wl87whmkkqp058lwzlwv0wydddizsni9m94f6kxgl5ahia1sc")))) (properties `((upstream-name . "spatstat.explore"))) (build-system r-build-system) (propagated-inputs (list r-abind r-goftest r-matrix r-nlme r-spatstat-data r-spatstat-geom r-spatstat-random r-spatstat-sparse r-spatstat-utils)) (home-page "https://spatstat.org/") (synopsis "Exploratory data analysis for the spatstat family") (description "This package implements functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the @code{spatstat} family of packages. Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.") (license license:gpl2+))) (define-public r-spatstat-model (package (name "r-spatstat-model") (version "3.2-8") (source (origin (method url-fetch) (uri (cran-uri "spatstat.model" version)) (sha256 (base32 "1x03fy921rq8dyr6jkpwnx7pf7fc5593mvnl8r1gz3sypnmp6p4d")))) (properties `((upstream-name . "spatstat.model"))) (build-system r-build-system) (propagated-inputs (list r-abind r-goftest r-matrix r-mgcv r-nlme r-rpart r-spatstat-data r-spatstat-explore r-spatstat-geom r-spatstat-random r-spatstat-sparse r-spatstat-utils r-tensor)) (home-page "https://spatstat.org/") (synopsis "Parametric statistical modelling for the spatstat family") (description "This package implements functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the spatstat family of packages. Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.") (license license:gpl2+))) (define-public r-spatstat-utils (package (name "r-spatstat-utils") (version "3.0-4") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 "1i1w1ys29s22jfjvliqnbw3zi6zar8bxxz3r8za182p2w0wqwhax")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) (home-page "https://www.spatstat.org") (synopsis "Utility functions for spatstat") (description "This package contains utility functions for the @code{spatstat} package which may also be useful for other purposes.") (license license:gpl2+))) (define-public r-spatstat-sparse (package (name "r-spatstat-sparse") (version "3.0-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.sparse" version)) (sha256 (base32 "0scdk3ns4nl1v1avbggnsinfpvl4i8391qy3x1iwxvkimr14xg3b")))) (properties `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) (propagated-inputs (list r-abind r-matrix r-spatstat-utils r-tensor)) (home-page "https://spatstat.org/") (synopsis "Sparse three-dimensional arrays and linear algebra utilities") (description "This package defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.") (license license:gpl2+))) (define-public r-spatstat-data (package (name "r-spatstat-data") (version "3.0-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 "0fxd266rza07s73fj1n4rd4i7x1bv1ll36iikxzjhnlh3vjc0hkn")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-spatstat-utils)) (home-page "https://www.spatstat.org") (synopsis "Datasets for spatstat") (description "This package contains all the datasets for the @code{spatstat} package.") (license license:gpl2+))) (define-public r-spatstat-geom (package (name "r-spatstat-geom") (version "3.2-7") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 "13k85918zd2n64mxjwlgzd986zvs3is8vg06k9i195yymfrik65y")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils)) (home-page "https://spatstat.org/") (synopsis "Geometrical functionality of the spatstat package") (description "This is a subset of the original spatstat package, containing the user-level code from spatstat which performs geometrical operations, except for the geometry of linear networks.") (license license:gpl2+))) (define-public r-spatstat-core (package (name "r-spatstat-core") (version "2.4-4") (source (origin (method url-fetch) (uri (cran-uri "spatstat.core" version)) (sha256 (base32 "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373")))) (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs (list r-abind r-goftest r-matrix r-mgcv r-nlme r-rpart r-spatstat-data r-spatstat-geom r-spatstat-random r-spatstat-sparse r-spatstat-utils r-tensor)) (home-page "https://spatstat.org/") (synopsis "Core functionality of the spatstat package") (description "This is a subset of the original spatstat package, containing all of the user-level code from spatstat, except for the code for linear networks.") (license license:gpl2+))) (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") (version "3.1-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 "1ybjl5ccp9r5ilbihwzk93zcm46pbpldn3nfbfpdw458xh894r3q")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-spatstat-data r-spatstat-explore r-spatstat-geom r-spatstat-model r-spatstat-random r-spatstat-sparse r-spatstat-utils)) (home-page "https://spatstat.org/") (synopsis "Linear networks functionality of the spatstat package") (description "This is a subset of the spatstat package, containing its functionality for spatial data on a linear network.") (license license:gpl2+))) (define-public r-spatstat-random (package (name "r-spatstat-random") (version "3.2-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.random" version)) (sha256 (base32 "01rsh7z9prsdrqlbc2761sf54w24z7jzj64ijfzy8l5ca56fxij8")))) (properties `((upstream-name . "spatstat.random"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils)) (home-page "https://spatstat.org/") (synopsis "Random Generation Functionality for the 'spatstat' Family") (description "This package provides functionality for random generation of spatial data in the spatstat family of packages. It generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes (simple sequential inhibition, Matern inhibition models, Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox processes, product shot noise cluster processes) and simulation of Gibbs point processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler).") (license license:gpl2+))) (define-public r-spatstat (package (name "r-spatstat") (version "3.0-7") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 "1h6fnri3ma5kgzkwv4lr2i2jvsx8sg4am3rgzb29h7l89x59yxrk")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-explore r-spatstat-geom r-spatstat-linnet r-spatstat-model r-spatstat-random r-spatstat-utils)) (home-page "https://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description "This package provides a comprehensive toolbox for analysing Spatial Point Patterns. It is focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. It also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. It supports spatial covariate data such as pixel images and contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.") (license license:gpl2+))) (define-public r-gaston (package (name "r-gaston") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "gaston" version)) (sha256 (base32 "1knjyw2dsarljj2zsqp3hi6hk6m90sfqp2l535h3arj70l3rq9x4")))) (properties `((upstream-name . "gaston"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp r-rcppeigen r-rcppparallel)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gaston/") (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models") (description "This is a package for the manipulation of genetic data (SNPs). Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix, @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms for linear mixed models (AIREML).") (license license:gpl3))) (define-public r-cpp11 (package (name "r-cpp11") (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 "0i234s1g1vc6m2sqxia5r1gaca05znjv4bff5dj74fach9k147c0")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/cpp11") (synopsis "C++11 Interface for R's C Interface") (description "This package provides a header only, C++11 interface to R's C interface. Compared to other approaches @code{cpp11} strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with @code{ALTREP} vectors.") (license license:expat))) (define-public r-rcpptoml (package (name "r-rcpptoml") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "RcppTOML" version)) (sha256 (base32 "1ak3dwzdrmq9kd30i12fy582rsn5xfljw214liv1w8l2rbwr24rp")))) (properties `((upstream-name . "RcppTOML"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://dirk.eddelbuettel.com/code/rcpp.toml.html") (synopsis "Rcpp bindings to TOML parser") (description "The TOML configuration format specifies an excellent format suitable for both human editing as well as the common uses of a machine-readable format. This package provides Rcpp bindings to a TOML parser.") (license license:gpl2+))) (define-public r-rcppziggurat (package (name "r-rcppziggurat") (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "RcppZiggurat" version)) (sha256 (base32 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w")))) (properties `((upstream-name . "RcppZiggurat"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppgsl)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/") (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations") (description "The Ziggurat generator for normally distributed random numbers, originally proposed by Marsaglia and Tsang (2000, @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few times starting with Leong et al (2005, @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an aggregation for comparing different implementations in order to provide a 'faster but good enough' alternative for use with R and C++ code.") (license license:gpl2+))) (define-public r-rfast (package (name "r-rfast") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 "1zqq4k85i0nbzndkh0iiq3k83ly0mpl3pn4wkka6qxfvk6n6rr7r")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel r-rcppziggurat)) (home-page "https://github.com/RfastOfficial/Rfast") (synopsis "Collection of efficient and fast R functions") (description "This package provides a collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.") (license license:gpl2+))) (define-public r-rffc (package (name "r-rffc") (version "1.0") (source (origin (method url-fetch) (uri (string-append "https://download.r-forge.r-project.org/src/contrib/" "rfFC_" version ".tar.gz")) (sha256 (base32 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g")))) (build-system r-build-system) (propagated-inputs (list r-randomforest)) (home-page "https://r-forge.r-project.org/projects/rffc/") (synopsis "Random Forest Feature Contributions") (description "This package provides functions for extracting feature contributions from a random forest model from package @code{randomForest}. Feature contributions provide detailed information about the relationship between data variables and the predicted value returned by random forest model.") (license license:gpl2))) (define-public r-clusterr (package (name "r-clusterr") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 "1bs1sl3yy90zx4ni0lhvdivzfas6i4v9203m59njvk5df9x82ffp")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gmp r-lifecycle r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/mlampros/ClusterR") (synopsis "Clustering") (description "This package provides Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of @code{RcppArmadillo} to speed up the computationally intensive parts of the functions. For more information, see @enumerate @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, @url{https://doi.org/10.18637/jss.v001.i04}; @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital Library, @url{https://doi.org/10.1145/1772690.1772862}; @item \"Armadillo: a template-based C++ library for linear algebra\" by Sanderson et al (2016), The Journal of Open Source Software, @url{https://doi.org/10.21105/joss.00026}; @item \"Clustering by Passing Messages Between Data Points\" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, @url{https://doi.org/10.1126/science.1136800}. @end enumerate ") (license license:gpl3))) (define-public r-spectrum (package (name "r-spectrum") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "Spectrum" version)) (sha256 (base32 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw")))) (properties `((upstream-name . "Spectrum"))) (build-system r-build-system) (propagated-inputs (list r-clusterr r-diptest r-ggplot2 r-rfast)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Spectrum/") (synopsis "Fast adaptive spectral clustering for single and multi-view data") (description "This package provides a self-tuning spectral clustering method for single or multi-view data. Spectrum uses a new type of adaptive density aware kernel that strengthens connections in the graph based on common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to integrate different data sources and reduce noise. Spectrum uses either the eigengap or multimodality gap heuristics to determine the number of clusters. The method is sufficiently flexible so that a wide range of Gaussian and non-Gaussian structures can be clustered with automatic selection of K.") (license license:agpl3+))) (define-public r-nabor (package (name "r-nabor") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "nabor" version)) (sha256 (base32 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7")))) (properties `((upstream-name . "nabor"))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/nabor/") (synopsis "Wrapper for K nearest neighbour library for low dimensions") (description "This package provides an R wrapper for libnabo, an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is designed as a drop-in replacement for the RANN function @code{nn2}. In addition, objects which include the k-d tree search structure can be returned to speed up repeated queries of the same set of target points.") (license license:bsd-3))) (define-public r-nada (package (name "r-nada") (version "1.6-1.1") (source (origin (method url-fetch) (uri (cran-uri "NADA" version)) (sha256 (base32 "0jp4mqr77cx7q5lff84s6wb0dwjy9mi0jyhbjc5fsx50bdczc3v7")))) (properties `((upstream-name . "NADA"))) (build-system r-build-system) (propagated-inputs (list r-survival)) (home-page "https://cran.r-project.org/package=NADA") (synopsis "Nondetects and data analysis for environmental data") (description "This package contains methods described by Dennis Helsel in his book @emph{Nondetects and Data Analysis: Statistics for Censored Environmental Data}.") (license license:gpl2+))) (define-public r-naturalsort (package (name "r-naturalsort") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "naturalsort" version)) (sha256 (base32 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/naturalsort/") (synopsis "Natural ordering") (description "This package provides functions related to human natural ordering. It handles adjacent digits in a character sequence as a number so that natural sort function arranges a character vector by their numbers, not digit characters.") (license license:bsd-3))) (define-public r-visdat (package (name "r-visdat") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "visdat" version)) (sha256 (base32 "1675az0lfvmwzh9c3fknnk0n2kz1w7hy0kdj3a37n5j1knxwsjhh")))) (build-system r-build-system) (propagated-inputs (list r-cli r-dplyr r-forcats r-ggplot2 r-glue r-magrittr r-purrr r-readr r-scales r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://visdat.njtierney.com/") (synopsis "Preliminary Visualisation of Data") (description "This package provides procedures to create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using @code{ggplot2}.") (license license:expat))) (define-public r-visnetwork (package (name "r-visnetwork") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "visNetwork" version)) (sha256 (base32 "116w3l65lgv18xzav5zz1pbgwpwck66n9cjpja9axrl9zi19vja7")) (snippet '(for-each delete-file '("inst/htmlwidgets/lib/vis/vis-network.min.js" "inst/htmlwidgets/lib/export/FileSaver/FileSaver.min.js" "inst/common-docs-files/js/jquery.url.min.js"))))) (properties `((upstream-name . "visNetwork"))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) ;; The inst directory contains some minified JavaScript ;; files. Regenerate them from sources. (with-directory-excursion "inst/" (call-with-values (lambda () (unzip2 `((,(search-input-file inputs "/FileSaver.js") "htmlwidgets/lib/export/FileSaver/FileSaver.min.js") (,(search-input-file inputs "/url.js") "common-docs-files/js/jquery.url.min.js") (,(assoc-ref inputs "vis-network.js") "htmlwidgets/lib/vis/vis-network.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-htmltools r-htmlwidgets r-jsonlite r-magrittr)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ;; The included file has no version information but was created ;; at around the same time as version 9.1.0. ("vis-network.js" ,(origin (method url-fetch) (uri "https://unpkg.com/vis-network@9.1.0/dist/vis-network.js") (sha256 (base32 "0vh2zf221ildsr5ly9idxi3jpqx61j3phbz5kdd801i0crqk4yj0")))) ;; Version 1.2.0 is a few months more recent than what ;; visNetwork bundles. ("filesaver.js" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/eligrey/FileSaver.js/") (commit "1.2.0"))) (file-name (git-file-name "FileSaver.js" "1.2.0")) (sha256 (base32 "07mw01056fk36pganhs27y8rl5y5hrdsm945pwbbvmdjnzq4ijny")))) ("jquery-url.js" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/websanova/js-url/") (commit "v1.8.6"))) (file-name (git-file-name "js-url.js" "1.8.6")) (sha256 (base32 "0pxqjwqf9avd4d99csgny8xf5c65kyqjnm24pwm4ca1zghsl9wyr")))))) (home-page "https://datastorm-open.github.io/visNetwork/") (synopsis "Network Visualization using vis.js Library") (description "This package provides an R interface to the vis.js JavaScript charting library. It allows an interactive visualization of networks.") (license license:expat))) (define-public r-muhaz (package (name "r-muhaz") (version "1.2.6.4") (source (origin (method url-fetch) (uri (cran-uri "muhaz" version)) (sha256 (base32 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g")))) (properties `((upstream-name . "muhaz"))) (build-system r-build-system) (propagated-inputs (list r-survival)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/muhaz/") (synopsis "Hazard function estimation in survival analysis") (description "This package produces a smooth estimate of the hazard function for censored data.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-flexsurv (package (name "r-flexsurv") (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "flexsurv" version)) (sha256 (base32 "1qshsii5fqpx4l113vr4lx9ijxhcr8494lx3ixjdbzy58077adb6")))) (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-desolve r-dplyr r-generics r-ggplot2 r-magrittr r-matrix r-mstate r-muhaz r-mvtnorm r-numderiv r-purrr r-quadprog r-rcpp r-rlang r-rstpm2 r-statmod r-survival r-tibble r-tidyr r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://github.com/chjackson/flexsurv-dev") (synopsis "Flexible parametric survival and multi-state models") (description "This package provides flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.") (license license:gpl2+))) (define-public r-transphylo (package (name "r-transphylo") (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "TransPhylo" version)) (sha256 (base32 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy")))) (properties `((upstream-name . "TransPhylo"))) (build-system r-build-system) (propagated-inputs (list r-ape r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TransPhylo/") (synopsis "Inference of transmission tree from a dated phylogeny") (description "This is a package to infer transmission trees from a dated phylogeny. It includes methods to simulate and analyze outbreaks. The methodology is described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)} and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.") (license license:gpl2+))) (define-public r-km-ci (package (name "r-km-ci") (version "0.5-6") (source (origin (method url-fetch) (uri (cran-uri "km.ci" version)) (sha256 (base32 "18sc9vhbdgks8lhk2nfxkkayh8j4j227hl63fm5p04f7z4wm6wc1")))) (properties `((upstream-name . "km.ci"))) (build-system r-build-system) (propagated-inputs (list r-survival)) (home-page "https://cran.r-project.org/web/packages/km.ci/") (synopsis "Confidence intervals for the Kaplan-Meier estimator") (description "This package computes various @dfn{confidence intervals} (CI) for the Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner.") (license license:gpl2+))) (define-public r-kmsurv (package (name "r-kmsurv") (version "0.1-5") (source (origin (method url-fetch) (uri (cran-uri "KMsurv" version)) (sha256 (base32 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm")))) (properties `((upstream-name . "KMsurv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/KMsurv/") (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis") (description "This package provides data sets and functions for Klein and Moeschberger (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\", Springer.") (license license:gpl3+))) (define-public r-survmisc (package (name "r-survmisc") (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "survMisc" version)) (sha256 (base32 "014cf7sfndmib9jmj0p3h67sr750k2pvw7m865zwdpvlqddi44fr")))) (properties `((upstream-name . "survMisc"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-ggplot2 r-gridextra r-km-ci r-kmsurv r-knitr r-survival r-xtable r-zoo)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/survMisc/") (synopsis "Miscellaneous functions for survival data") (description "This package provides a collection of functions to help in the analysis of right-censored survival data. These extend the methods available in the @code{survival} package.") (license license:gpl2))) (define-public r-exactranktests (package (name "r-exactranktests") (version "0.8-35") (source (origin (method url-fetch) (uri (cran-uri "exactRankTests" version)) (sha256 (base32 "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y")))) (properties `((upstream-name . "exactRankTests"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/exactRankTests/") (synopsis "Exact distributions for rank and permutation tests") (description "This package computes exact conditional p-values and quantiles using an implementation of the Shift-Algorithm by Streitberg & Roehmel.") (license license:gpl2+))) (define-public r-maxstat (package (name "r-maxstat") (version "0.7-25") (source (origin (method url-fetch) (uri (cran-uri "maxstat" version)) (sha256 (base32 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg")))) (properties `((upstream-name . "maxstat"))) (build-system r-build-system) (propagated-inputs (list r-exactranktests r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/maxstat/") (synopsis "Maximally selected rank statistics") (description "This package provides maximally selected rank statistics with several p-value approximations.") (license license:gpl2+))) (define-public r-survminer (package (name "r-survminer") (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "survminer" version)) (sha256 (base32 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz")))) (properties `((upstream-name . "survminer"))) (build-system r-build-system) (propagated-inputs (list r-broom r-dplyr r-ggplot2 r-ggpubr r-ggtext r-gridextra r-magrittr r-maxstat r-purrr r-rlang r-scales r-survival r-survmisc r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://rpkgs.datanovia.com/survminer/index.html") (synopsis "Drawing survival curves using ggplot2") (description "This package contains the function @code{ggsurvplot()} for easily drawing beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot adjusted curves for Cox model and to visually examine Cox model assumptions.") (license license:gpl2))) (define-public r-forge (package (name "r-forge") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "forge" version)) (sha256 (base32 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa")))) (properties `((upstream-name . "forge"))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-rlang)) (home-page "https://cran.r-project.org/web/packages/forge/") (synopsis "Cast values into shape") (description "This package provides helper functions with a consistent interface to coerce and verify the types and shapes of values for input checking.") (license license:asl2.0))) (define-public r-config (package (name "r-config") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "config" version)) (sha256 (base32 "0r8hjg7jrhr9lncb82xmq2slygv3slacd2w8ds6shnvdp3122p3v")))) (properties `((upstream-name . "config"))) (build-system r-build-system) (propagated-inputs (list r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/config") (synopsis "Manage environment specific configuration values") (description "This package lets you manage configuration values across multiple environments (e.g. development, test, production). It reads values using a function that determines the current environment and returns the appropriate value.") (license license:gpl3))) (define-public r-confintr (package (name "r-confintr") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "confintr" version)) (sha256 (base32 "0gi9cnk2cd67vmywrkb19g6f9gr8k999kg0k03khad7lgqp4l43s")))) (properties `((upstream-name . "confintr"))) (build-system r-build-system) (propagated-inputs (list r-boot)) (native-inputs (list r-knitr)) (home-page "https://github.com/mayer79/confintr") (synopsis "Confidence intervals") (description "This package calculates classic and/or bootstrap confidence intervals for many parameters such as the population mean, variance, @dfn{interquartile range} (IQR), @dfn{median absolute deviation} (MAD), skewness, kurtosis, Cramer's V, odds ratio, R-squared, quantiles (including median), proportions, different types of correlation measures, difference in means, quantiles and medians. Many of the classic confidence intervals are described in Smithson, M. (2003, ISBN: 978-0761924999). Bootstrap confidence intervals are calculated with the R package @code{boot}. Both one- and two-sided intervals are supported.") (license license:gpl2+))) (define-public r-adaptivesparsity (package (name "r-adaptivesparsity") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "AdaptiveSparsity" version)) (sha256 (base32 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91")))) (properties `((upstream-name . "AdaptiveSparsity"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'link-against-armadillo (lambda _ (substitute* "src/Makevars" (("PKG_LIBS=" prefix) (string-append prefix "-larmadillo"))) #t))))) (propagated-inputs (list r-mass r-matrix r-rcpp r-rcpparmadillo)) (inputs (list armadillo)) (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity") (synopsis "Adaptive sparsity models") (description "This package implements the Figueiredo machine learning algorithm for adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian geometric models.") (license license:lgpl3+))) (define-public r-add2ggplot (package (name "r-add2ggplot") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "add2ggplot" version)) (sha256 (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0")))) (properties `((upstream-name . "add2ggplot"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot)) (native-inputs (list r-knitr)) (home-page "https://github.com/JiaxiangBU/add2ggplot") (synopsis "Extension for ggplot2") (description "This package provides tools to create themes and color palettes for the package ggplot2.") (license license:expat))) (define-public r-diffusionmap (package (name "r-diffusionmap") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "diffusionMap" version)) (sha256 (base32 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j")))) (properties `((upstream-name . "diffusionMap"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-scatterplot3d)) (home-page "https://www.r-project.org") (synopsis "Diffusion map") (description "This package implements the diffusion map method of data parametrization, including creation and visualization of diffusion maps, clustering with diffusion K-means and regression using the adaptive regression model.") (license license:gpl2))) (define-public r-igraph (package (name "r-igraph") (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 "1f1v8pv3slmjw11w6a97885114whw6ykky3jviwj1rrqzcvwq3j1")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) (inputs (list glpk gmp libxml2 zlib)) (propagated-inputs (list r-cli r-cpp11 r-lifecycle r-magrittr r-matrix r-pkgconfig r-rlang)) (home-page "https://igraph.org") (synopsis "Network analysis and visualization") (description "This package provides routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.") (license license:gpl2+))) (define-public r-workflows (package (name "r-workflows") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 "10a1my6glvc32zxrar1ir699lwav7iz2ji4s6g9iprjndf3nm8ms")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs (list r-cli r-generics r-glue r-hardhat r-lifecycle r-modelenv r-parsnip r-rlang r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/workflows") (synopsis "Modeling workflows") (description "A workflow is an object that can bundle together your pre-processing, modeling, and post-processing requests. For example, if you have a @code{recipe} and @code{parsnip} model, these can be combined into a workflow. The advantages are: @enumerate @item You don’t have to keep track of separate objects in your workspace. @item The recipe prepping and model fitting can be executed using a single call to @code{fit()}. @item If you have custom tuning parameter settings, these can be defined using a simpler interface when combined with @code{tune}. @item In the future, workflows will be able to add post-processing operations, such as modifying the probability cutoff for two-class models. @end enumerate ") (license license:expat))) (define-public r-lobstr (package (name "r-lobstr") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "lobstr" version)) (sha256 (base32 "060p7b7i2qx09d7nf0kdl85r9j886fivrkrsl2bn10cggvnk7icv")))) (properties `((upstream-name . "lobstr"))) (build-system r-build-system) (propagated-inputs (list r-cpp11 r-crayon r-prettyunits r-rlang)) (home-page "https://github.com/r-lib/lobstr") (synopsis "Visualize R data structures with trees") (description "This package provides a set of tools for inspecting and understanding R data structures inspired by @code{str}. It includes @code{ast} for visualizing abstract syntax trees, @code{ref} for showing shared references, @code{cst} for showing call stack trees, and @code{obj_size} for computing object sizes.") (license license:gpl3))) (define-public r-gpfit (package (name "r-gpfit") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "GPfit" version)) (sha256 (base32 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby")))) (properties `((upstream-name . "GPfit"))) (build-system r-build-system) (propagated-inputs (list r-lattice r-lhs)) (home-page "https://cran.r-project.org/web/packages/GPfit/") (synopsis "Gaussian Processes modeling") (description "This package provides a computationally stable approach of fitting a @dfn{Gaussian Process} (GP) model to a deterministic simulator.") (license license:gpl2))) (define-public r-yardstick (package (name "r-yardstick") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "yardstick" version)) (sha256 (base32 "0aqxnxhyy0bdfm09b7jpzba6c4g5r6l4h48q2xfxsm353nni7wgb")))) (properties `((upstream-name . "yardstick"))) (build-system r-build-system) (propagated-inputs (list r-cli r-dplyr r-generics r-hardhat r-lifecycle r-rlang r-tibble r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/yardstick") (synopsis "Tidy characterizations of model performance") (description "This package provides tidy tools for quantifying how well a model fits to a data set such as confusion matrices, class probability curve summaries, and regression metrics (e.g., RMSE).") (license license:gpl2))) (define-public r-warp (package (name "r-warp") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "warp" version)) (sha256 (base32 "1gj65kgs7x63f6y2vnv13k293b52k4afbmdlcam635h9vs8da2h2")))) (properties `((upstream-name . "warp"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/DavisVaughan/warp") (synopsis "Group dates") (description "This package provides tooling to group dates by a variety of periods including: yearly, monthly, by second, by week of the month, and more. The groups are defined in such a way that they also represent the distance between dates in terms of the period. This extracts valuable information that can be used in further calculations that rely on a specific temporal spacing between observations.") (license license:expat))) (define-public r-scico (package (name "r-scico") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "scico" version)) (sha256 (base32 "1c6905y62s03kiah8ykhkag275pn06ihk5szldib2621ysrj2wb4")))) (properties `((upstream-name . "scico"))) (build-system r-build-system) (propagated-inputs (list r-scales)) (home-page "https://github.com/thomasp85/scico") (synopsis "Colour Palettes Based on the Scientific Colour-Maps") (description "This package provides colour choice in information visualisation. It important in order to avoid being mislead by inherent bias in the used colour palette. This package provides access to the perceptually uniform and colour-blindness friendly palettes developed by Fabio Crameri and released under the \"Scientific Colour-Maps\" moniker. The package contains 24 different palettes and includes both diverging and sequential types.") (license license:expat))) (define-public r-slider (package (name "r-slider") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "slider" version)) (sha256 (base32 "1c19lk0ddh5qh0jzx7178l314zyygmlpmbvn7670bcmdbxwjc2i0")))) (properties `((upstream-name . "slider"))) (build-system r-build-system) (propagated-inputs (list r-cli r-rlang r-vctrs r-warp)) (native-inputs (list r-knitr)) (home-page "https://github.com/DavisVaughan/slider") (synopsis "Sliding window functions") (description "This package provides type-stable rolling window functions over any R data type. Cumulative and expanding windows are also supported. For more advanced usage, an index can be used as a secondary vector that defines how sliding windows are to be created.") (license license:expat))) (define-public r-rlist (package (name "r-rlist") (version "0.4.6.2") (source (origin (method url-fetch) (uri (cran-uri "rlist" version)) (sha256 (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb")))) (properties `((upstream-name . "rlist"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml)) (home-page "https://renkun-ken.github.io/rlist/") (synopsis "Toolbox for Non-Tabular Data Manipulation") (description "This package provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.") (license license:expat))) (define-public r-rsample (package (name "r-rsample") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 "1vayyj6cijq1ag9r7fpcjfzrgkqhb4zxgajz78hz8dq01q3bgjg0")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs (list r-cli r-dplyr r-furrr r-generics r-glue r-lifecycle r-pillar r-purrr r-rlang r-slider r-tibble r-tidyr r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://rsample.tidymodels.org") (synopsis "General resampling infrastructure") (description "This package provides classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).") (license license:gpl2))) (define-public r-dicedesign (package (name "r-dicedesign") (version "1.10") (source (origin (method url-fetch) (uri (cran-uri "DiceDesign" version)) (sha256 (base32 "0gf76f4jy8lbmw045q3ncs4ly07clh6gdfbmlnyk45wcgch3nm06")))) (properties `((upstream-name . "DiceDesign"))) (build-system r-build-system) (home-page "http://dice.emse.fr/") (synopsis "Designs of computer experiments") (description "This package provides tools to create some specific @code{Space-Filling Design} (SFD) and to test their quality.") (license license:gpl3))) (define-public r-dicekriging (package (name "r-dicekriging") (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "DiceKriging" version)) (sha256 (base32 "0jfb2li6b93fkwgjkr4jwxnvv7zb0aqk9lkf2mnv2awzh0r16pdb")))) (properties `((upstream-name . "DiceKriging"))) (build-system r-build-system) (home-page "https://dicekrigingclub.github.io/www/") (synopsis "Kriging methods for computer experiments") (description "This is a package for the estimation, validation and prediction of kriging models.") (license license:gpl2+))) (define-public r-dials (package (name "r-dials") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "dials" version)) (sha256 (base32 "1zj8f47jzgaydp3cff96w0kx1gm208vyq3f77p3g59nc01r0wri4")))) (properties `((upstream-name . "dials"))) (build-system r-build-system) (propagated-inputs (list r-cli r-dicedesign r-dplyr r-glue r-hardhat r-lifecycle r-pillar r-purrr r-rlang r-scales r-tibble r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://dials.tidymodels.org/") (synopsis "Tools for creating tuning parameter values") (description "Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.") (license license:gpl2))) (define-public r-tune (package (name "r-tune") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "tune" version)) (sha256 (base32 "12z1h574ymg9r3q19h5nhbkmzb5p3ckz7xvp6p0yra1mdmzcq0v9")))) (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs (list r-cli r-dials r-dplyr r-foreach r-generics r-ggplot2 r-glue r-gpfit r-hardhat r-lifecycle r-parsnip r-purrr r-recipes r-rlang r-rsample r-tibble r-tidyr r-tidyselect r-vctrs r-withr r-workflows r-yardstick)) (home-page "https://github.com/tidymodels/tune") (synopsis "Tidy tuning tools") (description "The ability to tune models is important. @code{tune} contains functions and classes to be used in conjunction with other @code{tidymodels} packages for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.") (license license:expat))) (define-public r-workflowsets (package (name "r-workflowsets") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "workflowsets" version)) (sha256 (base32 "1rv82lx1vmhjqlim7y5vpfsa7mb6msvkhiz17hxr5k9244ykmbhi")))) (properties `((upstream-name . "workflowsets"))) (build-system r-build-system) (propagated-inputs (list r-cli r-dplyr r-hardhat r-generics r-ggplot2 r-glue r-lifecycle r-parsnip r-pillar r-prettyunits r-purrr r-rlang r-rsample r-tibble r-tidyr r-tune r-vctrs r-withr r-workflows)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/workflowsets") (synopsis "Create a collection of tidymodels workflows") (description "A workflow is a combination of a model and preprocessors (e.g, a formula, recipe, etc.). In order to try different combinations of these, an object can be created that contains many workflows. There are functions to create workflows en masse as well as training them and visualizing the results.") (license license:expat))) (define-public r-tidyposterior (package (name "r-tidyposterior") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "tidyposterior" version)) (sha256 (base32 "1yi0pihglp683dmfg0bn9lnb0qsl2xprj3al65v642rcfzrr7h4h")))) (properties `((upstream-name . "tidyposterior"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-generics r-ggplot2 r-purrr r-rlang r-rsample r-rstanarm r-tibble r-tidyr r-tune r-vctrs r-workflowsets)) (native-inputs (list r-knitr)) (home-page "https://tidyposterior.tidymodels.org") (synopsis "Bayesian analysis to compare models using resampling statistics") (description "This package can be used to conduct post hoc analyses of resampling results generated by models. For example, if two models are evaluated with the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there are 10 paired statistics. These can be used to make comparisons between models without involving a test set.") (license license:gpl2))) (define-public r-tidypredict (package (name "r-tidypredict") (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "tidypredict" version)) (sha256 (base32 "1h05gm6fwjh6v9qqi9jbislf008h7d50k003qymb0x9gz6p75qgy")))) (properties `((upstream-name . "tidypredict"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-generics r-knitr r-purrr r-rlang r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://tidypredict.tidymodels.org") (synopsis "Run predictions inside the database") (description "This package parses a fitted R model object, and returns a formula in Tidy Eval code that calculates the predictions. It works with several database backends because it leverages @code{dplyr} and @code{dbplyr} for the final SQL translation of the algorithm. It currently supports @code{lm()}, @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()}, @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.") (license license:gpl3))) (define-public r-janeaustenr (package (name "r-janeaustenr") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "janeaustenr" version)) (sha256 (base32 "1ap8p1lpbj2wz90mpf1vbyzhv2spzv03bi8lwzpsir2y77hjxhxl")))) (properties `((upstream-name . "janeaustenr"))) (build-system r-build-system) (home-page "https://github.com/juliasilge/janeaustenr") (synopsis "Jane Austen's complete novels") (description "This package provides the full texts for Jane Austen's six completed novels, ready for text analysis. These novels are \"Sense and Sensibility\", \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\", and \"Persuasion\".") (license license:expat))) (define-public r-janitor (package (name "r-janitor") (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "janitor" version)) (sha256 (base32 "1bmsyrmy833kzj3s9s6207f54bx1ca0ianwhiyrlp0jfbqcd1m99")))) (properties `((upstream-name . "janitor"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-hms r-lifecycle r-lubridate r-magrittr r-purrr r-rlang r-snakecase r-stringi r-stringr r-tidyr r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://github.com/sfirke/janitor") (synopsis "Simple tools for examining and cleaning dirty data") (description "The main janitor functions can: perfectly format @code{data.frame column} names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and isolate duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Excel. This package follows the principles of the \"tidyverse\" and works well with the pipe function @code{%>%}. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness. Advanced R users can already do everything covered here, but with janitor they can do it faster and save their thinking for the fun stuff.") (license license:expat))) (define-public r-tokenizers (package (name "r-tokenizers") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "tokenizers" version)) (sha256 (base32 "0a8wm4cff3hrll991h2rimw79kpf2jsn78y7yksdk8m18931wmr4")))) (properties `((upstream-name . "tokenizers"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-snowballc r-stringi)) (native-inputs (list r-knitr)) (home-page "https://lincolnmullen.com/software/tokenizers/") (synopsis "Fast, consistent tokenization of natural language text") (description "This is a package for converting natural language text into tokens. It includes tokenizers for shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, shingled characters, lines, tweets, Penn Treebank, regular expressions, as well as functions for counting characters, words, and sentences, and a function for splitting longer texts into separate documents, each with the same number of words. The tokenizers have a consistent interface, and the package is built on the @code{stringi} and @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.") (license license:expat))) (define-public r-hunspell (package (name "r-hunspell") (version "3.0.3") (source (origin (method url-fetch) (uri (cran-uri "hunspell" version)) (sha256 (base32 "1ws2hhrn3iw89vs17q9claf0cip5hy6rbgdr4dcjmzrdlrri9apx")))) (properties `((upstream-name . "hunspell"))) (build-system r-build-system) (propagated-inputs (list r-digest r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/hunspell#readme") (synopsis "High-performance stemmer, tokenizer, and spell checker") (description "This package provides a low-level spell checker and morphological analyzer based on the famous @code{hunspell} library. The package can analyze or check individual words as well as parse text, LaTeX, HTML or XML documents. For a more user-friendly interface use the @code{spelling} package which builds on this package to automate checking of files, documentation and vignettes in all common formats.") ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or ;; MPL; in addition to these licenses the rest of the R wrapper is also ;; available under the Expat license. (license (list license:gpl2 license:lgpl2.1 license:mpl1.1 license:expat)))) (define-public r-tidytext (package (name "r-tidytext") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "tidytext" version)) (sha256 (base32 "05f8209qx1rvddnkl0h05yig09xahs8lqgq9w5dvdiwarji50rsj")))) (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs (list r-cli r-dplyr r-generics r-janeaustenr r-lifecycle r-matrix r-purrr r-rlang r-stringr r-tibble r-tokenizers r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/juliasilge/tidytext") (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools") (description "This is a package for text mining for word processing and sentiment analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (license license:expat))) (define-public r-parsnip (package (name "r-parsnip") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "parsnip" version)) (sha256 (base32 "1j0bkmv2m4rxmnpq3rqha5jccjxai11m5392hb4dgzni7in36h92")))) (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs (list r-cli r-dplyr r-generics r-ggplot2 r-globals r-glue r-hardhat r-lifecycle r-magrittr r-pillar r-prettyunits r-purrr r-rlang r-tibble r-tidyr r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://parsnip.tidymodels.org") (synopsis "Common API to modeling and analysis functions") (description "This package provides a common interface to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. R, Spark, Stan, etc).") (license license:gpl2))) (define-public r-infer (package (name "r-infer") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "infer" version)) (sha256 (base32 "1zs1c22zc255m23in99cqp2chpdkski002rywmkdzwf6nd96mly7")))) (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs (list r-broom r-dplyr r-generics r-ggplot2 r-glue r-magrittr r-patchwork r-purrr r-rlang r-tibble r-tidyr r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/infer") (synopsis "Tidy statistical inference") (description "The objective of this package is to perform inference using an expressive statistical grammar that coheres with the Tidy design framework.") (license license:cc0))) (define-public r-modeldata (package (name "r-modeldata") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "modeldata" version)) (sha256 (base32 "15d29497bbarb3qyib4g584hscfviv0cg62195s26qg1q6l022ac")))) (properties `((upstream-name . "modeldata"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-mass r-purrr r-rlang r-tibble)) (home-page "https://modeldata.tidymodels.org") (synopsis "Data sets useful for modeling packages") (description "This package provides data sets used for demonstrating or testing model-related packages.") (license license:expat))) (define-public r-modeest (package (name "r-modeest") (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "modeest" version)) (sha256 (base32 "087dw0013y4m7fcl06mxylh9lnp6acysl80d80r9srv4pw4r950s")))) (properties `((upstream-name . "modeest"))) (build-system r-build-system) (propagated-inputs (list r-fbasics r-stable r-stabledist r-statip)) (home-page "https://github.com/paulponcet/modeest") (synopsis "Mode estimations for univariate data or distributions") (description "The package provides estimators of the mode of univariate unimodal (and sometimes multimodal) data and values of the modes of usual probability distributions.") (license license:gpl3))) (define-public r-conflicted (package (name "r-conflicted") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "conflicted" version)) (sha256 (base32 "121h4b4rms23szcfs1nrbgdk812d61vhrmwn9lgpsgnsaaxqd6y9")))) (properties `((upstream-name . "conflicted"))) (build-system r-build-system) (propagated-inputs (list r-cli r-memoise r-rlang)) (home-page "https://github.com/r-lib/conflicted") (synopsis "Alternative conflict resolution strategy") (description "R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. The @code{conflicted} package takes a different approach, making every conflict an error and forcing you to choose which function to use.") (license license:gpl3))) (define-public r-tidymodels (package (name "r-tidymodels") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "tidymodels" version)) (sha256 (base32 "1ilmxxmbi9czxwv8n6xajaww9047h34i9vy2dmglj7nqply8wzl0")))) (properties `((upstream-name . "tidymodels"))) (build-system r-build-system) (propagated-inputs (list r-broom r-cli r-conflicted r-dials r-dplyr r-ggplot2 r-hardhat r-infer r-modeldata r-parsnip r-purrr r-recipes r-rlang r-rsample r-rstudioapi r-tibble r-tidyr r-tune r-workflows r-workflowsets r-yardstick)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/tidymodels") (synopsis "Tidy collection for modeling and statistical analysis") (description "The tidy modeling \"verse\" is a collection of packages for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse.") (license license:gpl3))) (define-public r-lsa (package (name "r-lsa") (version "0.73.3") (source (origin (method url-fetch) (uri (cran-uri "lsa" version)) (sha256 (base32 "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh")))) (properties `((upstream-name . "lsa"))) (build-system r-build-system) (propagated-inputs (list r-snowballc)) (home-page "https://cran.r-project.org/package=lsa") (synopsis "Latent semantic analysis") (description "The basic idea of latent semantic analysis (LSA) is, that text do have a higher order (=latent semantic) structure which, however, is obscured by word usage (e.g. through the use of synonyms or polysemy). By using conceptual indices that are derived statistically via a truncated singular value decomposition (a two-mode factor analysis) over a given document-term matrix, this variability problem can be overcome.") (license license:gpl2+))) (define-public r-mlecens (package (name "r-mlecens") (version "0.1-7") (source (origin (method url-fetch) (uri (cran-uri "MLEcens" version)) (sha256 (base32 "1kdnm5ilfn5fclry3f1d518761hykrqgjhv69kc881r2fpcfa1lv")))) (properties `((upstream-name . "MLEcens"))) (build-system r-build-system) (home-page "https://stat.ethz.ch/~maathuis/") (synopsis "Computation of the MLE for bivariate (interval) censored data") (description "This package contains functions to compute the nonparametric @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly. To be more precise, we consider the situation where we observe a set of rectangles that are known to contain the unobservable realizations of (X,Y). We compute the MLE based on such a set of rectangles. The methods can also be used for univariate censored data (see data set @code{cosmesis}), and for censored data with competing risks (see data set @code{menopause}). The package also provides functions to visualize the observed data and the MLE.") (license license:gpl2+))) (define-public r-metafor (package (name "r-metafor") (version "4.4-0") (source (origin (method url-fetch) (uri (cran-uri "metafor" version)) (sha256 (base32 "1m4762fn4zbjpnx9vxyy9gvzyzn3avxnqpzmbj45w8241g3s1b32")))) (properties `((upstream-name . "metafor"))) (build-system r-build-system) (propagated-inputs (list r-mathjaxr r-matrix r-metadat r-nlme r-numderiv r-pbapply)) (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/web/packages/metafor/") (synopsis "Meta-analysis package for R") (description "This package provides a comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e. mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g. due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g. due to phylogenetic relatedness) can also be conducted.") (license license:gpl2+))) (define-public r-altmeta (package (name "r-altmeta") (version "4.1") (source (origin (method url-fetch) (uri (cran-uri "altmeta" version)) (sha256 (base32 "01v308389wqzp35icrp9ssb4y4gxwjzl600qw47c6rmm6s2mxzjh")))) (properties `((upstream-name . "altmeta"))) (build-system r-build-system) (propagated-inputs (list r-coda r-lme4 r-matrix r-metafor r-rjags)) (home-page "https://cran.r-project.org/web/packages/altmeta/") (synopsis "Alternative meta-analysis methods") (description "This package provides alternative statistical methods for meta-analysis, including: @enumerate @item bivariate generalized linear mixed models for synthesizing odds ratios, relative risks, and risk differences @item heterogeneity tests and measures that are robust to outliers; @item measures, tests, and visualization tools for publication bias or small-study effects; @item meta-analysis of diagnostic tests for synthesizing sensitivities, specificities, etc.; @item meta-analysis methods for synthesizing proportions; @item models for multivariate meta-analysis. @end enumerate ") (license license:gpl2+))) (define-public r-perm (package (name "r-perm") (version "1.0-0.4") (source (origin (method url-fetch) (uri (cran-uri "perm" version)) (sha256 (base32 "1sbvc9pd8j4wigblncd5jsgfnphp4kz1jy3acyivcclh79wh27jn")))) (properties `((upstream-name . "perm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/perm/") (synopsis "Exact or asymptotic permutation tests") (description "This package provides several methods for performing permutation tests. It has three main functions, to perform linear permutation tests. These tests are tests where the test statistic is the sum of the product of a covariate (usually group indicator) and the scores.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-qtl (package (name "r-qtl") (version "1.66") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 "10fnc3ms97rdqsqxz5jpvg2cmrwmz69wjxxs3h65r1yhy94pssnl")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") (description "R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs). Using a hidden Markov model, R/qtl estimates genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.") (license license:gpl3))) (define-public r-qtl2 (package (name "r-qtl2") (version "0.34") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 (base32 "1h3wim850b2xk09z9vgnyfp20k7vg94zf7szcrlw5nf1w9gn4wzy")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-rcpp r-rcppeigen r-rsqlite r-yaml)) (home-page "https://kbroman.org/qtl2/") (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") (description "This package provides a set of tools to perform @dfn{Quantitative Trait Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the @code{R/qtl} package to better handle high-dimensional data and complex cross designs. Broman et al. (2018) .") (license license:gpl3))) (define-public r-seqminer (package (name "r-seqminer") (version "9.3") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 "07dig3ydybmi55qy1zpkxpw568midgc1bzdl3k36734yqnsp2sjs")))) (build-system r-build-system) (inputs (list zlib)) (home-page "http://seqminer.genomic.codes") (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") (description "This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") ;; Any version of the GPL is acceptable (license (list license:gpl2+ license:gpl3+)))) (define-public r-maldiquant (package (name "r-maldiquant") (version "1.22.1") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 "0721j8lzv6ywv0hf8rjw446dmvl18gm5ymf5a35fg9vnprfsalha")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/MALDIquant") (synopsis "Quantitative analysis of mass spectrometry data") (description "This package provides a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.") (license license:gpl3+))) (define-public r-scattermore (package (name "r-scattermore") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "scattermore" version)) (sha256 (base32 "1l820rc4ncmqd5sacdc420xf6r5dh34sbhgzzgq7a4yx1dxshd2m")))) (properties `((upstream-name . "scattermore"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/exaexa/scattermore") (synopsis "Scatterplots with more points") (description "This package provides C-based tools for converting large scatterplot data to rasters. It speeds up plotting of data with millions of points.") (license license:gpl3+))) (define-public r-seuratobject (package (name "r-seuratobject") (version "5.0.1") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 "0hgrymldcqja40prr23gwx1c7lvwjjwcla3dld6x8wzkzqh1gkjs")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs (list r-future r-future-apply r-generics r-lifecycle r-matrix r-progressr r-rcpp r-rcppeigen r-rlang r-sp r-spam)) (home-page "https://satijalab.org/seurat") (synopsis "Data structures for single cell data") (description "This package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.") (license license:gpl3))) ;; This is for r-seurat5 (define-public r-seurat5object (let ((commit "185884ae527d6ce71cb51d2e84a630030e8439a3") (revision "1")) (package (inherit r-seuratobject) (name "r-seurat5object") (version (git-version "4.9.9.9084" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mojaveazure/seurat-object") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1nbai31gjsgiaazb4jhpqw8h04nm8xd131fng7zcw11kspj54n9z")) ;; This file triggers renv, which we don't want to use. (snippet '(delete-file ".Rprofile")))) (propagated-inputs (list r-future r-future-apply r-generics r-lifecycle r-matrix r-progressr r-rcpp r-rcppeigen r-rlang r-sp r-spam))))) (define-public r-seurat (package (name "r-seurat") (version "5.0.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 "038mqnavn3gxxx41yzq0q7gfnnx15dizryv8l374zwavpqsb84q7")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-cowplot r-fastdummies r-fitdistrplus r-future r-future-apply r-generics r-ggplot2 r-ggrepel r-ggridges r-httr r-ica r-igraph r-irlba r-jsonlite r-kernsmooth r-leiden r-lifecycle r-lmtest r-mass r-matrix r-matrixstats r-miniui r-patchwork r-pbapply r-plotly r-png r-progressr r-purrr r-rann r-rcolorbrewer r-rcpp r-rcppannoy r-rcppeigen r-rcpphnsw r-rcppprogress r-reticulate r-rlang r-rocr r-rspectra r-rtsne r-scales r-scattermore r-sctransform r-seuratobject r-shiny r-spatstat-explore r-spatstat-geom r-tibble r-uwot)) (home-page "https://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description "This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.") (license license:gpl3))) ;; Seurat5 is only available via the seurat5 branch. It will replace r-seurat ;; eventually once it has been released to CRAN. (define-public r-seurat5 (let ((commit "9d59c02042b9ae4f182fbde84cc8b18c0873ef4d") (revision "1")) (package (inherit r-seurat) (name "r-seurat5") (version (git-version "4.9.9.9044" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/satijalab/seurat") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0y4wl6aanq9scn2clazlxsar35g64v4sfy561j43fq1i85na7m4i")))) (propagated-inputs (list r-cluster r-cowplot r-fastdummies r-fitdistrplus r-future r-future-apply r-generics r-ggplot2 r-ggrepel r-ggridges r-httr r-ica r-igraph r-irlba r-jsonlite r-kernsmooth r-leiden r-lifecycle r-lmtest r-mass r-matrix r-matrixstats r-miniui r-patchwork r-pbapply r-plotly r-png r-progressr r-rann r-rcolorbrewer r-rcpp r-rcppannoy r-rcppeigen r-rcpphnsw r-rcppprogress r-reticulate r-rlang r-rocr r-rspectra r-rtsne r-scales r-scattermore r-sctransform r-seurat5object r-shiny r-spatstat-explore r-spatstat-geom r-tibble r-uwot))))) (define-public r-seuratdisk (let ((commit "877d4e18ab38c686f5db54f8cd290274ccdbe295") (revision "1")) (package (name "r-seuratdisk") (version (git-version "0.0.0.9021" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mojaveazure/seurat-disk") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0ma9qk95symk95slp8klriqg64d8klqf1634y93ml74icarxw1dm")))) (properties `((upstream-name . "SeuratDisk"))) (build-system r-build-system) (propagated-inputs (list r-cli r-crayon r-hdf5r r-matrix r-r6 r-rlang r-seurat r-seuratobject r-stringi r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mojaveazure/seurat-disk") (synopsis "Interfaces for HDF5-based single cell file formats") (description "The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. This package also supports rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.") (license license:gpl3)))) (define-public r-seuratdata (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5") (revision "1")) (package (name "r-seuratdata") (version (git-version "0.2.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/satijalab/seurat-data") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9")))) (properties `((upstream-name . "SeuratData"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases ;; When there is no HOME directory, this package will fail to load ;; the included list of packages. (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-cli r-crayon r-rappdirs)) (home-page "https://github.com/satijalab/seurat-data") (synopsis "Install and manage Seurat datasets") (description "Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages.") (license license:gpl3)))) (define-public r-phangorn (package (name "r-phangorn") (version "2.11.1") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 "086lxqzqx1n3237h9q28r54libaz2xk9h3f6vfj8l49yw356w28h")))) (build-system r-build-system) (propagated-inputs (list r-ape r-digest r-fastmatch r-generics r-igraph r-matrix r-quadprog r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/KlausVigo/phangorn") (synopsis "Phylogenetic analysis in R") (description "Phangorn is a package for phylogenetic analysis in R. It supports estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.") (license license:gpl2+))) (define-public r-diversitree (package (name "r-diversitree") (version "0.10-0") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 "1xl2swbmgpni2y2divl29xh702b88kxgcswa47g62ny59gh2fdn1")))) (build-system r-build-system) (inputs (list fftw gsl)) (propagated-inputs (list r-ape r-desolve r-rcpp r-subplex)) (home-page "https://www.zoology.ubc.ca/prog/diversitree") (synopsis "Comparative 'phylogenetic' analyses of diversification") (description "This package contains a number of comparative \"phylogenetic\" methods, mostly focusing on analysing diversification and character evolution. Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) (define-public r-calculus (package (name "r-calculus") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 "1p80bgg6896z798cx7nwqbwd0rxdv27kamaw1gw0hv4lpqsr7q10")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/eguidotti/calculus") (synopsis "High dimensional numerical and symbolic calculus") (description "Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, accurate high-order derivatives, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.") (license license:gpl3))) (define-public r-decon (package (name "r-decon") (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "decon" version)) (sha256 (base32 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs")))) (properties `((upstream-name . "decon"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/decon/") (synopsis "Deconvolution Estimation in Measurement Error Models") (description "This package contains a collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement error model, where the goal is to estimate the density or distribution function from contaminated data; (2) nonparametric regression model with errors-in-variables. The R functions allow the measurement errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the \"Fast Fourier Transform\" (FFT) algorithm for density estimation with error-free data to the deconvolution kernel estimation. Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.") (license license:gpl3+))) (define-public r-densestbayes (package (name "r-densestbayes") (version "1.0-2.2") (source (origin (method url-fetch) (uri (cran-uri "densEstBayes" version)) (sha256 (base32 "0ydnjyprv8fz037nkfvjd8w6hg4a19lbnq4kl7yankxksjfdyqc3")))) (properties `((upstream-name . "densEstBayes"))) (build-system r-build-system) (propagated-inputs (list r-bh r-mass r-nlme r-rcpp r-rcpparmadillo r-rcppeigen r-rcppparallel r-rstan r-rstantools r-stanheaders)) (home-page "https://cran.r-project.org/package=densEstBayes") (synopsis "Density estimation via Bayesian inference engines") (description "Bayesian density estimates for univariate continuous random samples are provided using the Bayesian inference engine paradigm. The engine options are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field variational Bayes and slice sampling. The methodology is described in Wand and Yu (2020), arXiv:2009.06182.") (license license:gpl2+))) (define-public r-locpol (package (name "r-locpol") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "locpol" version)) (sha256 (base32 "1bip9x45kdnwc14rvk3ckzfbs32yc2wiid1ypmbbin4mk7364zxk")))) (properties `((upstream-name . "locpol"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/locpol/") (synopsis "Kernel Local Polynomial Regression") (description "Computes local polynomial estimators for the regression and also density. It comprises several different utilities to handle kernel estimators.") (license license:gpl2+))) (define-public r-lpme (package (name "r-lpme") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "lpme" version)) (sha256 (base32 "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb")))) (properties `((upstream-name . "lpme"))) (build-system r-build-system) (propagated-inputs (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/lpme/") (synopsis "Nonparametric Estimation of Measurement Error Models") (description "Provide nonparametric methods for mean regression model, modal regression and conditional density estimation in the presence/absence of measurement error. Bandwidth selection is also provided for each method.") (license license:gpl2+))) (define-public r-aws-signature (package (name "r-aws-signature") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "aws.signature" version)) (sha256 (base32 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp")))) (properties `((upstream-name . "aws.signature"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-digest)) (home-page "https://github.com/cloudyr/aws.signature") (synopsis "Amazon Web Services Request Signatures") (description "This package generates version 2 and 4 request signatures for Amazon Web Services (AWS) and provides a mechanism for retrieving credentials from environment variables, AWS credentials files, and EC2 instance metadata. For use on EC2 instances, the package 'aws.ec2metadata' is suggested.") (license license:gpl2+))) (define-public r-aws-s3 (package (name "r-aws-s3") (version "0.3.21") (source (origin (method url-fetch) (uri (cran-uri "aws.s3" version)) (sha256 (base32 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx")))) (properties `((upstream-name . "aws.s3"))) (build-system r-build-system) (propagated-inputs (list r-aws-signature r-base64enc r-curl r-digest r-httr r-xml2)) (home-page "https://github.com/cloudyr/aws.s3") (synopsis "AWS S3 Client Package") (description "This package provides a simple client package for the Amazon Web Services (AWS) Simple Storage Service (S3) REST API.") (license license:gpl2+))) (define-public r-lgr (package (name "r-lgr") (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "lgr" version)) (sha256 (base32 "09x1vw6cnc1c0p0ylcz1q1vcxyaf1kljhh7ni3gl5jm19zii2h4c")))) (build-system r-build-system) (propagated-inputs (list r-r6)) (native-inputs (list r-knitr)) (home-page "https://s-fleck.github.io/lgr/") (synopsis "Fully featured logging framework") (description "This package offers a flexible, feature-rich yet light-weight logging framework based on @code{R6} classes. It supports hierarchical loggers, custom log levels, arbitrary data fields in log events, logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as well as email and push notifications.") (license license:expat))) (define-public r-mhg (package (name "r-mhg") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "mHG" version)) (sha256 (base32 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki")))) (properties `((upstream-name . "mHG"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=mHG") (synopsis "Minimum-hypergeometric test") (description "This package runs a minimum-hypergeometric (mHG) test as described in \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.") (license license:gpl2))) (define-public r-mlr (package (name "r-mlr") (version "2.19.1") (source (origin (method url-fetch) (uri (cran-uri "mlr" version)) (sha256 (base32 "00jjhvaqifj6glqsyzixlp56bvlch5smck8kk3klcmwx9pasyllx")))) (properties `((upstream-name . "mlr"))) (build-system r-build-system) (inputs (list gdal geos glu gmp gsl jags mpfr openmpi proj udunits)) (propagated-inputs (list r-backports r-bbmisc r-checkmate r-data-table r-ggplot2 r-parallelmap r-paramhelpers r-stringi r-survival r-xml)) (native-inputs (list r-knitr)) (home-page "https://mlr.mlr-org.com") (synopsis "Machine learning in R") (description "This package provides an interface to a large number of classification and regression techniques. These techniques include machine-readable parameter descriptions. There is also an experimental extension for survival analysis, clustering and general, example-specific cost-sensitive learning. Also included: @itemize @item Generic resampling, including cross-validation, bootstrapping and subsampling; @item Hyperparameter tuning with modern optimization techniques, for single- and multi-objective problems; @item Filter and wrapper methods for feature selection; @item Extension of basic learners with additional operations common in machine learning, also allowing for easy nested resampling. @end itemize Most operations can be parallelized.") (license license:bsd-2))) (define-public r-mlrmbo (package (name "r-mlrmbo") (version "1.1.5.1") (source (origin (method url-fetch) (uri (cran-uri "mlrMBO" version)) (sha256 (base32 "16fwj7m28g4km7yalqppxmh3lw2jln0z072l6awia38qkdg6xwhc")))) (properties `((upstream-name . "mlrMBO"))) (build-system r-build-system) (propagated-inputs (list r-backports r-bbmisc r-checkmate r-data-table r-lhs r-mlr r-parallelmap r-paramhelpers r-smoof)) (native-inputs (list r-knitr)) (home-page "https://github.com/mlr-org/mlrMBO") (synopsis "Model-based optimization with mlr") (description "This package is a flexible and comprehensive R toolbox for model-based optimization. It implements Efficient Global Optimization Algorithm for single- and multi-objective optimization. It supports mixed parameters. The machine learning toolbox mlr offers regression learners. It provides various infill criteria and features batch proposal, parallel execution, visualization, and logging. Its modular implementation allows easy customization by the user.") (license license:bsd-2))) (define-public r-mlr3measures (package (name "r-mlr3measures") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3measures" version)) (sha256 (base32 "0k0i1xx63lds1870p2ljy1dlp2i376gdd0sq9s4xiqljqjb8va57")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-prroc)) (home-page "https://mlr3measures.mlr-org.com/") (synopsis "Performance measures for mlr3") (description "This package implements multiple performance measures for supervised learning. It includes over 40 measures for regression and classification. Additionally, meta information about the performance measures can be queried, e.g. what the best and worst possible performances scores are.") (license license:lgpl3))) (define-public r-mlr3misc (package (name "r-mlr3misc") (version "0.13.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 "0b565hy86bcgjv8k9qipkcgsag6jiiv1jx5lgi1iddcf8rg6bind")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-r6)) (home-page "https://mlr3misc.mlr-org.com/") (synopsis "Helper functions for mlr3") (description "@code{mlr3misc} provides frequently used helper functions and assertions used in @code{mlr3} and its companion packages. It comes with helper functions for functional programming, for printing, to work with @code{data.table}, as well as some generally useful @code{R6} classes. This package also supersedes the package @code{BBmisc}.") (license license:lgpl3))) (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") (version "0.5.0-2") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 "0iv09qmr1gpipcylw8mp1y7kqjljy8p5sx466l1wxfaqkf7kw15j")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-lgr r-mlr3 r-mlr3misc r-paradox r-r6 r-withr)) (native-inputs (list r-knitr)) (home-page "https://mlr3pipelines.mlr-org.com/") (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}") (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse set of pipelining operators (PipeOps) that can be composed into graphs. Operations exist for data preprocessing, model fitting, and ensemble learning. Graphs can themselves be treated as @code{mlr3} Learners and can therefore be resampled, benchmarked, and tuned.") (license license:lgpl3))) (define-public r-mlr3ordinal (let ((commit "736e3a39be6b7088b650297cc6d90208ec58c0d7") (revision "1")) (package (name "r-mlr3ordinal") (version (git-version "0.1.0-9000" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mlr-org/mlr3ordinal") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0ipf6n4m6giicn0x7f3lrfmbqkhw8zkz32hzq2xf209wndkqhqm1")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-mlr3 r-mlr3misc r-mlr3pipelines r-nloptr r-ordinal r-paradox r-r6)) (home-page "https://mlr3ordinal.mlr-org.com/") (synopsis "Ordinal Regression for mlr3") (description "This package extends @code{mlr3} with support for performing ordinal regression.") (license license:expat)))) (define-public r-paradox (package (name "r-paradox") (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 "0igza40ycirnf5chs7z2nnh0w6d48v4wv102zn2vnvh0kkvgv3hd")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) (home-page "https://paradox.mlr-org.com/") (synopsis "Define and work with parameter spaces for complex algorithms") (description "With this package it is possible to define parameter spaces, constraints and dependencies for arbitrary algorithms, and to program on such spaces. It also includes statistical designs and random samplers. Objects are implemented as @code{R6} classes.") (license license:lgpl3))) (define-public r-mlr3 (package (name "r-mlr3") (version "0.17.2") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 "0kcny3wxc7qc2538hxxdzs9bw4pq55s4abhlnpf1r13b2gkns323")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-evaluate r-future r-future-apply r-lgr r-mlbench r-mlr3measures r-mlr3misc r-palmerpenguins r-paradox r-parallelly r-r6 r-rhpcblasctl r-uuid)) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") (description "@code{mlr3} enables efficient, object-oriented programming on the building blocks of machine learning. It provides @code{R6} objects for tasks, learners, resamplings, and measures. The package is geared towards scalability and larger datasets by supporting parallelization and out-of-memory data-backends like databases. While @code{mlr3} focuses on the core computational operations, add-on packages provide additional functionality.") (license license:lgpl3))) (define-public r-mlr3learners (package (name "r-mlr3learners") (version "0.5.8") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 "0q44qmd9zfc68jl2zz684rx9744g83vd7z40dck8cdvnnrxcff5g")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-mlr3 r-mlr3misc r-paradox r-r6)) (home-page "https://mlr3learners.mlr-org.com/") (synopsis "Recommended Learners for @code{mlr3}") (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba} with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.") (license license:lgpl3))) (define-public r-bbotk (package (name "r-bbotk") (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 "1ddr5w7n68d3imcrm0ipgk1waml8zj4szi566dmmiqvlpzpgdr3p")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-lgr r-mlr3misc r-paradox r-r6)) (native-inputs (list r-knitr)) (home-page "https://bbotk.mlr-org.com") (synopsis "Black-Box Optimization Toolkit") (description "This package provides a common framework for optimization of black-box functions for other packages, e.g. @code{mlr3}. It offers various optimization methods e.g. grid search, random search and generalized simulated annealing.") (license license:lgpl3))) (define-public r-mlr3tuning (package (name "r-mlr3tuning") (version "0.19.2") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 "1d27m6yzwr7chpf19q6mwpj2fyz9vv8k6nbg8z9615hmbp96lan5")))) (build-system r-build-system) (propagated-inputs (list r-bbotk r-checkmate r-data-table r-lgr r-mlr3 r-mlr3misc r-paradox r-r6)) (native-inputs (list r-knitr)) (home-page "https://mlr3tuning.mlr-org.com/") (synopsis "Tuning for @code{mlr3}") (description "@code{mlr3tuning} implements methods for hyperparameter tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various termination criteria can be set and combined. The class @code{AutoTuner} provides a convenient way to perform nested resampling in combination with @code{mlr3}.") (license license:lgpl3))) (define-public r-fontliberation (package (name "r-fontliberation") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "fontLiberation" version)) (sha256 (base32 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc")))) (properties `((upstream-name . "fontLiberation"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fontLiberation") (synopsis "Liberation fonts") (description "This package provides a placeholder for the Liberation fontset intended for the fontquiver package. This fontset covers the 12 combinations of families (sans, serif, mono) and faces (plain, bold, italic, bold italic) supported in R graphics devices.") (license license:silofl1.1))) (define-public r-fontbitstreamvera (package (name "r-fontbitstreamvera") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "fontBitstreamVera" version)) (sha256 (base32 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j")))) (properties `((upstream-name . "fontBitstreamVera"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fontBitstreamVera") (synopsis "Fonts for fontquiver") (description "This package is a placeholder for the Bitstream Vera font. It is intended for the fontquiver package.") (license (license:fsdg-compatible "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts" "The Font Software may be sold as part of a larger software package but no copy of one or more of the Font Software typefaces may be sold by itself.")))) (define-public r-fontquiver (package (name "r-fontquiver") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "fontquiver" version)) (sha256 (base32 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm")))) (properties `((upstream-name . "fontquiver"))) (build-system r-build-system) (propagated-inputs (list r-fontbitstreamvera r-fontliberation)) (home-page "https://cran.r-project.org/package=fontquiver") (synopsis "Set of installed fonts") (description "This package provides a set of fonts. This is useful when you want to avoid system fonts to make sure your outputs are reproducible.") (license license:gpl3))) (define-public r-freetypeharfbuzz (package (name "r-freetypeharfbuzz") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "freetypeharfbuzz" version)) (sha256 (base32 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7")))) (properties `((upstream-name . "freetypeharfbuzz"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'prepare-static-libraries (lambda* (#:key inputs #:allow-other-keys) (mkdir-p "src/target/include") (let ((freetype (assoc-ref inputs "static-freetype")) (harfbuzz (assoc-ref inputs "static-harfbuzz"))) (substitute* "src/Makevars.in" (("include @MK_FILE@") "") ; do not build static libs (("^HB_STATIC_LIB =.*") (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n")) (("^FT_STATIC_LIB =.*") (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n"))) (copy-recursively (string-append freetype "/include") "src/target/include") (copy-recursively (string-append harfbuzz "/include") "src/target/include"))))))) (propagated-inputs (list r-fontquiver)) ;; This may defeat the purpose of this package as our versions of freetype ;; and harfbuzz obviously differ from the tarballs offered by this ;; project. On the other hand, Guix arguably does a better job at ;; "ensur[ing] deterministic computation". (native-inputs `(("static-freetype" ,(package (inherit (static-package freetype)) (arguments `(#:configure-flags (list "--enable-static=yes" "--with-pic=yes" "--without-zlib" "--without-bzip2" "--without-png" "--without-harfbuzz"))))) ("static-harfbuzz" ,(package (inherit (static-package harfbuzz)) (arguments `(#:tests? #false ; fail because shared library is disabled #:configure-flags (list "--enable-static=yes" "--enable-shared=no" "--with-pic=yes" "--with-freetype=yes" "--without-icu" "--without-cairo" "--without-fontconfig" "--without-glib"))))))) (inputs (list zlib)) (home-page "https://cran.r-project.org/package=freetypeharfbuzz") (synopsis "Deterministic computation of text box metrics") (description "Unlike other tools that dynamically link to the Cairo stack, freetypeharfbuzz is statically linked to specific versions of the FreeType and harfbuzz libraries. This ensures deterministic computation of text box extents for situations where reproducible results are crucial (for instance unit tests of graphics).") (license license:gpl3))) (define-public r-vdiffr (package (name "r-vdiffr") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "vdiffr" version)) (sha256 (base32 "1ljj94swqgs8pvicdrlals6pckm7knwfvxxmmbhhi2zfcxdjwhzd")))) (properties `((upstream-name . "vdiffr"))) (build-system r-build-system) (inputs (list libpng zlib)) (propagated-inputs (list r-cpp11 r-diffobj r-glue r-htmltools r-lifecycle r-rlang r-testthat r-xml2)) (home-page "https://github.com/r-lib/vdiffr") (synopsis "Visual regression testing and graphical diffing") (description "This package is an extension to the testthat package that makes it easy to add graphical unit tests. It provides a Shiny application to manage the test cases.") (license license:gpl3))) (define-public r-highlight (package (name "r-highlight") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "highlight" version)) (sha256 (base32 "06sirfmkdl355rfr5bb475829v7zx1spkz82vi31vl55jzijq54m")))) (properties `((upstream-name . "highlight"))) (build-system r-build-system) (home-page "https://github.com/hadley/highlight") (synopsis "Syntax highlighter for R code") (description "This package provides a syntax highlighter for R code based on the results of the R parser. It supports rendering in HTML and LaTeX markup. It includes a custom Sweave driver performing syntax highlighting of R code chunks.") (license license:gpl3+))) (define-public r-clustree (package (name "r-clustree") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "clustree" version)) (sha256 (base32 "05yizn8hcf4nsibypxahp2mz64sy10vli776mi0d2gvfb5p4kwmm")))) (properties `((upstream-name . "clustree"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-dplyr r-ggplot2 r-ggraph r-ggrepel r-igraph r-rlang r-tidygraph r-viridis)) (native-inputs (list r-knitr)) (home-page "https://github.com/lazappi/clustree") (synopsis "Visualize clusterings at different resolutions") (description "Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualization for interrogating clusterings as resolution increases.") (license license:gpl3))) (define-public r-textshaping (package (name "r-textshaping") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 "0hpcjz66ykji89g2lzpp6hfkz10388py8vn2ss08n4xl3yz4v4ps")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs (list freetype fribidi harfbuzz zlib)) (propagated-inputs (list r-cpp11 r-systemfonts)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/textshaping") (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping") (description "This package provides access to the text shaping functionality in the HarfBuzz library and the bidirectional algorithm in the Fribidi library. This is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the @code{systemfonts} package.") (license license:expat))) (define-public r-ragg (package (name "r-ragg") (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 "17qc53scxf02f8hlpyirsjdav4wjh3mk6q04npf82y0j5mk1hynp")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs (list freetype libjpeg-turbo libpng libtiff zlib)) (propagated-inputs (list r-systemfonts r-textshaping)) (native-inputs (list pkg-config)) (home-page "https://ragg.r-lib.org") (synopsis "Graphic devices based on AGG") (description "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The ragg package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the @code{grDevices} package.") (license license:expat))) (define-public r-downlit (package (name "r-downlit") (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "downlit" version)) (sha256 (base32 "1gdk6rj3539vnm979spd8py0rpvlaniyiy336abi39g8xjcbw3vc")))) (properties `((upstream-name . "downlit"))) (build-system r-build-system) (propagated-inputs (list r-brio r-desc r-digest r-evaluate r-fansi r-memoise r-rlang r-vctrs r-withr r-yaml)) (home-page "https://downlit.r-lib.org/") (synopsis "Syntax highlighting and automatic linking") (description "This package provides syntax highlighting of R code, specifically designed for the needs of RMarkdown packages like @code{pkgdown}, @code{hugodown}, and @code{bookdown}. It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.") (license license:expat))) (define-public r-pkgdown (package (name "r-pkgdown") (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 "0sim3fwayf4mpxqi8y9v7clnkzs56amhxsc75lc1k0zskn374f7k")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-bslib r-callr r-cli r-desc r-digest r-downlit r-fs r-httr r-jsonlite r-magrittr r-memoise r-purrr r-ragg r-rlang r-rmarkdown r-tibble r-whisker r-withr r-xml2 r-yaml)) (native-inputs (list r-knitr)) (home-page "https://pkgdown.r-lib.org") (synopsis "Make static HTML documentation for an R package") (description "The goal of this package is to generate an attractive and useful website from a source package. @code{pkgdown} converts your documentation, vignettes, README file, and more to HTML making it easy to share information about your package online.") (license license:expat))) (define-public r-prereg (package (name "r-prereg") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "prereg" version)) (sha256 (base32 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw")))) (properties `((upstream-name . "prereg"))) (build-system r-build-system) (propagated-inputs (list r-rmarkdown ;; The package provides a custom LaTex template in ;; inst/rmd/prereg_form.tex, which depends on these packages: texlive-amsmath texlive-booktabs texlive-etoolbox texlive-fancyhdr texlive-fancyvrb texlive-geometry texlive-graphics texlive-iftex texlive-listings texlive-polyglossia texlive-threeparttable texlive-titlesec texlive-titling texlive-tools texlive-ulem texlive-upquote (texlive-updmap.cfg (list texlive-lm)))) (home-page "https://github.com/crsh/prereg") (synopsis "R Markdown Templates to preregister Scientific Studies") (description "This package provides a collection of templates to author preregistration documents for scientific studies in PDF format.") (license license:gpl3))) (define-public r-ez (package (name "r-ez") (version "4.4-0") (source (origin (method url-fetch) (uri (cran-uri "ez" version)) (sha256 (base32 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq")))) (properties `((upstream-name . "ez"))) (build-system r-build-system) (propagated-inputs (list r-car r-ggplot2 r-lme4 r-mass r-matrix r-mgcv r-plyr r-reshape2 r-scales r-stringr)) (home-page "https://github.com/mike-lawrence/ez") (synopsis "Easy Analysis and Visualization of Factorial Experiments") (description "Facilitates easy analysis of factorial experiments, including purely within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs, and mixed within-and-between-Ss designs. The functions in this package aim to provide simple, intuitive and consistent specification of data analysis and visualization. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Finally, this package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. The bootstrap function obtains predictions either by cell means or by more advanced/powerful mixed effects models, yielding predictions and confidence intervals that may be easily visualized at any level of the experiment's design.") (license license:gpl2+))) (define-public r-qdapregex (package (name "r-qdapregex") (version "0.7.8") (source (origin (method url-fetch) (uri (cran-uri "qdapRegex" version)) (sha256 (base32 "1pf1cz03i6sn83d1aaj4cv4jfavs6k81nn5sy7b0aw4i1hpkyiwz")))) (properties `((upstream-name . "qdapRegex"))) (build-system r-build-system) (propagated-inputs (list r-stringi)) (home-page "https://trinker.github.com/qdapRegex/") (synopsis "Regular Expression Removal, Extraction, and Replacement Tools") (description "This package provides a collection of regular expression tools associated with the @code{qdap} package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, citations, person tags, phone numbers, times, and zip codes.") (license license:gpl2))) (define-public r-mgsub (package (name "r-mgsub") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "mgsub" version)) (sha256 (base32 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9")))) (properties `((upstream-name . "mgsub"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=mgsub") (synopsis "Safe, Multiple, Simultaneous String Substitution") (description "Designed to enable simultaneous substitution in strings in a safe fashion. Safe means it does not rely on placeholders (which can cause errors in same length matches).") (license license:expat))) (define-public r-textshape (package (name "r-textshape") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "textshape" version)) (sha256 (base32 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds")))) (properties `((upstream-name . "textshape"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-slam r-stringi)) (home-page "https://github.com/trinker/textshape") (synopsis "Tools for Reshaping Text") (description "Tools that can be used to reshape and restructure text data.") (license license:gpl2))) (define-public r-syuzhet (package (name "r-syuzhet") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "syuzhet" version)) (sha256 (base32 "0cpjg16hwn6843jdxp4h94qjw1wwwblvjzg30w54rac08m62nkxg")))) (properties `((upstream-name . "syuzhet"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-dtt r-nlp r-rlang r-textshape r-tidyr r-zoo)) (native-inputs (list r-knitr)) (home-page "https://github.com/mjockers/syuzhet") (synopsis "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text") (description "Extracts sentiment and sentiment-derived plot arcs from text using a variety of sentiment dictionaries conveniently packaged for consumption by R users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing} developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif M. and Turney, Peter D. Applicable references are available in @file{README.md} and in the documentation for the @code{get_sentiment} function. The package also provides a hack for implementing Stanford's coreNLP sentiment parser. The package provides several methods for plot arc normalization.") (license license:gpl3))) (define-public r-lexicon (package (name "r-lexicon") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "lexicon" version)) (sha256 (base32 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c")))) (properties `((upstream-name . "lexicon"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-syuzhet)) (home-page "https://github.com/trinker/lexicon") (synopsis "Lexicons for Text Analysis") (description "This package provides a collection of lexical hash tables, dictionaries, and word lists.") (license license:gpl3))) (define-public r-english (package (name "r-english") (version "1.2-6") (source (origin (method url-fetch) (uri (cran-uri "english" version)) (sha256 (base32 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9")))) (properties `((upstream-name . "english"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=english") (synopsis "Translate Integers into English") (description "Allow numbers to be presented in an English language version, one, two, three, ... Ordinals are also available, first, second, third, ... and indefinite article choice, \"a\" or \"an\".") (license license:gpl2))) (define-public r-textclean (package (name "r-textclean") (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "textclean" version)) (sha256 (base32 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz")))) (properties `((upstream-name . "textclean"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-english r-glue r-lexicon r-mgsub r-qdapregex r-stringi r-textshape)) (home-page "https://github.com/trinker/textclean") (synopsis "Text Cleaning Tools") (description "Tools to clean and process text. Tools are geared at checking for substrings that are not optimal for analysis and replacing or removing them (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or extracting them into new variables. For example, emoticons are often used in text but not always easily handled by analysis algorithms. The @code{replace_emoticon()} function replaces emoticons with word equivalents.") (license license:gpl2))) (define-public r-striprtf (package (name "r-striprtf") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "striprtf" version)) (sha256 (base32 "1c8z2qf1kp43ir4dmyxq6hc46dclq8vx3ggkj02p8j1icjswm9bh")))) (properties `((upstream-name . "striprtf"))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-rcpp r-stringr)) (home-page "https://github.com/kota7/striprtf") (synopsis "Extract Text from RTF File") (description "Extracts plain text from @dfn{Rich Text Format} (RTF) file.") (license license:expat))) (define-public r-ndjson (package (name "r-ndjson") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "ndjson" version)) (sha256 (base32 "18j5bibranvbv84hvbsg6glmvhfancdsf2w6j99n3nw53bcgb12d")) (modules '((guix build utils))) (snippet '(begin ;; unvendor gzstream (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h")) #t)))) (properties `((upstream-name . "ndjson"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-gzstream (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Makevars" (("PKG_LIBS = " all) (string-append all "-lgzstream "))) #t))))) (inputs (list zlib gzstream)) (propagated-inputs (list r-data-table r-rcpp r-tibble)) (home-page "https://gitlab.com/hrbrmstr/ndjson") (synopsis "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader") (description "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many modern ndjson files contain large numbers of records. These constructs may not be columnar in nature, but it is often useful to read in these files and \"flatten\" the structure out to enable working with the data in an R @code{data.frame}-like context. Functions are provided that make it possible to read in plain ndjson files or compressed (@code{gz}) ndjson files and either validate the format of the records or create \"flat\" @code{data.table} structures from them.") (license license:expat))) (define-public r-streamr (package (name "r-streamr") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "streamR" version)) (sha256 (base32 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix")))) (properties `((upstream-name . "streamR"))) (build-system r-build-system) (propagated-inputs (list r-ndjson r-rcurl r-rjson)) (home-page "https://cran.r-project.org/package=streamR") (synopsis "Access to Twitter Streaming API via R") (description "This package provides functions to access Twitter's filter, sample, and user streams, and to parse the output into data frames.") (license license:gpl2))) (define-public r-strex (package (name "r-strex") (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "strex" version)) (sha256 (base32 "1vz5zrvf052bg2y48yvkci4hciknvyw5gpbvnklgyny5lzlqvyiq")))) (properties `((upstream-name . "strex"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-magrittr r-rlang r-stringi r-stringr)) (native-inputs (list r-knitr)) (home-page "https://rorynolan.github.io/strex/") (synopsis "Extra string manipulation functions") (description "Strex is a collection of string manipulation functions not provided by the @code{stringi} or @code{stringr} packages. The foremost of these is the extraction of numbers from strings. There are many other handy functionalities in strex.") (license license:gpl3))) (define-public r-readods (package (name "r-readods") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "readODS" version)) (sha256 (base32 "1znp039wfbq8bbjj9pdkl8hwnhm9x5n8c7y5b53xmpnaqxx5agiz")))) (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-cpp11 r-readr r-stringi r-tibble r-vctrs r-zip)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=readODS") (synopsis "Read and Write ODS Files") (description "This package lets you import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame. It also supports writing data frames to an ODS file.") (license license:gpl3))) (define-public r-qpdf (package (name "r-qpdf") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "qpdf" version)) (sha256 (base32 "0xp9x11jpih59s0skfswi5chmv1p8zhz4f66w0nxfx4jhyj0bjfr")) (modules '((guix build utils))) (snippet '(begin ;; unvendor libqpdf (delete-file-recursively "src/libqpdf") (delete-file-recursively "src/include/qpdf"))))) (properties `((upstream-name . "qpdf"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'configure (lambda _ (setenv "EXTERNAL_QPDF" "1")))))) (inputs (list libjpeg-turbo qpdf zlib)) (propagated-inputs (list r-askpass r-curl r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://github.com/ropensci/qpdf") (synopsis "Split, Combine and Compress PDF Files") (description "Content-preserving transformations transformations of PDF files such as split, combine, and compress. This package interfaces directly to the @code{qpdf} C++ API and does not require any command line utilities. Note that @code{qpdf} does not read actual content from PDF files: to extract text and data you need the @code{pdftools} package.") (license license:asl2.0))) (define-public r-pbdmpi (package (name "r-pbdmpi") (version "0.5-1") (source (origin (method url-fetch) (uri (cran-uri "pbdMPI" version)) (sha256 (base32 "047pxra6n3pacyqg5qdg8dbz32s8bq8z9dyi5rvs0ax76vr1v8v4")))) (properties `((upstream-name . "pbdMPI"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs (list openmpi)) (propagated-inputs (list r-float)) (native-inputs (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "Programming with Big Data -- Interface to MPI") (description "This package provides an efficient interface to MPI by utilizing S4 classes and methods with a focus on @dfn{Single Program/Multiple Data} (SPMD) parallel programming style, which is intended for batch parallel execution.") (license license:mpl2.0))) (define-public r-pdftools (package (name "r-pdftools") (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 "0r1c91qrva8lz0gs717llzs6zjiqjrdjhi71asf9bmx600hpp78b")))) (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs (list zlib poppler)) (propagated-inputs (list r-qpdf r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://docs.ropensci.org/pdftools/") (synopsis "Text Extraction, Rendering and Converting of PDF Documents") (description "This package provides utilities based on @code{libpoppler} for extracting text, fonts, attachments and metadata from a PDF file. It also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.") (license license:expat))) (define-public r-antiword (package (name "r-antiword") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "antiword" version)) (sha256 (base32 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2")) (modules '((guix build utils))) (snippet '(begin ;; unvendor libantiword (delete-file-recursively "src") #t)))) (properties `((upstream-name . "antiword"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-antiword (lambda* (#:key inputs #:allow-other-keys) (substitute* "R/antiword.R" (("system.file\\(\"bin\", package = \"antiword\"\\)") (string-append "\"" (assoc-ref inputs "antiword") "/bin\""))) #t))))) (inputs (list antiword)) (propagated-inputs (list r-sys)) (home-page "https://github.com/ropensci/antiword#readme") (synopsis "Extract Text from Microsoft Word Documents") (description "Wraps the @code{AntiWord} utility to extract text from Microsoft Word documents. The utility only supports the old @code{doc} format, not the new xml based @code{docx} format. Use the @code{xml2} package to read the latter.") (license license:gpl2))) (define-public r-readtext (package (name "r-readtext") (version "0.90") (source (origin (method url-fetch) (uri (cran-uri "readtext" version)) (sha256 (base32 "01hscqmjb3fz4iqqgi0l2s1z48a53a25jnsxb0cdd631c97alqrh")))) (properties `((upstream-name . "readtext"))) (build-system r-build-system) (propagated-inputs (list r-antiword r-data-table r-digest r-httr r-jsonlite r-pdftools r-pillar r-readods r-readxl r-streamr r-stringi r-striprtf r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/quanteda/readtext") (synopsis "Import and Handling for Plain and Formatted Text Files") (description "This package provides functions for importing and handling text files and formatted text files with additional meta-data, such including @code{.csv}, @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc}, @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.") (license license:gpl3))) (define-public r-packcircles (package (name "r-packcircles") (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "packcircles" version)) (sha256 (base32 "0fjc575i1vxjp2v4niv2syqqk0d609wm86gkq9rvgmch841x40ps")))) (properties `((upstream-name . "packcircles"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/mbedward/packcircles") (synopsis "Circle Packing") (description "Algorithms to find arrangements of non-overlapping circles.") (license license:expat))) ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on ;; its own. (define-public r-lwgeom (package (name "r-lwgeom") (version "0.2-13") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 "0rqw2nhac832b9v2hdz6wwc51iykh86x5qrq0azlibr9q242i0ph")))) (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs (list geos proj sqlite zlib)) (propagated-inputs (list r-rcpp r-sf r-units)) (native-inputs (list pkg-config)) (home-page "https://github.com/r-spatial/lwgeom/") (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features") (description "Access to selected functions found in @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (license license:gpl2))) (define-public r-stars (package (name "r-stars") (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 "0mqd2dfa8jhxjmfphvv3rkw2lri5sz49042asj5lyln3wkylqjj2")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs (list r-abind r-classint r-rlang r-sf r-units)) (native-inputs (list r-knitr)) (home-page "https://r-spatial.github.io/stars/") (synopsis "Spatiotemporal Arrays, Raster and Vector Data Cubes") (description "Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.") (license license:asl2.0))) (define-public r-tmaptools (package (name "r-tmaptools") (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "tmaptools" version)) (sha256 (base32 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx")))) (properties `((upstream-name . "tmaptools"))) (build-system r-build-system) (propagated-inputs (list r-dichromat r-lwgeom r-magrittr r-rcolorbrewer r-sf r-stars r-units r-viridislite r-xml)) (home-page "https://github.com/mtennekes/tmaptools") (synopsis "Thematic Map Tools") (description "Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates @code{tmap}, the package for visualizing thematic maps.") (license license:gpl3))) (define-public r-rworldmap (package (name "r-rworldmap") (version "1.3-8") (source (origin (method url-fetch) (uri (cran-uri "rworldmap" version)) (sha256 (base32 "007avjl7jhllybp82illrn8v38a85j6xbzk5pvykfx8ayx4wc3m6")))) (properties `((upstream-name . "rworldmap"))) (build-system r-build-system) (propagated-inputs (list r-fields r-raster r-sp r-terra)) (home-page "https://github.com/AndySouth/rworldmap/") (synopsis "Mapping Global Data") (description "Enables mapping of country level and gridded user datasets.") (license license:gpl2+))) (define-public r-rtweet (package (name "r-rtweet") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "rtweet" version)) (sha256 (base32 "18ynravc5vz7ywm1n7ww48gx06dndcishl6lq8nqajxsjwiphq3r")))) (properties `((upstream-name . "rtweet"))) (build-system r-build-system) (propagated-inputs (list r-bit64 r-curl r-httr r-httr2 r-jsonlite r-lifecycle r-progress r-rlang r-tibble r-withr)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/rtweet/") (synopsis "Collect Twitter data") (description "This package implements tools designed to collect and organize Twitter data via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream Application Program Interfaces (API)}.") (license license:expat))) (define-public r-intervals (package (name "r-intervals") (version "0.15.4") (source (origin (method url-fetch) (uri (cran-uri "intervals" version)) (sha256 (base32 "13wzwg5yc1wr8ww8bhv9x5ha78yajsfmb9phq4nbgrxkmbiy3h2h")))) (properties `((upstream-name . "intervals"))) (build-system r-build-system) (home-page "https://github.com/edzer/intervals") (synopsis "Tools for Working with Points and Intervals") (description "Tools for working with and comparing sets of points and intervals.") (license license:artistic2.0))) (define-public r-eyelinker (package (name "r-eyelinker") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "eyelinker" version)) (sha256 (base32 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71")))) (properties `((upstream-name . "eyelinker"))) (build-system r-build-system) (propagated-inputs (list r-intervals r-readr r-stringi r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/a-hurst/eyelinker") (synopsis "Import ASC Files from EyeLink Eye Trackers") (description "Imports plain-text ASC data files from EyeLink eye trackers into (relatively) tidy data frames for analysis and visualization.") (license license:gpl3))) (define-public r-btm (package (name "r-btm") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "BTM" version)) (sha256 (base32 "0lal2fr2lpaky03hrc1gb15kky3s5sr9rbkmrp3v9g2iksd7b5yb")))) (properties `((upstream-name . "BTM"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/bnosac/BTM") (synopsis "Biterm Topic Models for Short Text") (description "Biterm Topic Models find topics in collections of short texts. It is a word co-occurrence based topic model that learns topics by modeling word-word co-occurrences patterns which are called biterms. This in contrast to traditional topic models like Latent Dirichlet Allocation and Probabilistic Latent Semantic Analysis which are word-document co-occurrence topic models. A biterm consists of two words co-occurring in the same short text window. This context window can for example be a twitter message, a short answer on a survey, a sentence of a text or a document identifier. The techniques are explained in detail in the paper 'A Biterm Topic Model For Short Text' by Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\ BTM-WWW13.pdf}.") (license license:asl2.0))) (define-public r-delaporte (package (name "r-delaporte") (version "8.3.0") (source (origin (method url-fetch) (uri (cran-uri "Delaporte" version)) (sha256 (base32 "1g499xrb3hhd9xrzbxm1d911hm06mfn119xxmcr6f47vsz15ksvy")))) (properties `((upstream-name . "Delaporte"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://github.com/aadler/Delaporte") (synopsis "Statistical functions for the Delaporte distribution") (description "This package provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution with parameterization based on Vose (2008). The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.") (license license:bsd-2))) (define-public r-rjsonio (package (name "r-rjsonio") (version "1.3-1.9") (source (origin (method url-fetch) (uri (cran-uri "RJSONIO" version)) (sha256 (base32 "1kiy36hjzh5if5npqv5mdvkr5pdfg3ibj178gr0kz1r81i5h6wzi")))) (properties `((upstream-name . "RJSONIO"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=RJSONIO") (synopsis "Serialize R objects to JSON") (description "This is a package that allows conversion to and from data in JavaScript Object Notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to the @code{rjson} package.") (license license:bsd-3))) (define-public r-revgeo (package (name "r-revgeo") (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "revgeo" version)) (sha256 (base32 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55")))) (properties `((upstream-name . "revgeo"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) (home-page "https://cran.r-project.org/package=revgeo") (synopsis "Reverse geocoding") (description "The @code{revgeo} procedure allows you to use the Photon geocoder for OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with minimal hassle.") (license license:gpl3+))) (define-public r-qpcr (package (name "r-qpcr") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "qpcR" version)) (sha256 (base32 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv")))) (properties `((upstream-name . "qpcR"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase)) (home-page "https://cran.r-project.org/package=qpcR") (synopsis "Modelling and analysis of real-time PCR data") (description "This is a package for model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).") (license license:gpl2+))) (define-public r-textplot (package (name "r-textplot") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "textplot" version)) (sha256 (base32 "1ag2h365zsx0fxbl05s2yfhf1q13p40akvbqg4qwsb5ynh2a56bf")))) (properties `((upstream-name . "textplot"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-lattice r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/bnosac/textplot") (synopsis "Text Plots") (description "Visualise complex relations in texts. This is done by providing functionalities for displaying text co-occurrence networks, text correlation networks, dependency relationships as well as text clustering. Feel free to join the effort of providing interesting text visualisations.") (license license:gpl2))) (define-public r-gsa (package (name "r-gsa") (version "1.03.2") (source (origin (method url-fetch) (uri (cran-uri "GSA" version)) (sha256 (base32 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p")))) (properties `((upstream-name . "GSA"))) (build-system r-build-system) (home-page "https://statweb.stanford.edu/~tibs/GSA/") (synopsis "Gene set analysis") (description "This package lets you determine the significance of pre-defined sets of genes with respect to an outcome variable, such as a group indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) (define-public r-gsalib (package (name "r-gsalib") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "gsalib" version)) (sha256 (base32 "145zyc2sqa0acn9crilpw5njms7w7ca3jgl499lhsahlb6ws98rx")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gsalib") (synopsis "Utility functions for GATK") (description "This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.") (license license:expat))) (define-public r-randomforestsrc (package (name "r-randomforestsrc") (version "2.9.3") (source (origin (method url-fetch) (uri (cran-uri "randomForestSRC" version)) (sha256 (base32 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw")))) (properties `((upstream-name . "randomForestSRC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/randomForestSRC/") (synopsis "Random forests for survival, regression, and classification") (description "This package implements fast OpenMP parallel computing of Breiman's random forests for survival, competing risks, regression and classification based on Ishwaran and Kogalur's popular random survival forests (RSF) package. It handles missing data and now includes multivariate, unsupervised forests, quantile regression and solutions for class imbalanced data. It provides a fast interface using subsampling and confidence regions for variable importance.") (license license:gpl3+))) (define-public r-contfrac (package (name "r-contfrac") (version "1.1-12") (source (origin (method url-fetch) (uri (cran-uri "contfrac" version)) (sha256 (base32 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm")))) (properties `((upstream-name . "contfrac"))) (build-system r-build-system) (home-page "https://github.com/RobinHankin/contfrac") (synopsis "Continued Fractions") (description "Various utilities for evaluating continued fractions.") (license license:gpl2))) (define-public r-elliptic (package (name "r-elliptic") (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "elliptic" version)) (sha256 (base32 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn")))) (properties `((upstream-name . "elliptic"))) (build-system r-build-system) (inputs (list pari-gp)) (propagated-inputs (list r-mass)) (home-page "https://github.com/RobinHankin/elliptic") (synopsis "Weierstrass and Jacobi Elliptic Functions") (description "A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.") (license license:gpl2))) (define-public r-hypergeo (package (name "r-hypergeo") (version "1.2-13") (source (origin (method url-fetch) (uri (cran-uri "hypergeo" version)) (sha256 (base32 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd")))) (properties `((upstream-name . "hypergeo"))) (build-system r-build-system) (propagated-inputs (list r-contfrac r-desolve r-elliptic)) (home-page "https://cran.r-project.org/web/packages/hypergeo/") (synopsis "The Gauss Hypergeometric Function") (description "The Gaussian hypergeometric function for complex numbers.") (license license:gpl2))) (define-public r-gganimate (package (name "r-gganimate") (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "gganimate" version)) (sha256 (base32 "1jabs9qr0319w508kdsk5nmzfhl6nzykpp1by7l639yfvrfqcbd1")))) (properties `((upstream-name . "gganimate"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'absolute-paths (lambda* (#:key inputs #:allow-other-keys) (substitute* "R/renderers.R" (("'ffmpeg'") (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'")))))))) (inputs ;; For video output. (list ffmpeg)) (propagated-inputs (list r-ggplot2 r-glue r-progress r-rlang r-scales r-stringi r-tweenr ;; For GIF/SVG output. gifski is faster, but depends on Rust. r-magick ;; For HTML output. r-base64enc r-htmltools)) (native-inputs (list r-knitr)) (home-page "https://gganimate.com") (synopsis "Grammar of Animated Graphics") (description "This package extends the grammar of graphics as implemented by @code{ggplot2} to include the description of animation. It does this by providing a range of new grammar classes that can be added to the plot object in order to customise how it should change with time.") (license license:expat))) ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle ;; it, because its C++ libtz.so is built with different compiler flags than ;; ours. (define-public r-tzdb (package (name "r-tzdb") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "tzdb" version)) (sha256 (base32 "08rskp7kv2w5pfnrxzswgkdsrg1g0pq3n64q7i3gvpdx85hccls2")))) (properties `((upstream-name . "tzdb"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) (home-page "https://github.com/r-lib/tzdb") (synopsis "Time Zone Database Information") (description "This package provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the @code{date} library. @code{date} provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.") (license license:expat))) (define-public r-vroom (package (name "r-vroom") (version "1.6.5") (source (origin (method url-fetch) (uri (cran-uri "vroom" version)) (sha256 (base32 "0qapkgn5k9g07l48scgln8y1k6fkkzsq5la5fjfh9if9b0ga5p3v")))) (properties `((upstream-name . "vroom"))) (build-system r-build-system) (propagated-inputs (list r-bit64 r-cli r-cpp11 r-crayon r-glue r-hms r-lifecycle r-progress r-rlang r-tibble r-tidyselect r-tzdb r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://vroom.r-lib.org") (synopsis "Read and Write Rectangular Text Data") (description "This package reads and writes data files like @acronym{CSV}, @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing step, then reads the values lazily, so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.") (license license:expat))) (define-public r-rmisc (package (name "r-rmisc") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "Rmisc" version)) (sha256 (base32 "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x")))) (build-system r-build-system) (propagated-inputs (list r-plyr r-lattice)) (home-page "https://cran.r-project.org/web/packages/Rmisc/") (synopsis "Ryan Miscellaneous") (description "The Rmisc library contains functions for data analysis and utility operations.") (license license:gpl3))) (define-public r-rsq (package (name "r-rsq") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "rsq" version)) (sha256 (base32 "01b9rl2ng1sq0ibpfsf50agkwh01pfpw354vvgdjd0lzh9dxmsgp")))) (properties `((upstream-name . "rsq"))) (build-system r-build-system) (propagated-inputs (list r-deming r-deriv r-lme4 r-mass r-matrix r-nlme)) (home-page "https://cran.r-project.org/package=rsq") (synopsis "R-squared and related measures") (description "Calculate generalized R-squared, partial R-squared, and partial correlation coefficients for generalized linear (mixed) models (including quasi models with well defined variance functions).") (license license:gpl2))) (define-public r-webutils (package (name "r-webutils") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "webutils" version)) (sha256 (base32 "0g3zrbwiyq9z0chc66dr8gndqs0xdqkc49bpisbb7ns3g0fkl92i")))) (properties `((upstream-name . "webutils"))) (build-system r-build-system) (propagated-inputs (list r-curl r-jsonlite)) (home-page "https://github.com/jeroen/webutils") (synopsis "Utility functions for developing web applications") (description "This package parses HTTP request data in @code{application/json}, @code{multipart/form-data}, or @code{application/x-www-form-urlencoded} format. It includes an example of hosting and parsing HTML form data in R using either @code{httpuv} or @code{Rhttpd}.") (license license:expat))) (define-public r-protolite (package (name "r-protolite") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "protolite" version)) (sha256 (base32 "1sccyyf89bban3b83yxzkcyqpgcp7ggm9lirxixzjj433baj9vsk")))) (properties `((upstream-name . "protolite"))) (build-system r-build-system) (inputs (list protobuf)) (propagated-inputs (list r-jsonlite r-rcpp)) (native-inputs (list protobuf pkg-config)) (home-page "https://github.com/jeroen/protolite") (synopsis "Highly optimized protocol buffer serializers") (description "This package provides pure C++ implementations for reading and writing several common data formats based on Google protocol-buffers. It currently supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for binary geojson, and @code{mvt.proto} for vector tiles. This package uses the auto-generated C++ code by protobuf-compiler, hence the entire serialization is optimized at compile time. The @code{RProtoBuf} package on the other hand uses the protobuf runtime library to provide a general-purpose toolkit for reading and writing arbitrary protocol-buffer data in R.") (license license:expat))) (define-public r-opencpu (package (name "r-opencpu") (version "2.2.11") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 (base32 "1hdvfbzc8xmv8hrmchad590f91s4vq1nq83wi2ffh4n7q6ixr03s")) (snippet '(for-each delete-file '("inst/test/jquery-1.10.2.min.js" "inst/test/bootstrap/js/bootstrap.min.js"))))) (properties `((upstream-name . "opencpu") (updater-ignored-inputs . ("apparmor")) (updater-extra-native-inputs . ("js-jquery")))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/test/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-jquery") "jquery-1.10.2.min.js") ("bootstrap/js/bootstrap.js" "bootstrap/js/bootstrap.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (inputs (list pandoc)) (propagated-inputs (list r-brew r-curl r-evaluate r-httpuv r-jsonlite r-knitr r-mime r-openssl r-protolite r-rappdirs r-remotes r-rlang r-sys r-vctrs r-webutils r-zip)) (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) ("r-r-rsp" ,r-r-rsp) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.10.2.js") (sha256 (base32 "0ah5ivczcv62rj8bxwam7ar0f4il544jbn983vwfvkykl506gpla")))))) (home-page "https://www.opencpu.org") (synopsis "API for embedded scientific computing") (description "This package provides a system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP API for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user stack based on Apache2.") (license license:asl2.0))) (define-public r-exactextractr (package (name "r-exactextractr") (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "exactextractr" version)) (sha256 (base32 "1pj3145c20r4hnyyrynzmps96a4fpgn408lrl6b9bs79y33c6zwv")))) (properties `((upstream-name . "exactextractr"))) (build-system r-build-system) (inputs (list geos)) (propagated-inputs (list r-raster r-rcpp r-sf)) (native-inputs (list r-knitr)) (home-page "https://isciences.gitlab.io/exactextractr/") (synopsis "Fast extraction from raster datasets using polygons") (description "This package provides a replacement for the @code{extract} function from the @code{raster} package that is suitable for extracting raster values using @code{sf} polygons.") (license license:asl2.0))) (define-public r-stringfish (package (name "r-stringfish") (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "stringfish" version)) (sha256 (base32 "14vrg6mkwwgw1klgpvjn7936yfxav55rainz71xjjih2j21vq21n")))) (properties `((upstream-name . "stringfish"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppparallel)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/traversc/stringfish") (synopsis "Alternative string implementation") (description "This package provides an extendable, performant and multithreaded @code{alt-string} implementation backed by C++ vectors and strings.") (license license:gpl3))) (define-public r-rapiserialize (package (name "r-rapiserialize") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "RApiSerialize" version)) (sha256 (base32 "02k0l8bi849b2102ysb102xky4p84i9v2r4w6fab7bgf32wvph4w")))) (properties `((upstream-name . "RApiSerialize"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=RApiSerialize") (synopsis "R API serialization") (description "This package provides other packages with access to the internal R serialization code. Access to this code is provided at the C function level by using the registration of native function mechanism. Client packages simply include a single header file RApiSerializeAPI.h provided by this package.") (license license:gpl2+))) (define-public r-qs (package (name "r-qs") (version "0.25.7") (source (origin (method url-fetch) (uri (cran-uri "qs" version)) (sha256 (base32 "0a0jay9p2k0ahf08s94dr1w66qhbgzs87vkaanwkd4j6lvijncz7")))) (properties `((upstream-name . "qs"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; Our zstd is at 1.5.0, but this package bundles 1.5.2. (add-after 'unpack 'use-older-zstd (lambda _ (substitute* "configure" (("100502") "100500"))))))) (inputs (list lz4 (list zstd "lib"))) (propagated-inputs (list r-rapiserialize r-rcpp r-stringfish)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/traversc/qs") (synopsis "Quick serialization of R objects") (description "This package provides functions for quickly writing and reading any R object to and from disk.") (license license:gpl3))) (define-public r-rgeos (package (name "r-rgeos") (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "rgeos" version)) (sha256 (base32 "04fyrqdpb4cz9kjqh1cxbpqh1ana7l8zh7wdzxassgzxjvgc80wx")))) (properties `((upstream-name . "rgeos"))) (build-system r-build-system) (inputs (list geos)) (propagated-inputs (list r-sp)) (home-page "https://cran.r-project.org/package=rgeos") (synopsis "Interface to Geometry Engine (GEOS)") (description "This package provides an R interface to Geometry Engine (GEOS) using the C API for topology operations on geometries.") (license license:gpl2+))) (define-public r-tfruns (package (name "r-tfruns") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "tfruns" version)) (sha256 (base32 "1xk7dl51xd1h54798xwycvxmn77jv80in61hanm36zk0024wpxg8")))) (properties `((upstream-name . "tfruns"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-config r-jsonlite r-magrittr r-reticulate r-rlang r-rstudioapi r-tidyselect r-whisker r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/tfruns") (synopsis "Training run tools for TensorFlow") (description "Create and manage unique directories for each TensorFlow training run. This package provides a unique, time stamped directory for each run along with functions to retrieve the directory of the latest run or latest several runs.") (license license:asl2.0))) (define-public r-tfautograph (package (name "r-tfautograph") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "tfautograph" version)) (sha256 (base32 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2")))) (properties `((upstream-name . "tfautograph"))) (build-system r-build-system) (inputs (list tensorflow)) (propagated-inputs (list r-backports r-reticulate)) (home-page "https://t-kalinowski.github.io/tfautograph/") (synopsis "Autograph R for Tensorflow") (description "This package lets you translate R control flow expressions into Tensorflow graphs.") (license license:gpl3))) (define-public r-tensorflow (package (name "r-tensorflow") (version "2.14.0") (source (origin (method url-fetch) (uri (cran-uri "tensorflow" version)) (sha256 (base32 "1zv7b3r8c2nzyrq295pvdf3kv2mz7cmm4adck508qr12rb9d5ybx")))) (properties `((upstream-name . "tensorflow"))) (build-system r-build-system) (inputs (list tensorflow)) (propagated-inputs (list r-config r-lifecycle r-processx r-reticulate r-rstudioapi r-tfautograph r-tfruns r-yaml)) (home-page "https://github.com/rstudio/tensorflow") (synopsis "R interface to TensorFlow") (description "R interface to TensorFlow a library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them.") (license license:asl2.0))) (define-public r-keras (package (name "r-keras") (version "2.13.0") (source (origin (method url-fetch) (uri (cran-uri "keras" version)) (sha256 (base32 "1xjmkrz06rh8767pfqi81fgkljkyb4i7bzllahw7b62b9s2wp38l")))) (properties `((upstream-name . "keras"))) (build-system r-build-system) (propagated-inputs (list r-generics r-glue r-magrittr r-r6 r-reticulate r-rlang r-tensorflow r-tfruns r-zeallot)) (native-inputs (list r-knitr)) (home-page "https://keras.rstudio.com") (synopsis "R Interface to 'Keras'") (description "This package provides an interface to Keras, a high-level neural networks API. Keras was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.") (license license:expat))) (define-public r-zzlite (package (name "r-zzlite") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "zzlite" version)) (sha256 (base32 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps")))) (properties `((upstream-name . "zzlite"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zzlite") (synopsis "Wrapper for the Zamzar file conversion API") (description "This package provides a minor collection of HTTP wrappers for the Zamzar file conversion API. The wrappers makes it easy to utilize the API and thus convert between more than 100 different file formats (ranging from audio files, images, movie formats, etc., etc.) through an R session.") (license license:gpl3))) (define-public r-ztree (package (name "r-ztree") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "zTree" version)) (sha256 (base32 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y")))) (properties `((upstream-name . "zTree"))) (build-system r-build-system) (propagated-inputs (list r-plyr)) (home-page "https://cran.r-project.org/package=zTree") (synopsis "Functions to import data from z-Tree into R") (description "This package provides tools for reading @code{.xls} and @code{.sbj} files which are written by the proprietary program z-Tree for developing and carrying out economic experiments.") (license license:gpl3))) (define-public r-distributionutils (package (name "r-distributionutils") (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "DistributionUtils" version)) (sha256 (base32 "1mv3p7hm02q3mhrw5165gc2d77ighnykyfn6ibxvkc3ii2m9xrri")))) (properties `((upstream-name . "DistributionUtils"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=DistributionUtils") (synopsis "Distribution utilities") (description "This package provides utilities for dealing with distributions. Functionality includes sample skewness and kurtosis, log-histogram, tail plots, moments by integration, changing the point about which a moment is calculated, functions for testing distributions using inversion tests and the Massart inequality. Also included is an implementation of the incomplete Bessel K function.") (license license:gpl2+))) (define-public r-ztpln (package (name "r-ztpln") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "ztpln" version)) (sha256 (base32 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr")))) (properties `((upstream-name . "ztpln"))) (build-system r-build-system) (propagated-inputs (list r-distributionutils r-mixtools r-rcpp r-rcppeigen r-rcppnumerical)) (native-inputs (list r-knitr)) (home-page "https://github.com/mattocci27/ztpln") (synopsis "Zero-truncated Poisson lognormal distribution") (description "This package provides functions for obtaining the density, random variates and maximum likelihood estimates of the Zero-truncated Poisson lognormal distribution and their mixture distribution.") (license license:expat))) (define-public r-zscorer (package (name "r-zscorer") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "zscorer" version)) (sha256 (base32 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn")))) (properties `((upstream-name . "zscorer"))) (build-system r-build-system) (propagated-inputs (list r-shiny)) (native-inputs (list r-knitr)) (home-page "https://github.com/nutriverse/zscorer") (synopsis "Child Anthropometry z-Score Calculator") (description "This package provides a tool for calculating z-scores and centiles for weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age, head circumference-for-age, age circumference-for-age, subscapular skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth Standards.") (license license:agpl3+))) (define-public r-zra (package (name "r-zra") (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "ZRA" version)) (sha256 (base32 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi")))) (properties `((upstream-name . "ZRA"))) (build-system r-build-system) (propagated-inputs (list r-dygraphs r-forecast)) (home-page "https://cran.r-project.org/package=ZRA") (synopsis "Dynamic plots for time series forecasting") (description "This package combines a forecast of a time series, using the function @code{forecast}, with the dynamic plots from @code{dygraphs}.") (license license:gpl2+))) (define-public r-rfigshare (package (name "r-rfigshare") (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "rfigshare" version)) (sha256 (base32 "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j")))) (properties `((upstream-name . "rfigshare"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-httpuv r-httr r-rjsonio r-xml r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/rfigshare") (synopsis "R Interface to figshare") (description "This package provides an interface to figshare, a scientific repository to archive and assign DOIs to data, software, figures, and more.") (license license:cc0))) (define-public r-dismo (package (name "r-dismo") (version "1.3-14") (source (origin (method url-fetch) (uri (cran-uri "dismo" version)) (sha256 (base32 "1msc75xnc9lbnn8pivd5j4jvb1b9p3xgybfm2ak2mpb2aplz5837")) (snippet '(for-each delete-file (list "inst/java/dismo.jar" "inst/java/maxent.jar"))))) (properties `((upstream-name . "dismo"))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) ((guix build ant-build-system) #:prefix java:)) #:imported-modules (cons '(guix build ant-build-system) %r-build-system-modules) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'build-jars (lambda* (#:key inputs #:allow-other-keys) (let ((maxent (search-input-file inputs "/share/java/maxent/maxent.jar"))) (install-file maxent "inst/java/") (with-directory-excursion "java" (invoke "javac" "-cp" maxent "mebridge.java") (invoke "jar" "cvf" "../inst/java/dismo.jar" "mebridge.class"))))) (add-after 'install 'strip-jar-timestamps (assoc-ref java:%standard-phases 'strip-jar-timestamps))))) (inputs (list java-maxent)) (propagated-inputs (list r-raster r-rcpp r-sp r-terra)) (native-inputs (list `(,icedtea-8 "jdk") zip)) (home-page "https://rspatial.org/raster/sdm/") (synopsis "Species distribution modeling") (description "This package provides methods for species distribution modeling, i.e., predicting the environmental similarity of any site to that of the locations of known occurrences of a species.") (license license:gpl3+))) (define-public r-zoon (package (name "r-zoon") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "zoon" version)) (sha256 (base32 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip")))) (properties `((upstream-name . "zoon"))) (build-system r-build-system) (propagated-inputs (list r-dismo r-plyr r-randomforest r-raster r-rcurl r-rfigshare r-rgdal r-roxygen2 r-rworldmap r-sp r-testthat)) (native-inputs (list r-knitr)) (home-page "https://github.com/zoonproject/zoon") (synopsis "Reproducible, accessible and shareable species distribution modelling") (description "This package reads user submitted modules from an online repository, runs full species distribution modelling workflows and returns output that is fully reproducible.") (license license:bsd-3))) (define-public r-paws-common (package (name "r-paws-common") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 "05rld34brjc32p9f9cbqyyh208rh9idnyih33cpw7bz7bfyicnqm")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-curl r-digest r-httr r-jsonlite r-rcpp r-xml2)) (home-page "https://cran.r-project.org/package=paws.common") (synopsis "Paws low-level Amazon Web Services API") (description "This package provides functions for making low-level API requests to Amazon Web Services. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).") (license license:asl2.0))) (define-public r-paws-customer-engagement (package (name "r-paws-customer-engagement") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.customer.engagement" version)) (sha256 (base32 "1380waqavwga17fvdzfpag4snzynkykh3pnia5bi73476y7myj5h")))) (properties `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services customer engagement services") (description "This package provides an interface to Amazon Web Services customer engagement services, including Simple Email Service, Connect contact center service, and more.") (license license:asl2.0))) (define-public r-paws-cost-management (package (name "r-paws-cost-management") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.cost.management" version)) (sha256 (base32 "1j9zi73y9ng5m6wlws4crfv4j6b8qxk1m9g1hd286g4gg852g80y")))) (properties `((upstream-name . "paws.cost.management"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services cost management services") (description "This package provides an interface to Amazon Web Services cost management services, including cost and usage reports, budgets, pricing, and more.") (license license:asl2.0))) (define-public r-paws-developer-tools (package (name "r-paws-developer-tools") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.developer.tools" version)) (sha256 (base32 "177q7x8l9asyidpc7j20xwpyk0bd9x9m20cy4qzlnnmr14anyvjm")))) (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services developer tools services") (description "This package provides an interface to Amazon Web Services developer tools services, including version control, continuous integration and deployment, and more.") (license license:asl2.0))) (define-public r-paws-end-user-computing (package (name "r-paws-end-user-computing") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.end.user.computing" version)) (sha256 (base32 "0qz5kps9819yfqjdqjmv7wx70ll7xayfxmd5dc867k14i41f91cm")))) (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services end user computing services") (description "This package provides an interface to Amazon Web Services end user computing services, including collaborative document editing, mobile intranet, and more.") (license license:asl2.0))) (define-public r-paws-application-integration (package (name "r-paws-application-integration") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 "1sgzp0yr1jsmbyzyk26m762rhpxb89wrwqqvrrw3xr1ib0cg06ah")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services application integration services") (description "This package provides an interface to Amazon Web Services application integration services, including Simple Queue Service (SQS) message queue, Simple Notification Service (SNS) publish/subscribe messaging, and more.") (license license:asl2.0))) (define-public r-paws-security-identity (package (name "r-paws-security-identity") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.security.identity" version)) (sha256 (base32 "01gh761ykc4h81whn649bm28b01njqm1kjqkn9l4n7hhnalddy06")))) (properties `((upstream-name . "paws.security.identity"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services security, identity, and compliance services") (description "This package provides an interface to Amazon Web Services security, identity, and compliance services, including the Identity and Access Management (IAM) service for managing access to services and resources, and more.") (license license:asl2.0))) (define-public r-paws-analytics (package (name "r-paws-analytics") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.analytics" version)) (sha256 (base32 "07nwa39mn749a9rqb683wf19kd8si7ksws87annbldmd57r072l8")))) (properties `((upstream-name . "paws.analytics"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services analytics services") (description "This package provides an interface to Amazon Web Services analytics services, including Elastic MapReduce Hadoop and Spark big data service, Elasticsearch search engine, and more.") (license license:asl2.0))) (define-public r-paws-machine-learning (package (name "r-paws-machine-learning") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.machine.learning" version)) (sha256 (base32 "0zcw758xsw2360571dj215gyd1amaxx07i58h1r6r5zys940lxis")))) (properties `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services machine learning services") (description "This package provides an interface to Amazon Web Services machine learning services, including SageMaker managed machine learning service, natural language processing, speech recognition, translation, and more.") (license license:asl2.0))) (define-public r-paws-management (package (name "r-paws-management") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.management" version)) (sha256 (base32 "0k40lrgxx91bijj3648zsgj55x120mhmx8dyx3hm2yvh2k96ks7h")))) (properties `((upstream-name . "paws.management"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services management and governance services") (description "This package provides an interface to Amazon Web Services management and governance services, including CloudWatch application and infrastructure monitoring, Auto Scaling for automatically scaling resources, and more.") (license license:asl2.0))) (define-public r-paws-networking (package (name "r-paws-networking") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.networking" version)) (sha256 (base32 "0qs6bp0vlbazxir9jmdcnazh90yrvhrw6k9046id73hw1j7h5zaf")))) (properties `((upstream-name . "paws.networking"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services networking and content delivery services") (description "This package provides an interface to Amazon Web Services networking and content delivery services, including Route 53 Domain Name System service, CloudFront content delivery, load balancing, and more.") (license license:asl2.0))) (define-public r-paws-database (package (name "r-paws-database") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.database" version)) (sha256 (base32 "0nlkbnyxd3znmvqxqb3w43sznacmikq32d9fihyc1dx7ghvmf61z")))) (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services Database Services") (description "This package provides an interface to Amazon Web Services database services, including Relational Database Service (RDS), DynamoDB NoSQL database, and more.") (license license:asl2.0))) (define-public r-paws-storage (package (name "r-paws-storage") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.storage" version)) (sha256 (base32 "0v2g1shv9m4h2fz2lvjad479g3nmxc92wlyrxj4s7fifzzs2pd97")))) (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services storage services") (description "This package provides an interface to Amazon Web Services storage services, including Simple Storage Service (S3).") (license license:asl2.0))) (define-public r-paws-compute (package (name "r-paws-compute") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 "1vsxwzqgk0004nmfy79pd0zc208fczay95p7h16mzqgds9586ma1")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services compute services") (description "This package provides an interface to Amazon Web Services compute services, including Elastic Compute Cloud (EC2), Lambda functions-as-a-service, containers, batch processing, and more.") (license license:asl2.0))) (define-public r-paws (package (name "r-paws") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws" version)) (sha256 (base32 "1l9pjmfnhqgzxghxz22fbqc43x9am6d21f982p2sykxv271yclhf")))) (properties `((upstream-name . "paws"))) (build-system r-build-system) (propagated-inputs (list r-paws-analytics r-paws-application-integration r-paws-common r-paws-compute r-paws-cost-management r-paws-customer-engagement r-paws-database r-paws-developer-tools r-paws-end-user-computing r-paws-machine-learning r-paws-management r-paws-networking r-paws-security-identity r-paws-storage)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services software development kit") (description "This package provides an interface to Amazon Web Services, including storage, database, and compute services, such as Simple Storage Service (S3), DynamoDB NoSQL database, and Lambda functions-as-a-service.") (license license:asl2.0))) (define-public r-zoomgroupstats (package (name "r-zoomgroupstats") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "zoomGroupStats" version)) (sha256 (base32 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966")))) (properties `((upstream-name . "zoomGroupStats"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-dplyr r-lubridate r-magick r-openxlsx r-paws r-pbapply r-stringr r-syuzhet)) (native-inputs (list r-knitr)) (home-page "http://zoomgroupstats.org") (synopsis "Analyze text, audio, and video from Zoom meetings") (description "This package provides utilities for processing and analyzing the files that are exported from a recorded Zoom meeting. This includes analyzing data captured through video cameras and microphones, the text-based chat, and meta-data. You can analyze aspects of the conversation among meeting participants and their emotional expressions throughout the meeting.") (license license:expat))) (define-public r-zoom (package (name "r-zoom") (version "2.0.6") (source (origin (method url-fetch) (uri (cran-uri "zoom" version)) (sha256 (base32 "05ikad4j1qi5y8mn77n9bw7d6ic3api9d7mbcn855w8xcc69ja4q")))) (properties `((upstream-name . "zoom"))) (build-system r-build-system) (home-page "https://github.com/cbarbu/R-package-zoom") (synopsis "Spatial data visualization tool") (description "This package provides @code{zm}, a utility that allows you to zoom/navigate any plot when called with any active plot.") (license license:gpl3+))) (define-public r-zoolog (package (name "r-zoolog") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "zoolog" version)) (sha256 (base32 "06g44gjk9w73996n4h1a2q8kcd6q2mvm1vhx0iq0785gvrz18pj9")))) (properties `((upstream-name . "zoolog"))) (build-system r-build-system) (propagated-inputs (list r-rdpack r-stringi)) (native-inputs (list r-knitr)) (home-page "https://josempozo.github.io/zoolog/") (synopsis "Zooarchaeological analysis with log-ratios") (description "This package includes functions and reference data to generate and manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from measurements obtained on zooarchaeological material. Log ratios are used to compare the relative (rather than the absolute) dimensions of animals from archaeological contexts. The zoolog package is also able to seamlessly integrate data and references with heterogeneous nomenclature, which is internally managed by a zoolog thesaurus.") (license license:gpl3))) (define-public r-filehash (package (name "r-filehash") (version "2.4-5") (source (origin (method url-fetch) (uri (cran-uri "filehash" version)) (sha256 (base32 "0b52bnsqp65s3r4aw9mvfwfnjmsrqq8ndcadwig547nn9mwy47iv")))) (properties `((upstream-name . "filehash"))) (build-system r-build-system) (propagated-inputs (list r-digest)) (home-page "http://github.com/rdpeng/filehash") (synopsis "Simple key-value database") (description "This package implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow filehash databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets.") (license license:gpl2+))) (define-public r-mlearning (package (name "r-mlearning") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "mlearning" version)) (sha256 (base32 "0fh28i36smpybhzd2kni435m7wf20i3yib6h7jy173r1v5adzkba")))) (properties `((upstream-name . "mlearning"))) (build-system r-build-system) (propagated-inputs (list r-class r-e1071 r-ipred r-mass r-nnet r-randomforest r-rpart)) (home-page "https://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description "This package provides a unified interface to various machine learning algorithms. Confusion matrices are provided too.") (license license:gpl2+))) (define-public r-zooimage (package (name "r-zooimage") (version "5.5.2") (source (origin (method url-fetch) (uri (cran-uri "zooimage" version)) (sha256 (base32 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8")))) (properties `((upstream-name . "zooimage"))) (build-system r-build-system) (propagated-inputs (list r-digest r-dt r-filehash r-jpeg r-mass r-mda r-mlearning r-png r-shiny r-svdialogs r-svmisc r-tiff)) (home-page "https://www.sciviews.org/zooimage") (synopsis "Analysis of numerical plankton images") (description "This package provides a solution for analyzing digital images of plankton. In combination with ImageJ, an image analysis system, it processes digital images, measures individuals, trains for automatic classification of taxa, and finally, measures plankton samples (abundances, total and partial size spectra or biomasses, etc.).") (license license:gpl2+))) (define-public r-zooarch (package (name "r-zooarch") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "zooaRch" version)) (sha256 (base32 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc")))) (properties `((upstream-name . "zooaRch"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zooaRch") (synopsis "Analytical Tools for Zooarchaeological Data") (description "The analysis and inference of faunal remains recovered from archaeological sites concerns the field of zooarchaeology. The zooaRch package provides analytical tools to make inferences on zooarchaeological data. Functions in this package allow users to read, manipulate, visualize, and analyze zooarchaeological data.") (license license:gpl2+))) (define-public r-zonebuilder (package (name "r-zonebuilder") (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "zonebuilder" version)) (sha256 (base32 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn")))) (properties `((upstream-name . "zonebuilder"))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-sf)) (native-inputs (list r-knitr)) (home-page "https://github.com/zonebuilders/zonebuilder") (synopsis "Create and explore geographic zoning systems") (description "This package provides functions, documentation and example data to help divide geographic space into discrete polygons (zones). The functions are motivated by research into the merits of different zoning systems. A flexible @code{ClockBoard} zoning system is provided, which breaks-up space by concentric rings and radial lines emanating from a central point.") (license license:gpl3))) (define-public r-zonator (package (name "r-zonator") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "zonator" version)) (sha256 (base32 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k")))) (properties `((upstream-name . "zonator"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal)) (native-inputs (list r-knitr)) (home-page "https://cbig.github.io/zonator/") (synopsis "Utilities for Zonation spatial conservation prioritization") (description "Create new analysis setups and deal with results of Zonation conservation prioritization software.") (license license:bsd-2))) (define-public r-mmwrweek (package (name "r-mmwrweek") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "MMWRweek" version)) (sha256 (base32 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s")))) (properties `((upstream-name . "MMWRweek"))) (build-system r-build-system) (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf") (synopsis "Convert dates to MMWR day, week, and year") (description "The first day of any MMWR week is Sunday. MMWR week numbering is sequential beginning with 1 and incrementing with each week to a maximum of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at least four days in the calendar year. This package provides functionality to convert dates to MMWR day, week, and year and the reverse.") (license license:gpl2+))) (define-public r-cccd (package (name "r-cccd") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "cccd" version)) (sha256 (base32 "0cxh19jqappc6zq9nz3m40ybdmsp12mf7yvflsz96wks3ly2ld4y")))) (properties `((upstream-name . "cccd"))) (build-system r-build-system) (propagated-inputs (list r-deldir r-fnn r-igraph r-proxy)) (home-page "https://cran.r-project.org/package=cccd") (synopsis "Class cover catch digraphs") (description "This package provides tools to create Class Cover Catch Digraphs, neighborhood graphs, and relatives.") (license license:gpl2+))) (define-public r-crul (package (name "r-crul") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "crul" version)) (sha256 (base32 "18n9ga0ah628k83qin75ys0wipc9dgc25xnafcj400jp85g42l4f")))) (properties `((upstream-name . "crul"))) (build-system r-build-system) (propagated-inputs (list r-curl r-httpcode r-jsonlite r-mime r-r6 r-urltools)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/crul") (synopsis "HTTP client") (description "This package provides a simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's @code{faraday} gem.") (license license:expat))) (define-public r-gistr (package (name "r-gistr") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "gistr" version)) (sha256 (base32 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp")))) (properties `((upstream-name . "gistr"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-crul r-dplyr r-httr r-jsonlite r-knitr r-magrittr r-rmarkdown)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/gistr") (synopsis "Work with Gists in browser") (description "This package allows the user to create new Github gists, update gists with new files, rename files, delete files, get and delete gists, star and un-star them, fork them, open a gist in your default browser, get an embed code for a gist, list gist commits, and get rate limit information when authenticated.") (license license:expat))) (define-public r-rbokeh (package (name "r-rbokeh") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "rbokeh" version)) (sha256 (base32 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q")) (snippet '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js" "inst/htmlwidgets/lib/bokehjs/bokeh.min.js"))))) (properties `((upstream-name . "rbokeh"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/bokehjs" (let ((mapping `((,(assoc-ref inputs "js-bokeh-widgets") . "bokeh-widgets.min.js") (,(assoc-ref inputs "js-bokeh") . "bokeh.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (propagated-inputs (list r-digest r-gistr r-hexbin r-htmlwidgets r-jsonlite r-lazyeval r-magrittr r-maps r-pryr r-scales)) ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml. (native-inputs `(("esbuild" ,esbuild) ("js-bokeh-widgets" ,(origin (method url-fetch) (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js") (sha256 (base32 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy")))) ("js-bokeh" ,(origin (method url-fetch) (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js") (sha256 (base32 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q")))) ("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/rbokeh/") (synopsis "R interface for the Bokeh visualization library") (description "This package provides a native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.") (license license:expat))) (define-public r-fauxpas (package (name "r-fauxpas") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "fauxpas" version)) (sha256 (base32 "1xhyws6nr9ayir4sykvhyaf1aprx9rjm2xyb3p5ikd26l5hp7l44")))) (properties `((upstream-name . "fauxpas"))) (build-system r-build-system) (propagated-inputs (list r-httpcode r-r6 r-whisker)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/fauxpas") (synopsis "HTTP error helpers") (description "This package provides HTTP error helpers. Methods are included for general purpose HTTP error handling, as well as individual methods for every HTTP status code, both via status code numbers as well as their descriptive names. It supports the ability to adjust behavior to stop, message or warning. It includes the ability to use a custom whisker template to have any configuration of status code, short description, and verbose message.") (license license:expat))) (define-public r-webmockr (package (name "r-webmockr") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "webmockr" version)) (sha256 (base32 "1a590fyzmag1p6c9a82yp93wd1s4jdznk0416i0pv8r5jwarkdv7")))) (properties `((upstream-name . "webmockr"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-crul r-curl r-fauxpas r-jsonlite r-magrittr r-r6 r-urltools)) (home-page "https://github.com/ropensci/webmockr") (synopsis "Stubbing and setting expectations on HTTP Requests") (description "This is a package for stubbing and setting expectations on HTTP requests. It includes tools for stubbing HTTP requests, including expected request conditions and response conditions. You can match on HTTP method, query parameters, request body, headers and more. It can be used for unit tests or outside of a testing context.") (license license:expat))) (define-public r-iotools (package (name "r-iotools") (version "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "iotools" version)) (sha256 (base32 "12xlf31aawj5sxanb2m63r665a9x5v87q4ig8qkvaygpdg51gycw")))) (properties `((upstream-name . "iotools"))) (build-system r-build-system) (home-page "https://www.rforge.net/iotools") (synopsis "I/O tools for streaming") (description "This package provides basic I/O tools for streaming and data parsing.") ;; GPL 2 or GPL 3. (license license:gpl3))) (define-public r-wordspace (package (name "r-wordspace") (version "0.2-8") (source (origin (method url-fetch) (uri (cran-uri "wordspace" version)) (sha256 (base32 "17fqd4zrsklv2ik3lg00x66yasfh1kyhs3k9ri6lrk56wwv6hzb2")))) (properties `((upstream-name . "wordspace"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-iotools r-mass r-matrix r-rcpp r-sparsesvd)) (native-inputs (list r-knitr)) (home-page "https://wordspace.r-forge.r-project.org/") (synopsis "Distributional semantic models in R") (description "The wordspace package turns R into an interactive laboratory for empirical research on @dfn{distributional semantic models} (DSM). It consists of a small set of carefully designed functions, most of which @itemize @item encapsulate non-trivial R operations in a user-friendly manner or @item provide efficient and memory-lean C implementations of key operations. @end itemize ") (license license:gpl3))) (define-public r-maxlik (package (name "r-maxlik") (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "maxLik" version)) (sha256 (base32 "0pdigfpyiqacj2ydhpn5w1h89dz1ydk0syzs25lsgdi40sz0bvkw")))) (properties `((upstream-name . "maxLik"))) (build-system r-build-system) (propagated-inputs (list r-generics r-misctools r-sandwich)) (home-page "https://cran.r-project.org/package=maxLik") (synopsis "Maximum Likelihood Estimation and related tools") (description "This package provides functions for @dfn{Maximum Likelihood} (ML) estimation, non-linear optimization, and related tools. It includes a unified way to call different optimizers, and classes and methods to handle the results from the Maximum Likelihood viewpoint. It also includes a number of convenience tools for testing and developing your own models.") (license license:gpl2+))) (define-public r-misctools (package (name "r-misctools") (version "0.6-28") (source (origin (method url-fetch) (uri (cran-uri "miscTools" version)) (sha256 (base32 "089vb57ynqzqa9ppalqfgn0n5wazfjng2kc7z4wgb2ll40hjyk5x")))) (properties `((upstream-name . "miscTools"))) (build-system r-build-system) (propagated-inputs (list r-digest)) (home-page "http://www.micEcon.org") (synopsis "Miscellaneous tools and utilities") (description "This package provides miscellaneous small tools and utilities. Many of them facilitate the work with matrices, e.g. inserting rows or columns, creating symmetric matrices, or checking for semidefiniteness. Other tools facilitate the work with regression models, e.g. extracting the standard errors, obtaining the number of (estimated) parameters, or calculating R-squared values.") (license license:gpl2+))) (define-public r-mockery (package (name "r-mockery") (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "mockery" version)) (sha256 (base32 "1hs550i2nqnn1yyx2sd7babamkq3sm7cxiwzcj8wlps5yah208h7")))) (properties `((upstream-name . "mockery"))) (build-system r-build-system) (propagated-inputs (list r-testthat)) (native-inputs (list r-knitr)) (home-page "https://github.com/jfiksel/mockery") (synopsis "Mocking library for R") (description "The two main functionalities of this package are creating mock objects (functions) and selectively intercepting calls to a given function that originate in some other function. It can be used with any testing framework available for R. Mock objects can be injected with either this package's own @code{stub} function or a similar @code{with_mock} facility present in the @code{testthat} package.") (license license:expat))) (define-public r-zoltr (package (name "r-zoltr") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "zoltr" version)) (sha256 (base32 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar")))) (properties `((upstream-name . "zoltr"))) (build-system r-build-system) (propagated-inputs (list r-base64url r-dplyr r-httr r-jsonlite r-magrittr r-mmwrweek r-mockery r-readr r-rlang r-webmockr)) (native-inputs (list r-knitr)) (home-page "https://github.com/reichlab/zoltr") (synopsis "Interface to the Zoltar forecast repository API") (description "Zoltar is a website that provides a repository of model forecast results in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time series forecasts for prediction challenges of interest to the modeling community. This package provides functions for working with the Zoltar API, including connecting and authenticating, getting information about projects, models, and forecasts, deleting and uploading forecast data, and downloading scores.") (license license:gpl3))) (define-public r-zoib (package (name "r-zoib") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "zoib" version)) (sha256 (base32 "1px4jjjpn6ikngzlxz1i6fgld9cy5lv6nqn1bjin4q6sqqixyx2j")))) (properties `((upstream-name . "zoib"))) (build-system r-build-system) (propagated-inputs (list r-abind r-coda r-formula r-rjags)) (home-page "https://www.r-project.org") (synopsis "Bayesian inference for beta regression") (description "This package lets you fit beta regression and zero-or-one inflated beta regression and obtain Bayesian inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.") (license license:gpl3+))) (define-public r-logger (package (name "r-logger") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "logger" version)) (sha256 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg")))) (properties `((upstream-name . "logger"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://daroczig.github.io/logger/") (synopsis "Lightweight and flexible logging utility") (description "Inspired by the the @code{futile.logger} R package and @code{logging} Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.") (license license:agpl3+))) (define-public r-fasterize (package (name "r-fasterize") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "fasterize" version)) (sha256 (base32 "1d63q77hfbn2ly8cwsik4gaavdhidpi7idf7qj2y5bi9xhd10kyl")))) (properties `((upstream-name . "fasterize"))) (build-system r-build-system) (propagated-inputs (list r-raster r-rcpp r-rcpparmadillo r-wk)) (native-inputs (list r-knitr)) (home-page "https://github.com/ecohealthalliance/fasterize") (synopsis "Fast Polygon to Raster Conversion") (description "This package provides a drop-in replacement for @code{rasterize} from the @code{raster} package that takes sf-type objects, and is much faster. There is support for the main options provided by the @code{rasterize} function, including setting the field used and background value, and options for aggregating multi-layer rasters.") (license license:expat))) (define-public r-bien (package (name "r-bien") (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "BIEN" version)) (sha256 (base32 "17zrj5ckxaz4mdbgywxi8kf51ssbf2md1d2azf30dh96kzc2ayps")))) (properties `((upstream-name . "BIEN"))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-ape r-dbi r-doparallel r-fasterize r-foreach r-raster r-rpostgresql r-sf r-terra)) (home-page "https://cran.r-project.org/package=BIEN") (synopsis "Tools for accessing the BIEN database") (description "This package provides tools for accessing the Botanical Information and Ecology Network (BIEN) database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data. This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.") (license license:expat))) (define-public r-varhandle (package (name "r-varhandle") (version "2.0.6") (source (origin (method url-fetch) (uri (cran-uri "varhandle" version)) (sha256 (base32 "0xy5w7cz9sb0xmxvzajg4sf0ip2ihxc5nimh10awchvkywzgsyjf")))) (properties `((upstream-name . "varhandle"))) (build-system r-build-system) (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle") (synopsis "Functions for robust variable handling") (description "This package contains some functions to help users (especially data explorers) to make more sense of their variables and take the most out of variables and hardware resources. Functions in this package are supposed to be efficient and easy to use.") (license license:gpl2+))) (define-public r-ggh4x (package (name "r-ggh4x") (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "ggh4x" version)) (sha256 (base32 "114xvlpdhnsdnw1g89yls3z80dxcj9fah09kvfddhlwbqbknxjxf")))) (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-gtable r-lifecycle r-rlang r-scales r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/teunbrand/ggh4x") (synopsis "Extension for ggplot2") (description "This package is a @code{ggplot2} extension. It provides some utility functions that do not entirely fit within the grammar of graphics concept. The package extends @code{ggpplots} facets through customisation, by setting individual scales per panel, resizing panels and providing nested facets. It also allows multiple colour, fill scales per plot and hosts a smaller collection of stats, geoms and axis guides.") (license license:expat))) (define-public r-gghalves (package (name "r-gghalves") (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "gghalves" version)) (sha256 (base32 "1qsxq2zbz4zcpqc7949apznn9f2c959jwwx010bl4gf2p6vchfx7")))) (properties `((upstream-name . "gghalves"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gtable)) (native-inputs (list r-knitr)) (home-page "https://github.com/erocoar/gghalves") (synopsis "Compose half-half plots using your favourite geoms") (description "This package provides a @code{ggplot2} extension for easy plotting of half-half geom combinations. Think half boxplot and half jitterplot, or half violinplot and half dotplot.") (license license:expat))) (define-public r-zoeppritz (package (name "r-zoeppritz") (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "zoeppritz" version)) (sha256 (base32 "0bl1hrghyv5vjs02r2f5k9p7l4ialwdpl7si14lz8lbb0r1a6fwq")))) (properties `((upstream-name . "zoeppritz"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=zoeppritz") (synopsis "Seismic reflection and scattering coefficients for waves") (description "The @code{r-zoeppritz} package calculates and plots scattering matrix coefficients or scattering amplitudes, for seismological P and S-waves at an interface.") (license license:gpl2+))) (define-public r-metadat (package (name "r-metadat") (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "metadat" version)) (sha256 (base32 "1f7mb3pw5d0akr09jjva06ay223izhpzbr21bapnw99x1kiybk7h")))) (properties `((upstream-name . "metadat"))) (build-system r-build-system) (propagated-inputs (list r-mathjaxr)) (home-page "https://github.com/wviechtb/metadat") (synopsis "Meta-Analysis Datasets") (description "This package provides a collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.") (license license:gpl2+))) (define-public r-mathjaxr (package (name "r-mathjaxr") (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "mathjaxr" version)) (sha256 (base32 "0yf1sfkb2kjsplipl2v4k2gp20li9xzsynclg228sy0v243pdi7c")) (modules '((guix build utils))) (snippet '(begin (delete-file-recursively "src/mathjax/es5/input") (delete-file-recursively "src/mathjax/es5/output") (delete-file "src/mathjax/es5/tex-chtml-full.js"))))) (properties `((upstream-name . "mathjaxr"))) (build-system r-build-system) (arguments (list #:phases `(modify-phases %standard-phases (add-after 'unpack 'use-js-mathjax (lambda* (#:key inputs #:allow-other-keys) (symlink (search-input-directory inputs "/share/javascript/mathjax/es5/output") "src/mathjax/es5/output") (symlink (search-input-directory inputs "/share/javascript/mathjax/es5/input") "src/mathjax/es5/input") (symlink (search-input-file inputs "/share/javascript/mathjax/es5/tex-chtml-full.js") "src/mathjax/es5/tex-chtml-full.js")))))) (inputs (list js-mathjax-for-r-mathjaxr)) (home-page "https://github.com/wviechtb/mathjaxr") (synopsis "Use Mathjax in Rd Files") (description "This package provides MathJax and macros to enable its use within Rd files for rendering equations in the HTML help files.") (license (list license:asl2.0 license:gpl3)))) (define-public r-spacefillr (package (name "r-spacefillr") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "spacefillr" version)) (sha256 (base32 "0raaw9ib8b2dzkh4w28wpxcgxs7ky328yaayb64lc39syf7g19dv")))) (properties `((upstream-name . "spacefillr"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/tylermorganwall/spacefillr") (synopsis "Space-Filling Random and Quasi-Random Sequences") (description "@code{spacefillr} enables generation of random and quasi-random space-filling sequences. It supports the following sequences: Halton, Sobol, Owen-scrambled Sobol, Owen-scrambled Sobol with errors distributed as blue noise, progressive jittered, progressive multi-jittered (PMJ), PMJ with blue noise, PMJ02, and PMJ02 with blue noise. The package also includes a C++ API.") (license license:expat))) (define-public r-spacetime (package (name "r-spacetime") (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "spacetime" version)) (sha256 (base32 "1kr12pbi6hqns30kqy4jv5pcm3lgfcfyc2gwaak1jbg894csahhr")))) (properties `((upstream-name . "spacetime"))) (build-system r-build-system) (propagated-inputs (list r-intervals r-lattice r-sp r-xts r-zoo)) (native-inputs (list r-knitr)) (home-page "https://github.com/edzer/spacetime/") (synopsis "Classes and methods for spatio-temporal data") (description "@command{spacetime} provides classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal matching or aggregation, retrieving coordinates, print, summary, etc.") (license license:gpl2+))) (define-public r-gstat (package (name "r-gstat") (version "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "gstat" version)) (sha256 (base32 "09ax28di93r4r334qwdp84i95809lkr6587w4xlgpvsma7k0bcj8")))) (properties `((upstream-name . "gstat"))) (build-system r-build-system) (propagated-inputs (list r-fnn r-lattice r-sp r-sf r-sftime r-spacetime r-stars r-zoo)) (home-page "https://github.com/r-spatial/gstat/") (synopsis "Spatial and spatio-temporal geostatistical modelling, prediction and simulation") (description "This package enables variogram modelling, including: simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; and sequential Gaussian or indicator (co)simulation. It includes variogram and variogram map plotting utility functions, and supports @command{sf} and @command{stars}.") (license license:gpl2+))) (define-public r-automap (package (name "r-automap") (version "1.1-9") (source (origin (method url-fetch) (uri (cran-uri "automap" version)) (sha256 (base32 "0hrsdynjxv0n5n1pbdk05rgrcwfd0g5p9pgdbicx4ljk73nhl1zk")))) (properties `((upstream-name . "automap"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gstat r-lattice r-reshape r-sf r-sp r-stars)) (home-page "https://cran.r-project.org/package=automap") (synopsis "Automatic interpolation package") (description "@command{automap} performs an automatic interpolation by automatically estimating the variogram and then calling @command{gstat}.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-cartogram (package (name "r-cartogram") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "cartogram" version)) (sha256 (base32 "1vkcp8k9ajrnm14p2fqrcb4vk67503zd0w51h8amcljg3p21wzkl")))) (properties `((upstream-name . "cartogram"))) (build-system r-build-system) (propagated-inputs (list r-packcircles r-sf)) (home-page "https://github.com/sjewo/cartogram/") (synopsis "Create cartograms with R") (description "This package enables construction of continuous and non-contiguous area cartograms.") (license license:gpl3))) (define-public r-measurements (package (name "r-measurements") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "measurements" version)) (sha256 (base32 "061xjwsacsk8vblva4s09xdrvd7kfgxydnpgr7imigyny01c5bh9")))) (properties `((upstream-name . "measurements"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/measurements/") (synopsis "Tools for units of measurement") (description "This package provides a collection of tools to make working with physical measurements easier. One can convert between metric and imperial units, or calculate a dimension's unknown value from other dimensions' measurements.") (license license:gpl3))) (define-public r-sungeo (package (name "r-sungeo") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "SUNGEO" version)) (sha256 (base32 "1sy9kw3nr69jf33034kcnv418lqyz6sfrd01646i7dfsm64aydp2")) (modules '((guix build utils))) (snippet '(begin ;; Fortunately, the package does not actually use ;; rmapshaper, which has got a js/node dependency. ;; The only occurrence is in R/point2poly_tess.R, ;; where it is commented out. (substitute* "DESCRIPTION" (("rmapshaper,") "")) (substitute* "NAMESPACE" (("importFrom\\(rmapshaper,ms_dissolve\\) ") "")))))) (properties `((upstream-name . "SUNGEO"))) (build-system r-build-system) (propagated-inputs (list r-automap r-cartogram r-data-table r-dplyr r-httr r-jsonlite r-measurements r-packcircles r-purrr r-rann r-raster r-rcpp r-rcurl r-rlang r-sf r-sp r-spdep r-stringr r-terra)) (home-page "https://github.com/zhukovyuri/SUNGEO/") (synopsis "Sub-National Geospatial Data Archive: Geoprocessing Toolkit") (description "Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System.") (license license:gpl2))) ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar ;;; functionality or similar names. ;;;