;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2016, 2017 Ben Woodcroft ;;; Copyright © 2017, 2018 Roel Janssen ;;; Copyright © 2017, 2018, 2019 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 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 Wiktor Żelazny ;;; ;;; 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 git-download) #:use-module (guix utils) #:use-module (guix build-system r) #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #: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 graph) #: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 lisp) #: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 pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xorg)) (define-public r-clipr (package (name "r-clipr") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903")))) (build-system r-build-system) (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-ellipsis (package (name "r-ellipsis") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "ellipsis" version)) (sha256 (base32 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b")))) (build-system r-build-system) (propagated-inputs `(("r-rlang" ,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-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-matrix-utils (package (name "r-matrix-utils") (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "Matrix.utils" version)) (sha256 (base32 "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va")))) (properties `((upstream-name . "Matrix.utils"))) (build-system r-build-system) (propagated-inputs `(("r-grr" ,r-grr) ("r-matrix" ,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-sys (package (name "r-sys") (version "3.3") (source (origin (method url-fetch) (uri (cran-uri "sys" version)) (sha256 (base32 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6")))) (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-askpass (package (name "r-askpass") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "askpass" version)) (sha256 (base32 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) (build-system r-build-system) (propagated-inputs `(("r-sys" ,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-vegan (package (name "r-vegan") (version "2.5-6") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-knitr" ,r-knitr) ; needed for vignettes ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) ("r-permute" ,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-tidyverse (package (name "r-tidyverse") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "tidyverse" version)) (sha256 (base32 "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-dbplyr" ,r-dbplyr) ("r-dplyr" ,r-dplyr) ("r-forcats" ,r-forcats) ("r-ggplot2" ,r-ggplot2) ("r-haven" ,r-haven) ("r-hms" ,r-hms) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-modelr" ,r-modelr) ("r-purrr" ,r-purrr) ("r-readr" ,r-readr) ("r-readxl" ,r-readxl) ("r-reprex" ,r-reprex) ("r-rlang" ,r-rlang) ("r-rstudioapi" ,r-rstudioapi) ("r-rvest" ,r-rvest) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-xml2" ,r-xml2))) (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-rvest (package (name "r-rvest") (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 (base32 "0ji5lk8g1gbv4d9c4jg1fg6rgsqrrwkm05j1id7drdw9kqdifgj1")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) ("r-magrittr" ,r-magrittr) ("r-selectr" ,r-selectr) ("r-xml2" ,r-xml2))) (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 "0.4-1") (source (origin (method url-fetch) (uri (cran-uri "selectr" version)) (sha256 (base32 "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr) ("r-r6" ,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-reprex (package (name "r-reprex") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-clipr" ,r-clipr) ("r-fs" ,r-fs) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-whisker" ,r-whisker) ("r-withr" ,r-withr))) (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-callr (package (name "r-callr") (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 "12dbqzjngbyaqdyw0yq1blyfx8pagcvx1vqj2jm451hs25nhdrnh")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) ("r-processx" ,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-readxl (package (name "r-readxl") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) ("r-progress" ,r-progress) ("r-rcpp" ,r-rcpp) ("r-tibble" ,r-tibble))) (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-modelr (package (name "r-modelr") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "modelr" version)) (sha256 (base32 "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (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-httpuv (package (name "r-httpuv") (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-later" ,r-later) ("r-promises" ,r-promises) ("r-r6" ,r-r6) ("r-rcpp" ,r-rcpp))) (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-jsonlite (package (name "r-jsonlite") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8")))) (build-system r-build-system) (home-page "http://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 "0.15") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) ("r-jsonlite" ,r-jsonlite) ("r-mime" ,r-mime) ("r-xfun" ,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-htmltools (package (name "r-htmltools") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-rcpp" ,r-rcpp) ("r-rlang" ,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 "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-yaml" ,r-yaml))) (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 "1.13.2") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 (base32 "0h6jslchlx1dzqqdb70c3n9xlapcym9ykycvr0hc4q3450y8qmvh")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) ("r-rstudioapi" ,r-rstudioapi) ("r-stringr" ,r-stringr))) (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 "4.2") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 "0xh227gvb056wlipjxxbf555z1i1qcs7rr1igvs6k6645y9irrlp")))) (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" (("#ifdef _WIN32") "#if 1")) #t))))) (inputs `(("libcurl" ,curl) ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config))) (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") (source (origin (method url-fetch) (uri (cran-uri "hwriter" version)) (sha256 (base32 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb")))) (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 "0.2.20") (source (origin (method url-fetch) (uri (cran-uri "rjson" version)) (sha256 (base32 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) (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-shiny (package (name "r-shiny") (version "1.2.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/rstudio/shiny.git") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4")))) (build-system r-build-system) (arguments `(#: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) (delete-file old) (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 "bootstrap/shim/respond.min.js" (string-append (assoc-ref inputs "js-respond") "/share/javascript/respond.min.js")) (replace-file "bootstrap/shim/html5shiv.min.js" (string-append (assoc-ref inputs "js-html5shiv") "/share/javascript/html5shiv.min.js")) (replace-file "json2-min.js" (string-append (assoc-ref inputs "js-json2") "/share/javascript/json2.min.js")) (replace-file "strftime/strftime-min.js" (string-append (assoc-ref inputs "js-strftime") "/share/javascript/strftime.min.js")) (replace-file "highlight/highlight.pack.js" (string-append (assoc-ref inputs "js-highlight") "/share/javascript/highlight.min.js")) (replace-file "datatables/js/jquery.dataTables.min.js" (string-append (assoc-ref inputs "js-datatables") "/share/javascript/jquery.dataTables.min.js")) (replace-file "selectize/js/selectize.min.js" (string-append (assoc-ref inputs "js-selectize") "/share/javascript/selectize.min.js")) (replace-file "selectize/js/es5-shim.min.js" (string-append (assoc-ref inputs "js-es5-shim") "/share/javascript/es5-shim.min.js")) (for-each (match-lambda ((source . target) (delete-file 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") ("shiny.js" . "shiny.min.js") ("jquery.js" . "jquery.min.js"))))) #t))))) (propagated-inputs `(("r-crayon" ,r-crayon) ("r-httpuv" ,r-httpuv) ("r-mime" ,r-mime) ("r-jsonlite" ,r-jsonlite) ("r-xtable" ,r-xtable) ("r-digest" ,r-digest) ("r-htmltools" ,r-htmltools) ("r-r6" ,r-r6) ("r-sourcetools" ,r-sourcetools))) (inputs `(("js-datatables" ,js-datatables) ("js-html5shiv" ,js-html5shiv) ("js-json2" ,js-json2) ("js-respond" ,js-respond) ("js-selectize" ,js-selectize) ("js-strftime" ,js-strftime) ("js-highlight" ,js-highlight) ("js-es5-shim" ,js-es5-shim))) (native-inputs `(("uglify-js" ,uglify-js))) (home-page "http://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))) ;; 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 "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "shinyTree" version)) (sha256 (base32 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3")) (modules '((guix build utils))) (snippet '(begin ;; 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")) #t)))) (properties `((upstream-name . "shinyTree"))) (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 'replace-minified-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/jsTree-3.3.7/" (symlink (string-append (assoc-ref inputs "js-requirejs") "/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) (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs `(("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-promises" ,r-promises) ("r-shiny" ,r-shiny) ("r-stringr" ,r-stringr))) (inputs `(("js-requirejs" ,js-requirejs))) (native-inputs `(("uglify-js" ,uglify-js) ("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 "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. (arguments `(#:modules ((guix build utils) (guix build r-build-system) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'generate-minified-javascript (lambda _ (with-directory-excursion "inst/AdminLTE" (delete-file "app.min.js") (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js"))) (call-with-output-file "app.min.js" (lambda (port) (dump-port minified port)))))))))) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-promises" ,r-promises) ("r-shiny" ,r-shiny))) (native-inputs `(("uglify-js" ,uglify-js))) (home-page "http://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 "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 (base32 "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs `(("r-fs" ,r-fs) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-shiny" ,r-shiny) ("r-tibble" ,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 "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "shinythemes" version)) (sha256 (base32 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf")))) (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) (propagated-inputs `(("r-shiny" ,r-shiny))) (home-page "http://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 "0.8.7") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a")))) (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/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")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-htmltools" ,r-htmltools) ("r-tidyr" ,r-tidyr))) (native-inputs `(("uglify-js" ,uglify-js) ("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 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))))) (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.git") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) (build-system r-build-system) (propagated-inputs `(("r-d3r" ,r-d3r) ("r-htmlwidgets" ,r-htmlwidgets) ("r-shiny" ,r-shiny) ("r-magrittr" ,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-crosstalk (package (name "r-crosstalk") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "crosstalk" version)) (sha256 (base32 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-lazyeval" ,r-lazyeval) ("r-r6" ,r-r6) ("r-shiny" ,r-shiny))) (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 "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "Rook" version)) (sha256 (base32 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) (properties `((upstream-name . "Rook"))) (build-system r-build-system) (propagated-inputs `(("r-brew" ,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 `(("r-htmltools" ,r-htmltools) ("r-shiny" ,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 `(("r-hms" ,r-hms) ("r-rcpp" ,r-rcpp) ("r-tibble" ,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-maps (package (name "r-maps") (version "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "maps" version)) (sha256 (base32 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr")))) (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 "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,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:non-copyleft ; The C code "https://www.gnu.org/licenses/license-list.en.html#lucent102" "Lucent Public License Version 1.02"))))) (define-public r-rgooglemaps (package (name "r-rgooglemaps") (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs `(("r-png" ,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-geosphere (package (name "r-geosphere") (version "1.5-10") (source (origin (method url-fetch) (uri (cran-uri "geosphere" version)) (sha256 (base32 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan")))) (build-system r-build-system) (propagated-inputs `(("r-sp" ,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-ggmap (package (name "r-ggmap") (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggmap" version)) (sha256 (base32 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) (build-system r-build-system) (propagated-inputs `(("r-bitops" ,r-bitops) ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jpeg" ,r-jpeg) ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) ("r-png" ,r-png) ("r-purrr" ,r-purrr) ("r-rgooglemaps" ,r-rgooglemaps) ("r-rjson" ,r-rjson) ("r-scales" ,r-scales) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,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 "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-forcats" ,r-forcats) ("r-hms" ,r-hms) ("r-rcpp" ,r-rcpp) ("r-readr" ,r-readr) ("r-tibble" ,r-tibble))) (home-page "https://haven.tidyverse.org") (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files") (description "This package lets you mport foreign statistical formats into R via the embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (license license:expat))) (define-public r-amap (package (name "r-amap") (version "0.8-17") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "5.3") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-nlme" ,r-nlme) ("r-rcpp" ,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 `(("r-curl" ,r-curl) ("r-httr" ,r-httr) ("r-plyr" ,r-plyr) ("r-progress" ,r-progress) ("r-readr" ,r-readr) ("r-xml" ,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 "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9")))) (build-system r-build-system) (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 "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag")))) (build-system r-build-system) (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-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 `(("r-boot" ,r-boot))) (home-page "http://www.sciviews.org/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-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 "2.7-2") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7")))) (build-system r-build-system) (home-page "http://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 "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498")))) (build-system r-build-system) (home-page "http://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 "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-desc" ,r-desc) ("r-prettyunits" ,r-prettyunits) ("r-r6" ,r-r6) ("r-rprojroot" ,r-rprojroot) ("r-withr" ,r-withr))) (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 "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii")))) (build-system r-build-system) (propagated-inputs `(("r-desc" ,r-desc) ("r-pkgbuild" ,r-pkgbuild) ("r-rlang" ,r-rlang) ("r-rprojroot" ,r-rprojroot) ("r-rstudioapi" ,r-rstudioapi) ("r-withr" ,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-rcpp (package (name "r-rcpp") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "http://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-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 "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "bindrcpp" version)) (sha256 (base32 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) (build-system r-build-system) (propagated-inputs `(("r-bindr" ,r-bindr) ("r-plogr" ,r-plogr) ("r-rcpp" ,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 "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "AUC" version)) (sha256 (base32 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7")))) (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 "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "calibrate" version)) (sha256 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,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 "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl")))) (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 "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "GlobalOptions" version)) (sha256 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2")))) (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (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 "0.4.8") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) ("r-globaloptions" ,r-globaloptions) ("r-shape" ,r-shape))) (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-powerlaw (package (name "r-powerlaw") (version "0.70.2") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs `(("r-vgam" ,r-vgam))) (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-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 "1.12.0") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 "0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-viridis" ,r-viridis))) (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-getoptlong (package (name "r-getoptlong") (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs `(("perl" ,perl))) (propagated-inputs `(("r-globaloptions" ,r-globaloptions) ("r-rjson" ,r-rjson))) (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 "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "fastmatch" version)) (sha256 (base32 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) (build-system r-build-system) (home-page "http://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 "2.2-14") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) (home-page "http://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 "0.12.7") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit) ("r-fastmatch" ,r-fastmatch) ("r-ff" ,r-ff))) (home-page "http://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 "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "prettyunits" version)) (sha256 (base32 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-magrittr" ,r-magrittr))) (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-reshape (package (name "r-reshape") (version "0.8.8") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp))) (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-progress (package (name "r-progress") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "progress" version)) (sha256 (base32 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l")))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon) ("r-hms" ,r-hms) ("r-prettyunits" ,r-prettyunits) ("r-r6" ,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 "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-plyr" ,r-plyr) ("r-progress" ,r-progress) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape" ,r-reshape) ("r-rlang" ,r-rlang))) (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 "0.4-23") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x")))) (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 "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) (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-rmtstat (package (name "r-rmtstat") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "RMTstat" version)) (sha256 (base32 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1")))) (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 "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"") #:phases (modify-phases %standard-phases (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs `(("openmpi" ,openmpi))) (native-inputs `(("pkg-config" ,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-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 `(("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,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 "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429")))) (build-system r-build-system) (home-page "http://www.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-extremes (package (name "r-extremes") (version "2.0-10") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 "08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs `(("r-distillery" ,r-distillery) ("r-lmoments" ,r-lmoments))) (home-page "http://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 "0.9-37") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (native-inputs `(("gfortran" ,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 "1.2") (source (origin (method url-fetch) (uri (cran-uri "idr" version)) (sha256 (base32 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb")))) (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-inline (package (name "r-inline") (version "0.3.15") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z")))) (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-bbmle (package (name "r-bbmle") (version "1.0.20") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-numderiv" ,r-numderiv))) (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 "1.3.11") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q")))) (build-system r-build-system) (propagated-inputs `(("r-bbmle" ,r-bbmle) ("r-coda" ,r-coda) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp))) (home-page "http://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 "5.6.13.3") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6")))) (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 "1.5.5.3") (source (origin (method url-fetch) (uri (cran-uri "limSolve" version)) (sha256 (base32 "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg")))) (properties `((upstream-name . "limSolve"))) (build-system r-build-system) (propagated-inputs `(("r-lpsolve" ,r-lpsolve) ("r-mass" ,r-mass) ("r-quadprog" ,r-quadprog))) (native-inputs `(("gfortran" ,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-fitdistrplus (package (name "r-fitdistrplus") (version "1.0-14") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-npsurv" ,r-npsurv) ("r-survival" ,r-survival))) (home-page "http://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 "1.7-6") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-rcpp" ,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-suppdists (package (name "r-suppdists") (version "1.1-9.4") (source (origin (method url-fetch) (uri (cran-uri "SuppDists" version)) (sha256 (base32 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw")))) (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-ksamples (package (name "r-ksamples") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "kSamples" version)) (sha256 (base32 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms")))) (properties `((upstream-name . "kSamples"))) (build-system r-build-system) (propagated-inputs `(("r-suppdists" ,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 "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "CVST" version)) (sha256 (base32 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5")))) (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs `(("r-kernlab" ,r-kernlab) ("r-matrix" ,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-squarem (package (name "r-squarem") (version "2017.10-1") (source (origin (method url-fetch) (uri (cran-uri "SQUAREM" version)) (sha256 (base32 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv")))) (properties `((upstream-name . "SQUAREM"))) (build-system r-build-system) (home-page "http://www.jhsph.edu/agingandhealth/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-lava (package (name "r-lava") (version "1.6.6") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) ("r-squarem" ,r-squarem) ("r-survival" ,r-survival))) (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-drr (package (name "r-drr") (version "0.0.3") (source (origin (method url-fetch) (uri (cran-uri "DRR" version)) (sha256 (base32 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl")))) (properties `((upstream-name . "DRR"))) (build-system r-build-system) (propagated-inputs `(("r-cvst" ,r-cvst) ("r-kernlab" ,r-kernlab) ("r-matrix" ,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 "2018.04.18") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb")))) (build-system r-build-system) (propagated-inputs `(("r-kernsmooth" ,r-kernsmooth) ("r-lava" ,r-lava) ("r-rcpp" ,r-rcpp) ("r-survival" ,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 "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs `(("r-drr" ,r-drr) ("r-magrittr" ,r-magrittr))) (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-timedate (package (name "r-timedate") (version "3043.102") (source (origin (method url-fetch) (uri (cran-uri "timeDate" version)) (sha256 (base32 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p")))) (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 "1.5-9") (source (origin (method url-fetch) (uri (cran-uri "magic" version)) (sha256 (base32 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,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-rmysql (package (name "r-rmysql") (version "0.10.17") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs `(("mariadb" ,mariadb) ("zlib" ,zlib))) (propagated-inputs `(("r-dbi" ,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-rpostgresql (package (name "r-rpostgresql") (version "0.6-2") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) (properties `((upstream-name . "RPostgreSQL"))) (build-system r-build-system) (inputs `(("postgresql" ,postgresql))) (propagated-inputs `(("r-dbi" ,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-linprog (package (name "r-linprog") (version "0.9-2") (source (origin (method url-fetch) (uri (cran-uri "linprog" version)) (sha256 (base32 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9")))) (build-system r-build-system) (propagated-inputs `(("r-lpsolve" ,r-lpsolve))) (home-page "http://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 "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 "1mx5n5mw63nij4n6crs9165mlls4fnh1ipw5ch467rjsidgl0mg8")))) (build-system r-build-system) (propagated-inputs `(("r-magic" ,r-magic) ("r-linprog" ,r-linprog) ("r-lpsolve" ,r-lpsolve) ("r-rcpp" ,r-rcpp) ("r-rcppprogress" ,r-rcppprogress))) (home-page "http://geometry.r-forge.r-project.org/") (synopsis "Mesh generation and surface tesselation") (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 "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-class" ,r-class) ("r-geometry" ,r-geometry) ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-robustbase" ,r-robustbase) ("r-sfsmisc" ,r-sfsmisc))) (native-inputs `(("gfortran" ,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 "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "gower" version)) (sha256 (base32 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg")))) (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 `(("r-rcpp" ,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 "0.9-9") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) ("r-mass" ,r-mass) ("r-nnet" ,r-nnet) ("r-prodlim" ,r-prodlim) ("r-rpart" ,r-rpart) ("r-survival" ,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 "1.8.12") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) ("r-lattice" ,r-lattice) ("r-mnormt" ,r-mnormt) ("r-nlme" ,r-nlme))) (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 "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "generics" version)) (sha256 (base32 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) (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 "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) ("r-nlme" ,r-nlme) ("r-purrr" ,r-purrr) ("r-reshape2" ,r-reshape2) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (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 "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) ("r-glue" ,r-glue) ("r-gower" ,r-gower) ("r-ipred" ,r-ipred) ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-tidyselect" ,r-tidyselect) ("r-timedate" ,r-timedate) ("r-withr" ,r-withr))) (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") (source (origin (method url-fetch) (uri (cran-uri "pdist" version)) (sha256 (base32 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd")))) (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 "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-rcpp" ,r-rcpp) ("r-scales" ,r-scales))) (home-page "http://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-corrplot (package (name "r-corrplot") (version "0.84") (source (origin (method url-fetch) (uri (cran-uri "corrplot" version)) (sha256 (base32 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd")))) (build-system r-build-system) (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-stringdist (package (name "r-stringdist") (version "0.9.5.5") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi")))) (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 sting 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-ucminf (package (name "r-ucminf") (version "1.1-4") (source (origin (method url-fetch) (uri (cran-uri "ucminf" version)) (sha256 (base32 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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-ordinal (package (name "r-ordinal") (version "2019.4-25") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-numderiv" ,r-numderiv) ("r-ucminf" ,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 "2.6-10") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-ordinal" ,r-ordinal) ("r-survival" ,r-survival))) (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 "1.6") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "0.3-7") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) ("r-jomo" ,r-jomo) ("r-pan" ,r-pan))) (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 "3.6.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mitml" ,r-mitml) ("r-nnet" ,r-nnet) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-rpart" ,r-rpart) ("r-survival" ,r-survival))) (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 "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "truncnorm" version)) (sha256 (base32 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9")))) (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-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 `(("r-truncnorm" ,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 "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs `(("r-mice" ,r-mice) ("r-rcpp" ,r-rcpp) ("r-rsolnp" ,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 "2.2-5.6") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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-venndiagram (package (name "r-venndiagram") (version "1.6.20") (source (origin (method url-fetch) (uri (cran-uri "VennDiagram" version)) (sha256 (base32 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775")))) (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs `(("r-futile-logger" ,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 "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv")))) (build-system r-build-system) (propagated-inputs `(("r-sm" ,r-sm) ("r-zoo" ,r-zoo))) (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 `(("r-rcpp" ,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 "0.11-2") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,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 "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "PerformanceAnalytics" version)) (sha256 (base32 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd")))) (properties `((upstream-name . "PerformanceAnalytics"))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog) ("r-xts" ,r-xts) ("r-zoo" ,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 "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-mass" ,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 "1.4-4") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) ("r-lmtest" ,r-lmtest) ("r-mass" ,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-ica (package (name "r-ica") (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "ica" version)) (sha256 (base32 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7")))) (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-dtw (package (name "r-dtw") (version "1.21-3") (source (origin (method url-fetch) (uri (cran-uri "dtw" version)) (sha256 (base32 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s")))) (build-system r-build-system) (propagated-inputs `(("r-proxy" ,r-proxy))) (home-page "http://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 "1.1-221.1") (source (origin (method url-fetch) (uri (cran-uri "SDMTools" version)) (sha256 (base32 "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q")))) (properties `((upstream-name . "SDMTools"))) (build-system r-build-system) (propagated-inputs `(("r-r-utils" ,r-r-utils))) (home-page "http://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 "0.3-41") (source (origin (method url-fetch) (uri (cran-uri "scatterplot3d" version)) (sha256 (base32 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc")))) (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 "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-scales" ,r-scales) ("r-withr" ,r-withr))) (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 `(("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,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-cli (package (name "r-cli") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-crayon" ,r-crayon))) (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 "0.4") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9")))) (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-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 `(("r-crayon" ,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 "3.4.1") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) ("r-r6" ,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-tsp (package (name "r-tsp") (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,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 "0.1-1") (source (origin (method url-fetch) (uri (cran-uri "qap" version)) (sha256 (base32 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 `(("r-cluster" ,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-webshot (package (name "r-webshot") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,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 "1.2-8") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-colorspace" ,r-colorspace) ("r-dendextend" ,r-dendextend) ("r-gclus" ,r-gclus) ("r-gplots" ,r-gplots) ("r-mass" ,r-mass) ("r-qap" ,r-qap) ("r-registry" ,r-registry) ("r-tsp" ,r-tsp))) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://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 "0.10") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 "065ygh046ah43p5aqyrkv2vkxcnvnb4j7blfdygysg6hmqzp4pbv")))) (build-system r-build-system) (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 "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) (build-system r-build-system) (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-vctrs (package (name "r-vctrs") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-digest" ,r-digest) ("r-ellipsis" ,r-ellipsis) ("r-glue" ,r-glue) ("r-rlang" ,r-rlang) ("r-zeallot" ,r-zeallot))) (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 "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-fansi" ,r-fansi) ("r-rlang" ,r-rlang) ("r-utf8" ,r-utf8) ("r-vctrs" ,r-vctrs))) (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-uuid (package (name "r-uuid") (version "0.1-2") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx")))) (build-system r-build-system) (home-page "http://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 "0.16") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 "1dadq9l0527v038b1k1dyfs0dklsgxnmplls3qhqprfgskif8mga")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,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-metap (package (name "r-metap") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-rdpack" ,r-rdpack))) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description "The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.") (license license:gpl2))) (define-public r-network (package (name "r-network") (version "1.15") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) ("r-tibble" ,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-statnet-common (package (name "r-statnet-common") (version "4.3.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) (propagated-inputs `(("r-coda" ,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-sna (package (name "r-sna") (version "2.4") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2")))) (build-system r-build-system) (propagated-inputs `(("r-network" ,r-network) ("r-statnet-common" ,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-ttr (package (name "r-ttr") (version "0.23-5") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-xts" ,r-xts) ("r-zoo" ,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-leaps (package (name "r-leaps") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "leaps" version)) (sha256 (base32 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "splus2R" version)) (sha256 (base32 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz")))) (properties `((upstream-name . "splus2R"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (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 "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "ifultools" version)) (sha256 (base32 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-splus2r" ,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 "2.0-2") (source (origin (method url-fetch) (uri (cran-uri "sapa" version)) (sha256 (base32 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds")))) (build-system r-build-system) (propagated-inputs `(("r-ifultools" ,r-ifultools) ("r-splus2r" ,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 "0.4-15") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-ttr" ,r-ttr) ("r-xts" ,r-xts) ("r-zoo" ,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 "0.10-47") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog) ("r-quantmod" ,r-quantmod) ("r-zoo" ,r-zoo))) (native-inputs `(("gfortran" ,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 `(("r-ifultools" ,r-ifultools) ("r-mass" ,r-mass) ("r-splus2r" ,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 "1.2") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q")))) (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs `(("r-leaps" ,r-leaps) ("r-locfit" ,r-locfit) ("r-mgcv" ,r-mgcv))) (home-page "http://www.stat.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 "1.8.11") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,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-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 `(("r-ifultools" ,r-ifultools) ("r-mass" ,r-mass) ("r-sapa" ,r-sapa) ("r-scatterplot3d" ,r-scatterplot3d) ("r-splus2r" ,r-splus2r) ("r-wmtsa" ,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-urca (package (name "r-urca") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "urca" version)) (sha256 (base32 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732")))) (build-system r-build-system) (propagated-inputs `(("r-nlme" ,r-nlme))) (native-inputs `(("gfortran" ,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 "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "trend" version)) (sha256 (base32 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q")))) (build-system r-build-system) (propagated-inputs `(("r-extradistr" ,r-extradistr))) (native-inputs `(("gfortran" ,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 "0.999-4") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,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-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 `(("r-expm" ,r-expm) ("r-matrix" ,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-phontools (package (name "r-phontools") (version "0.2-2.1") (source (origin (method url-fetch) (uri (cran-uri "phonTools" version)) (sha256 (base32 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7")))) (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 "0.60-9") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-cubature" ,r-cubature) ("r-quadprog" ,r-quadprog) ("r-quantreg" ,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 `(("r-complexplus" ,r-complexplus) ("r-expm" ,r-expm) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-phontools" ,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-heatmaply (package (name "r-heatmaply") (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 "1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-colorspace" ,r-colorspace) ("r-dendextend" ,r-dendextend) ("r-ggplot2" ,r-ggplot2) ("r-htmlwidgets" ,r-htmlwidgets) ("r-magrittr" ,r-magrittr) ("r-plotly" ,r-plotly) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-scales" ,r-scales) ("r-seriation" ,r-seriation) ("r-viridis" ,r-viridis) ("r-webshot" ,r-webshot))) (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 `(("zlib" ,zlib) ("hdf5" ,hdf5))) (native-inputs `(("which" ,which))) (propagated-inputs `(("r-rcpp" ,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 `(("r-httr" ,r-httr) ("r-r-methodss3" ,r-r-methodss3) ("r-r-oo" ,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-import (package (name "r-import") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "import" version)) (sha256 (base32 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji")))) (build-system r-build-system) (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 "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs `(("r-shiny" ,r-shiny) ("r-jsonlite" ,r-jsonlite))) (home-page "http://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-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 `(("r-backports" ,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-radiant-data (package (name "r-radiant-data") (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg")) (modules '((guix build utils))) (snippet '(begin ;; Delete files that are under CC-NC-SA. (delete-file-recursively "inst/app/tools/help") #t)))) (properties `((upstream-name . "radiant.data"))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-broom" ,r-broom) ("r-car" ,r-car) ("r-curl" ,r-curl) ("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-import" ,r-import) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-markdown" ,r-markdown) ("r-plotly" ,r-plotly) ("r-psych" ,r-psych) ("r-readr" ,r-readr) ("r-readxl" ,r-readxl) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-rstudioapi" ,r-rstudioapi) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-shinyfiles" ,r-shinyfiles) ("r-shinyace" ,r-shinyace) ("r-stringi" ,r-stringi) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-writexl" ,r-writexl))) (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 "1.1-7.3") (source (origin (method url-fetch) (uri (cran-uri "AlgDesign" version)) (sha256 (base32 "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz")))) (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-signal (package (name "r-signal") (version "0.7-6") (source (origin (method url-fetch) (uri (cran-uri "signal" version)) (sha256 (base32 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (native-inputs `(("gfortran" ,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-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 `(("r-proto" ,r-proto))) (home-page "http://gsubfn.googlecode.com") (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 `(("r-chron" ,r-chron) ("r-dbi" ,r-dbi) ("r-gsubfn" ,r-gsubfn) ("r-proto" ,r-proto) ("r-rsqlite" ,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 "4.8.0") (source (origin (method url-fetch) (uri (cran-uri "VIM" version)) (sha256 (base32 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw")))) (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) ("r-colorspace" ,r-colorspace) ("r-data-table" ,r-data-table) ("r-e1071" ,r-e1071) ("r-laeken" ,r-laeken) ("r-mass" ,r-mass) ("r-nnet" ,r-nnet) ("r-ranger" ,r-ranger) ("r-rcpp" ,r-rcpp) ("r-robustbase" ,r-robustbase) ("r-sp" ,r-sp) ("r-vcd" ,r-vcd))) (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 allows to 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 "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny")))) (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 `(("r-ttr" ,r-ttr))) (home-page "http://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 "0.6") (source (origin (method url-fetch) (uri (cran-uri "riverplot" version)) (sha256 (base32 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z")))) (build-system r-build-system) (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 `(("r-zoo" ,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-catdap (package (name "r-catdap") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "catdap" version)) (sha256 (base32 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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-arules (package (name "r-arules") (version "1.6-4") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,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 "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "parsedate" version)) (sha256 (base32 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr")))) (build-system r-build-system) (propagated-inputs `(("r-rematch2" ,r-rematch2))) (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 "2.1") (source (origin (method url-fetch) (uri (cran-uri "abc" version)) (sha256 (base32 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) (build-system r-build-system) (propagated-inputs `(("r-abc-data" ,r-abc-data) ("r-locfit" ,r-locfit) ("r-mass" ,r-mass) ("r-nnet" ,r-nnet) ("r-quantreg" ,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 "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb")))) (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-openxlsx (package (name "r-openxlsx") (version "4.1.0.1") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 "1lflygpi1z4rlb1c6g6wsmi334maiiy7jhpg6ph4sw8lpvg12w4b")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-zip" ,r-zip))) (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 "0.5.16") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-data-table" ,r-data-table) ("r-foreign" ,r-foreign) ("r-haven" ,r-haven) ("r-openxlsx" ,r-openxlsx) ("r-readxl" ,r-readxl) ("r-tibble" ,r-tibble))) (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 "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 "1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) ("r-lattice" ,r-lattice) ("r-sp" ,r-sp))) (home-page "http://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-later (package (name "r-later") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang))) (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 "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "promises" version)) (sha256 (base32 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8")))) (build-system r-build-system) (propagated-inputs `(("r-later" ,r-later) ("r-magrittr" ,r-magrittr) ("r-r6" ,r-r6) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang))) (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 "1.0.18") (source (origin (method url-fetch) (uri (cran-uri "doSNOW" version)) (sha256 (base32 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh")))) (properties `((upstream-name . "doSNOW"))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach) ("r-iterators" ,r-iterators) ("r-snow" ,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-snowfall (package (name "r-snowfall") (version "1.84-6.1") (source (origin (method url-fetch) (uri (cran-uri "snowfall" version)) (sha256 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) (build-system r-build-system) (propagated-inputs `(("r-snow" ,r-snow))) (home-page "http://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-rappdirs (package (name "r-rappdirs") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "rappdirs" version)) (sha256 (base32 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g")))) (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-learnr (package (name "r-learnr") (version "0.9.2.1") (source (origin (method url-fetch) (uri (cran-uri "learnr" version)) (sha256 (base32 "0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-markdown" ,r-markdown) ("r-rappdirs" ,r-rappdirs) ("r-rmarkdown" ,r-rmarkdown) ("r-rprojroot" ,r-rprojroot) ("r-shiny" ,r-shiny) ("r-withr" ,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 `(("r-car" ,r-car) ("r-cluster" ,r-cluster) ("r-fractal" ,r-fractal) ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-np" ,r-np) ("r-powerplus" ,r-powerplus) ("r-robust" ,r-robust) ("r-trend" ,r-trend) ("r-tsa" ,r-tsa) ("r-urca" ,r-urca) ("r-vim" ,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-reticulate (package (name "r-reticulate") (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs `(("r-jsonlite" ,r-jsonlite) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (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 "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) (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-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 `(("r-ggplot2" ,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 "2.9") (source (origin (method url-fetch) (uri (cran-uri "ggsci" version)) (sha256 (base32 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-scales" ,r-scales))) (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 "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,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-ggpubr (package (name "r-ggpubr") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 "0i81mmz4qn9yzcgfa6dhkcrx4ddlflkm2c3b40isc8all43rm8rn")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-ggsci" ,r-ggsci) ("r-ggsignif" ,r-ggsignif) ("r-glue" ,r-glue) ("r-gridextra" ,r-gridextra) ("r-magrittr" ,r-magrittr) ("r-polynom" ,r-polynom) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-tidyr" ,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 "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ellipse" version)) (sha256 (base32 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs")))) (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 `(("gfortran" ,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 "1.42") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) ("r-cluster" ,r-cluster) ("r-ellipse" ,r-ellipse) ("r-flashclust" ,r-flashclust) ("r-lattice" ,r-lattice) ("r-leaps" ,r-leaps) ("r-mass" ,r-mass) ("r-scatterplot3d" ,r-scatterplot3d))) (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 "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "factoextra" version)) (sha256 (base32 "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-cluster" ,r-cluster) ("r-dendextend" ,r-dendextend) ("r-factominer" ,r-factominer) ("r-ggplot2" ,r-ggplot2) ("r-ggpubr" ,r-ggpubr) ("r-ggrepel" ,r-ggrepel) ("r-reshape2" ,r-reshape2) ("r-tidyr" ,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-fansi (package (name "r-fansi") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,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") (source (origin (method url-fetch) (uri (cran-uri "NbClust" version)) (sha256 (base32 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c")))) (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 "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f")))) (build-system r-build-system) (inputs `(("hdf5" ,hdf5) ("zlib" ,zlib))) (propagated-inputs `(("r-bit64" ,r-bit64) ("r-r6" ,r-r6))) (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 `(("r-iterators" ,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-polynom (package (name "r-polynom") (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "polynom" version)) (sha256 (base32 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5")))) (build-system r-build-system) (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-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 "4-9") (source (origin (method url-fetch) (uri (cran-uri "rjags" version)) (sha256 (base32 "1vrmxxfnia2mkmfkp5yaq5qrlh4xg3ggab6fnj14mrp1231wb91a")))) (build-system r-build-system) (propagated-inputs `(("r-coda" ,r-coda))) (inputs `(("jags" ,jags))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://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-rdpack (package (name "r-rdpack") (version "0.11-0") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs `(("r-bibtex" ,r-bibtex) ("r-gbrd" ,r-gbrd))) (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 "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 "005kaxjhr40shpav2pg7s7gj8f49579r7rbgwlncbwv16nn0rbbg")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-digest" ,r-digest) ("r-htmltools" ,r-htmltools) ("r-magrittr" ,r-magrittr) ("r-r6" ,r-r6) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-uuid" ,r-uuid) ("r-xml2" ,r-xml2) ("r-zip" ,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-abn (package (name "r-abn") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) (propagated-inputs `(("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-nnet" ,r-nnet) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rjags" ,r-rjags))) (home-page "http://www.r-bayesian-networks.org") (synopsis "Modelling multivariate data with additive bayesian networks") (description "Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a @dfn{generalized linear model} (GLM). Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. This package provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data.") (license license:gpl2+))) (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") (source (origin (method url-fetch) (uri (cran-uri "ACDm" version)) (sha256 (base32 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil")))) (properties `((upstream-name . "ACDm"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-rsolnp" ,r-rsolnp) ("r-zoo" ,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 "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "overlap" version)) (sha256 (base32 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy")))) (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 "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "snakecase" version)) (sha256 (base32 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r")))) (build-system r-build-system) (propagated-inputs `(("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr))) (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 `(("r-data-table" ,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-insight (package (name "r-insight") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 "1izqh4j0gzyk25cga67gs0i6rl0j471h5y2c3y1maz79r32fs7fd")))) (build-system r-build-system) (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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) ("r-insight" ,r-insight) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-tidyselect" ,r-tidyselect))) (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 "2.8.2") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-insight" ,r-insight) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-sjlabelled" ,r-sjlabelled) ("r-tidyselect" ,r-tidyselect))) (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-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 "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "moonBook" version)) (sha256 (base32 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6")))) (properties `((upstream-name . "moonBook"))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) ("r-nortest" ,r-nortest) ("r-purrr" ,r-purrr) ("r-sjmisc" ,r-sjmisc) ("r-stringr" ,r-stringr) ("r-survival" ,r-survival))) (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 "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 "1q6x9mfk5gikqjbbra1dn8hs1rq5ws99jdjav3m113gx9f2j5yxh")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-data-table" ,r-data-table) ("r-gdtools" ,r-gdtools) ("r-htmltools" ,r-htmltools) ("r-knitr" ,r-knitr) ("r-officer" ,r-officer) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-xml2" ,r-xml2))) (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 "1.1") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46")))) (build-system r-build-system) (inputs `(("zlib" ,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-biasedurn (package (name "r-biasedurn") (version "1.07") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) (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-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 `(("r-ggdendro" ,r-ggdendro) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-rcolorbrewer" ,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 "1.20.3") (source (origin (method url-fetch) (uri (cran-uri "getopt" version)) (sha256 (base32 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk")))) (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 "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy")))) (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 "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs `(("r-findpython" ,r-findpython) ("r-jsonlite" ,r-jsonlite) ("r-r6" ,r-r6))) (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 "2.2.6.1") (source (origin (method url-fetch) (uri (cran-uri "hash" version)) (sha256 (base32 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056")))) (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 `(("r-psych" ,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 "3.9.0") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw")))) (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 "4.6-2") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-plyr" ,r-plyr))) (home-page "http://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 `(("r-dbi" ,r-dbi) ("r-doby" ,r-doby) ("r-rsqlite" ,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 "1.6") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs `(("r-basix" ,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 "1.15.3") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp))) (home-page "http://expasy.org/tools/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 "1.7") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 `(("r-plotrix" ,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 "0.1-45") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 (base32 "0xvj8va6xd7zkn3l4a5ad7v62s7xmkz8frq7gpcl3b6vqwckkaw4")))) (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 "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-codetools" ,r-codetools) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-knitr" ,r-knitr) ("r-miniui" ,r-miniui) ("r-shiny" ,r-shiny) ("r-webshot" ,r-webshot))) (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 `(("r-pbapply" ,r-pbapply) ("r-xtable" ,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") (source (origin (method url-fetch) (uri (cran-uri "infotheo" version)) (sha256 (base32 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv")))) (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-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 `(("r-rcpp" ,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 `(("r-mass" ,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 "1.8") (source (origin (method url-fetch) (uri (cran-uri "abcrf" version)) (sha256 (base32 "0r31ki89z8zzcffm0yvd2zw3q96rk6g6fnwwkql902mgajbrha1f")))) (build-system r-build-system) (propagated-inputs `(("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-ranger" ,r-ranger) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-readr" ,r-readr) ("r-stringr" ,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 "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "abctools" version)) (sha256 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) (build-system r-build-system) (propagated-inputs `(("r-abc" ,r-abc) ("r-abind" ,r-abind) ("r-hmisc" ,r-hmisc) ("r-plyr" ,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 "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "ggstance" version)) (sha256 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-rlang" ,r-rlang) ("r-withr" ,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-mosaiccore (package (name "r-mosaiccore") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "mosaicCore" version)) (sha256 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z")))) (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-lazyeval" ,r-lazyeval) ("r-mass" ,r-mass) ("r-rlang" ,r-rlang) ("r-tidyr" ,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-ggformula (package (name "r-ggformula") (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "ggformula" version)) (sha256 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-ggstance" ,r-ggstance) ("r-magrittr" ,r-magrittr) ("r-mosaiccore" ,r-mosaiccore) ("r-rlang" ,r-rlang) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (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 "0.17.0") (source (origin (method url-fetch) (uri (cran-uri "mosaicData" version)) (sha256 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9")))) (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 "3.0-7") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-sp" ,r-sp))) (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 "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "mosaic" version)) (sha256 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-ggdendro" ,r-ggdendro) ("r-ggformula" ,r-ggformula) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-glue" ,r-glue) ("r-gridextra" ,r-gridextra) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-lazyeval" ,r-lazyeval) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-mosaiccore" ,r-mosaiccore) ("r-mosaicdata" ,r-mosaicdata) ("r-readr" ,r-readr) ("r-tidyr" ,r-tidyr))) (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 `(("r-lattice" ,r-lattice) ("r-mosaic" ,r-mosaic) ("r-nlme" ,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 "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "svGUI" version)) (sha256 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc")))) (properties `((upstream-name . "svGUI"))) (build-system r-build-system) (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 "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "svDialogs" version)) (sha256 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97")))) (properties `((upstream-name . "svDialogs"))) (build-system r-build-system) (inputs `(("yad" ,yad) ("zenity" ,zenity))) (propagated-inputs `(("r-rstudioapi" ,r-rstudioapi) ("r-svgui" ,r-svgui))) (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 `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,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 "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx")))) (build-system r-build-system) (propagated-inputs `(("r-future" ,r-future) ("r-globals" ,r-globals) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang))) (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 "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "abjutils" version)) (sha256 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv")))) (build-system r-build-system) (propagated-inputs `(("r-devtools" ,r-devtools) ("r-dplyr" ,r-dplyr) ("r-furrr" ,r-furrr) ("r-future" ,r-future) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-magrittr" ,r-magrittr) ("r-progress" ,r-progress) ("r-purrr" ,r-purrr) ("r-readr" ,r-readr) ("r-rlang" ,r-rlang) ("r-rstudioapi" ,r-rstudioapi) ("r-scales" ,r-scales) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,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 `(("r-mass" ,r-mass) ("r-matrix" ,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 `(("r-cluster" ,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 `(("r-kernlab" ,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 "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "parmigene" version)) (sha256 (base32 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d")))) (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-pscl (package (name "r-pscl") (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "pscl" version)) (sha256 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,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 `(("r-mice" ,r-mice) ("r-pscl" ,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 "0.4.16") (source (origin (method url-fetch) (uri (cran-uri "mhsmm" version)) (sha256 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,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 "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "nleqslv" version)) (sha256 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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-physicalactivity (package (name "r-physicalactivity") (version "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "PhysicalActivity" version)) (sha256 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln")))) (properties `((upstream-name . "PhysicalActivity"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") (synopsis "Procesing accelerometer data for physical activity measurement") (description "This @code{r-physicalactivity} package provides a function @code{wearingMarking} for classification of monitor 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 `(("r-circlize" ,r-circlize) ("r-dbi" ,r-dbi) ("r-ggplot2" ,r-ggplot2) ("r-iterators" ,r-iterators) ("r-mhsmm" ,r-mhsmm) ("r-nleqslv" ,r-nleqslv) ("r-physicalactivity" ,r-physicalactivity) ("r-plyr" ,r-plyr) ("r-r-utils" ,r-r-utils) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rsqlite" ,r-rsqlite) ("r-zoo" ,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 `(("r-dbi" ,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-magick (package (name "r-magick") (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) ("zlib" ,zlib))) (propagated-inputs `(("r-curl" ,r-curl) ("r-magrittr" ,r-magrittr) ("r-rcpp" ,r-rcpp))) (native-inputs `(("pkg-config" ,pkg-config))) (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 "3.36") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-matrix" ,r-matrix) ("r-minqa" ,r-minqa) ("r-mitools" ,r-mitools) ("r-numderiv" ,r-numderiv) ("r-survival" ,r-survival))) (home-page "http://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-dvmisc (package (name "r-dvmisc") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "dvmisc" version)) (sha256 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv")))) (build-system r-build-system) (propagated-inputs `(("r-cubature" ,r-cubature) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-mass" ,r-mass) ("r-mvtnorm" ,r-mvtnorm) ("r-pracma" ,r-pracma) ("r-purrr" ,r-purrr) ("r-rbenchmark" ,r-rbenchmark) ("r-rcpp" ,r-rcpp) ("r-survey" ,r-survey))) (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 `(("r-dvmisc" ,r-dvmisc) ("r-rcpp" ,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 `(("r-ape" ,r-ape) ("r-powerlaw" ,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-abundant (package (name "r-abundant") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "abundant" version)) (sha256 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) (build-system r-build-system) (propagated-inputs `(("r-quic" ,r-quic))) (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 `(("r-data-table" ,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 "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9")))) (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 "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,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 "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-survival" ,r-survival))) (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 "1.4-10") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-mvtnorm" ,r-mvtnorm) ("r-sandwich" ,r-sandwich) ("r-survival" ,r-survival) ("r-th-data" ,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-emmeans (package (name "r-emmeans") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 "1fpawaxnmj67md169a9mzrnnh2d0c973xydfg6hw865933jil9lq")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) ("r-mvtnorm" ,r-mvtnorm) ("r-numderiv" ,r-numderiv) ("r-plyr" ,r-plyr) ("r-xtable" ,r-xtable))) (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 "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "pwr" version)) (sha256 (base32 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,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 "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 (base32 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,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 "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,r-libcoin) ("r-matrixstats" ,r-matrixstats) ("r-modeltools" ,r-modeltools) ("r-multcomp" ,r-multcomp) ("r-mvtnorm" ,r-mvtnorm) ("r-survival" ,r-survival))) (home-page "http://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 "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w")))) (build-system r-build-system) (inputs `(("pandoc" ,ghc-pandoc) ("pandoc-citeproc" ,ghc-pandoc-citeproc))) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges) ("r-glue" ,r-glue) ("r-reshape2" ,r-reshape2) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyselect" ,r-tidyselect))) (home-page "http://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 "1.7.15") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) ("r-rcppeigen" ,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 "0.17.6") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 "11z1wfi0d74d1rld0320l3vmv6rl41wa0v9bjc44rk06yc90wld2")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-emmeans" ,r-emmeans) ("r-insight" ,r-insight) ("r-lme4" ,r-lme4) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-modelr" ,r-modelr) ("r-parameters" ,r-parameters) ("r-performance" ,r-performance) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-sjlabelled" ,r-sjlabelled) ("r-sjmisc" ,r-sjmisc) ("r-tidyr" ,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 "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) ("r-matrix" ,r-matrix) ("r-nlme" ,r-nlme) ("r-rcppeigen" ,r-rcppeigen) ("r-tmb" ,r-tmb))) (native-inputs `(("r-knitr" ,r-knitr))) ; 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 "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 "0r453zb106hj9w53jjgckxqajjf7shlrgv10gjxsv8if6qybdz5b")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight))) (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 "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-insight" ,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 "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 "0idfycjk05gyykfp9ibmhxfcjvd01ikh1dl0fb4nqw6znw3ar0xp")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-insight" ,r-insight) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-sjlabelled" ,r-sjlabelled) ("r-sjmisc" ,r-sjmisc))) (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-sjplot (package (name "r-sjplot") (version "2.7.2") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 "1kx1qqgp4fhwwwpqn9mv8m1pnpjxfs7ww36ns7j1ja4a7ydwn2hp")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-forcats" ,r-forcats) ("r-ggeffects" ,r-ggeffects) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-glmmtmb" ,r-glmmtmb) ("r-insight" ,r-insight) ("r-knitr" ,r-knitr) ("r-lme4" ,r-lme4) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-modelr" ,r-modelr) ("r-nlme" ,r-nlme) ("r-performance" ,r-performance) ("r-psych" ,r-psych) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-sjlabelled" ,r-sjlabelled) ("r-sjmisc" ,r-sjmisc) ("r-sjstats" ,r-sjstats) ("r-tidyr" ,r-tidyr))) (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-gh (package (name "r-gh") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) ("r-ini" ,r-ini) ("r-jsonlite" ,r-jsonlite))) (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 "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://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-usethis (package (name "r-usethis") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy")))) (build-system r-build-system) (propagated-inputs `(("r-clipr" ,r-clipr) ("r-clisymbols" ,r-clisymbols) ("r-crayon" ,r-crayon) ("r-curl" ,r-curl) ("r-desc" ,r-desc) ("r-fs" ,r-fs) ("r-gh" ,r-gh) ("r-git2r" ,r-git2r) ("r-glue" ,r-glue) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-rprojroot" ,r-rprojroot) ("r-rstudioapi" ,r-rstudioapi) ("r-whisker" ,r-whisker) ("r-withr" ,r-withr) ("r-yaml" ,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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "sessioninfo" version)) (sha256 (base32 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-withr" ,r-withr))) (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 "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49")))) (build-system r-build-system) (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 `(("r-processx" ,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 "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-desc" ,r-desc) ("r-digest" ,r-digest) ("r-pkgbuild" ,r-pkgbuild) ("r-prettyunits" ,r-prettyunits) ("r-r6" ,r-r6) ("r-rprojroot" ,r-rprojroot) ("r-sessioninfo" ,r-sessioninfo) ("r-withr" ,r-withr) ("r-xopen" ,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 "1.0") (source (origin (method url-fetch) (uri (cran-uri "rapportools" version)) (sha256 (base32 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) (build-system r-build-system) (propagated-inputs `(("r-pander" ,r-pander) ("r-plyr" ,r-plyr) ("r-reshape" ,r-reshape))) (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 "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "pander" version)) (sha256 (base32 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-rcpp" ,r-rcpp))) (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 "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a")))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-dplyr" ,r-dplyr) ("r-htmltools" ,r-htmltools) ("r-lubridate" ,r-lubridate) ("r-magick" ,r-magick) ("r-matrixstats" ,r-matrixstats) ("r-pander" ,r-pander) ("r-pryr" ,r-pryr) ("r-rapportools" ,r-rapportools) ("r-rcurl" ,r-rcurl) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (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 "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "lsei" version)) (sha256 (base32 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "0.4-0") (source (origin (method url-fetch) (uri (cran-uri "npsurv" version)) (sha256 (base32 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20")))) (build-system r-build-system) (propagated-inputs `(("r-lsei" ,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-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 `(("r-mvtnorm" ,r-mvtnorm) ("r-rcpp" ,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-tweedie (package (name "r-tweedie") (version "2.3.2") (source (origin (method url-fetch) (uri (cran-uri "tweedie" version)) (sha256 (base32 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("gsl" ,gsl))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (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 "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-rcppgsl" ,r-rcppgsl) ("r-statmod" ,r-statmod) ("r-tweedie" ,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 "0.25-1") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) ("r-lme4" ,r-lme4) ("r-lmertest" ,r-lmertest) ("r-pbkrtest" ,r-pbkrtest) ("r-reshape2" ,r-reshape2))) (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 "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "lmerTest" version)) (sha256 (base32 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b")))) (properties `((upstream-name . "lmerTest"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-numderiv" ,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 `(("r-afex" ,r-afex) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-lmertest" ,r-lmertest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-mgcv" ,r-mgcv) ("r-pbkrtest" ,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-weights (package (name "r-weights") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "weights" version)) (sha256 (base32 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c")))) (build-system r-build-system) (propagated-inputs `(("r-gdata" ,r-gdata) ("r-hmisc" ,r-hmisc) ("r-mice" ,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-rcppannoy (package (name "r-rcppannoy") (version "0.0.13") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 "1jibp9b07c5ka1kif0nl7f168hxfvysj32wnmnxg85l663hmvm8j")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (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 "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppHNSW" version)) (sha256 (base32 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,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 "4.4.4") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "http://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 "1.16.1") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 "083sb24anyd4sw0il3x07pqn9rbx5y5ayqass6mz8x443rnjvphd")))) (build-system r-build-system) (inputs `(("netcdf" ,netcdf) ("zlib" ,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-biocmanager (package (name "r-biocmanager") (version "1.30.8") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 (base32 "0pqgb7j4aqpcp3bapl313rmyxxj3j96s9csip4f65444gjy5r2x2")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (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))) (define-public r-rgl (package (name "r-rgl") (version "0.100.30") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("freetype" ,freetype) ("libpng" ,libpng) ("glu" ,glu) ("libx11" ,libx11) ("ghc-pandoc" ,ghc-pandoc) ("zlib" ,zlib))) (propagated-inputs `(("r-crosstalk" ,r-crosstalk) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) ("r-manipulatewidget" ,r-manipulatewidget) ("r-shiny" ,r-shiny))) (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 "0.1-10") (source (origin (method url-fetch) (uri (cran-uri "multicool" version)) (sha256 (base32 "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,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-misc3d (package (name "r-misc3d") (version "0.8-4") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) (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-ks (package (name "r-ks") (version "1.11.5") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 (base32 "06ymx244yknmpl6935l4pafqbm4gcbpnhqg7rinql6rrfr9mcrag")))) (build-system r-build-system) (propagated-inputs `(("r-fnn" ,r-fnn) ("r-kernlab" ,r-kernlab) ("r-kernsmooth" ,r-kernsmooth) ("r-matrix" ,r-matrix) ("r-mclust" ,r-mclust) ("r-mgcv" ,r-mgcv) ("r-multicool" ,r-multicool) ("r-mvtnorm" ,r-mvtnorm))) (home-page "http://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 "1.2.13") (source (origin (method url-fetch) (uri (cran-uri "feature" version)) (sha256 (base32 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra")))) (build-system r-build-system) (propagated-inputs `(("r-ks" ,r-ks) ("r-misc3d" ,r-misc3d) ("r-rgl" ,r-rgl))) (home-page "http://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 "1.10-1") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-coda" ,r-coda) ("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-nlme" ,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 "0.4-93") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-mvtnorm" ,r-mvtnorm))) (native-inputs `(("gfortran" ,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") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92")))) (build-system r-build-system) (propagated-inputs `(("r-circular" ,r-circular) ("r-insol" ,r-insol) ("r-pbapply" ,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 "2.14-1") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b")))) (build-system r-build-system) (propagated-inputs `(("r-subplex" ,r-subplex))) (home-page "http://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-fmsb (package (name "r-fmsb") (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5")))) (build-system r-build-system) (home-page "http://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 "http://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 "2.1-6") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m")))) (build-system r-build-system) (inputs `(("gsl" ,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-softimpute (package (name "r-softimpute") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "softImpute" version)) (sha256 (base32 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq")))) (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,gfortran))) (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-fftwtools (package (name "r-fftwtools") (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "fftwtools" version)) (sha256 (base32 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6")))) (build-system r-build-system) (inputs `(("fftw" ,fftw))) (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 "0.1-5") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) (build-system r-build-system) (inputs `(("libtiff" ,libtiff) ("libjpeg" ,libjpeg) ("zlib" ,zlib))) (home-page "http://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 "0.2-0") (source (origin (method url-fetch) (uri (cran-uri "NLP" version)) (sha256 (base32 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w")))) (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 "0.7-6") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-nlp" ,r-nlp) ("r-rcpp" ,r-rcpp) ("r-slam" ,r-slam) ("r-xml2" ,r-xml2))) (home-page "http://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-waveslim (package (name "r-waveslim") (version "1.7.5.1") (source (origin (method url-fetch) (uri (cran-uri "waveslim" version)) (sha256 (base32 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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-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 `(("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ;; The "tm" package is only "suggested" according to CRAN, but the ;; wordcloud package cannot be loaded without it. ("r-tm" ,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") (source (origin (method url-fetch) (uri (cran-uri "colorRamps" version)) (sha256 (base32 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z")))) (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 "0.2.8") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 (base32 "1hkddl8kj1g01dy7xiracx81f6b405b3ga2qp4wlrl552b9xxpby")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) ("r-dplyr" ,r-dplyr) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble))) (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 "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 (base32 "15222q3sglq0mad5q806p99fhrb96qizmpqw35fa1rb148f95paf")))) (build-system r-build-system) (propagated-inputs `(("r-biocmanager" ,r-biocmanager) ("r-rlang" ,r-rlang))) (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-docopt (package (name "r-docopt") (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "docopt" version)) (sha256 (base32 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068")))) (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") (source (origin (method url-fetch) (uri (cran-uri "sparsesvd" version)) (sha256 (base32 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,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 "0.3-2") (source (origin (method url-fetch) (uri (cran-uri "speedglm" version)) (sha256 (base32 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-matrix" ,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") (source (origin (method url-fetch) (uri (cran-uri "densityClust" version)) (sha256 (base32 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13")))) (properties `((upstream-name . "densityClust"))) (build-system r-build-system) (propagated-inputs `(("r-fnn" ,r-fnn) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gridextra" ,r-gridextra) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rtsne" ,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 `(("r-docopt" ,r-docopt) ("r-matrix" ,r-matrix) ("r-slam" ,r-slam) ("r-sparsesvd" ,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-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 `(("r-bh" ,r-bh) ("r-irlba" ,r-irlba) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,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 "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "corpcor" version)) (sha256 (base32 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf")))) (build-system r-build-system) (home-page "http://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 "0.15-0") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 "1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen))) (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 "1.6.0.2") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-matrix" ,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 `(("r-lars" ,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 `(("r-data-table" ,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 "0.0.8") (source (origin (method url-fetch) (uri (cran-uri "TFMPvalue" version)) (sha256 (base32 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,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-rnifti (package (name "r-rnifti") (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,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 "1.6.2") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 (base32 "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m")))) (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 `(("r-ore" ,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 "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i")))) (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs `(("r-ore" ,r-ore) ("r-reportr" ,r-reportr) ("r-rnifti" ,r-rnifti) ("r-shades" ,r-shades))) (home-page "http://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-grimport (package (name "r-grimport") (version "0.9-2") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 "0n3y6dzy8s0ifvyrgwbly6cl14lmgd54dyi74s5i984apszpsp16")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs `(("ghostscript" ,ghostscript))) (propagated-inputs `(("r-xml" ,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 "0.1-5") (source (origin (method url-fetch) (uri (cran-uri "grImport2" version)) (sha256 (base32 "0dyb3nrrvxnkk9q5b136bdivcz1jj3ajx1kscm3k0kkpqjif0pls")))) (properties `((upstream-name . "grImport2"))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-jpeg" ,r-jpeg) ("r-png" ,r-png) ("r-xml" ,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 "3.0.8") (source (origin (method url-fetch) (uri (cran-uri "kohonen" version)) (sha256 (base32 "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-rcpp" ,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 "1.4") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "0.0-18") (source (origin (method url-fetch) (uri (cran-uri "Iso" version)) (sha256 (base32 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid")))) (properties `((upstream-name . "Iso"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://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-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 `(("r-devtools" ,r-devtools) ("r-kohonen" ,r-kohonen) ("r-mass" ,r-mass) ("r-pls" ,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 "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "ALS" version)) (sha256 (base32 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) (properties `((upstream-name . "ALS"))) (build-system r-build-system) (propagated-inputs `(("r-iso" ,r-iso) ("r-nnls" ,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 "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "strucchange" version)) (sha256 (base32 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x")))) (build-system r-build-system) (propagated-inputs `(("r-sandwich" ,r-sandwich) ("r-zoo" ,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 "0.4-11") (source (origin (method url-fetch) (uri (cran-uri "pixmap" version)) (sha256 (base32 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) (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 "1.1") (source (origin (method url-fetch) (uri (cran-uri "rapidjsonr" version)) (sha256 (base32 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd")))) (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 "2.5") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) (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 "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx")))) (build-system r-build-system) (propagated-inputs `(("r-fs" ,r-fs) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-rlang" ,r-rlang) ("r-withr" ,r-withr))) (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 "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "bigrquery" version)) (sha256 (base32 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-bit64" ,r-bit64) ("r-curl" ,r-curl) ("r-dbi" ,r-dbi) ("r-gargle" ,r-gargle) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-prettyunits" ,r-prettyunits) ("r-progress" ,r-progress) ("r-rapidjsonr" ,r-rapidjsonr) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble))) (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 "0.5-13.5") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn")))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-CC (lambda _ (setenv "CC" "gcc") #t))))) (inputs `(("gmp" ,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 "0.7-2") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs `(("mpfr" ,mpfr))) (propagated-inputs `(("r-gmp" ,r-gmp))) (home-page "http://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-assertive-base (package (name "r-assertive-base") (version "0.0-7") (source (origin (method url-fetch) (uri (cran-uri "assertive.base" version)) (sha256 (base32 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh")))) (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 "0.0-4") (source (origin (method url-fetch) (uri (cran-uri "assertive.properties" version)) (sha256 (base32 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw")))) (properties `((upstream-name . "assertive.properties"))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,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 `(("r-assertive-base" ,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 `(("r-assertive-base" ,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 `(("r-assertive-base" ,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 `(("r-assertive-base" ,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 "0.0-4") (source (origin (method url-fetch) (uri (cran-uri "assertive.reflection" version)) (sha256 (base32 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj")))) (properties `((upstream-name . "assertive.reflection"))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,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 `(("r-assertive-base" ,r-assertive-base) ("r-assertive-properties" ,r-assertive-properties) ("r-codetools" ,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 `(("r-assertive-base" ,r-assertive-base) ("r-assertive-numbers" ,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 "0.0-3") (source (origin (method url-fetch) (uri (cran-uri "assertive.code" version)) (sha256 (base32 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) (properties `((upstream-name . "assertive.code"))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,r-assertive-base) ("r-assertive-properties" ,r-assertive-properties) ("r-assertive-types" ,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 "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.datetimes" version)) (sha256 (base32 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78")))) (properties `((upstream-name . "assertive.datetimes"))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,r-assertive-base) ("r-assertive-types" ,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 `(("r-assertive-base" ,r-assertive-base) ("r-assertive-types" ,r-assertive-types) ("r-stringi" ,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 `(("r-assertive-base" ,r-assertive-base) ("r-assertive-strings" ,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 `(("r-assertive-base" ,r-assertive-base) ("r-assertive-strings" ,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 `(("r-assertive-base" ,r-assertive-base) ("r-assertive-strings" ,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 "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "assertive" version)) (sha256 (base32 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3")))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,r-assertive-base) ("r-assertive-code" ,r-assertive-code) ("r-assertive-data" ,r-assertive-data) ("r-assertive-data-uk" ,r-assertive-data-uk) ("r-assertive-data-us" ,r-assertive-data-us) ("r-assertive-datetimes" ,r-assertive-datetimes) ("r-assertive-files" ,r-assertive-files) ("r-assertive-matrices" ,r-assertive-matrices) ("r-assertive-models" ,r-assertive-models) ("r-assertive-numbers" ,r-assertive-numbers) ("r-assertive-properties" ,r-assertive-properties) ("r-assertive-reflection" ,r-assertive-reflection) ("r-assertive-sets" ,r-assertive-sets) ("r-assertive-strings" ,r-assertive-strings) ("r-assertive-types" ,r-assertive-types) ("r-knitr" ,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 "1.0-0") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "2.3-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 (base32 "194n5mgvyms9ckjqixl3h33apii8h9kqspqg2si9k741k578qb3w")))) (build-system r-build-system) (propagated-inputs `(("r-dotcall64" ,r-dotcall64))) (native-inputs `(("gfortran" ,gfortran))) (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 "9.9") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 (base32 "1qbqdqq76xgnlbc9z643zn4s8k493h1jmav2f465hfvp63306br6")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,r-maps) ("r-spam" ,r-spam))) (native-inputs `(("gfortran" ,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 "2.0-7.2") (source (origin (method url-fetch) (uri (cran-uri "SpatialExtremes" version)) (sha256 (base32 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8")))) (properties `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) (propagated-inputs `(("r-fields" ,r-fields) ("r-maps" ,r-maps))) (home-page "http://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 `(("r-car" ,r-car) ("r-gtools" ,r-gtools) ("r-mass" ,r-mass) ("r-multcomp" ,r-multcomp) ("r-plotrix" ,r-plotrix) ("r-scales" ,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 `(("gfortran" ,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") (source (origin (method url-fetch) (uri (cran-uri "survivalROC" version)) (sha256 (base32 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) (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-longitudinal (package (name "r-longitudinal") (version "1.1.12") (source (origin (method url-fetch) (uri (cran-uri "longitudinal" version)) (sha256 (base32 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l")))) (build-system r-build-system) (propagated-inputs `(("r-corpcor" ,r-corpcor))) (home-page "http://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 "1.2.13") (source (origin (method url-fetch) (uri (cran-uri "GeneNet" version)) (sha256 (base32 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p")))) (properties `((upstream-name . "GeneNet"))) (build-system r-build-system) (propagated-inputs `(("r-corpcor" ,r-corpcor) ("r-fdrtool" ,r-fdrtool) ("r-longitudinal" ,r-longitudinal))) (home-page "http://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 "2.16.11.2") (source (origin (method url-fetch) (uri (cran-uri "rbamtools" version)) (sha256 (base32 "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-refgenome" ,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-protviz (package (name "r-protviz") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) (inputs `(("perl" ,perl) ("python-2" ,python-2))) (propagated-inputs `(("r-rcpp" ,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 "2.2-9") (source (origin (method url-fetch) (uri (cran-uri "cmprsk" version)) (sha256 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival))) (native-inputs `(("gfortran" ,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 "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "etm" version)) (sha256 (base32 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-lattice" ,r-lattice) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/etm") (synopsis "Empirical transition matrix") (description "The @dfn{empirical transition matrix} (etm) package permits to estimate 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 "2.38") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs `(("r-cmprsk" ,r-cmprsk) ("r-data-table" ,r-data-table) ("r-etm" ,r-etm) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-mgcv" ,r-mgcv) ("r-numderiv" ,r-numderiv) ("r-plyr" ,r-plyr) ("r-survival" ,r-survival) ("r-zoo" ,r-zoo))) (home-page "http://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 `(("r-mass" ,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 "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "huge" version)) (sha256 (base32 "18f8w4hdp9fdi2k5ip6fnrn5z47w4ybgxs2m6a7jdvd2v4wfdr69")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,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 `(("r-epi" ,r-epi) ("r-genenet" ,r-genenet) ("r-glmnet" ,r-glmnet) ("r-mass" ,r-mass) ("r-ppls" ,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 "0.9-6") (source (origin (method url-fetch) (uri (cran-uri "mcmc" version)) (sha256 (base32 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4")))) (build-system r-build-system) (home-page "http://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 "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1")))) (build-system r-build-system) (native-inputs `(("r-r-rsp" ,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 "0.12.4") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,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-future (package (name "r-future") (version "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-globals" ,r-globals) ("r-listenv" ,r-listenv))) (native-inputs `(("r-r-rsp" ,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 "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (propagated-inputs `(("r-future" ,r-future) ("r-globals" ,r-globals))) (native-inputs `(("r-r-rsp" ,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-rsvd (package (name "r-rsvd") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "rsvd" version)) (sha256 (base32 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,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 `(("r-codetools" ,r-codetools) ("r-crayon" ,r-crayon) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-tibble" ,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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "capushe" version)) (sha256 (base32 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,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 "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach) ("r-iterators" ,r-iterators) ("r-pkgmaker" ,r-pkgmaker) ("r-rngtools" ,r-rngtools))) (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 "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "blockmodeling" version)) (sha256 (base32 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2")))) (build-system r-build-system) (propagated-inputs `(("r-doparallel" ,r-doparallel) ("r-dorng" ,r-dorng) ("r-foreach" ,r-foreach) ("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,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 `(("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-plyr" ,r-plyr) ("r-scales" ,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))) ;; 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") (source (origin (method url-fetch) (uri (cran-uri "shinyBS" version)) (sha256 (base32 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji")))) (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 `(("r-htmltools" ,r-htmltools) ("r-shiny" ,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-outliers (package (name "r-outliers") (version "0.14") (source (origin (method url-fetch) (uri (cran-uri "outliers" version)) (sha256 (base32 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn")))) (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 "3.1-4") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo))) (home-page "http://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 "0.36.1") (source (origin (method url-fetch) (uri (cran-uri "tensorA" version)) (sha256 (base32 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7")))) (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 `(("r-rspectra" ,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 "1.40-2") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i")))) (build-system r-build-system) (propagated-inputs `(("r-bayesm" ,r-bayesm) ("r-energy" ,r-energy) ("r-robustbase" ,r-robustbase) ("r-tensora" ,r-tensora))) (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 "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "cobs" version)) (sha256 (base32 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb")))) (build-system r-build-system) (propagated-inputs `(("r-quantreg" ,r-quantreg) ("r-sparsem" ,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 `(("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,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 "5.1-5") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,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 "1.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjs" version)) (sha256 (base32 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-shiny" ,r-shiny))) (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 "1.0") (source (origin (method url-fetch) (uri (cran-uri "colourpicker" version)) (sha256 (base32 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi")))) (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-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")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-miniui" ,r-miniui) ("r-shiny" ,r-shiny) ("r-shinyjs" ,r-shinyjs))) (native-inputs `(("uglify-js" ,uglify-js) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.3.1.js") (sha256 (base32 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) ("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 "0.9") (source (origin (method url-fetch) (uri (cran-uri "ggExtra" version)) (sha256 (base32 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj")))) (properties `((upstream-name . "ggExtra"))) (build-system r-build-system) (propagated-inputs `(("r-colourpicker" ,r-colourpicker) ("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-miniui" ,r-miniui) ("r-r6" ,r-r6) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-shinyjs" ,r-shinyjs))) (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-minpack-lm (package (name "r-minpack-lm") (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) (native-inputs `(("gfortran" ,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") (source (origin (method url-fetch) (uri (cran-uri "moments" version)) (sha256 (base32 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra")))) (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 "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "msir" version)) (sha256 (base32 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb")))) (build-system r-build-system) (propagated-inputs `(("r-mclust" ,r-mclust))) (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 `(("gfortran" ,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 "0.6-5") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-mnormt" ,r-mnormt) ("r-numderiv" ,r-numderiv) ("r-pbivnorm" ,r-pbivnorm))) (home-page "http://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 "0.5-2") (source (origin (method url-fetch) (uri (cran-uri "nonnest2" version)) (sha256 (base32 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6")))) (build-system r-build-system) (propagated-inputs `(("r-compquadform" ,r-compquadform) ("r-lavaan" ,r-lavaan) ("r-mvtnorm" ,r-mvtnorm) ("r-sandwich" ,r-sandwich))) (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 "0.9-51") (source (origin (method url-fetch) (uri (cran-uri "penalized" version)) (sha256 (base32 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-survival" ,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 `(("r-mass" ,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 "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "nor1mix" version)) (sha256 (base32 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w")))) (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 "1.2") (source (origin (method url-fetch) (uri (cran-uri "beanplot" version)) (sha256 (base32 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9")))) (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 "0.3-3") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs `(("zeromq" ,zeromq) ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,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 "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-pillar" ,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 "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "IRdisplay" version)) (sha256 (base32 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli")))) (properties `((upstream-name . "IRdisplay"))) (build-system r-build-system) (propagated-inputs `(("r-repr" ,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 "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp")))) (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")) #t)))))) (inputs `(("jupyter" ,jupyter))) (propagated-inputs `(("r-crayon" ,r-crayon) ("r-digest" ,r-digest) ("r-evaluate" ,r-evaluate) ("r-irdisplay" ,r-irdisplay) ("r-jsonlite" ,r-jsonlite) ("r-pbdzmq" ,r-pbdzmq) ("r-repr" ,r-repr) ("r-uuid" ,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") (source (origin (method url-fetch) (uri (cran-uri "gmodels" version)) (sha256 (base32 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) (build-system r-build-system) (propagated-inputs `(("r-gdata" ,r-gdata) ("r-mass" ,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 "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (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-valr (package (name "r-valr") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-rcpp" ,r-rcpp) ("r-readr" ,r-readr) ("r-rlang" ,r-rlang) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble))) (home-page "http://github.com/rnabioco/valr") (synopsis "Genome interval arithmetic in R") (description "This package enables you to read and manipulate genome intervals and signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.") (license license:expat))) (define-public r-rematch2 (package (name "r-rematch2") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "rematch2" version)) (sha256 (base32 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq")))) (build-system r-build-system) (propagated-inputs `(("r-tibble" ,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") (source (origin (method url-fetch) (uri (cran-uri "picante" version)) (sha256 (base32 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) ("r-nlme" ,r-nlme) ("r-vegan" ,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 `(("r-checkmate" ,r-checkmate) ("r-nnet" ,r-nnet) ("r-purrr" ,r-purrr) ("r-r6" ,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 "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtable" ,r-gtable) ("r-knitr" ,r-knitr) ("r-lattice" ,r-lattice) ("r-plyr" ,r-plyr) ("r-scales" ,r-scales))) (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 `(("r-ggplot2" ,r-ggplot2) ("r-qtl" ,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 `(("r-data-table" ,r-data-table) ("r-r-utils" ,r-r-utils) ("r-testthat" ,r-testthat) ("r-venndiagram" ,r-venndiagram) ("r-yaml" ,r-yaml) ("bedops" ,bedops) ("bedtools" ,bedtools) ("htslib" ,htslib))) ; for tabix (native-inputs `(("r-knitr" ,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-sets (package (name "r-sets") (version "1.0-18") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl")))) (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 "1.9-19") (source (origin (method url-fetch) (uri (cran-uri "partitions" version)) (sha256 (base32 "1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx")))) (build-system r-build-system) (propagated-inputs `(("r-gmp" ,r-gmp) ("r-polynom" ,r-polynom))) (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 "1.2-6") (source (origin (method url-fetch) (uri (cran-uri "Brobdingnag" version)) (sha256 (base32 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r")))) (properties `((upstream-name . "Brobdingnag"))) (build-system r-build-system) (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-untb (package (name "r-untb") (version "1.7-4") (source (origin (method url-fetch) (uri (cran-uri "untb" version)) (sha256 (base32 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6")))) (build-system r-build-system) (propagated-inputs `(("r-brobdingnag" ,r-brobdingnag) ("r-partitions" ,r-partitions) ("r-polynom" ,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 "http://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 `(("r-combinat" ,r-combinat) ("r-mvtnorm" ,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 `(("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,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 "3.6-1") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-segmented" ,r-segmented))) (inputs `(("zlib" ,zlib))) (home-page "http://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 "0.6-5") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh")))) (build-system r-build-system) (inputs `(("udunits" ,udunits))) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (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-classint (package (name "r-classint") (version "0.4-2") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) ("r-e1071" ,r-e1071) ("r-kernsmooth" ,r-kernsmooth))) (native-inputs `(("gfortran" ,gfortran))) (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 "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (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 "0.1-23") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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-sf (package (name "r-sf") (version "0.8-0") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) ("geos" ,geos) ("proj" ,proj.4) ("zlib" ,zlib))) (propagated-inputs `(("r-classint" ,r-classint) ("r-dbi" ,r-dbi) ("r-magrittr" ,r-magrittr) ("r-rcpp" ,r-rcpp) ("r-units" ,r-units))) (native-inputs `(("pkg-config" ,pkg-config))) (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-spdep (package (name "r-spdep") (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-coda" ,r-coda) ("r-deldir" ,r-deldir) ("r-expm" ,r-expm) ("r-gmodels" ,r-gmodels) ("r-learnbayes" ,r-learnbayes) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-nlme" ,r-nlme) ("r-sf" ,r-sf) ("r-sp" ,r-sp) ("r-spdata" ,r-spdata))) (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 "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-ape" ,r-ape) ("r-boot" ,r-boot) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-igraph" ,r-igraph) ("r-mass" ,r-mass) ("r-reshape2" ,r-reshape2) ("r-seqinr" ,r-seqinr) ("r-shiny" ,r-shiny) ("r-spdep" ,r-spdep) ("r-vegan" ,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 "0.12") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p")))) (build-system r-build-system) (propagated-inputs `(("r-adegenet" ,r-adegenet) ("r-ape" ,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-rmetasim (package (name "r-rmetasim") (version "3.1.7") (source (origin (method url-fetch) (uri (cran-uri "rmetasim" version)) (sha256 (base32 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-adegenet" ,r-adegenet) ("r-gtools" ,r-gtools) ("r-pegas" ,r-pegas))) (home-page "https://cran.r-project.org/web/packages/rmetasim") (synopsis "Individual-based population genetic simulation environment") (description "This package provides an interface between R and the metasim simulation engine. The simulation environment is documented in: Strand, A.(2002), Metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics.") ;; Any GPL version (license license:gpl2+))) (define-public r-genetics (package (name "r-genetics") (version "1.3.8.1.2") (source (origin (method url-fetch) (uri (cran-uri "genetics" version)) (sha256 (base32 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh")))) (build-system r-build-system) (propagated-inputs `(("r-combinat" ,r-combinat) ("r-gdata" ,r-gdata) ("r-gtools" ,r-gtools) ("r-mass" ,r-mass) ("r-mvtnorm" ,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 `(("r-genetics" ,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 "1.1.16") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 (base32 "0d49h7if8h6d784nsnqqxakg19kvl8cmz8k53901m2h0c0amlfxa")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "5.1-3.1") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 (base32 "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-hmisc" ,r-hmisc) ("r-htmltable" ,r-htmltable) ("r-htmltools" ,r-htmltools) ("r-lattice" ,r-lattice) ("r-multcomp" ,r-multcomp) ("r-nlme" ,r-nlme) ("r-polspline" ,r-polspline) ("r-quantreg" ,r-quantreg) ("r-rpart" ,r-rpart) ("r-sparsem" ,r-sparsem) ("r-survival" ,r-survival))) (native-inputs `(("gfortran" ,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-haplo-stats (package (name "r-haplo-stats") (version "1.7.9") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs `(("r-rms" ,r-rms))) (native-inputs `(("r-r-rsp" ,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 "1.0-32") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci")))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "ibdreg" version)) (sha256 (base32 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g")))) (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 `(("r-ibdreg" ,r-ibdreg) ("r-mgcv" ,r-mgcv) ("r-nlme" ,r-nlme) ("r-qtl" ,r-qtl) ("r-wgaim" ,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-ldheatmap (package (name "r-ldheatmap") (version "0.99-7") (source (origin (method url-fetch) (uri (cran-uri "LDheatmap" version)) (sha256 (base32 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc")))) (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs `(("r-genetics" ,r-genetics) ("r-rcpp" ,r-rcpp) ("r-snpstats" ,r-snpstats))) (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html") (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") (description "This package provides tools to produce a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot.") (license license:gpl3))) (define-public r-hwde (package (name "r-hwde") (version "0.67") (source (origin (method url-fetch) (uri (cran-uri "hwde" version)) (sha256 (base32 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy")))) (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 "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "tdthap" version)) (sha256 (base32 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k")))) (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 `(("r-rcurl" ,r-rcurl) ("r-xml" ,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 "0.14") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 "1jiq2d292y0l3f4npyfzfpnmb0sqxsl212kkjfbjg5301h0na762")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) ("r-tinytex" ,r-tinytex) ("r-xfun" ,r-xfun) ("pandoc" ,ghc-pandoc))) (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 "1.6.4") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d")))) (build-system r-build-system) (propagated-inputs `(("r-getopt" ,r-getopt))) (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-wgcna (package (name "r-wgcna") (version "1.68") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-doparallel" ,r-doparallel) ("r-dynamictreecut" ,r-dynamictreecut) ("r-fastcluster" ,r-fastcluster) ("r-foreach" ,r-foreach) ("r-go-db" ,r-go-db) ("r-hmisc" ,r-hmisc) ("r-impute" ,r-impute) ("r-rcpp" ,r-rcpp) ("r-robust" ,r-robust) ("r-survival" ,r-survival) ("r-matrixstats" ,r-matrixstats) ("r-preprocesscore" ,r-preprocesscore))) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis "Weighted correlation network analysis") (description "This package provides functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. It includes functions for rudimentary data cleaning, construction and summarization of correlation networks, module identification and functions for relating both variables and modules to sample traits. It also includes a number of utility functions for data manipulation and visualization.") (license license:gpl2+))) (define-public r-kernlab (package (name "r-kernlab") (version "0.9-27") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn")))) (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 "0.04-22") (source (origin (method url-fetch) (uri (cran-uri "hierfstat" version)) (sha256 (base32 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-adegenet" ,r-adegenet) ("r-gtools" ,r-gtools))) (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 "1.2-8") (source (origin (method url-fetch) (uri (cran-uri "hapassoc" version)) (sha256 (base32 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s")))) (build-system r-build-system) (home-page "http://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 "2.8") (source (origin (method url-fetch) (uri (cran-uri "sampling" version)) (sha256 (base32 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m")))) (build-system r-build-system) (propagated-inputs `(("r-lpsolve" ,r-lpsolve) ("r-mass" ,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 "2.3.2") (source (origin (method url-fetch) (uri (cran-uri "R2HTML" version)) (sha256 (base32 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9")))) (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 allows to parse 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 "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2")))) (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (ice-9 match)) #:phases (modify-phases %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")) (match (find-files (string-append jdk "/jre/lib/") "libjvm.so") ((lib) (setenv "JAVA_LIBS" lib)) (_ (error "Could not find libjvm.so")))) #t))))) (inputs `(("icu4c" ,icu4c) ("jdk" ,icedtea-8 "jdk") ("pcre" ,pcre) ("zlib" ,zlib))) (home-page "http://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 "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "svMisc" version)) (sha256 (base32 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2")))) (properties `((upstream-name . "svMisc"))) (build-system r-build-system) (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 `(("r-rcpp" ,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 "1.3.7") (source (origin (method url-fetch) (uri (cran-uri "Rttf2pt1" version)) (sha256 (base32 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja")))) (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 "0.17") (source (origin (method url-fetch) (uri (cran-uri "extrafont" version)) (sha256 (base32 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g")))) (build-system r-build-system) (propagated-inputs `(("r-extrafontdb" ,r-extrafontdb) ("r-rttf2pt1" ,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 `(("r-extrafont" ,r-extrafont) ("r-ggplot2" ,r-ggplot2) ("r-hmisc" ,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-msigdbr (package (name "r-msigdbr") (version "7.0.1") (source (origin (method url-fetch) (uri (cran-uri "msigdbr" version)) (sha256 (base32 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble))) (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 "0.4-1") (source (origin (method url-fetch) (uri (cran-uri "gridGraphics" version)) (sha256 (base32 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p")))) (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 "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "farver" version)) (sha256 (base32 "1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (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-ggplotify (package (name "r-ggplotify") (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gridgraphics" ,r-gridgraphics) ("r-rvcheck" ,r-rvcheck))) (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 "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "triebeard" version)) (sha256 (base32 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (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 "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "tweenr" version)) (sha256 (base32 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg")))) (build-system r-build-system) (propagated-inputs `(("r-farver" ,r-farver) ("r-magrittr" ,r-magrittr) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang))) (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 "1.10-0") (source (origin (method url-fetch) (uri (cran-uri "polyclip" version)) (sha256 (base32 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,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-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 `(("r-rcpp" ,r-rcpp) ("r-triebeard" ,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 "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "ggforce" version)) (sha256 (base32 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-mass" ,r-mass) ("r-polyclip" ,r-polyclip) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-tidyselect" ,r-tidyselect) ("r-tweenr" ,r-tweenr) ("r-withr" ,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. Thi package aims to be a collection of mainly new statistics and geometries that fills this gap.") (license license:expat))) (define-public r-europepmc (package (name "r-europepmc") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "europepmc" version)) (sha256 (base32 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-plyr" ,r-plyr) ("r-progress" ,r-progress) ("r-purrr" ,r-purrr) ("r-urltools" ,r-urltools) ("r-xml2" ,r-xml2))) (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 "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggraph" version)) (sha256 (base32 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-ggforce" ,r-ggforce) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-graphlayouts" ,r-graphlayouts) ("r-gtable" ,r-gtable) ("r-igraph" ,r-igraph) ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-tidygraph" ,r-tidygraph) ("r-viridis" ,r-viridis))) (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-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 `(("r-randomforest" ,r-randomforest))) (home-page "http://ligarto.org/rdiaz/Software/Software.html") (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 `(("r-cluster" ,r-cluster) ("r-survival" ,r-survival))) (native-inputs `(("gfortran" ,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 "1.0.2-2.1") (source (origin (method url-fetch) (uri (cran-uri "rda" version)) (sha256 (base32 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639")))) (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 "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "ggvis" version)) (sha256 (base32 "1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-dplyr" ,r-dplyr) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-shiny" ,r-shiny))) (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 "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "gbm" version)) (sha256 (base32 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6")))) (build-system r-build-system) (propagated-inputs `(("r-gridextra" ,r-gridextra) ("r-lattice" ,r-lattice) ("r-survival" ,r-survival))) (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 "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "threejs" version)) (sha256 (base32 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi")))) (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-85") "htmlwidgets/lib/threejs-85/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 "uglify-js" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-crosstalk" ,r-crosstalk) ("r-htmlwidgets" ,r-htmlwidgets) ("r-igraph" ,r-igraph))) (native-inputs `(("uglify-js" ,uglify-js) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.3.1.js") (sha256 (base32 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) ("js-threejs-85" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js") (sha256 (base32 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl")))))) (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 "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "mlbench" version)) (sha256 (base32 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl")))) (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 "1.0-22") (source (origin (method url-fetch) (uri (cran-uri "mpm" version)) (sha256 (base32 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk")))) (build-system r-build-system) (propagated-inputs `(("r-kernsmooth" ,r-kernsmooth) ("r-mass" ,r-mass))) (home-page "http://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 "0.1-7") (source (origin (method url-fetch) (uri (cran-uri "png" version)) (sha256 (base32 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) (build-system r-build-system) (inputs `(("libpng" ,libpng) ("zlib" ,zlib))) (home-page "http://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 "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "ggcorrplot" version)) (sha256 (base32 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,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-flexdashboard (package (name "r-flexdashboard") (version "0.5.1.1") (source (origin (method url-fetch) (uri (cran-uri "flexdashboard" version)) (sha256 (base32 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x")))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (srfi srfi-26) (ice-9 popen) (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 #t "Processing ~a --> ~a~%" source target) (delete-file target) (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) ("r-shiny" ,r-shiny))) (native-inputs `(("uglify-js" ,uglify-js) ("js-raphael" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js") (sha256 (base32 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x")))) ("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")))) ("js-featherlight" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js") (sha256 (base32 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb")))))) (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 `(("r-polynom" ,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 "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "mapplots" version)) (sha256 (base32 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p")))) (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 "4.3") (source (origin (method url-fetch) (uri (cran-uri "PMCMR" version)) (sha256 (base32 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij")))) (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 `(("r-digest" ,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-rex (package (name "r-rex") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "rex" version)) (sha256 (base32 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x")))) (build-system r-build-system) (propagated-inputs `(("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr))) (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-sctransform (package (name "r-sctransform") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p")))) (build-system r-build-system) (propagated-inputs `(("r-future" ,r-future) ("r-future-apply" ,r-future-apply) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-reshape2" ,r-reshape2))) (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 "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-cli" ,r-cli) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rematch2" ,r-rematch2) ("r-rlang" ,r-rlang) ("r-rprojroot" ,r-rprojroot) ("r-tibble" ,r-tibble) ("r-withr" ,r-withr) ("r-xfun" ,r-xfun))) (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 "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "pbmcapply" version)) (sha256 (base32 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz")))) (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 "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "blme" version)) (sha256 (base32 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,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 "0.9.11") (source (origin (method url-fetch) (uri (cran-uri "batchtools" version)) (sha256 (base32 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-base64url" ,r-base64url) ("r-brew" ,r-brew) ("r-checkmate" ,r-checkmate) ("r-data-table" ,r-data-table) ("r-digest" ,r-digest) ("r-fs" ,r-fs) ("r-progress" ,r-progress) ("r-r6" ,r-r6) ("r-rappdirs" ,r-rappdirs) ("r-stringi" ,r-stringi) ("r-withr" ,r-withr))) (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 "0.3-57") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,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 "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "sitmo" version)) (sha256 (base32 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (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 "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "dqrng" version)) (sha256 (base32 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) ("r-sitmo" ,r-sitmo))) (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-dalex (package (name "r-dalex") (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 "0iiwkf0pfdb90lf1xhv43qd32z3cjmkmf0ly9841n5lldkjazy3h")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) (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 "2.1") (source (origin (method url-fetch) (uri (cran-uri "enrichR" version)) (sha256 (base32 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1")))) (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) ("r-rjson" ,r-rjson))) (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 "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs `(("r-misc3d" ,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-ggfortify (package (name "r-ggfortify") (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 "1wk9j0xg5hj9i1vf62qjiphv8cbsgq7y6baay3pfl3wyb2dwgci0")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-scales" ,r-scales) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (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 "1.2.12") (source (origin (method url-fetch) (uri (cran-uri "RefManageR" version)) (sha256 (base32 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp")))) (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs `(("r-bibtex" ,r-bibtex) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-lubridate" ,r-lubridate) ("r-plyr" ,r-plyr) ("r-stringr" ,r-stringr) ("r-xml2" ,r-xml2))) (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 `(("r-assertthat" ,r-assertthat) ("r-curl" ,r-curl) ("r-httr" ,r-httr) ("r-miniui" ,r-miniui) ("r-refmanager" ,r-refmanager) ("r-rstudioapi" ,r-rstudioapi) ("r-shiny" ,r-shiny) ("r-shinyjs" ,r-shinyjs) ("r-yaml" ,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 "0.90.0.2") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) ("r-stringi" ,r-stringi))) (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 "0.2.3.1") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d")))) (build-system r-build-system) (propagated-inputs `(("r-openssl" ,r-openssl) ("r-rcpp" ,r-rcpp) ("r-reticulate" ,r-reticulate) ("r-rspectra" ,r-rspectra))) (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 "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 "1y9wpzs92d1fl2x5figfywd48lkyhwx37j542z0rf6ckrl46n89n")))) (build-system r-build-system) (propagated-inputs `(("r-dqrng" ,r-dqrng) ("r-fnn" ,r-fnn) ("r-irlba" ,r-irlba) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppannoy" ,r-rcppannoy) ("r-rcppparallel" ,r-rcppparallel) ("r-rcppprogress" ,r-rcppprogress) ("r-rspectra" ,r-rspectra))) (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 "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "kableExtra" version)) (sha256 (base32 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i")))) (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-glue" ,r-glue) ("r-htmltools" ,r-htmltools) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) ("r-readr" ,r-readr) ("r-rmarkdown" ,r-rmarkdown) ("r-rstudioapi" ,r-rstudioapi) ("r-rvest" ,r-rvest) ("r-scales" ,r-scales) ("r-stringr" ,r-stringr) ("r-viridislite" ,r-viridislite) ("r-webshot" ,r-webshot) ("r-xml2" ,r-xml2))) (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 `(("gfortran" ,gfortran))) (home-page "http://www-stat.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-rhpcblasctl (package (name "r-rhpcblasctl") (version "0.18-205") (source (origin (method url-fetch) (uri (cran-uri "RhpcBLASctl" version)) (sha256 (base32 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp")))) (properties `((upstream-name . "RhpcBLASctl"))) (build-system r-build-system) (home-page "http://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 "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix) ("r-reticulate" ,r-reticulate))) (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-patchwork ;; There has been no public release yet. (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242") (revision "1")) (package (name "r-patchwork") (version (git-version "0.0.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/thomasp85/patchwork.git") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable))) (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 mathmatical operators for combining multiple plots.") (license license:expat)))) (define-public r-liger (package (name "r-liger") (version "0.4.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/MacoskoLab/liger.git") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx")) (modules '((guix build utils))) (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") #t)))) (build-system r-build-system) (arguments `(#: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$")) (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar" (find-files "." "\\.class$")) #t))))) (propagated-inputs `(("r-cowplot" ,r-cowplot) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-hmisc" ,r-hmisc) ("r-ica" ,r-ica) ("r-irlba" ,r-irlba) ("r-matrix" ,r-matrix) ("r-mclust" ,r-mclust) ("r-patchwork" ,r-patchwork) ("r-plyr" ,r-plyr) ("r-rann-l1" ,r-rann-l1) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-riverplot" ,r-riverplot) ("r-rtsne" ,r-rtsne) ("r-snow" ,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) ("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-harmony ;; There are no tagged commits (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a") (revision "1")) (package (name "r-harmony") (version (git-version "1.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/immunogenomics/harmony") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-irlba" ,r-irlba) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppprogress" ,r-rcppprogress) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (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 "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "covr" version)) (sha256 (base32 "160w0m2d06kdd8dar57lpph39rxx55xwncbpl3b21l7j9drh1s5f")))) (properties `((upstream-name . "covr"))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon) ("r-digest" ,r-digest) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-rex" ,r-rex) ("r-withr" ,r-withr) ("r-yaml" ,r-yaml))) (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 "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (inputs `(("fontconfig" ,fontconfig) ("freetype" ,freetype) ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config))) (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 "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo))) (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 allow to emphasize hidden group structures in networks or focus on specific nodes.") (license license:expat))) (define-public r-tidygraph (package (name "r-tidygraph") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "tidygraph" version)) (sha256 (base32 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn")))) (properties `((upstream-name . "tidygraph"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-igraph" ,r-igraph) ("r-magrittr" ,r-magrittr) ("r-pillar" ,r-pillar) ("r-r6" ,r-r6) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,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 `(("r-ggplot2" ,r-ggplot2) ("r-matrix" ,r-matrix) ("r-seurat" ,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 "2.6") (source (origin (method url-fetch) (uri (cran-uri "assertr" version)) (sha256 (base32 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-mass" ,r-mass) ("r-rlang" ,r-rlang))) (native-inputs `(("r-knitr" ,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 "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 "1mgggb3l67wgjiccq4y84wbs2dw9qk01akd553yiwbwky9rpawgh")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-insight" ,r-insight))) (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 "1.4-6") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 (base32 "0lj1dax56dxxsj1hindxcvgz169p9dxd0y4wjypbyr01nja8rz4d")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs `(("gdal" ,gdal) ("proj.4" ,proj.4) ("zlib" ,zlib))) (propagated-inputs `(("r-sp" ,r-sp))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://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") (source (origin (method url-fetch) (uri (cran-uri "insol" version)) (sha256 (base32 "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5")))) (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs `(("r-raster" ,r-raster) ("r-rgdal" ,r-rgdal))) (native-inputs `(("gfortran" ,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 "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n")))) (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs `(("r-glue" ,r-glue) ("r-rlang" ,r-rlang))) (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 "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "assertable" version)) (sha256 (base32 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table))) (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)))