;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2016, 2017 Ben Woodcroft ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2017 Raoul Bonnal ;;; Copyright © 2018 Vijayalakshmi Vedantham ;;; Copyright © 2018 Sahithi Yarlagadda ;;; Copyright © 2018 Sandeep Subramanian ;;; Copyright © 2018 Charlie Ritter ;;; Copyright © 2018 Konrad Hinsen ;;; Copyright © 2018, 2020, 2021, 2022 Mădălin Ionel Patrașcu ;;; Copyright © 2018 Laura Lazzati ;;; Copyright © 2018 Leo Famulari ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2018, 2019 Brett Gilio ;;; Copyright © 2019 Nicolò Balzarotti ;;; Copyright © 2019, 2020, 2021 Wiktor Żelazny ;;; Copyright © 2019 Arne Babenhauserheide ;;; Copyright © 2019, 2020 Efraim Flashner ;;; Copyright © 2020 Todor Kondić ;;; Copyright © 2020 Danjela Lura ;;; Copyright © 2020 Naga Malleswari ;;; Copyright © 2020 Eric Brown ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Rafael Luque Leiva ;;; Copyright © 2020, 2021 Lars-Dominik Braun ;;; Copyright © 2020 Vinicius Monego ;;; Copyright © 2020 Antoine Côté ;;; Copyright © 2020 Arun Isaac ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020, 2021, 2022 Simon Tournier ;;; Copyright © 2020 Aniket Patil ;;; Copyright © 2021 Marcel Schilling ;;; Copyright © 2021 Guillaume Le Vaillant ;;; Copyright © 2022 Navid Afkhami ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . (define-module (gnu packages cran) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) #:use-module (gnu packages compression) #:use-module (gnu packages crypto) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages 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 libevent) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) #:use-module (gnu packages node) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) #:use-module (gnu packages tcl) #:use-module (gnu packages tex) #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages uglifyjs) #:use-module (gnu packages version-control) #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) (define-public r-afpt (package (name "r-afpt") (version "1.1.0.1") (source (origin (method url-fetch) (uri (cran-uri "afpt" version)) (sha256 (base32 "0cg5cdm9nl1hs6f3j0ljpw4bkqvh3ksyj615b9nnbqs5k28lyds9")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-fingerprint (package (name "r-fingerprint") (version "3.5.7") (source (origin (method url-fetch) (uri (cran-uri "fingerprint" version)) (sha256 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic")))) (properties `((upstream-name . "fingerprint"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fingerprint") (synopsis "Functions to Operate on Binary Fingerprint Data") (description "This package provides functions to manipulate binary fingerprints of arbitrary length. A fingerprint is represented by an object of S4 class @code{fingerprint}. The bitwise logical functions in R are overridden so that they can be used directly with @code{fingerprint} objects. A number of distance metrics are also available. Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded. Arbitrary fingerprint formats can be handled via line handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-fpeek (package (name "r-fpeek") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "fpeek" version)) (sha256 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii")))) (properties `((upstream-name . "fpeek"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/davidgohel/fpeek") (synopsis "Check text files content at a glance") (description "This package provides tools to help working with text files. It can return the number of lines; print the first and last lines; convert encoding. Operations are made without reading the entire file before starting, resulting in good performances with large files.") 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The main tools are: @enumerate @item @code{g:GOSt}, functional enrichment analysis and visualization of gene lists; @item @code{g:Convert}, gene/protein/transcript identifier conversion across various namespaces; @item @code{g:Orth}, orthology search across species; @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions, genes and variant effects. @end enumerate This package is an R interface corresponding to the 2019 update of @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and higher.") (license license:gpl2+))) (define-public r-oenb (package (name "r-oenb") (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "oenb" version)) (sha256 (base32 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5")))) (properties `((upstream-name . 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It contains functions to assist with organic or biological mass spectrometry data analysis. Mass spectral libraries are available as companion packages.") (license license:bsd-2))) (define-public r-scales (package (name "r-scales") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 (base32 "1pq2rrix6a5gsi8xw38viiydp1bsxxmcmyy7dv9q8gkb1qj50p8q")))) (build-system r-build-system) (propagated-inputs (list r-farver r-labeling r-lifecycle r-munsell r-rcolorbrewer r-rlang r-r6 r-viridislite)) (home-page "https://github.com/hadley/scales") (synopsis "Scale functions for visualization") (description "This package provides graphical scales that map data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends.") 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For ease of use, the @code{parDist} function extends the signature of the @code{dist} function and uses the same parameter naming conventions as distance methods of existing R packages.") (license license:gpl2+))) (define-public r-pheatmap (package (name "r-pheatmap") (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "pheatmap" version)) (sha256 (base32 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) (build-system r-build-system) (propagated-inputs (list r-gtable r-rcolorbrewer r-scales)) (home-page "https://cran.r-project.org/web/packages/pheatmap") (synopsis "Pretty heatmaps") (description "This package provides an implementation of heatmaps that offers more control over dimensions and appearance.") (license license:gpl2+))) (define-public r-pnwcolors (package (name "r-pnwcolors") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "PNWColors" version)) (sha256 (base32 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj")))) (properties `((upstream-name . "PNWColors"))) (build-system r-build-system) (home-page "https://github.com/jakelawlor/PNWColors") (synopsis "Color palettes for data visualizations") (description "This package provides color palettes. They are checked for colorblind accessibility from hue, saturation, and lightness value scaling using the Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.") (license license:cc0))) (define-public r-plotfunctions (package (name "r-plotfunctions") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "plotfunctions" version)) (sha256 (base32 "0asmxw8283fpvl83h478j5nyg59xqifqaa8f2f6l199gvvswhhg2")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-polychrome (package (name "r-polychrome") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "Polychrome" version)) (sha256 (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg")))) (properties `((upstream-name . "Polychrome"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-scatterplot3d)) (native-inputs (list r-knitr)) (home-page "http://oompa.r-forge.r-project.org/") (synopsis "Qualitative palettes with many colors") (description "This package provides tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors. See Coombes and colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.") (license license:asl2.0))) (define-public r-ecp (package (name "r-ecp") (version "3.1.3") (source (origin (method url-fetch) (uri (cran-uri "ecp" version)) (sha256 (base32 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/ecp/") (synopsis "Multiple change-point analysis of multivariate data") (description "This package implements various procedures for finding multiple change-points. Two methods make use of dynamic programming and pruning, with no distributional assumptions other than the existence of certain absolute moments in one method. Hierarchical and exact search methods are included. All methods return the set of estimated change-points as well as other summary information.") 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Most R users don't need to use this package directly, but other R packages (e.g. shiny, rmarkdown, etc.) depend on this package to avoid bundling redundant copies of jQuery.") (license license:expat))) (define-public r-sass (package (name "r-sass") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "sass" version)) (sha256 (base32 "1fq8wqnxmx10lg0dh4qzmxdkhd22fjh8vhassapxb1chsimwn3w5")))) (properties `((upstream-name . "sass"))) (build-system r-build-system) (propagated-inputs (list r-fs r-htmltools r-r6 r-rappdirs r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/sass") (synopsis "Syntactically Awesome Style Sheets (SASS)") (description "This package provides an SCSS compiler, powered by the libsass library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the Sass CSS extension language, which is stable, powerful, and CSS compatible.") (license license:expat))) (define-public r-saver (package (name "r-saver") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "SAVER" version)) (sha256 (base32 "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158")))) (properties `((upstream-name . "SAVER"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-glmnet r-iterators r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/mohuangx/SAVER") (synopsis "Recovery of gene expression profile in noisy and sparse scRNA-seq data") (description "This package is an implementation of a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. In @dfn{single-cell RNA sequencing} (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. This package @dfn{single-cell analysis via expression recovery} (SAVER) implements an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.") (license license:gpl2))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-bslib (package (name "r-bslib") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z")) (snippet '(for-each delete-file '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js" "inst/lib/bs3/assets/javascripts/bootstrap.min.js" "inst/lib/bs4/dist/js/bootstrap.bundle.min.js" "inst/lib/bs5/dist/js/bootstrap.bundle.min.js"))))) (properties `((upstream-name . "bslib"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/lib/" (call-with-values (lambda () (unzip2 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js" "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js") ("bs-colorpicker/js/bootstrap-colorpicker.js" "bs-colorpicker/js/bootstrap-colorpicker.min.js") ("bs3/assets/javascripts/bootstrap.js" "bs3/assets/javascripts/bootstrap.min.js") (,(assoc-ref inputs "js-bootstrap4-bundle") "bs4/dist/js/bootstrap.bundle.min.js") (,(assoc-ref inputs "js-bootstrap5-bundle") "bs5/dist/js/bootstrap.bundle.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass)) (native-inputs `(("esbuild" ,esbuild) ("js-bootstrap4-bundle" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js") (sha256 (base32 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1")))) ("js-bootstrap5-bundle" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.0.2/dist/js/bootstrap.bundle.js") (sha256 (base32 "06vin94nqw1vzs4zrqcms8z9js9fckbj8gwyx07awm8jkjhnqfhl")))))) (home-page "https://rstudio.github.io/bslib/") (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") (description "This package simplifies custom CSS styling of both shiny and rmarkdown via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their various Bootswatch themes. An interactive widget is also provided for previewing themes in real time.") (license license:expat))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-shiny (package (name "r-shiny") (version "1.7.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/rstudio/shiny") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7")) (snippet '(for-each delete-file '("inst/www/shared/bootstrap/js/bootstrap.min.js" "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO "inst/www/shared/datatables/js/jquery.dataTables.min.js" "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js" "inst/www/shared/highlight/highlight.pack.js" "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js" "inst/www/shared/jquery.min.js" "inst/www/shared/jqueryui/jquery-ui.min.js" "inst/www/shared/legacy/jquery.min.js" "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js" "inst/www/shared/selectize/js/selectize.min.js" "inst/www/shared/shiny.min.js" "inst/www/shared/showdown/compressed/showdown.js" "inst/www/shared/strftime/strftime-min.js"))))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules (,@%r-build-system-modules (guix build minify-build-system)) #:phases (modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda* (#:key inputs #:allow-other-keys) (let ((replace-file (lambda (old new) (format #t "replacing ~a with ~a\n" old new) (symlink new old)))) ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ ;; contain just data. They are not minified code, so we don't ;; replace them. (with-directory-excursion "inst/www/shared" (replace-file "strftime/strftime-min.js" (search-input-file inputs "/share/javascript/strftime.min.js")) (replace-file "highlight/highlight.pack.js" (search-input-file inputs "/share/javascript/highlight.min.js")) (replace-file "datatables/js/jquery.dataTables.min.js" (search-input-file inputs "/share/javascript/jquery.dataTables.min.js")) (replace-file "selectize/js/selectize.min.js" (search-input-file inputs "/share/javascript/selectize.min.js")) (for-each (match-lambda ((source . target) (minify source #:target target))) `(("jqueryui/jquery-ui.js" . "jqueryui/jquery-ui.min.js") ("datepicker/js/bootstrap-datepicker.js" . "datepicker/js/bootstrap-datepicker.min.js") ("ionrangeslider/js/ion.rangeSlider.js" . "ionrangeslider/js/ion.rangeSlider.min.js") ("bootstrap/js/bootstrap.js" . "bootstrap/js/bootstrap.min.js") (,(assoc-ref inputs "js-bootstrap-accessibility") . "bootstrap/accessibility/js/bootstrap-accessibility.min.js") ("shiny.js" . "shiny.min.js") ("jquery.js" . "jquery.min.js") ("legacy/jquery.js" . "legacy/jquery.min.js") ("selectize/accessibility/js/selectize-plugin-a11y.js" . "selectize/accessibility/js/selectize-plugin-a11y.min.js") ("showdown/src/showdown.js" . "showdown/compressed/showdown.js")))))))))) (propagated-inputs (list r-bslib r-cachem r-commonmark r-crayon r-ellipsis r-fastmap r-fontawesome r-glue r-htmltools r-httpuv r-jsonlite r-later r-lifecycle r-mime r-promises r-r6 r-rlang r-sourcetools r-withr r-xtable)) (inputs (list js-datatables js-selectize js-strftime js-highlight)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("gfortran" ,gfortran) ("js-bootstrap-accessibility" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\ v1.0.7/_site/plugins/js/bootstrap-accessibility.js") (sha256 (base32 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8")))))) (home-page "https://shiny.rstudio.com") (synopsis "Easy interactive web applications with R") (description "Makes it incredibly easy to build interactive web applications with R. Automatic \"reactive\" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.") (license license:artistic2.0))) (define-public r-shinyhelper (package (name "r-shinyhelper") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "shinyhelper" version)) (sha256 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp")))) (properties `((upstream-name . "shinyhelper"))) (build-system r-build-system) (propagated-inputs (list r-markdown r-shiny)) (home-page "https://cran.r-project.org/package=shinyhelper") (synopsis "Easily add Markdown help files to shiny app elements") (description "This package creates a lightweight way to add markdown helpfiles to Shiny apps, using modal dialog boxes, with no need to observe each help button separately.") (license license:gpl3))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-shinytree (package (name "r-shinytree") (version "0.2.7") (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 (search-input-file inputs "/share/javascript/require.min.js") "libs/require.js") (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-jquery") "libs/jquery.js") ("jstree.js" "jstree.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr)) (inputs (list js-requirejs)) (native-inputs `(("uglifyjs" ,node-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 "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'generate-minified-javascript (lambda _ (with-directory-excursion "inst/AdminLTE" (let ((target "app.min.js") (source "app.js")) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs (list r-htmltools r-promises r-shiny)) (native-inputs (list esbuild)) (home-page "https://rstudio.github.io/shinydashboard/") (synopsis "Create dashboards with shiny") (description "This package provides an extension to the Shiny web application framework for R, making it easy to create attractive dashboards.") ;; This package includes software that was released under the Expat ;; license, but the whole package is released under GPL version 2 or ;; later. (license license:gpl2+))) (define-public r-shinyfiles (package (name "r-shinyfiles") (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 (base32 "1l4a4v9ivxkj2vx6xw4z3pk7a8px23icppcgvgpybibq2j74pglg")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs (list r-fs r-htmltools r-jsonlite r-shiny r-tibble)) (home-page "https://github.com/thomasp85/shinyFiles") (synopsis "Server-side file system viewer for Shiny") (description "This package provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to \"download\" files to a temporary location. Both file and folder selection as well as file saving is available.") (license license:gpl2+))) (define-public r-shinythemes (package (name "r-shinythemes") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "shinythemes" version)) (sha256 (base32 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip")))) (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) (propagated-inputs (list r-shiny)) (home-page "https://rstudio.github.io/shinythemes/") (synopsis "Themes for Shiny") (description "This package provides themes for use with Shiny. It includes several Bootstrap themes, which are packaged for use with Shiny applications.") ;; The package is released under version 3 of the GPL, but it includes ;; source files that are covered by the Expat license. It also includes ;; fonts under SIL or the ASL. (license (list license:gpl3 license:expat license:silofl1.1 license:asl2.0)))) ;; The package sources include minified variants of d3.js and non-minified ;; source code of d3-jetpack. (define-public r-d3r (package (name "r-d3r") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva")))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/d3/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "d3.v3.js") "v3/dist/d3.min.js") (,(assoc-ref inputs "d3.v4.js") "v4/dist/d3.min.js") (,(assoc-ref inputs "d3.v5.js") "v5/dist/d3.min.js") (,(assoc-ref inputs "d3.v6.js") "v6/dist/d3.min.js") (,(assoc-ref inputs "d3.v7.js") "v7/dist/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-dplyr r-htmltools r-rlang r-tidyr)) (native-inputs `(("esbuild" ,esbuild) ("d3.v3.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v3.js") (sha256 (base32 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))) ("d3.v5.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v5.js") (sha256 (base32 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))) ("d3.v6.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v6.js") (sha256 (base32 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9")))) ("d3.v7.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v7.js") (sha256 (base32 "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description "This package provides a suite of functions to help ease the use of the d3.js visualization library in R. These helpers include @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame} R objects into the JSON format that the d3.js library expects.") (license license:bsd-3))) ;; We use the latest commit here because the last release was in 2016 while ;; the latest commit was in 2018. (define-public r-sankeyd3 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc") (revision "1")) (package (name "r-sankeyd3") (version (git-version "0.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/fbreitwieser/sankeyD3") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) (build-system r-build-system) (propagated-inputs (list r-d3r r-htmlwidgets r-shiny r-magrittr)) (home-page "https://github.com/fbreitwieser/sankeyD3") (synopsis "Sankey network graphs from R") (description "This package provides an R library to generate Sankey network graphs in R and Shiny via the D3 visualization library.") ;; The R code is licensed under GPLv3+. It includes the non-minified ;; JavaScript source code of d3-sankey, which is released under the ;; 3-clause BSD license. (license (list license:gpl3+ license:bsd-3))))) (define-public r-wesanderson (package (name "r-wesanderson") (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "wesanderson" version)) (sha256 (base32 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2")))) (properties `((upstream-name . "wesanderson"))) (build-system r-build-system) (home-page "https://github.com/karthik/wesanderson") (synopsis "Wes Anderson color palette generator") (description "This package provides color palettes that have been generated mostly from Wes Anderson movies.") (license license:expat))) (define-public r-gg-gap (package (name "r-gg-gap") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "gg.gap" version)) (sha256 (base32 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h")))) (properties `((upstream-name . "gg.gap"))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-ggplot2)) (home-page "https://github.com/ChrisLou-bioinfo/gg.gap") (synopsis "Define segments on the y-axis for ggplot2") (description "The @code{gg.gap} function enables you to define segments for the y-axis in a ggplot2 plot.") (license license:gpl3))) (define-public r-mbess (package (name "r-mbess") (version "4.9.0") (source (origin (method url-fetch) (uri (cran-uri "MBESS" version)) (sha256 (base32 "0qmyvjx2zn5hlzdbz8c94g8l4707swhn7sq9mxkdqiydmflzv0b5")))) (properties `((upstream-name . "MBESS"))) (build-system r-build-system) (propagated-inputs (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools)) (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html") (synopsis "Methods for designing research studies") (description "This package implements methods that are useful in designing research studies and analyzing data, with particular emphasis on methods that are developed for or used within the behavioral, educational, and social sciences (broadly defined). That being said, many of the methods implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a suite of functions for a variety of related topics, such as effect sizes, confidence intervals for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size planning (from the @dfn{accuracy in parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk point estimation perspectives), mediation analysis, various properties of distributions, and a variety of utility functions.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-homologene (package (name "r-homologene") (version "1.4.68.19.3.27") (source (origin (method url-fetch) (uri (cran-uri "homologene" version)) (sha256 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh")))) (properties `((upstream-name . 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(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 "1.4.5.3") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs (list r-png r-sp)) (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. 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"RcppThread"))) (build-system r-build-system) (home-page "https://github.com/tnagler/RcppThread") (synopsis "R threading in C++") (description "This package provides a C++11-style thread class and thread pool that can safely be interrupted from R.") (license license:expat))) (define-public r-rcppnumerical (package (name "r-rcppnumerical") (version "0.4-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen)) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis"Numerical computing libraries integration with @code{Rcpp}") (description "This package provides a collection of libraries for numerical computing (numerical integration, optimization, etc.) and their integration with @code{Rcpp}.") (license license:gpl2+))) (define-public r-rcppxptrutils (package (name "r-rcppxptrutils") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "RcppXPtrUtils" version)) (sha256 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l")))) (properties `((upstream-name . "RcppXPtrUtils"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/Enchufa2/RcppXPtrUtils") (synopsis "XPtr add-ons for Rcpp") (description "This package provides the means to compile user-supplied C++ functions with Rcpp and retrieve an @code{XPtr} that can be passed to other C++ components.") (license license:expat))) (define-public r-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 (list r-bindr r-plogr r-rcpp)) (home-page "https://github.com/krlmlr/bindrcpp") (synopsis "Rcpp interface to active bindings") (description "This package provides an easy way to fill an environment with active bindings that call a C++ function.") (license license:expat))) (define-public r-auc (package (name "r-auc") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "AUC" version)) (sha256 (base32 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3")))) (properties `((upstream-name . "AUC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AUC") (synopsis "Compute the area under the curve of selected measures") (description "This package includes functions to compute the area under the curve of selected measures: the area under the sensitivity curve (AUSEC), the area under the specificity curve (AUSPC), the area under the accuracy curve (AUACC), and the area under the receiver operating characteristic curve (AUROC). The curves can also be visualized. Support for partial areas is provided.") (license license:gpl2+))) (define-public r-calibrate (package (name "r-calibrate") (version "1.7.7") (source (origin (method url-fetch) (uri (cran-uri "calibrate" version)) (sha256 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/calibrate") (synopsis "Calibration of scatterplot and biplot axes") (description "This is a package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots.") (license license:gpl2))) (define-public r-shape (package (name "r-shape") (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/shape") (synopsis "Functions for plotting graphical shapes") (description "This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...") (license license:gpl3+))) (define-public r-globaloptions (package (name "r-globaloptions") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "GlobalOptions" version)) (sha256 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7")))) (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/GlobalOptions") (synopsis "Generate functions to get or set global options") (description "This package provides more controls on the option values such as validation and filtering on the values, making options invisible or private.") (license license:gpl2+))) (define-public r-circlize (package (name "r-circlize") (version "0.4.15") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn")))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-globaloptions r-shape)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/circlize") (synopsis "Circular visualization") (description "Circular layout is an efficient way to visualise huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. Its flexibility is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.") (license license:gpl2+))) (define-public r-powerlaw (package (name "r-powerlaw") (version "0.70.6") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs (list r-pracma)) (native-inputs (list r-knitr)) (home-page "https://github.com/csgillespie/poweRlaw") (synopsis "Tools for the analysis of heavy tailed distributions") (description "This package provides an implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.") ;; Any of these GPL versions. (license (list license:gpl2 license:gpl3)))) (define-public r-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 "1.15.2") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-magrittr r-viridis)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/dendextend") (synopsis "Extending 'dendrogram' functionality in R") (description "This package offers a set of functions for extending @code{dendrogram} objects in R, letting you visualize and compare trees of hierarchical clusterings. You can adjust a tree's graphical parameters (the color, size, type, etc of its branches, nodes and labels) and visually and statistically compare different dendrograms to one another.") ;; Any of these versions (license (list license:gpl2 license:gpl3)))) (define-public r-getoptlong (package (name "r-getoptlong") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs (list perl)) (propagated-inputs (list r-crayon r-globaloptions r-rjson)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/GetoptLong") (synopsis "Parsing command-line arguments and variable interpolation") (description "This is yet another command-line argument parser which wraps the powerful Perl module @code{Getopt::Long} and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.") (license license:gpl2+))) (define-public r-fastmatch (package (name "r-fastmatch") (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "fastmatch" version)) (sha256 (base32 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx")))) (build-system r-build-system) (home-page "https://www.rforge.net/fastmatch") (synopsis "Fast match function") (description "This package provides a fast @code{match} replacement for cases that require repeated look-ups. It is slightly faster that R's built-in @code{match} function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.") (license license:gpl2))) (define-public r-ff (package (name "r-ff") (version "4.0.7") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa")))) (build-system r-build-system) (propagated-inputs (list 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 "0.13.3") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk")))) (build-system r-build-system) (propagated-inputs (list r-bit r-fastmatch r-ff)) (home-page "https://github.com/edwindj/ffbase") (synopsis "Basic statistical functions for package 'ff'") (description "This package extends the out of memory vectors of @code{ff} with statistical functions and other utilities to ease their usage.") (license license:gpl3))) (define-public r-prettyunits (package (name "r-prettyunits") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "prettyunits" version)) (sha256 (base32 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/prettyunits") (synopsis "Pretty, human readable formatting of quantities") (description "This package provides tools for pretty, human readable formatting of quantities.") 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(license license:gpl2))) (define-public r-reshape (package (name "r-reshape") (version "0.8.9") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br")))) (build-system r-build-system) (propagated-inputs (list r-plyr)) (home-page "http://had.co.nz/reshape") (synopsis "Flexibly reshape data") (description "Flexibly restructure and aggregate data using just two functions: @code{melt} and @code{cast}. This package provides them.") (license license:expat))) (define-public r-restrserve (package (name "r-restrserve") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "RestRserve" version)) (sha256 (base32 "1ydsdgy6mxl0zqk7xqf4v6if5nf2qv7k48q340fhaqyjk2gd60p7")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-digest r-jsonlite r-mime r-r6 r-rcpp r-rserve r-uuid)) (native-inputs (list r-knitr)) (home-page "https://restrserve.org") (synopsis "R web API framework") (description "RestRserve is an R web API framework for building high-performance AND robust microservices and app backends. With Rserve backend on UNIX-like systems it is parallel by design. It will handle incoming requests in parallel - each request in a separate fork.") 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(license license:gpl2+))) (define-public r-proxy (package (name "r-proxy") (version "0.4-26") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 "0k8sr24mjfvxp12sf1j9228ah3ngy15nqmm0jw14x5s32f1assv7")))) (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 "1.4-7") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 "1bdi06n5zkjnnyh0rallf04s0vlcx9rg9p5q7s6vfqvkf19nk501")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/sp") (synopsis "Classes and methods for spatial data") (description "This package provides classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. 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(license license:gpl2))) (define-public r-distillery (package (name "r-distillery") (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b")))) (build-system r-build-system) (home-page "https://ral.ucar.edu/staff/ericg/") (synopsis "Functions for confidence intervals and object information") (description "This package provides some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with the packages extRemes and SpatialVx.") (license license:gpl2+))) (define-public r-etrunct (package (name "r-etrunct") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "etrunct" version)) (sha256 (base32 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr")))) (properties `((upstream-name . 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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 "0.3.19") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") (description "This package provides functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and @code{.Call} calling conventions.") ;; Any version of the LGPL. (license license:lgpl3+))) (define-public r-inum (package (name "r-inum") (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "inum" version)) (sha256 (base32 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz")))) (build-system r-build-system) (propagated-inputs (list r-libcoin)) (home-page "https://cran.r-project.org/web/packages/inum/") (synopsis "Interval and enum-type representation of vectors") (description "This package provides an enum-type representation of vectors and representation of intervals, including a method of coercing variables in data frames.") (license license:gpl2))) (define-public r-invgamma (package (name "r-invgamma") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "invgamma" version)) (sha256 (base32 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a")))) (properties `((upstream-name . "invgamma"))) (build-system r-build-system) (home-page "https://github.com/dkahle/invgamma") (synopsis "Inverse gamma distribution") (description "This package provides a light weight implementation of the standard distribution functions for the inverse gamma distribution, wrapping those for the gamma distribution in the @code{stats} package.") (license license:gpl2))) (define-public r-bdsmatrix (package (name "r-bdsmatrix") (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "bdsmatrix" version)) (sha256 (base32 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5")))) (properties `((upstream-name . "bdsmatrix"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bdsmatrix/") (synopsis "Routines for block diagonal symmetric matrices") (description "This package provides procedures to work with block diagonal symmetric matrices, a special case of sparse matrices.") (license license:lgpl2.0))) (define-public r-bbmle (package (name "r-bbmle") (version "1.0.25") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46")))) (build-system r-build-system) (propagated-inputs (list r-bdsmatrix r-lattice r-mass r-matrix r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description "This package provides methods and functions for fitting maximum likelihood models in R. This package modifies and extends the @code{mle} classes in the @code{stats4} package.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-emdbook (package (name "r-emdbook") (version "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6")))) (build-system r-build-system) (propagated-inputs (list r-bbmle r-coda r-lattice r-mass r-plyr)) (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 "5.6.15") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6")))) (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 "1.5.6") (source (origin (method url-fetch) (uri (cran-uri "limSolve" version)) (sha256 (base32 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr")))) (properties `((upstream-name . "limSolve"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-mass r-quadprog)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/limSolve") (synopsis "Solving linear inverse models") (description "This package provides functions that: @enumerate @item find the minimum/maximum of a linear or quadratic function, @item sample an underdetermined or overdetermined system, @item solve a linear system Ax=B for the unknown x. @end enumerate It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.") ;; Any GPL version. (license (list license:gpl2+ license:gpl3+)))) (define-public r-fitdistrplus (package (name "r-fitdistrplus") (version "1.1-8") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 "0nhgjvwya95v6b9khbsgp44lw10xg35w61lmka1v6wq7yh827izk")))) (build-system r-build-system) (propagated-inputs (list r-mass r-survival)) (native-inputs (list r-knitr)) (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 "1.7-10") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal")))) (build-system r-build-system) (propagated-inputs (list r-boot r-gsl r-rcpp)) (home-page "https://cran.r-project.org/web/packages/energy") (synopsis "Multivariate inference via the energy of data") (description "This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.") (license license:gpl2+))) (define-public r-suppdists (package (name "r-suppdists") (version "1.1-9.7") (source (origin (method url-fetch) (uri (cran-uri "SuppDists" version)) (sha256 (base32 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb")))) (properties `((upstream-name . "SuppDists"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/SuppDists") (synopsis "Supplementary distributions") (description "This package provides ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. In addition two random number generators of George Marsaglia are included.") (license license:gpl2+))) (define-public r-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 (list r-suppdists)) (home-page "https://cran.r-project.org/web/packages/kSamples") (synopsis "K-Sample rank tests and their combinations") (description "This package provides tools to compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples.") (license license:gpl2+))) (define-public r-cvst (package (name "r-cvst") (version "0.2-3") (source (origin (method url-fetch) (uri (cran-uri "CVST" version)) (sha256 (base32 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg")))) (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs (list r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/CVST") (synopsis "Fast cross-validation via sequential testing") (description "This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.") (license license:gpl2+))) (define-public r-squarem (package (name "r-squarem") (version "2021.1") (source (origin (method url-fetch) (uri (cran-uri "SQUAREM" version)) (sha256 (base32 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6")))) (properties `((upstream-name . "SQUAREM"))) (build-system r-build-system) (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html") (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms") (description "This package provides algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette.") (license license:gpl2+))) (define-public r-progressr (package (name "r-progressr") (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 (base32 "1p5s35rzh28n2id2lipgyqmh3wzib66m7x0pz9028y8cql8xr5ac")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs (list r-digest)) (home-page "https://progressr.futureverse.org") (synopsis "Inclusive, unifying API for progress updates") (description "This package provides a minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates.") (license license:gpl3+))) (define-public r-lava (package (name "r-lava") (version "1.6.10") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s")))) (build-system r-build-system) (propagated-inputs (list r-future-apply r-numderiv r-progressr r-squarem r-survival)) (native-inputs (list r-knitr)) (home-page "https://github.com/kkholst/lava") (synopsis "Latent variable models") (description "This package provides tools for the estimation and simulation of latent variable models.") (license license:gpl3))) (define-public r-drr (package (name "r-drr") (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "DRR" version)) (sha256 (base32 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-prodlim (package (name "r-prodlim") (version "2019.11.13") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8")))) (build-system r-build-system) (propagated-inputs (list r-kernsmooth r-lava r-rcpp r-survival)) (home-page "https://cran.r-project.org/web/packages/prodlim") (synopsis "Product-limit estimation for censored event history analysis") (description "This package provides a fast and user-friendly implementation of nonparametric estimators for censored event history (survival) analysis with the Kaplan-Meier and Aalen-Johansen methods.") (license license:gpl2+))) (define-public r-dimred (package (name "r-dimred") (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 "1z8fqdc8mslvfix8ngxs1y2yrvlanp5581hwp2nzldj6mk5kn15b")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-magic (package (name "r-magic") (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "magic" version)) (sha256 (base32 "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5")))) (build-system r-build-system) (propagated-inputs (list r-abind)) (home-page "https://github.com/RobinHankin/magic.git") (synopsis "Create and investigate magic squares") (description "This package provides a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.") (license license:gpl2))) (define-public r-rmysql (package (name "r-rmysql") (version "0.10.23") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-geometry (package (name "r-geometry") (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 "1n7m0djqlhrv01l98r76grkki6cv4k4q2z6c7fksqgq4r2l6a14i")))) (build-system r-build-system) (propagated-inputs (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress)) (home-page "http://geometry.r-forge.r-project.org/") (synopsis "Mesh generator and surface tessellator") (description "This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this. Currently the package only gives access to Delaunay triangulation and convex hull computation.") ;; The Qhull sources are included and are distributed under a custom ;; non-copyleft license. The R sources are released under GPL version 2. 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It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.") (license license:gpl2))) (define-public r-gower (package (name "r-gower") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "gower" version)) (sha256 (base32 "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/gower") (synopsis "Gower's distance") (description "This package provides tools to compute Gower's distance (or similarity) coefficient between records, and to compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.") (license license:gpl3))) (define-public r-rcpproll (package (name "r-rcpproll") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppRoll" version)) (sha256 (base32 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) (properties `((upstream-name . "RcppRoll"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppRoll") (synopsis "Efficient rolling and windowed operations") (description "This package provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.") 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(license license:gpl2+))) (define-public r-psych (package (name "r-psych") (version "2.2.5") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mnormt r-nlme)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/psych/") (synopsis "Procedures for psychological, psychometric, and personality research") (description "This package provides a general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics.") (license license:gpl2+))) (define-public r-generics (package (name "r-generics") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "generics" version)) (sha256 (base32 "162q9hdsnfcwjj255ahbi6v9vnyynvda7gb75p721y28j5xb7sk3")))) (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 "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 "16grzja9hz5mqpfzbp1r6zif1gp7swfadkm52340si9h8ifhk8b6")))) (build-system r-build-system) (propagated-inputs (list r-backports r-dplyr r-ellipsis r-generics r-ggplot2 r-glue r-purrr r-rlang r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") (description "This package provides tools to convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like @code{dplyr}, @code{tidyr} and @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which summarizes a model's statistical findings such as coefficients of a regression; @code{augment}, which adds columns to the original data such as predictions, residuals and cluster assignments; and @code{glance}, which provides a one-row summary of model-level statistics.") (license license:expat))) (define-public r-recipes (package (name "r-recipes") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 "1950rvva19ms6xy9d3jx94gzy589qprk115zjjd0ib4qxgip601x")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ellipsis r-generics r-glue r-gower r-hardhat r-ipred r-lifecycle r-lubridate r-magrittr r-matrix r-purrr r-rlang r-tibble r-tidyr r-tidyselect r-timedate r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description "Recipes is an extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis \"steps\". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.") (license license:gpl2))) (define-public r-pdist (package (name "r-pdist") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "pdist" version)) (sha256 (base32 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406")))) (build-system r-build-system) (home-page "https://github.com/jeffwong/pdist") (synopsis "Partitioned distance function") (description "Pdist computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling @code{dist}, but this creates unnecessary computation by computing the distances between a row of X and another row of X, and likewise for Y. Pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.") (license license:gpl3+))) (define-public r-ggrepel (package (name "r-ggrepel") (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-rlang r-scales)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/slowkow/ggrepel") (synopsis "Repulsive text and label geometries for ggplot2") (description "This package provides text and label geometries for ggplot2 that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.") (license license:gpl3))) (define-public r-coro (package (name "r-coro") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "coro" version)) (sha256 (base32 "14irld29dipgfd34y0k351daqg9vqpnpdx8m3pxmqr1aiyj5f5cv")))) (properties `((upstream-name . "coro"))) (build-system r-build-system) (propagated-inputs (list r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/coro") (synopsis "Coroutines for R") (description "This package provides coroutines for R, a family of functions that can be suspended and resumed later on. This includes async functions (which await) and generators (which yield). Async functions are based on the concurrency framework of the @code{promises} package. Generators are based on a dependency free iteration protocol defined in @code{coro} and are compatible with iterators from the @code{reticulate} package.") (license license:expat))) (define-public r-corrplot (package (name "r-corrplot") (version "0.92") (source (origin (method url-fetch) (uri (cran-uri "corrplot" version)) (sha256 (base32 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/taiyun/corrplot") (synopsis "Visualization of a correlation matrix") (description "This package provides a graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including choosing color, text labels, color labels, layout, etc.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-stringdist (package (name "r-stringdist") (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") (description "This package implements an approximate string matching version of R's native @code{match} function. It can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.") (license license:gpl3+))) (define-public r-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 (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ucminf/") (synopsis "General-purpose unconstrained non-linear optimization") (description "This package provides an implementation of an algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of @code{ucminf} is designed for easy interchange with the package @code{optim}.") (license license:gpl2+))) (define-public r-usedist (package (name "r-usedist") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "usedist" version)) (sha256 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj")))) (properties `((upstream-name . "usedist"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=usedist") (synopsis "Distance matrix utilities") (description "This package provides functions to re-arrange, extract, and work with distances.") (license license:gpl3))) (define-public r-useful (package (name "r-useful") (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "useful" version)) (sha256 (base32 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1")))) (properties `((upstream-name . "useful"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-dplyr r-ggplot2 r-magrittr r-matrix r-plyr r-purrr r-scales)) (home-page "https://github.com/jaredlander/useful") (synopsis "Collection of handy, useful functions") (description "This package provides a set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing parts of a @code{data.frame}, constructing formulas from text and building design and response matrices.") (license license:bsd-3))) (define-public r-ordinal (package (name "r-ordinal") (version "2019.12-10") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix r-numderiv r-ucminf)) (home-page "https://github.com/runehaubo/ordinal") (synopsis "Regression models for ordinal data") (description "This package provides an implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered models. Estimation is via maximum likelihood and mixed models are fitted with the Laplace approximation and adaptive Gauss-Hermite quadrature.") (license license:gpl2+))) (define-public r-jomo (package (name "r-jomo") (version "2.7-3") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 "0qq03zspmh8x2c8w882ynsw7wshr9b0fyrpwnqx5yc1xlzrqffcx")))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-mass r-ordinal r-survival r-tibble)) (home-page "https://cran.r-project.org/web/packages/jomo/") (synopsis "Multilevel Joint Modelling Multiple Imputation") (description "Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation @url{Carpenter and Kenward (2013), http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.") (license license:gpl2))) (define-public r-pan (package (name "r-pan") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pan/") (synopsis "Multiple imputation for multivariate panel or clustered data") (description "This package implements multiple imputation for multivariate panel or clustered data.") (license license:gpl3))) (define-public r-mitml (package (name "r-mitml") (version "0.4-3") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9")))) (build-system r-build-system) (propagated-inputs (list r-haven r-jomo r-pan)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/mitml/") (synopsis "Tools for multiple imputation in multilevel modeling") (description "This package provides tools for multiple imputation of missing data in multilevel modeling. It includes a user-friendly interface to the packages pan and jomo, and several functions for visualization, data management and the analysis of multiply imputed data sets.") (license license:gpl2+))) (define-public r-mice (package (name "r-mice") (version "3.14.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cpp11 r-dplyr r-generics r-lattice r-rcpp r-rlang r-tidyr r-withr)) (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 (list r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/Rsolnp/") (synopsis "General non-linear optimization") (description "The Rsolnp package implements a general non-linear augmented Lagrange multiplier method solver, a @dfn{sequential quadratic programming} (SQP) based solver).") ;; Any version of the GPL. (license license:gpl2+))) (define-public r-hardyweinberg (package (name "r-hardyweinberg") (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs (list r-mice r-nnet r-rcpp r-rsolnp)) (home-page "https://cran.r-project.org/package=HardyWeinberg") (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") (description "This package contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of diallelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.") (license license:gpl2+))) (define-public r-sm (package (name "r-sm") (version "2.2-5.7") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") (synopsis "Smoothing methods for nonparametric regression and density estimation") (description "This is software accompanying the book 'Applied Smoothing Techniques for Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford University Press. It provides smoothing methods for nonparametric regression and density estimation") (license license:gpl2+))) (define-public r-venndiagram (package (name "r-venndiagram") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "VennDiagram" version)) (sha256 (base32 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7")))) (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs (list r-futile-logger)) (home-page "https://cran.r-project.org/web/packages/VennDiagram/") (synopsis "Generate High-Resolution Venn and Euler Plots") (description "This package provides a set of functions to generate high-resolution Venn and Euler plots. It includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.") (license license:gpl2+))) (define-public r-vioplot (package (name "r-vioplot") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6")))) (build-system r-build-system) (propagated-inputs (list r-sm r-zoo)) (native-inputs (list r-knitr)) (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") (synopsis "Violin plot") (description "This package provides a violin plot, which is a combination of a box plot and a kernel density plot.") (license license:bsd-3))) (define-public r-rsofia (package (name "r-rsofia") (version "1.1") (source (origin (method url-fetch) ;; This package has been removed from CRAN, so we can ;; only fetch it from the archives. (uri (string-append "https://cran.r-project.org/src/" "contrib/Archive/RSofia/RSofia_" version ".tar.gz")) (sha256 (base32 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn")))) (properties `((upstream-name . "RSofia"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") (synopsis "Port of sofia-ml to R") (description "This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.") (license license:asl2.0))) (define-public r-xts (package (name "r-xts") (version "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://github.com/joshuaulrich/xts") (synopsis "Extensible time series") (description "This package provides for uniform handling of R's different time-based data classes by extending @code{zoo}, maximizing native format information preservation and allowing for user-level customization and extension, while simplifying cross-class interoperability.") (license license:gpl2+))) (define-public r-performanceanalytics (package (name "r-performanceanalytics") (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "PerformanceAnalytics" version)) (sha256 (base32 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq")))) (properties `((upstream-name . "PerformanceAnalytics"))) (build-system r-build-system) (propagated-inputs (list r-quadprog r-xts r-zoo)) (home-page "https://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.") ;; Either version may be picked. (license (list license:gpl2 license:gpl3)))) (define-public r-laeken (package (name "r-laeken") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mass)) (home-page "https://cran.r-project.org/web/packages/laeken/") (synopsis "Estimation of indicators on social exclusion and poverty") (description "This package provides tools for the estimation of indicators on social exclusion and poverty, as well as an implementation of Pareto tail modeling for empirical income distributions.") (license license:gpl2+))) (define-public r-vcd (package (name "r-vcd") (version "1.4-9") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55")))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-lmtest r-mass)) (home-page "https://cran.r-project.org/web/packages/vcd/") (synopsis "Visualizing categorical data") (description "This package provides visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was originally inspired by the book \"Visualizing Categorical Data\" by Michael Friendly and is now the main support package for a new book, \"Discrete Data Analysis with R\" by Michael Friendly and David Meyer (2015).") (license license:gpl2))) (define-public r-vcfr (package (name "r-vcfr") (version "1.12.0") (source (origin (method url-fetch) (uri (cran-uri "vcfR" version)) (sha256 (base32 "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx")))) (build-system r-build-system) (native-inputs (list r-knitr)) (inputs (list zlib)) (propagated-inputs (list r-ape r-dplyr r-magrittr r-memuse r-pinfsc50 r-rcpp r-stringr r-tibble r-vegan r-viridislite)) (home-page "https://github.com/knausb/vcfR") (synopsis "Manipulate and visualize VCF data") (description "This package facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R, a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file. It also may be converted into other popular R objects. This package provides a link between VCF data and familiar R software.") (license license:gpl3))) (define-public r-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 "1.22-3") (source (origin (method url-fetch) (uri (cran-uri "dtw" version)) (sha256 (base32 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z")))) (build-system r-build-system) (propagated-inputs (list 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 "1.1-221.2") (source (origin (method url-fetch) (uri (cran-uri "SDMTools" version)) (sha256 (base32 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh")))) (properties `((upstream-name . "SDMTools"))) (build-system r-build-system) (propagated-inputs (list r-r-utils)) (home-page "https://www.rforge.net/SDMTools/") (synopsis "Species distribution modelling tools") (description "This package provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.") (license license:gpl3+))) (define-public r-scatterplot3d (package (name "r-scatterplot3d") (version "0.3-41") (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 "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr r-scales r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description "Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) (define-public r-ggjoy (package (name "r-ggjoy") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggjoy" version)) (sha256 (base32 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggridges)) (home-page "https://github.com/clauswilke/ggjoy") (synopsis "Joyplots in ggplot2") (description "Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) (define-public r-cli (package (name "r-cli") (version "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 "0qqd4mscv8ndjbji7knprdlv2hhyk35gazagvapbjzq1p6yfpaf3")))) (build-system r-build-system) (propagated-inputs (list r-glue)) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") (description "This package provides a suite of tools designed to build attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (license license:expat))) (define-public r-argparser (package (name "r-argparser") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") (description "This package provides a cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script.") (license license:gpl3+))) (define-public r-debugme (package (name "r-debugme") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "debugme" version)) (sha256 (base32 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) (build-system r-build-system) (propagated-inputs (list r-crayon)) (home-page "https://github.com/r-lib/debugme#readme") (synopsis "Debug R packages") (description "This package allows the user to specify debug messages as special string constants, and control debugging of packages via environment variables.") (license license:expat))) (define-public r-processx (package (name "r-processx") (version "3.5.3") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 "0ail3w8n5g1ibdamgpxcfpla18kqkilmppiasm7ms67cavx2k5k7")))) (build-system r-build-system) (propagated-inputs (list r-ps r-r6)) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description "This package provides portable tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes and their children; restart processes. It can read the standard output and error of the processes, using non-blocking connections. @code{processx} can poll a process for standard output or error, with a timeout. It can also poll several processes at once.") (license license:expat))) (define-public r-tsp (package (name "r-tsp") (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 "022k0972kcxb0w6qhx09l9cif8fmpkpvwddvgxiy60bx343ywzia")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) (home-page "https://cran.r-project.org/web/packages/TSP/") (synopsis "Traveling salesperson problem (TSP)") (description "This package provides basic infrastructure and some algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the traveling salesman problem).") (license license:gpl3))) (define-public r-qap (package (name "r-qap") (version "0.1-1") (source (origin (method url-fetch) (uri (cran-uri "qap" version)) (sha256 (base32 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic assignment problem} (QAP). Currently only a simulated annealing heuristic is available.") (license license:gpl3))) (define-public r-gclus (package (name "r-gclus") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "gclus" version)) (sha256 (base32 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/gclus/") (synopsis "Clustering graphics") (description "This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices of merit, ordering functions, and enhanced versions of @code{pairs} and @code{parcoord} which color panels according to their merit level.") (license license:gpl2+))) (define-public r-webshot (package (name "r-webshot") (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p")))) (build-system r-build-system) (propagated-inputs (list r-callr r-jsonlite r-magrittr)) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description "Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and screenshot static as well as interactive R Markdown documents.") (license license:gpl2))) (define-public r-seriation (package (name "r-seriation") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 "0dlj0mqpg585m6i7yn0h878i8ag6pyqph98xkk42i2nvghpy01gr")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-colorspace r-gclus r-mass r-qap r-registry r-tsp)) (native-inputs (list gfortran)) (home-page "https://s2.smu.edu/IDA/seriation/") (synopsis "Infrastructure for ordering objects using seriation") (description "This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).") (license license:gpl3))) (define-public r-xfun (package (name "r-xfun") (version "0.31") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 "0dgjkrlwl6rxmvdn6s1xrbiaa53hkfx2s7rqrbrc7c6shbkg6sfi")))) (build-system r-build-system) ;; knitr itself depends on xfun #; (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") (description "This package provides miscellaneous functions commonly used in other packages maintained by Yihui Xie.") (license license:expat))) (define-public r-utf8 (package (name "r-utf8") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7")))) (build-system r-build-system) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description "This package provides tools to process and print UTF-8 encoded international text (Unicode). Input, validate, normalize, encode, format, and display.") (license license:asl2.0))) (define-public r-zeallot (package (name "r-zeallot") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "zeallot" version)) (sha256 (base32 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3")))) (build-system r-build-system) (home-page "https://github.com/nteetor/zeallot") (synopsis "Multiple, unpacking, and destructuring assignment") (description "This package provides a @code{%<-%} operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.") (license license:expat))) (define-public r-zlog (package (name "r-zlog") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "zlog" version)) (sha256 (base32 "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci")))) (properties `((upstream-name . "zlog"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zlog") (synopsis "Transformation for laboratory easurements") (description "The @code{zlog} package offers functions to transform laboratory measurements into standardised z or @math{z(log)-values}. Therefore the lower and upper reference limits are needed. If these are not known they could be estimated from a given sample.") (license license:gpl3+))) (define-public r-vctrs (package (name "r-vctrs") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/vctrs") (synopsis "Vector helpers") (description "There are three main goals to the @code{vctrs} package: @enumerate @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to @code{length()} and @code{class()}. These definitions are paired with a framework for type-coercion and size-recycling. @item To define type- and size-stability as desirable function properties, use them to analyse existing base function, and to propose better alternatives. This work has been particularly motivated by thinking about the ideal properties of @code{c()}, @code{ifelse()}, and @code{rbind()}. @item To provide a new @code{vctr} base class that makes it easy to create new S3 vectors. @code{vctrs} provides methods for many base generics in terms of a few new @code{vctrs} generics, making implementation considerably simpler and more robust. @end enumerate\n") (license license:gpl3))) (define-public r-pillar (package (name "r-pillar") (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 "1fqk18vc9ashf12gdqkdi6n1nj5lh324vwhgiib3b2fcb2bghhbq")))) (build-system r-build-system) (propagated-inputs (list r-cli r-crayon r-ellipsis r-fansi r-glue r-lifecycle r-rlang r-utf8 r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description "This package provides a @code{pillar} generic designed for formatting columns of data using the full range of colours provided by modern terminals.") (license license:gpl3))) (define-public r-pinfsc50 (package (name "r-pinfsc50") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "pinfsc50" version)) (sha256 (base32 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pinfsc50/") (synopsis "Genomic data for the plant pathogen Phytophthora infestans") (description "This package contains genomic data for the plant pathogen Phytophthora infestans. It includes a variant file, a sequence file and an annotation file. This package is intended to be used as example data for packages that work with genomic data.") (license license:gpl2+))) (define-public r-uuid (package (name "r-uuid") (version "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7")))) (build-system r-build-system) (home-page "https://www.rforge.net/uuid") (synopsis "Tools for generating and handling of UUIDs") (description "This package provides tools for generating and handling of @dfn{Universally Unique Identifiers} (UUIDs).") (license license:expat))) (define-public r-tinytex (package (name "r-tinytex") (version "0.39") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 "1v95pjxdq0ma90jji5yqh8ihlcf35cmrqx9v0z649zh0q9vrnbpj")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description "This package provides helper functions to install and maintain the LaTeX distribution named TinyTeX, a lightweight, cross-platform, portable, and easy-to-maintain version of TeX Live. This package also contains helper functions to compile LaTeX documents, and install missing LaTeX packages automatically.") (license license:expat))) (define-public r-tinytest (package (name "r-tinytest") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "tinytest" version)) (sha256 (base32 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s")))) (properties `((upstream-name . "tinytest"))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/tinytest") (synopsis "Lightweight unit testing framework") (description "This package provides a lightweight unit testing framework. Main features: @enumerate @item install tests with the package; @item test results are treated as data that can be stored and manipulated; @item test files are R scripts interspersed with test commands, that can be programmed over; @item fully automated build-install-test sequence for packages; @item skip tests when not run locally (e.g. on CRAN); @item flexible and configurable output printing; @item compare computed output with output stored with the package; @item run tests in parallel; @item extensible by other packages; @item report side effects. @end enumerate ") (license license:gpl3))) (define-public r-network (package (name "r-network") (version "1.17.2") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m")))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-statnet-common r-tibble)) (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description "This package provides tools to create and modify network objects. The @code{network} class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) (define-public r-stabs (package (name "r-stabs") (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "stabs" version)) (sha256 (base32 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/hofnerb/stabs") (synopsis "Stability selection with error control") (description "This package provides resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting. Both, standard stability selection (Meinshausen & Buhlmann, 2010) and complementary pairs stability selection with improved error bounds (Shah & Samworth, 2013) are implemented. The package can be combined with arbitrary user specified variable selection approaches.") (license license:gpl2))) (define-public r-rle (package (name "r-rle") (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "rle" version)) (sha256 (base32 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40")))) (properties `((upstream-name . "rle"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rle/") (synopsis "Common functions for run-length encoded vectors") (description "This package provides common @code{base} and @code{stats} methods for @code{rle} objects, aiming to make it possible to treat them transparently as vectors.") (license license:gpl3))) (define-public r-statnet-common (package (name "r-statnet-common") (version "4.6.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 "07djgc6qbxahiy5v15lfayxbj4188lxsb8xcs7hnbm2hic953bfx")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) (propagated-inputs (list r-coda)) (home-page "https://statnet.org") (synopsis "R scripts and utilities used by the Statnet software") (description "This package provides non-statistical utilities used by the software developed by the Statnet Project.") (license license:gpl3))) (define-public r-statcheck (package (name "r-statcheck") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "statcheck" version)) (sha256 (base32 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/statcheck/") (synopsis "Extract statistics from articles and recompute p-values") (description "This package can automatically extract statistical null-hypothesis significant testing (NHST) results from articles and recompute the p-values based on the reported test statistic and degrees of freedom to detect possible inconsistencies.") (license license:gpl2))) (define-public r-sna (package (name "r-sna") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s")))) (build-system r-build-system) (propagated-inputs (list r-network r-statnet-common)) (home-page "https://statnet.org") (synopsis "Tools for social network analysis") (description "This package provides a range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.") (license license:gpl2+))) (define-public r-tfisher (package (name "r-tfisher") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "TFisher" version)) (sha256 (base32 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx")))) (properties `((upstream-name . "TFisher"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-mvtnorm r-sn)) (home-page "https://cran.r-project.org/web/packages/TFisher/") (synopsis "Optimal thresholding Fisher's p-value combination method") (description "This package provides the @dfn{cumulative distribution function} (CDF), quantile, and statistical power calculator for a collection of thresholding Fisher's p-value combination methods, including Fisher's p-value combination method, truncated product method and, in particular, soft-thresholding Fisher's p-value combination method which is proven to be optimal in some context of signal detection. The p-value calculator for the omnibus version of these tests are also included.") (license license:gpl2))) (define-public r-ttr (package (name "r-ttr") (version "0.24.3") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs (list r-curl r-xts r-zoo)) (home-page "https://github.com/joshuaulrich/TTR") (synopsis "Technical trading rules") (description "This package provides functions and data to construct technical trading rules with R.") (license license:gpl2))) (define-public r-leaflet-providers (package (name "r-leaflet-providers") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "leaflet.providers" version)) (sha256 (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy")))) (properties `((upstream-name . "leaflet.providers"))) (build-system r-build-system) (home-page "https://github.com/rstudio/leaflet.providers") (synopsis "Leaflet map tile providers") (description "This package contains third-party map tile provider information from Leaflet.js, to be used with the @code{leaflet} R package. Additionally, @code{leaflet.providers} enables users to retrieve up-to-date provider information between package updates.") (license license:bsd-2))) ;; This package contains a lot of minified JavaScript with unclear provenance. ;; When upgrading please make sure that all minified JavaScript files are ;; removed in a snippet and that the replacement sources correspond to the ;; original minified scripts. (define-public r-leaflet (package (name "r-leaflet") (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "leaflet" version)) (sha256 (base32 "0xsng9n08i1w7qj4hbi706m6d8jm9ixrnwq5xac2s3csfm1s1xij")) (snippet '(for-each delete-file (list "inst/htmlwidgets/lib/leaflet/leaflet.js" "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js" "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js" "inst/htmlwidgets/lib/jquery/jquery.min.js" "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js" "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js" "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js" "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js" "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js" "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js" "inst/legacy/www/leaflet.js"))))) (properties `((upstream-name . 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These maps can be used directly from the R console, from RStudio, in Shiny applications and R Markdown documents.") (license license:gpl3))) (define-public r-leaps (package (name "r-leaps") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "leaps" version)) (sha256 (base32 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/leaps/") (synopsis "Regression subset selection") (description "This package provides tools for regression subset selection, including exhaustive search.") (license license:gpl2+))) (define-public r-splus2r (package (name "r-splus2r") (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "splus2R" version)) (sha256 (base32 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x")))) (properties `((upstream-name . 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(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 "0.4.20") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp")))) (build-system r-build-system) (propagated-inputs (list r-curl r-ttr r-xts r-zoo)) (home-page "https://cran.r-project.org/web/packages/quantmod/") (synopsis "Quantitative financial modelling framework") (description "This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.") (license license:gpl3))) (define-public r-tseries (package (name "r-tseries") (version "0.10-51") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5")))) (build-system r-build-system) (propagated-inputs (list r-quadprog r-quantmod r-zoo)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tseries/") (synopsis "Time series analysis and computational finance") (description "This package provides functions relating to time series analysis and computational finance.") (license license:gpl2))) (define-public r-wmtsa (package (name "r-wmtsa") (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "wmtsa" version)) (sha256 (base32 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) (build-system r-build-system) (propagated-inputs (list r-ifultools r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/wmtsa/") (synopsis "Wavelet methods for time series analysis") (description "This package provides software to accompany the book \"Wavelet Methods for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge University Press, 2000.") (license license:gpl2))) (define-public r-tsa (package (name "r-tsa") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb")))) (properties `((upstream-name . 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"extraDistr"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/twolodzko/extraDistr") (synopsis "Additional univariate and multivariate distributions") (description "This package implements density, distribution functions, quantile functions and random generation functions for a large number of univariate and multivariate distributions.") (license license:gpl2))) (define-public r-fractal (package (name "r-fractal") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "fractal" version)) (sha256 (base32 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) (build-system r-build-system) (propagated-inputs (list r-ifultools r-mass r-sapa r-scatterplot3d r-splus2r r-wmtsa)) (home-page "https://cran.r-project.org/web/packages/fractal/") (synopsis "Fractal time series modeling and analysis") (description "This package provides tools for stochastic fractal and deterministic chaotic time series analysis.") (license license:gpl2))) (define-public r-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 (list r-nlme)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/urca/") (synopsis "Unit root and cointegration tests for time series data") (description "This package provides unit root and cointegration tests encountered in applied econometric analysis.") (license license:gpl2+))) (define-public r-cubature (package (name "r-cubature") (version "2.0.4.4") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 "0sfmcy5xpa40w3qn0jbg7b802wksl5k8glz9jpx77n159wn3nyq8")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/bnaras/cubature") (synopsis "Adaptive multivariate integration over hypercubes") (description "This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both @code{hcubature} and @code{pcubature} routines in addition to a vector interface.") ;; The included cubature C library is released under GPLv2+, but the ;; wrapper declares the license to be GPLv3+. (license (list license:gpl2+ license:gpl3+)))) (define-public r-trend (package (name "r-trend") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "trend" version)) (sha256 (base32 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs")))) (build-system r-build-system) (propagated-inputs (list r-extradistr)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/trend/") (synopsis "Non-parametric trend tests and change-point detection") (description "The analysis of environmental data often requires the detection of trends and change-points. This package includes tests for trend detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman correlation trend test), change-point detection (Lanzante's test procedures, Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two sample Robust Rank-Order Distributional Test.") (license license:gpl3))) (define-public r-expm (package (name "r-expm") (version "0.999-6") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran)) (home-page "https://r-forge.r-project.org/projects/expm/") (synopsis "Tools for matrix exponentials and related quantities") (description "This package provides tools for the computation of the matrix exponential, logarithm, square root, and related quantities.") (license license:gpl2+))) (define-public r-complexplus (package (name "r-complexplus") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "complexplus" version)) (sha256 (base32 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) (build-system r-build-system) (propagated-inputs (list r-expm r-matrix)) (home-page "https://cran.r-project.org/web/packages/complexplus/") (synopsis "Functions of complex or real variables") (description "This package extends several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.") (license license:gpl2))) (define-public r-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 . 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(license license:bsd-2))) (define-public r-np (package (name "r-np") (version "0.60-11") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3")))) (build-system r-build-system) (propagated-inputs (list r-boot r-cubature r-quadprog r-quantreg)) (home-page "https://github.com/JeffreyRacine/R-Package-np") (synopsis "Non-parametric kernel smoothing methods for mixed data types") (description "This package provides non-parametric (and semi-parametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-powerplus (package (name "r-powerplus") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "powerplus" version)) (sha256 (base32 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) (build-system r-build-system) (propagated-inputs (list r-complexplus r-expm r-mass r-matrix r-phontools)) (home-page "https://cran.r-project.org/web/packages/powerplus/") (synopsis "Exponentiation operations") (description "This package provides tools for the computation of matrix and scalar exponentiation.") (license license:gpl2))) (define-public r-egg (package (name "r-egg") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "egg" version)) (sha256 (base32 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-heatmap3 (package (name "r-heatmap3") (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "heatmap3" version)) (sha256 (base32 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r")))) (build-system r-build-system) (propagated-inputs (list r-fastcluster)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/heatmap3/") (synopsis "Improved heatmap package") (description "This package provides an improved heatmap package. It is completely compatible with the original R function @code{heatmap}, and provides more powerful and convenient features.") (license license:gpl2+))) (define-public r-heatmaply (package (name "r-heatmaply") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-colorspace r-dendextend r-egg r-ggplot2 r-htmlwidgets r-magrittr r-plotly r-rcolorbrewer r-reshape2 r-scales r-seriation r-viridis r-webshot)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=heatmaply") (synopsis "Interactive cluster heat maps using plotly") (description "This package enables you to create interactive cluster heatmaps that can be saved as a stand-alone HTML file, embedded in R Markdown documents or in a Shiny app, and made available in the RStudio viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A heatmap is a popular graphical method for visualizing high-dimensional data, in which a table of numbers is encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by dendrograms.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-h5 (package (name "r-h5") (version "0.9.9") (source (origin (method url-fetch) (uri (cran-uri "h5" version)) (sha256 (base32 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs (list zlib hdf5)) (native-inputs (list which)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/mannau/h5") (synopsis "Interface to the HDF5 Library") (description "This package provides an S4 interface to the HDF5 library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. 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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.") 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(license license:gpl2+))) (define-public r-factoextra (package (name "r-factoextra") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "factoextra" version)) (sha256 (base32 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2")))) (build-system r-build-system) (propagated-inputs (list r-abind r-cluster r-dendextend r-factominer r-ggplot2 r-ggpubr r-ggrepel r-reshape2 r-tidyr)) (home-page "http://www.sthda.com/english/rpkgs/factoextra") (synopsis "Extract and visualize the results of multivariate data analyses") (description "This package provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.") (license license:gpl2))) (define-public r-fansi (package (name "r-fansi") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 "0sn0kflgcn2qrrv646pzqylm02cx8l5ws473ppmvla4xihyvi9w6")))) (build-system r-build-system) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/brodieG/fansi") (synopsis "ANSI control sequence aware string functions") (description "This package provides counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.") (license license:gpl2+))) (define-public r-nbclust (package (name "r-nbclust") (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "NbClust" version)) (sha256 (base32 "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-officer (package (name "r-officer") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 "0qmn62srh9zicgizyblanirbdva7f09g967yb86kfrn05ckh5y10")))) (build-system r-build-system) (propagated-inputs (list r-r6 r-uuid r-xml2 r-zip)) (home-page "https://davidgohel.github.io/officer") (synopsis "Manipulation of Word and PowerPoint documents") (description "This package provides tools to access and manipulate Word and PowerPoint documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. When working with PowerPoint presentations, slides can be added or removed; shapes inside slides can also be added or removed. When working with Word documents, a cursor can be used to help insert or delete content at a specific location in the document.") (license license:gpl3))) (define-public r-profilemodel (package (name "r-profilemodel") (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "profileModel" version)) (sha256 (base32 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i")))) (properties `((upstream-name . "profileModel"))) (build-system r-build-system) (home-page "https://github.com/ikosmidis/profileModel") (synopsis "Profiling inference functions for various model classes") (description "This package provides tools that can be used to calculate, evaluate, plot and use for inference the profiles of *arbitrary* inference functions for arbitrary @code{glm}-like fitted models with linear predictors. More information on the methods that are implemented can be found in Kosmidis (2008) @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.") (license license:gpl2+))) (define-public r-brglm (package (name "r-brglm") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "brglm" version)) (sha256 (base32 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an")))) (properties `((upstream-name . "brglm"))) (build-system r-build-system) (propagated-inputs (list r-profilemodel)) (home-page "https://github.com/ikosmidis/brglm") (synopsis "Bias reduction in binomial-response generalized linear models") (description "Fit generalized linear models with binomial responses using either an adjusted-score approach to bias reduction or maximum penalized likelihood where penalization is by Jeffreys invariant prior. These procedures return estimates with improved frequentist properties (bias, mean squared error) that are always finite even in cases where the maximum likelihood estimates are infinite (data separation). Fitting takes place by fitting generalized linear models on iteratively updated pseudo-data. 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(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 "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar")))) (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 "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 "13b5halfxc7nr57vkz3qmkkcpw1hr4xdk1mjh2cq8cvpnjz15qc3")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs (list r-findpython r-jsonlite r-r6)) (native-inputs (list r-knitr)) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description "This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.") (license license:gpl2+))) (define-public r-hash (package (name "r-hash") (version "2.2.6.2") (source (origin (method url-fetch) (uri (cran-uri "hash" version)) (sha256 (base32 "17scs675a86c34hjbxmwi8kny4yyv97x3515s449zafj2i0ad8vm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/hash/") (synopsis "Implementation of hash/associated arrays/dictionaries") (description "This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.") (license license:gpl2+))) (define-public r-orddom (package (name "r-orddom") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "orddom" version)) (sha256 (base32 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) (build-system r-build-system) (propagated-inputs (list r-psych)) (home-page "https://cran.r-project.org/web/packages/orddom/") (synopsis "Ordinal dominance statistics") (description "This package provides tools to compute ordinal, statistics and effect sizes as an alternative to mean comparison: Cliff's delta or success rate difference (SRD), Vargha and Delaney's A or the Area Under a Receiver Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's Common Language Effect Size (CLES) or Grissom & Kim's Probability of Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover, comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of Group (Non-)Overlap considerations.") (license license:gpl2))) (define-public r-deriv (package (name "r-deriv") (version "4.1.3") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") (synopsis "Symbolic differentiation") (description "This package provides an R-based solution for symbolic differentiation. It admits user-defined functions as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.") (license license:gpl3+))) (define-public r-doby (package (name "r-doby") (version "4.6.13") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs (list r-broom r-deriv r-dplyr r-ggplot2 r-magrittr r-mass r-matrix r-microbenchmark r-pbkrtest r-tibble)) (native-inputs (list r-knitr)) (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") (description "This package contains: @itemize @item facilities for working with grouped data: @code{do} something to data stratified @code{by} some variables. @item implementations of least-squares means, general linear contrasts, and @item miscellaneous other utilities. @end itemize\n") (license license:gpl2+))) (define-public r-refgenome (package (name "r-refgenome") (version "1.7.7") (source (origin (method url-fetch) (uri (cran-uri "refGenome" version)) (sha256 (base32 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5")))) (properties `((upstream-name . "refGenome"))) (build-system r-build-system) (propagated-inputs (list r-dbi r-doby r-rsqlite)) (home-page "https://cran.r-project.org/web/packages/refGenome/") (synopsis "Gene and splice site annotation using annotation data from Ensembl and UCSC") (description "This package contains functionality for importing and managing of downloaded genome annotation data from the Ensembl genome browser (European Bioinformatics Institute) and from the UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.") (license license:gpl2))) (define-public r-basix (package (name "r-basix") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "BASIX" version)) (sha256 (base32 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id")))) (properties `((upstream-name . "BASIX"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BASIX/") (synopsis "Efficient C/C++ toolset for R") (description "BASIX provides some efficient C/C++ implementations of native R procedures to speed up calculations in R.") (license license:gpl2))) (define-public r-blockfest (package (name "r-blockfest") (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs (list r-basix)) (home-page "https://cran.r-project.org/web/packages/BlockFeST/") (synopsis "Bayesian calculation of region-specific fixation index") (description "This package provides an R implementation of an extension of the BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.") (license license:gpl2))) (define-public r-proc (package (name "r-proc") (version "1.18.0") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs (list r-plyr r-rcpp)) (home-page "https://web.expasy.org/pROC/") (synopsis "Display and analyze ROC curves") (description "This package provides tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). The area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (license license:gpl3+))) (define-public r-rootsolve (package (name "r-rootsolve") (version "1.8.2.3") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/rootSolve/") (synopsis "Tools for the analysis of ordinary differential equations") (description "This package provides routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of @dfn{ordinary differential equations} (ODE). It includes routines that: @enumerate @item generate gradient and jacobian matrices (full and banded), @item find roots of non-linear equations by the Newton-Raphson method, @item estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running, @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). @end enumerate\n") (license license:gpl2+))) (define-public r-abcanalysis (package (name "r-abcanalysis") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ABCanalysis" version)) (sha256 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) (properties `((upstream-name . "ABCanalysis"))) (build-system r-build-system) (propagated-inputs (list r-plotrix)) (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") (synopsis "Computed ABC Analysis") (description "Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to the perception of losing information from a data set. This package provides tools to calculate these limits on the basis of the mathematical properties of the distribution of the analyzed items.") (license license:gpl3))) (define-public r-slam (package (name "r-slam") (version "0.1-50") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") (description "This package contains data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.") (license license:gpl2))) (define-public r-manipulatewidget (package (name "r-manipulatewidget") (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-codetools r-htmltools r-htmlwidgets r-knitr r-miniui r-shiny r-shinyjs r-webshot)) (native-inputs (list r-knitr)) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description "This package lets you create in just a few lines of R code a nice user interface to modify the data or the graphical parameters of one or multiple interactive charts. It is useful to quickly explore visually some data or for package developers to generate user interfaces easy to maintain.") (license license:gpl2+))) (define-public r-a3 (package (name "r-a3") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "A3" version)) (sha256 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) (properties `((upstream-name . "A3"))) (build-system r-build-system) (propagated-inputs (list r-pbapply r-xtable)) (home-page "https://cran.r-project.org/web/packages/A3/") (synopsis "Error metrics for predictive models") (description "This package supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward.") (license license:gpl2+))) (define-public r-infotheo (package (name "r-infotheo") (version "1.2.0.1") (source (origin (method url-fetch) (uri (cran-uri "infotheo" version)) (sha256 (base32 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0")))) (build-system r-build-system) (home-page "http://homepage.meyerp.com/software") (synopsis "Information-theoretic measures") (description "This package implements various measures of information theory based on several entropy estimators.") (license license:gpl3+))) (define-public r-nsprcomp (package (name "r-nsprcomp") (version "0.5.1-2") (source (origin (method url-fetch) (uri (cran-uri "nsprcomp" version)) (sha256 (base32 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f")))) (properties `((upstream-name . "nsprcomp"))) (build-system r-build-system) (home-page "https://sigg-iten.ch/research/") (synopsis "Non-negative and sparse PCA") (description "This package implements two methods for performing a constrained principal component analysis (PCA), where non-negativity and/or sparsity constraints are enforced on the principal axes (PAs). The function @code{nsprcomp} computes one principal component (PC) after the other. Each PA is optimized such that the corresponding PC has maximum additional variance not explained by the previous components. In contrast, the function @code{nscumcomp} jointly computes all PCs such that the cumulative variance is maximal. Both functions have the same interface as the @code{prcomp} function from the @code{stats} package (plus some extra parameters).") (license license:gpl2+))) (define-public r-cmplot (package (name "r-cmplot") (version "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") (synopsis "Circle Manhattan plot") (description "Circle Manhattan Plot is an R package that can lay out genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.") (license license:gpl2+))) (define-public r-precrec (package (name "r-precrec") (version "0.12.9") (source (origin (method url-fetch) (uri (cran-uri "precrec" version)) (sha256 (base32 "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm")))) (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-data-table r-ggplot2 r-gridextra r-rcpp r-withr)) (native-inputs (list r-knitr)) (home-page "https://evalclass.github.io/precrec/") (synopsis "Calculate accurate precision-recall and ROC curves") (description "This package provides tools for accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.") (license license:gpl3))) (define-public r-netrep (package (name "r-netrep") (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "NetRep" version)) (sha256 (base32 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd")))) (properties `((upstream-name . "NetRep"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bh r-foreach r-rcolorbrewer r-rcpp r-rcpparmadillo r-rhpcblasctl r-statmod)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=NetRep") (synopsis "Permutation testing network module preservation across datasets") (description "This package provides functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing.") (license license:gpl2))) (define-public r-intergraph (package (name "r-intergraph") (version "2.0-2") (source (origin (method url-fetch) (uri (cran-uri "intergraph" version)) (sha256 (base32 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc")))) (properties `((upstream-name . "intergraph"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-network)) (native-inputs (list r-knitr)) (home-page "http://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description "Functions implemented in this package allow coercing (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages @code{network} and @code{igraph}.") (license license:gpl3))) (define-public r-abcoptim (package (name "r-abcoptim") (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "ABCoptim" version)) (sha256 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) (properties `((upstream-name . "ABCoptim"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/gvegayon/ABCoptim/") (synopsis "Optimization of Artificial Bee Colony algorithm") (description "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms, and uses only common control parameters such as colony size and maximum cycle number. The @code{r-abcoptim} implements the Artificial bee colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. This version is a work-in-progress and is written in R code.") (license license:expat))) (define-public r-abcp2 (package (name "r-abcp2") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "ABCp2" version)) (sha256 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) (properties `((upstream-name . "ABCp2"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ABCp2/") (synopsis "Approximate Bayesian Computational Model for Estimating P2") (description "This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.") (license license:gpl2))) (define-public r-abcrf (package (name "r-abcrf") (version "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "abcrf" version)) (sha256 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27")))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-mass r-matrixstats r-ranger r-rcpp r-rcpparmadillo r-readr r-stringr)) (home-page "https://cran.r-project.org/web/packages/abcrf/") (synopsis "Approximate bayesian computation via random forests") (description "This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.") (license license:gpl2+))) (define-public r-abctools (package (name "r-abctools") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "abctools" version)) (sha256 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) (build-system r-build-system) (propagated-inputs (list r-abc r-abind r-hmisc r-plyr)) (home-page "https://github.com/dennisprangle/abctools/") (synopsis "Tools for ABC analyses") (description "This @code{r-abctools} package provides tools for approximate Bayesian computation including summary statistic selection and assessing coverage. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods to tune the choice of threshold.") (license license:gpl2+))) (define-public r-ggstance (package (name "r-ggstance") (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "ggstance" version)) (sha256 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr r-rlang r-withr)) (home-page "https://cran.r-project.org/web/packages/ggstance/") (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") (description "This package is a @code{r-ggplot2} extension that provides flipped components: @enumerate @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms; @item vertical versions of @code{r-ggplot2} positions. @end enumerate") (license license:gpl3))) (define-public r-ggnetwork (package (name "r-ggnetwork") (version "0.5.10") (source (origin (method url-fetch) (uri (cran-uri "ggnetwork" version)) (sha256 (base32 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v")))) (properties `((upstream-name . "ggnetwork"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggrepel r-igraph r-network r-sna)) (native-inputs (list r-knitr)) (home-page "https://github.com/briatte/ggnetwork") (synopsis "Geometries to plot networks with ggplot2") (description "This package provides geometries to plot network objects with the ggplot2 package.") (license license:gpl3))) (define-public r-cvauc (package (name "r-cvauc") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "cvAUC" version)) (sha256 (base32 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28")))) (properties `((upstream-name . "cvAUC"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-rocr)) (home-page "https://github.com/ledell/cvAUC") (synopsis "Cross-validated area under the ROC curve confidence intervals") (description "This package contains various tools for working with and evaluating cross-validated area under the ROC curve (AUC) estimators. The primary functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which report cross-validated AUC and compute confidence intervals for cross-validated AUC estimates based on influence curves for i.i.d. and pooled repeated measures data, respectively.") (license license:asl2.0))) (define-public r-gam (package (name "r-gam") (version "1.20.1") (source (origin (method url-fetch) (uri (cran-uri "gam" version)) (sha256 (base32 "1bbxiqfgi7jc9vw1hspw5q41d69nlw2v6k91zqlvmam5pvxcd1sp")))) (properties `((upstream-name . "gam"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=gam") (synopsis "Generalized additive models") (description "This package provides functions for fitting and working with generalized additive models, as described in chapter 7 of \"Statistical Models in S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive Models\" (Hastie and Tibshirani, 1990).") (license license:gpl2))) (define-public r-superlearner (package (name "r-superlearner") (version "2.0-28") (source (origin (method url-fetch) (uri (cran-uri "SuperLearner" version)) (sha256 (base32 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-furrr (package (name "r-furrr") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 "117xj66l14r08macwghgyibzm282ljv1afpa133h952gc70irs9z")))) (build-system r-build-system) (propagated-inputs (list r-future r-globals r-lifecycle r-purrr r-rlang r-vctrs)) (home-page "https://github.com/DavisVaughan/furrr") (synopsis "Apply mapping functions in parallel using futures") (description "This package provides implementations of the family of @code{map()} functions from the @code{purrr} package that can be resolved using any @code{future}-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.") (license license:lgpl2.1+))) (define-public r-abjutils (package (name "r-abjutils") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "abjutils" version)) (sha256 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-purrr r-rlang r-rstudioapi r-stringi r-stringr r-tidyr)) (home-page "https://github.com/abjur/abjutils/") (synopsis "Collection of tools for jurimetrical analysis") (description "This package implements general purpose tools, such as functions for sampling and basic manipulation of Brazilian lawsuits identification number. It also implements functions for text cleaning, such as accentuation removal.") (license license:expat))) (define-public r-abnormality (package (name "r-abnormality") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "abnormality" version)) (sha256 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/abnormality/") (synopsis "Measure a subject's abnormality with respect to a reference population") (description "This package contains functions to implement the methodology and considerations laid out by Marks et al. in the article \"Measuring abnormality in high dimensional spaces: applications in biomechanical gait analysis\". Using high-dimensional datasets to measure a subject's overall level of abnormality as compared to a reference population is often needed in outcomes research.") (license license:expat))) (define-public r-abodoutlier (package (name "r-abodoutlier") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "abodOutlier" version)) (sha256 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj")))) (properties `((upstream-name . "abodOutlier"))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/abodOutlier/") (synopsis "Angle-based outlier detection") (description "This package performs angle-based outlier detection on a given data frame. It offers three methods to process data: @enumerate @item full but slow implementation using all the data that has cubic complexity; @item a fully randomized method; @item a method using k-nearest neighbours. @end enumerate These algorithms are well suited for high dimensional data outlier detection.") (license license:expat))) (define-public r-abps (package (name "r-abps") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ABPS" version)) (sha256 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) (properties `((upstream-name . "ABPS"))) (build-system r-build-system) (propagated-inputs (list r-kernlab)) (home-page "https://cran.r-project.org/web/packages/ABPS/") (synopsis "Abnormal blood profile score to detect blood doping") (description "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS). The ABPS is a part of the Athlete biological passport program of the World anti-doping agency, which combines several blood parameters into a single score in order to detect blood doping. The package also contains functions to calculate other scores used in anti-doping programs, such as the ratio of hemoglobin to reticulocytes (OFF-score), as well as example data.") (license license:gpl2+))) (define-public r-parmigene (package (name "r-parmigene") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "parmigene" version)) (sha256 (base32 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/parmigene/") (synopsis "Mutual information estimation for gene network reconstruction") (description "This package provides a parallel estimation of the mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks.") (license license:agpl3+))) (define-public r-pscl (package (name "r-pscl") (version "1.5.5") (source (origin (method url-fetch) (uri (cran-uri "pscl" version)) (sha256 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://github.com/atahk/pscl/") (synopsis "Political science computational laboratory") (description "The @code{pscl} is an R package providing classes and methods for: @enumerate @item Bayesian analysis of roll call data (item-response models); @item elementary Bayesian statistics; @item maximum likelihood estimation of zero-inflated and hurdle models for count data; @item utility functions. @end enumerate") (license license:gpl2))) (define-public r-accelmissing (package (name "r-accelmissing") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "accelmissing" version)) (sha256 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) (build-system r-build-system) (propagated-inputs (list r-mice r-pscl)) (home-page "https://cran.r-project.org/web/packages/accelmissing/") (synopsis "Missing value imputation for accelerometer data") (description "This package provides a statistical method to impute the missing values in accelerometer data. The methodology includes both parametric and semi-parametric multiple imputations under the zero-inflated Poisson lognormal model. It also provides multiple functions to preprocess the accelerometer data previous to the missing data imputation. These include detecting the wearing and the non-wearing time, selecting valid days and subjects, and creating plots.") (license license:gpl2+))) (define-public r-mhsmm (package (name "r-mhsmm") (version "0.4.16") (source (origin (method url-fetch) (uri (cran-uri "mhsmm" version)) (sha256 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://github.com/jaredo/mhsmm/") (synopsis "Inference for hidden Markov and semi-Markov models") (description "The @code{r-mhsmm} package implements estimation and prediction methods for hidden Markov and semi-Markov models for multiple observation sequences. Such techniques are of interest when observed data is thought to be dependent on some unobserved (or hidden) state. Also, this package is suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.") (license license:gpl2+))) (define-public r-nleqslv (package (name "r-nleqslv") (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "nleqslv" version)) (sha256 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nleqslv/") (synopsis "Solve systems of nonlinear equations") (description "The @code{r-nleqslv} package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.") (license license:gpl2+))) (define-public r-physicalactivity (package (name "r-physicalactivity") (version "0.2-4") (source (origin (method url-fetch) (uri (cran-uri "PhysicalActivity" version)) (sha256 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40")))) (properties `((upstream-name . "PhysicalActivity"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") (synopsis "Processing accelerometer data for physical activity measurement") (description "This @code{r-physicalactivity} package provides a function @code{wearingMarking} for classification of monitored wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plots of accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. The revised package version 0.2-1 improved the functions regarding speed, robustness and add better support for time zones and daylight saving. In addition, several functions were added: @enumerate @item the @code{markDelivery} can classify days for ActiGraph delivery by mail; @item the @code{markPAI} can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. @end enumerate It also supports importing ActiGraph (AGD) files with @code{readActigraph} and @code{queryActigraph} functions.") (license license:gpl3+))) (define-public r-acc (package (name "r-acc") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "acc" version)) (sha256 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-dbi r-ggplot2 r-iterators r-mhsmm r-nleqslv r-physicalactivity r-plyr r-r-utils r-rcpp r-rcpparmadillo r-rsqlite r-zoo)) (home-page "https://cran.r-project.org/web/packages/acc/") (synopsis "Exploring accelerometer data") (description "This package processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also, includes functions to plot, analyze, and simulate accelerometer data.") 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(license license:expat))) (define-public r-magick (package (name "r-magick") (version "2.7.3") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3")))) (build-system r-build-system) (inputs (list imagemagick zlib)) (propagated-inputs (list r-curl r-magrittr r-rcpp)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/ropensci/magick") (synopsis "Advanced graphics and image-processing in R") (description "This package provides bindings to ImageMagick, a comprehensive image processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio, images are automatically previewed when printed to the console, resulting in an interactive editing environment.") (license license:expat))) (define-public r-survey (package (name "r-survey") (version "4.1-1") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-matrix r-minqa r-mitools r-numderiv 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-gee (package (name "r-gee") (version "4.13-23") (source (origin (method url-fetch) (uri (cran-uri "gee" version)) (sha256 (base32 "0v0fam678pqqkxmj95f1pwsi08y1rbz1wxnp1ig81jvpn0xpq8gq")))) (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/gee/") (synopsis "Generalized estimation equation solver") (description "This package provides a solver for generalized estimation equations.") (license license:gpl2))) (define-public r-tab (package (name "r-tab") (version "5.1.1") (source (origin (method url-fetch) (uri (cran-uri "tab" version)) (sha256 (base32 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv")))) (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-kableextra r-knitr r-mass r-survey)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tab/") (synopsis "Create summary tables for statistical reports") (description "This package contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards models. Functions are available to handle data from simple random samples as well as complex surveys.") (license license:gpl3+))) (define-public r-dvmisc (package (name "r-dvmisc") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dvmisc" version)) (sha256 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs (list r-cubature r-data-table r-dplyr r-ggplot2 r-mass r-mvtnorm r-pracma r-rbenchmark r-rcpp r-survey r-tab)) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description "This package implements faster versions of base R functions (e.g. mean, standard deviation, covariance, weighted mean), mostly written in C++, along with miscellaneous functions for various purposes (e.g. create the histogram with fitted probability density function or probability mass function curve, create the body mass index groups, assess the linearity assumption in logistic regression).") (license license:gpl2))) (define-public r-accelerometry (package (name "r-accelerometry") (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "accelerometry" version)) (sha256 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) (build-system r-build-system) (propagated-inputs (list r-dvmisc r-rcpp)) (home-page "https://cran.r-project.org/web/packages/accelerometry/") (synopsis "Functions for processing accelerometer data") (description "This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented.") (license license:gpl3))) (define-public r-absim (package (name "r-absim") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "AbSim" version)) (sha256 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) (properties `((upstream-name . "AbSim"))) (build-system r-build-system) (propagated-inputs (list r-ape r-powerlaw)) (home-page "https://cran.r-project.org/web/packages/AbSim/") (synopsis "Time resolved simulations of antibody repertoires") (description "This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins with an initial V-D-J recombination event, starting the first phylogenetic tree. Upon completion, the main loop of the algorithm begins, with each iteration representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.") (license license:gpl2))) (define-public r-quic (package (name "r-quic") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "QUIC" version)) (sha256 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) (properties `((upstream-name . "QUIC"))) (build-system r-build-system) (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") (synopsis "Regularized sparse inverse covariance matrix estimation") (description "This package implements the regularized Gaussian maximum likelihood estimation of the inverse of a covariance matrix. It uses Newton's method and coordinate descent to solve the regularized inverse covariance matrix estimation problem.") ;; The project home page states that the release is under GPLv3 or later. ;; The CRAN page only says GPL-3. (license license:gpl3+))) (define-public r-abundant (package (name "r-abundant") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "abundant" version)) (sha256 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd")))) (build-system r-build-system) (propagated-inputs (list r-glasso)) (home-page "https://cran.r-project.org/web/packages/abundant/") (synopsis "Abundant regression and high-dimensional principal fitted components") (description "This package provides tools to fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) @url{doi:10.1214/11-AOS962}.") ;; The DESCRIPTION file states GPL-2, but since it directly depends on a ;; GPLv3+ package (QUIC) this likely means GPLv2+. (license license:gpl2+))) (define-public r-ac3net (package (name "r-ac3net") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "Ac3net" version)) (sha256 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) (properties `((upstream-name . "Ac3net"))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/Ac3net/") (synopsis "Inferring directional conservative causal core gene networks") (description "This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.") (license license:gpl3+))) (define-public r-aca (package (name "r-aca") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "ACA" version)) (sha256 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) (properties `((upstream-name . "ACA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACA/") (synopsis "Abrupt change-point or aberration detection in point series") (description "This package offers an interactive function for the detection of breakpoints in series.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-acceptancesampling (package (name "r-acceptancesampling") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 (base32 "1ja1g0v8qvf7yj81x37wc6i7fkwpc573756jgvazazi8yf1gm12p")))) (properties `((upstream-name . "AcceptanceSampling"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") (synopsis "Creation and evaluation of acceptance sampling plans") (description "This @code{r-acceptancesampling} provides functionality for creating and evaluating acceptance sampling plans. Acceptance sampling is a methodology commonly used in quality control and improvement. International standards of acceptance sampling provide sampling plans for specific circumstances. The aim of this package is to provide an easy-to-use interface to visualize single, double or multiple sampling plans. In addition, methods have been provided to enable the user to assess sampling plans against pre-specified levels of performance, as measured by the probability of acceptance for a given level of quality in the lot.") (license license:gpl3+))) (define-public r-acclma (package (name "r-acclma") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ACCLMA" version)) (sha256 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) (properties `((upstream-name . "ACCLMA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACCLMA/") (synopsis "ACC & LMA graph plotting") (description "This package contains a function that imports data from a @acronym{CSV, Comma-Separated Values} file, or uses manually entered data from the format (x, y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration Curve} vs @acronym{LOI, Line of Independence} graph and @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main function is @code{plotLMA} (source file, header) that takes a data set and plots the appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a string) was passed, a manual data entry window is opened. The header parameter indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has a header row or not. The dataset should contain only one independent variable (x) and one dependent variable (y) and can contain a weight for each observation.") (license license:gpl2))) (define-public r-aspi (package (name "r-aspi") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "aspi" version)) (sha256 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/aspi/") (synopsis "Analysis of symmetry of parasitic infections") (description "This package provides tools for the analysis and visualization of bilateral asymmetry in parasitic infections.") (license license:gpl3+))) (define-public r-sandwich (package (name "r-sandwich") (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/sandwich/") (synopsis "Robust Covariance Matrix Estimators") (description "This package provides model-robust standard error estimators for cross-sectional, time series, clustered, panel, and longitudinal data.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-th-data (package (name "r-th-data") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs (list r-mass r-survival)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TH.data/") (synopsis "Shared data sets") (description "This package contains supporting data sets that are used in other packages maintained by Torsten Hothorn.") (license license:gpl3))) (define-public r-multcomp (package (name "r-multcomp") (version "1.4-19") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 "0mz5wdqrqpp2gqijfpp9rgfbq8yvxki4is8fbbc4qwdwryqp6d7h")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) (home-page "https://cran.r-project.org/web/packages/multcomp/") (synopsis "Simultaneous inference in general parametric models") (description "Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, Hothorn, Westfall, 2010, CRC Press).") (license license:gpl2))) (define-public r-multcompview (package (name "r-multcompview") (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "multcompView" version)) (sha256 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j")))) (properties `((upstream-name . "multcompView"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=multcompView") (synopsis "Visualizations of paired comparisons") (description "Convert a logical vector or a vector of p-values or a correlation, difference, or distance matrix into a display identifying the pairs for which the differences were not significantly different.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-emmeans (package (name "r-emmeans") (version "1.7.4-1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 "08g7ifqhwqa00hc850nwx03dp7isz0281ig6kvixc4xdahmkm8zp")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv r-xtable)) (native-inputs (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") (synopsis "Estimated marginal means, aka least-squares means") (description "This package provides tools to obtain @dfn{estimated marginal means} (EMMs) for many linear, generalized linear, and mixed models. It can be used to compute contrasts or linear functions of EMMs, trends, and comparisons of slopes.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-pwr (package (name "r-pwr") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "pwr" version)) (sha256 (base32 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/heliosdrm/pwr") (synopsis "Basic functions for power analysis") (description "This package provides power analysis functions along the lines of Cohen (1988).") (license license:gpl3+))) (define-public r-libcoin (package (name "r-libcoin") (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/libcoin") (synopsis "Linear test statistics for permutation inference") (description "This package provides basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999).") (license license:gpl2))) (define-public r-coin (package (name "r-coin") (version "1.4-2") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm")))) (build-system r-build-system) (propagated-inputs (list r-libcoin r-matrixstats r-modeltools r-multcomp r-mvtnorm 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 "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a")))) (build-system r-build-system) (inputs (list pandoc)) (native-inputs (list r-knitr)) (propagated-inputs (list r-dplyr r-ggplot2 r-ggridges r-glue r-posterior r-reshape2 r-rlang r-tibble r-tidyselect)) (home-page "https://mc-stan.org/bayesplot") (synopsis "Plotting for Bayesian models") (description "This package provides plotting functions for posterior analysis, model checking, and MCMC diagnostics. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling.") (license license:gpl3+))) (define-public r-tmb (package (name "r-tmb") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 "1mr5vwamw6ag1fhd83jyy6015296908qwshwq0fcphhiv60x579c")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcppeigen)) (home-page "http://tmb-project.org") (synopsis "Template model builder: a general random effect tool") (description "With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through BLAS and parallel user templates.") (license license:gpl2))) (define-public r-sjstats (package (name "r-sjstats") (version "0.18.1") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-broom r-dplyr r-effectsize r-emmeans r-insight r-lme4 r-magrittr r-mass r-modelr r-parameters r-performance r-purrr r-rlang r-sjlabelled r-sjmisc r-tidyr)) (home-page "https://github.com/strengejacke/sjstats") (synopsis "Functions for common statistical computations") (description "This package provides a collection of convenient functions for common statistical computations, which are not directly provided by R's @code{base} or @code{stats} packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort. Second, these shortcut functions are generic, and can be applied not only to vectors, but also to other objects as well. The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models, mixed effects models and Bayesian models.") (license license:gpl3))) (define-public r-glmmtmb (package (name "r-glmmtmb") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 "0xdjc3gx0cj098rrjzlsy9cccxzfvn029xh4ycpya4xjhxsykldr")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-matrix r-nlme r-numderiv r-rcppeigen r-tmb)) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description "Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via the Template Model Builder. Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.") (license license:agpl3+))) (define-public r-bayestestr (package (name "r-bayestestr") (version "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 "1fbkpagc5zznrafy7h68nhx43a1yg4v7242pbqjkd0h2481c101z")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs (list r-datawizard r-insight)) (native-inputs (list r-knitr)) (home-page "https://github.com/easystats/bayestestR") (synopsis "Describe Bayesian models and posterior distributions") (description "This package provides utilities to understand and describe posterior distributions and Bayesian models. It includes point-estimates such as @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest Density Interval} (HDI), and indices used for null-hypothesis testing (such as ROPE percentage and pd).") (license license:gpl3))) (define-public r-performance (package (name "r-performance") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 "1znr4i1pjv6z3lj6qrma2i3l94rz1z29w92mrxxfy3ch0s71crww")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) (home-page "https://easystats.github.io/performance/") (synopsis "Assessment of regression models performance") (description "This package provides utilities for computing measures to assess model quality, which are not directly provided by R's @code{base} or @code{stats} packages. These include e.g. measures like r-squared, intraclass correlation coefficient, root mean squared error or functions to check models for overdispersion, singularity or zero-inflation and more. Functions apply to a large variety of regression models, including generalized linear models, mixed effects models and Bayesian models.") (license license:gpl3))) (define-public r-ggeffects (package (name "r-ggeffects") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 "01yyfw7fkbxrp0gpwni5y8m4w9l3xckwc3crnvy1fqs1d6gwx3xx")))) (build-system r-build-system) (propagated-inputs (list r-insight r-mass r-sjlabelled)) (native-inputs (list r-knitr)) (home-page "https://github.com/strengejacke/ggeffects") (synopsis "Create tidy data frames of marginal effects for ggplot") (description "This package provides tools to compute marginal effects from statistical models and return the result as tidy data frames. These data frames are ready to use with the @code{ggplot2} package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are @code{ggpredict()} and @code{ggeffect()}. There is a generic @code{plot()} method to plot the results using @code{ggplot2}.") (license license:gpl3))) (define-public r-effectsize (package (name "r-effectsize") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 "07dbj7n9vwjkb7xrdj224lzc3ppr3jjdgyyilkj7gpkvgjgfrqhz")))) (properties `((upstream-name . 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User credentials are shared with command line git through the @code{git-credential} store and SSH keys stored on disk or ssh-agent.") (license license:expat))) (define-public r-usethis (package (name "r-usethis") (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i")))) (build-system r-build-system) (propagated-inputs (list r-cli r-clipr r-crayon r-curl r-desc r-fs r-gert r-gh r-glue r-jsonlite r-lifecycle r-purrr r-rappdirs r-rlang r-rprojroot r-rstudioapi r-whisker r-withr r-yaml)) (home-page "https://github.com/r-lib/usethis") (synopsis "Automate R package and project setup") (description "This package helps you to automate R package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, GitHub integration, licenses, Rcpp, RStudio projects, and more.") 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(license (list license:gpl2+ license:asl2.0)))) (define-public r-rcpphnsw (package (name "r-rcpphnsw") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppHNSW" version)) (sha256 (base32 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") (description "Hnswlib is a C++ library for approximate nearest neighbors. This package provides a minimal R interface by relying on the Rcpp package.") ;; hnswlib is released under Version 2.0 of the Apache License. (license (list license:gpl3 license:asl2.0)))) (define-public r-rcppparallel (package (name "r-rcppparallel") (version "5.1.5") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "https://rcppcore.github.io/RcppParallel/") (synopsis "Parallel programming tools for Rcpp") (description "This package provides high level functions for parallel programming with Rcpp. For example, the @code{parallelFor()} function can be used to convert the work of a standard serial @code{for} loop into a parallel one and the @code{parallelReduce()} function can be used for accumulating aggregates or other values.") 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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 "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "multicool" version)) (sha256 (base32 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/multicool/") (synopsis "Permutations of multisets in cool-lex order") (description "This package provides a set of tools to permute multisets without loops or hash tables and to generate integer partitions. Cool-lex order is similar to colexicographical order.") (license license:gpl2))) (define-public r-misc3d (package (name "r-misc3d") (version "0.9-1") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/misc3d/") (synopsis "Miscellaneous 3D Plots") (description "This package provides a collection of miscellaneous 3d plots, including isosurfaces.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-ks (package (name "r-ks") (version "1.13.5") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i")))) (build-system r-build-system) (propagated-inputs (list r-fnn r-kernlab r-kernsmooth r-matrix r-mclust r-mgcv r-multicool r-mvtnorm r-plot3d r-pracma)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description "This package provides kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-feature (package (name "r-feature") (version "1.2.15") (source (origin (method url-fetch) (uri (cran-uri "feature" version)) (sha256 (base32 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y")))) (build-system r-build-system) (propagated-inputs (list r-ks r-plot3d)) (native-inputs (list r-knitr)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Inferential feature significance for kernel density estimation") (description "The feature package contains functions to display and compute kernel density estimates, significant gradient and significant curvature regions. Significant gradient and/or curvature regions often correspond to significant features (e.g. local modes).") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-arm (package (name "r-arm") (version "1.12-2") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1")))) (build-system r-build-system) (propagated-inputs (list r-abind r-coda r-lme4 r-mass r-matrix r-nlme)) (home-page "https://cran.r-project.org/web/packages/arm/") (synopsis "Data analysis using regression and multilevel/hierarchical models") (description "This package provides functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.") (license license:gpl3+))) (define-public r-circular (package (name "r-circular") (version "0.4-95") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mvtnorm)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/circular/") (synopsis "Circular statistics") (description "This package provides tools for circular statistics, from \"Topics in circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.") (license license:gpl2+))) (define-public r-activity (package (name "r-activity") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3")))) (build-system r-build-system) (propagated-inputs (list r-insol 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 "2.18") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as")))) (build-system r-build-system) (propagated-inputs (list r-subplex)) (home-page "https://kingaa.github.io/ouch/") (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") (description "This package provides tools to fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.") (license license:gpl2+))) (define-public r-fmsb (package (name "r-fmsb") (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk")))) (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 "https://www.rmetrics.org") (synopsis "Stable distribution functions") (description "This package provides density, probability and quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.") 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"admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") (synopsis "Adrian Dusa's miscellaneous") (description "This package contains miscellaneous functions used to interpret and translate, factorize and negate Sum of Products expressions, for both binary and multi-value crisp sets, and to extract information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly flexible recoding routine and a more flexible alternative to the base function @code{with()}.") (license license:gpl3+))) (define-public r-sodium (package (name "r-sodium") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "sodium" version)) (sha256 (base32 "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q")))) (properties `((upstream-name . "sodium"))) (build-system r-build-system) (inputs (list libsodium)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/sodium") (synopsis "R bindings to the libsodium crypto library") (description "This package provides bindings to libsodium: a library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.") (license license:expat))) (define-public r-softimpute (package (name "r-softimpute") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "softImpute" version)) (sha256 (base32 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a")))) (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran r-knitr)) (home-page "https://cran.r-project.org/web/packages/softImpute") (synopsis "Matrix completion via iterative soft-thresholded SVD") (description "This package provides iterative methods for matrix completion that use nuclear-norm regularization. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank @dfn{single value decompositions} (SVDs) on large sparse centered matrices (i.e. principal components).") (license license:gpl2))) (define-public r-fftwtools (package (name "r-fftwtools") (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "fftwtools" version)) (sha256 (base32 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i")))) (build-system r-build-system) (inputs (list fftw)) (native-inputs (list pkg-config)) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description "This package provides a wrapper for several FFTW functions. It provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using the FFTW3 library. The package includes the functions @code{fftw()} and @code{mvfftw()} which are designed to mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. The FFT functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.") (license license:gpl2+))) (define-public r-tiff (package (name "r-tiff") (version "0.1-11") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq")))) (build-system r-build-system) (inputs (list libtiff libjpeg-turbo zlib)) (native-inputs (list pkg-config)) (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description "This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.") ;; Either of these two license versions. (license (list license:gpl2 license:gpl3)))) (define-public r-nlp (package (name "r-nlp") (version "0.2-1") (source (origin (method url-fetch) (uri (cran-uri "NLP" version)) (sha256 (base32 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-waveslim (package (name "r-waveslim") (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "waveslim" version)) (sha256 (base32 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://waveslim.blogspot.com") (synopsis "Basic wavelet routines for signal processing") (description "This package provides basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).") (license license:bsd-3))) (define-public r-wordcloud (package (name "r-wordcloud") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "wordcloud" version)) (sha256 (base32 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-rcpp ;; The "tm" package is only "suggested" according to CRAN, but the ;; wordcloud package cannot be loaded without it. r-tm)) (home-page "https://cran.r-project.org/web/packages/wordcloud") (synopsis "Word clouds") (description "This package provides functionality to create pretty word clouds, visualize differences and similarity between documents, and avoid over-plotting in scatter plots with text.") 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It also provides tidy interfaces to manipulate tree data.") (license license:artistic2.0))) (define-public r-rvcheck (package (name "r-rvcheck") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a")))) (build-system r-build-system) (propagated-inputs (list r-biocmanager r-yulab-utils)) (home-page "https://cran.r-project.org/web/packages/rvcheck") (synopsis "R package version check") (description "This package provides tools to check the latest release version of R and R packages (on CRAN, Bioconductor or Github).") 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(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 (list r-matrix)) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") (synopsis "Sparse truncated singular value decomposition") (description "This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported.") ;; SVDLIBC is released under BSD-2. The R interface is released under ;; BSD-3. 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(license license:gpl2+))) (define-public r-combinat (package (name "r-combinat") (version "0.0-8") (source (origin (method url-fetch) (uri (cran-uri "combinat" version)) (sha256 (base32 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/combinat") (synopsis "Combinatorics utilities") (description "This package provides assorted routines for combinatorics.") (license license:gpl2))) (define-public r-qlcmatrix (package (name "r-qlcmatrix") (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "qlcMatrix" version)) (sha256 (base32 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) (properties `((upstream-name . "qlcMatrix"))) (build-system r-build-system) (propagated-inputs (list r-docopt r-matrix r-slam r-sparsesvd)) (home-page "https://cran.r-project.org/web/packages/qlcMatrix") (synopsis "Sparse matrix functions for quantitative language comparison") (description "This package provides an extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for the special data format used for @dfn{quantitative language comparison} (QLC).") (license license:gpl3))) (define-public r-ddrtree (package (name "r-ddrtree") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "DDRTree" version)) (sha256 (base32 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) (properties `((upstream-name . "DDRTree"))) (build-system r-build-system) (propagated-inputs (list r-bh r-irlba r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/DDRTree") (synopsis "Learning principal graphs with DDRTree") (description "This package provides an implementation of the framework of @dfn{reversed graph embedding} (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of the data simultaneously. DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the ordering as well as the intrinsic structure of single cell genomics data. In general, it could be used to reconstruct the temporal progression as well as the bifurcation structure of any data type.") (license license:asl2.0))) (define-public r-corpcor (package (name "r-corpcor") (version "1.6.10") (source (origin (method url-fetch) (uri (cran-uri "corpcor" version)) (sha256 (base32 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i")))) (build-system r-build-system) (home-page "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 "0.16-1") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) (native-inputs (list r-knitr)) (home-page "https://github.com/yixuan/RSpectra") (synopsis "Solvers for large-scale Eigenvalue and SVD problems") (description "This package provides an R interface to the Spectra library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than @code{eigen()} if k << n.") ;; MPL 2 or later. (license license:mpl2.0))) (define-public r-vbsr (package (name "r-vbsr") (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "vbsr" version)) (sha256 (base32 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/vbsr") (synopsis "Variational Bayes spike regression regularized linear models") (description "This package provides an efficient algorithm for solving ultra-sparse regularized regression models using a variational Bayes algorithm with a spike prior. The algorithm is solved on a path, with coordinate updates, and is capable of generating very sparse models. Very general model diagnostics for controlling type-1 errors are also provided.") (license license:gpl2))) (define-public r-flare (package (name "r-flare") (version "1.7.0.1") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-lattice r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/flare") (synopsis "Family of Lasso regression implementations") (description "This package provides implementations of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear models.") (license license:gpl2))) (define-public r-lassopv (package (name "r-lassopv") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "lassopv" version)) (sha256 (base32 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) (build-system r-build-system) (propagated-inputs (list r-lars)) (home-page "https://github.com/lingfeiwang/lassopv") (synopsis "Non-parametric p-value estimation for predictors in Lasso") (description "This package enables you to estimate the p-values for predictors x against target variable y in Lasso regression, using the regularization strength when each predictor enters the active set of regularization path for the first time as the statistic.") (license license:gpl3))) (define-public r-splitstackshape (package (name "r-splitstackshape") (version "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "splitstackshape" version)) (sha256 (base32 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://github.com/mrdwab/splitstackshape") (synopsis "Stack and reshape datasets after splitting concatenated values") (description "Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The @code{concat.split} (cSplit) family of functions provided by this package splits such data into separate cells. This package also includes functions to stack groups of columns and to reshape wide data, even when the data are \"unbalanced\"---something which @code{reshape} (from base R) does not handle, and which @code{melt} and @code{dcast} from @code{reshape2} do not easily handle.") (license license:gpl3))) (define-public r-tfmpvalue (package (name "r-tfmpvalue") (version "0.0.8") (source (origin (method url-fetch) (uri (cran-uri "TFMPvalue" version)) (sha256 (base32 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/ge11232002/TFMPvalue") (synopsis "P-value computation for position weight matrices") (description "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match scores. TFMPvalue provides the accurate calculation of a p-value with a score threshold for position weight matrices, or the score with a given p-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) (define-public r-rncl (package (name "r-rncl") (version "0.8.6") (source (origin (method url-fetch) (uri (cran-uri "rncl" version)) (sha256 (base32 "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw")))) (build-system r-build-system) (propagated-inputs (list r-progress r-rcpp)) (home-page "https://github.com/fmichonneau/rncl") (synopsis "Interface to the Nexus class library") (description "This package provides an interface to the Nexus class library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s @code{phylo4(d)}. This functionality is demonstrated with @code{read_newick_phylo()} and @code{read_nexus_phylo()}.") (license license:bsd-2))) (define-public r-phylobase (package (name "r-phylobase") (version "0.8.10") (source (origin (method url-fetch) (uri (cran-uri "phylobase" version)) (sha256 (base32 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-rcpp r-rncl r-rnexml)) (native-inputs (list r-knitr)) (home-page "https://github.com/fmichonneau/phylobase") (synopsis "Base package for phylogenetic structures and comparative data") (description "This package provides a base @code{S4} class for comparative methods, incorporating one or more trees and trait data.") (license license:gpl2+))) (define-public r-rnexml (package (name "r-rnexml") (version "2.4.7") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb")))) (build-system r-build-system) (propagated-inputs (list r-ape r-dplyr r-httr r-lazyeval r-plyr r-reshape2 r-rlang r-stringi r-stringr r-tidyr r-uuid r-xml r-xml2)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/RNeXML/") (synopsis "Semantically rich I/O for the NeXML Format") (description "This package provides access to phyloinformatic data in NeXML format. The package should add new functionality to R such as the possibility to manipulate NeXML objects in more various and refined way and compatibility with @code{ape} objects.") (license license:bsd-3))) (define-public r-rnifti (package (name "r-rnifti") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 "0kkj9dby85iwnlqb7zwrh1xidlvqip7i1mbgckb5qg4b0a3zgibc")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/jonclayden/RNifti") (synopsis "Fast R and C++ access to NIfTI images") (description "This package provides very fast read and write access to images stored in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. It also provides a C/C++ API that can be used by other packages.") (license license:gpl2))) (define-public r-shades (package (name "r-shades") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "shades" version)) (sha256 (base32 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/shades") (synopsis "Simple color manipulation") (description "This package provides functions for easily manipulating colors, creating color scales and calculating color distances.") (license license:bsd-3))) (define-public r-ore (package (name "r-ore") (version "1.7.1.1") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") (description "This package provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.") (license license:bsd-3))) (define-public r-reportr (package (name "r-reportr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "reportr" version)) (sha256 (base32 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) (build-system r-build-system) (propagated-inputs (list r-ore)) (home-page "https://github.com/jonclayden/reportr") (synopsis "General message and error reporting system") (description "This package provides a system for reporting messages, which offers certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current \"output level\".") (license license:gpl2))) (define-public r-tractor-base (package (name "r-tractor-base") (version "3.3.3.1") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p")))) (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs (list r-ore r-reportr r-rnifti r-shades)) (home-page "https://www.tractor-mri.org.uk") (synopsis "Read, manipulate and visualize magnetic resonance images") (description "This package provides functions for working with magnetic resonance images. It supports reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualization; flexible image manipulation; metadata and sparse image handling.") (license license:gpl2))) (define-public r-grimport (package (name "r-grimport") (version "0.9-5") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs (list ghostscript)) (propagated-inputs (list r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport") (synopsis "Convert, import, and draw PostScript pictures") (description "This package provides functions for converting, importing, and drawing PostScript pictures in R plots.") (license license:gpl2+))) (define-public r-grimport2 (package (name "r-grimport2") (version "0.2-0") (source (origin (method url-fetch) (uri (cran-uri "grImport2" version)) (sha256 (base32 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1")))) (properties `((upstream-name . "grImport2"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-jpeg r-png r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport2/") (synopsis "Import SVG graphics") (description "This package provides functions for importing external vector images and drawing them as part of R plots. This package is different from the @code{grImport} package because, where that package imports PostScript format images, this package imports SVG format images. Furthermore, this package imports a specific subset of SVG, so external images must be preprocessed using a package like @code{rsvg} to produce SVG that this package can import. SVG features that are not supported by R graphics, such as gradient fills, can be imported and then exported via the @code{gridSVG} package.") (license license:gpl2+))) (define-public r-kohonen (package (name "r-kohonen") (version "3.0.11") (source (origin (method url-fetch) (uri (cran-uri "kohonen" version)) (sha256 (base32 "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/kohonen") (synopsis "Supervised and unsupervised self-organising maps") (description "This package provides functions to train @dfn{self-organising maps} (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.") (license license:gpl2+))) (define-public r-nnls (package (name "r-nnls") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nnls") (synopsis "Lawson-Hanson algorithm for non-negative least squares") (description "This package provides an R interface to the Lawson-Hanson implementation of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows the combination of non-negative and non-positive constraints.") (license license:gpl2+))) (define-public r-iso (package (name "r-iso") (version "0.0-18.1") (source (origin (method url-fetch) (uri (cran-uri "Iso" version)) (sha256 (base32 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g")))) (properties `((upstream-name . "Iso"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~rolf/") (synopsis "Functions to perform isotonic regression") (description "This package provides support for linear order and unimodal order (univariate) isotonic regression and bivariate isotonic regression with linear order on both variables.") (license license:gpl2+))) (define-public r-chemometricswithr (package (name "r-chemometricswithr") (version "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "ChemometricsWithR" version)) (sha256 (base32 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) (properties `((upstream-name . "ChemometricsWithR"))) (build-system r-build-system) (propagated-inputs (list r-devtools r-kohonen r-mass r-pls)) (home-page "https://github.com/rwehrens/CWR") (synopsis "Chemometrics with R") (description "This package provides functions and scripts used in the book \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences\" by Ron Wehrens, Springer (2011).") (license license:gpl2+))) (define-public r-als (package (name "r-als") (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "ALS" version)) (sha256 (base32 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) (properties `((upstream-name . "ALS"))) (build-system r-build-system) (propagated-inputs (list r-iso r-nnls)) (home-page "https://cran.r-project.org/web/packages/ALS") (synopsis "Multivariate curve resolution alternating least squares") (description "Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. This package provides an implementation of @dfn{multivariate curve resolution alternating least squares} (MCR-ALS). Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.") (license license:gpl2+))) (define-public r-strucchange (package (name "r-strucchange") (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "strucchange" version)) (sha256 (base32 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x")))) (build-system r-build-system) (propagated-inputs (list r-sandwich r-zoo)) (home-page "https://cran.r-project.org/web/packages/strucchange") (synopsis "Testing, monitoring, and dating structural changes") (description "This package provides tools for testing, monitoring and dating structural changes in (linear) regression models. It features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F statistics, respectively. It is possible to monitor incoming data online using fluctuation processes. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data.") ;; Either of these two GPL versions (license (list license:gpl2 license:gpl3)))) (define-public r-pixmap (package (name "r-pixmap") (version "0.4-12") (source (origin (method url-fetch) (uri (cran-uri "pixmap" version)) (sha256 (base32 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pixmap") (synopsis "Tools for bitmap images") (description "This package provides functions for importing, exporting, plotting and other manipulations of bitmapped images.") (license license:gpl2))) (define-public r-rapidjsonr (package (name "r-rapidjsonr") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "rapidjsonr" version)) (sha256 (base32 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rapidjsonr") (synopsis "JSON parser") (description "This package provides JSON parsing capability through the Rapidjson library.") (license license:expat))) (define-public r-ontologyindex (package (name "r-ontologyindex") (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k")))) (properties `((upstream-name . 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This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.") (license license:expat))) (define-public r-bigrquery (package (name "r-bigrquery") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "bigrquery" version)) (sha256 (base32 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-bit64 r-curl r-dbi r-gargle r-glue r-httr r-jsonlite r-lifecycle r-prettyunits r-progress r-rapidjsonr r-rcpp r-rlang r-tibble)) (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.") 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(license license:gpl3+))) (define-public r-rmpfr (package (name "r-rmpfr") (version "0.8-7") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 "1ljpbxvm4agbxnab5dfffbpw5k964hy3gw57dzydq1gpbxwdphlk")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs (list mpfr gmp)) (propagated-inputs (list r-gmp)) (native-inputs (list pkg-config)) (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.") 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(license license:gpl3+))) (define-public r-dotcall64 (package (name "r-dotcall64") (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") (synopsis "Enhanced foreign function interface supporting long vectors") (description "This package provides @code{.C64()}, an enhanced version of @code{.C()} and @code{.Fortran()} from the R foreign function interface. @code{.C64()} supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.") (license license:gpl2+))) (define-public r-spam (package (name "r-spam") (version "2.8-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 (base32 "1ann2a2ifr3z983fcg1c0pkgmbxz6a0ym5q1dmq1r382bd1pg0fr")))) (build-system r-build-system) (propagated-inputs (list r-dotcall64)) (native-inputs (list gfortran r-knitr)) (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. 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The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets.") (license license:gpl2+))) (define-public r-spatialextremes (package (name "r-spatialextremes") (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "SpatialExtremes" version)) (sha256 (base32 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3")))) (properties `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) (propagated-inputs (list r-fields r-maps)) (home-page "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 (list r-car r-gtools r-mass r-multcomp r-plotrix r-scales)) (home-page "https://cran.r-project.org/web/packages/drc") (synopsis "Analysis of dose-response curves") (description "This package provides a suite of flexible and versatile model fitting and after-fitting functions for the analysis of dose-response data.") (license license:gpl2+))) (define-public r-rmeta (package (name "r-rmeta") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "rmeta" version)) (sha256 (base32 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rmeta") (synopsis "Tools for meta-analysis") (description "This package provides functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. It draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.") 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(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 . 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(license license:gpl3))) (define-public r-cmprsk (package (name "r-cmprsk") (version "2.2-11") (source (origin (method url-fetch) (uri (cran-uri "cmprsk" version)) (sha256 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44")))) (build-system r-build-system) (propagated-inputs (list r-survival)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/cmprsk") (synopsis "Subdistribution analysis of competing risks") (description "This package provides tool for estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), A proportional hazards model for the subdistribution of a competing risk, JASA, 94:496-509.") (license license:gpl2+))) (define-public r-etm (package (name "r-etm") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "etm" version)) (sha256 (base32 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/etm") (synopsis "Empirical transition matrix") (description "The @dfn{empirical transition matrix} (etm) package estimates the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator.") (license license:expat))) (define-public r-epi (package (name "r-epi") (version "2.46") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 "0s3ij0rya4wd7k97kc4s3pwj1d1ypaxl1s7zqr6sa07hp4a8fzz0")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs (list r-cmprsk r-data-table r-dplyr r-etm r-magrittr r-mass r-matrix r-mgcv r-numderiv r-plyr r-survival r-zoo)) (home-page "https://BendixCarstensen.com/Epi/") (synopsis "Statistical analysis in epidemiology") (description "This package provides functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation, manipulation and simulation of multistate data - the Lexis suite of functions, which includes interfaces to the @code{mstate}, @code{etm} and @code{cmprsk} packages. It also contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.") (license license:gpl2))) (define-public r-ppls (package (name "r-ppls") (version "1.6-1.1") (source (origin (method url-fetch) (uri (cran-uri "ppls" version)) (sha256 (base32 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ppls") (synopsis "Penalized partial least squares") (description "This package contains linear and nonlinear regression methods based on partial least squares and penalization techniques. Model parameters are selected via cross-validation, and confidence intervals ans tests for the regression coefficients can be conducted via jackknifing.") (license license:gpl2+))) (define-public r-huge (package (name "r-huge") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "huge" version)) (sha256 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/huge") (synopsis "High-dimensional undirected graph estimation") (description "This package provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline.") (license license:gpl2))) (define-public r-parcor (package (name "r-parcor") (version "0.2-6") (source (origin (method url-fetch) (uri (cran-uri "parcor" version)) (sha256 (base32 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) (build-system r-build-system) (propagated-inputs (list r-epi r-genenet r-glmnet r-mass r-ppls)) (home-page "https://cran.r-project.org/web/packages/parcor") (synopsis "Regularized estimation of partial correlation matrices") (description "This package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso and Ridge regression based on cross-validation.") (license license:gpl2+))) (define-public r-mcmc (package (name "r-mcmc") (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "mcmc" version)) (sha256 (base32 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p")))) (build-system r-build-system) (home-page "https://www.stat.umn.edu/geyer/mcmc/") (synopsis "Markov chain Monte Carlo") (description "This package simulates continuous distributions of random vectors using @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are random walk Metropolis algorithm (function @code{metrop}), simulated tempering (function @code{temper}), and morphometric random walk Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity by change of variable.") (license license:expat))) (define-public r-listenv (package (name "r-listenv") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/listenv") (synopsis "Environments behaving (almost) as lists") (description "This package implements list environments. List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting.") (license license:lgpl2.1+))) (define-public r-globals (package (name "r-globals") (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 "15llx4233ihj4w815k7inc17530w9ja0mi29n1i0s2sr42j8jdpq")))) (build-system r-build-system) (propagated-inputs (list r-codetools)) (home-page "https://github.com/HenrikBengtsson/globals") (synopsis "Identify global objects in R expressions") (description "This package provides tools to identify global (\"unknown\" or \"free\") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.") (license license:lgpl2.1+))) (define-public r-parallelly (package (name "r-parallelly") (version "1.31.1") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 "1nhp66psk3m79is5qm4ppxkj7bdy46jr2h2pir22ia9ghhyzris0")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") (synopsis "Enhancements of the parallel package") (description "This package provides utility functions that enhance the @code{parallel} package and support the built-in parallel backends of the @code{future} package. For example, @code{availableCores} gives the number of CPU cores available to your R process as given by R options and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to @code{parallel::detectCores}. Another example is @code{makeClusterPSOCK}, which is backward compatible with @code{parallel::makePSOCKcluster} while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.") (license license:lgpl2.1+))) (define-public r-future (package (name "r-future") (version "1.26.1") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 "1mchjdvvwgs8v0iv8z5m6gav3xzvnq11h8qrc7lfnrb2x3d0np53")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-digest r-globals r-listenv r-parallelly)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future") (synopsis "Unified parallel and distributed processing in R") (description "The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify any code in order to switch from sequential on the local machine to, say, distributed processing on a remote compute cluster.") (license license:lgpl2.1+))) (define-public r-future-apply (package (name "r-future-apply") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 "1xb7qj8izjwmy4aa92p5f4cdbhgp220hrly3b5879f9hrv2w2rk1")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-future r-globals)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future.apply") (synopsis "Apply function to elements in parallel using futures") (description "This package provides implementations of @code{apply()}, @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()}, @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.") (license license:gpl2+))) (define-public r-rsvd (package (name "r-rsvd") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "rsvd" version)) (sha256 (base32 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "https://github.com/erichson/rSVD") (synopsis "Randomized singular value decomposition") (description "Low-rank matrix decompositions are fundamental tools and widely used for data analysis, dimension reduction, and data compression. Classically, highly accurate deterministic matrix algorithms are used for this task. However, the emergence of large-scale data has severely challenged our computational ability to analyze big data. The concept of randomness has been demonstrated as an effective strategy to quickly produce approximate answers to familiar problems such as the @dfn{singular value decomposition} (SVD). This package provides several randomized matrix algorithms such as the randomized singular value decomposition (@code{rsvd}), randomized principal component analysis (@code{rpca}), randomized robust principal component analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}), and the randomized CUR decomposition (@code{rcur}). In addition several plot functions are provided.") (license license:gpl3+))) (define-public r-sloop (package (name "r-sloop") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "sloop" version)) (sha256 (base32 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-crayon r-purrr r-rlang r-tibble)) (home-page "https://github.com/r-lib/sloop") (synopsis "Helpers for object-oriented programming in R") (description "This package provides a collection of helper functions designed to help you to better understand object oriented programming in R, particularly using @code{S3}.") (license license:gpl3))) (define-public r-capushe (package (name "r-capushe") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "capushe" version)) (sha256 (base32 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/capushe/index.html") (synopsis "Calibrating penalties using slope heuristics") (description "This package provides tools for the calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics.") (license license:gpl2+))) (define-public r-dorng (package (name "r-dorng") (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators 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 "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "blockmodeling" version)) (sha256 (base32 "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/blockmodeling") (synopsis "Generalized and classical blockmodeling of valued networks") (description "This package is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted.") (license license:gpl2+))) (define-public r-upsetr (package (name "r-upsetr") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "UpSetR" version)) (sha256 (base32 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im")))) (properties `((upstream-name . "UpSetR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-plyr r-scales)) (home-page "https://github.com/hms-dbmi/UpSetR") (synopsis "Visualize intersecting sets") (description "This package provides a more scalable alternative to Venn and Euler diagrams for visualizing intersecting sets. Create visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.") (license license:expat))) ;; This package includes a JavaScript file, which is not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinybs (package (name "r-shinybs") (version "0.61.1") (source (origin (method url-fetch) (uri (cran-uri "shinyBS" version)) (sha256 (base32 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a")))) (properties `((upstream-name . "shinyBS"))) (build-system r-build-system) ;; The tests spawn Shiny browser apps. They cannot be run ;; non-interactively. (arguments '(#:tests? #f)) (propagated-inputs (list r-htmltools r-shiny)) (home-page "https://ebailey78.github.io/shinyBS/") (synopsis "Twitter Bootstrap components for Shiny") (description "This package adds additional Twitter Bootstrap components to Shiny.") (license license:gpl3))) (define-public r-shinyjqui (package (name "r-shinyjqui") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "shinyjqui" version)) (sha256 (base32 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1")) (snippet '(for-each delete-file (list "inst/www/shinyjqui.min.js" "inst/www/jquery.ui.touch-punch.min.js"))))) (properties `((upstream-name . "shinyjqui"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www" (let ((mapping `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch") "/jquery.ui.touch-punch.js") . "jquery.ui.touch-punch.min.js") ("shinyjqui.js" . "shinyjqui.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (propagated-inputs (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ("js-jquery.ui.touch-punch" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/furf/jquery-ui-touch-punch") (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5"))) (sha256 (base32 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q")))))) (home-page "https://github.com/yang-tang/shinyjqui") (synopsis "jQuery UI interactions and effects for Shiny") (description "This is an extension to Shiny that brings interactions and animation effects from the jQuery UI library.") (license license:expat))) (define-public r-shinymanager (package (name "r-shinymanager") (version "1.0.400") (source (origin (method url-fetch) (uri (cran-uri "shinymanager" version)) (sha256 (base32 "1np2yp5pn8g9i4jhysfgprmdn13cpw4vaaagrd72rnk2r4hpmyx4")))) (properties `((upstream-name . "shinymanager"))) (build-system r-build-system) (propagated-inputs (list r-billboarder r-dbi r-dt r-htmltools r-openssl r-r-utils r-r6 r-rsqlite r-scrypt r-shiny)) (native-inputs (list r-knitr)) (home-page "https://github.com/datastorm-open/shinymanager") (synopsis "Authentication management for Shiny applications") (description "This package provides simple and secure authentification mechanism for single Shiny applications. Credentials are stored in an encrypted SQLite database.") (license license:gpl3))) (define-public r-outliers (package (name "r-outliers") (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "outliers" version)) (sha256 (base32 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/outliers/index.html") (synopsis "Tests for outliers") (description "This package provides a collection of some tests commonly used for identifying outliers.") (license license:gpl2+))) (define-public r-bayesm (package (name "r-bayesm") (version "3.1-4") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) (build-system r-build-system) (propagated-inputs (list r-rcpp 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 "0.36.2") (source (origin (method url-fetch) (uri (cran-uri "tensorA" version)) (sha256 (base32 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf")))) (properties `((upstream-name . "tensorA"))) (build-system r-build-system) (home-page "http://www.stat.boogaart.de/tensorA") (synopsis "Advanced tensor arithmetic with named indices") (description "This package provides convenience functions for advanced linear algebra with tensors and computation with datasets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, and parallel computations on sequences of tensors.") (license license:gpl2+))) (define-public r-rarpack (package (name "r-rarpack") (version "0.11-0") (source (origin (method url-fetch) (uri (cran-uri "rARPACK" version)) (sha256 (base32 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) (properties `((upstream-name . "rARPACK"))) (build-system r-build-system) (propagated-inputs (list r-rspectra)) (home-page "https://github.com/yixuan/rARPACK") (synopsis "Solvers for large scale eigenvalue and SVD problems") (description "This package was previously an R wrapper of the ARPACK library, and now a shell of the R package RSpectra, an R interface to the Spectra library for solving large scale eigenvalue/vector problems. The current version of rARPACK simply imports and exports the functions provided by RSpectra. New users of rARPACK are advised to switch to the RSpectra package.") (license license:bsd-3))) (define-public r-compositions (package (name "r-compositions") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v")))) (build-system r-build-system) (propagated-inputs (list r-bayesm r-mass r-robustbase r-tensora)) (native-inputs (list r-knitr)) (home-page "http://www.stat.boogaart.de/compositions") (synopsis "Compositional data analysis") (description "This package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations).") (license license:gpl2+))) (define-public r-cobs (package (name "r-cobs") (version "1.3-5") (source (origin (method url-fetch) (uri (cran-uri "cobs" version)) (sha256 (base32 "04f6a6gp11p93j2k35mbrfqgjx5qsgi3dj1085a5v5s0z6l7vbkz")))) (build-system r-build-system) (propagated-inputs (list r-quantreg r-sparsem)) (home-page "https://cran.r-project.org/web/packages/cobs") (synopsis "Constrained B-Splines (sparse matrix based)") (description "This package provides qualitatively constrained (regression) smoothing splines via linear programming and sparse matrices.") (license license:gpl2+))) (define-public r-drimpute (package (name "r-drimpute") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "DrImpute" version)) (sha256 (base32 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b")))) (properties `((upstream-name . "DrImpute"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "https://github.com/ikwak2/DrImpute") (synopsis "Imputing dropout events in single-cell RNA-Seq data") (description "This is an R package for imputing dropout events. Many statistical methods in cell type identification, visualization and lineage reconstruction do not account for dropout events. DrImpute can improve the performance of such software by imputing dropout events.") (license license:gpl3))) (define-public r-gamlss-dist (package (name "r-gamlss-dist") (version "6.0-3") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 (base32 "1gqjr419v8z2ygh0h1xz7bipnsbp820njzwq7z3r9f41rn1ym47c")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "http://www.gamlss.org/") (synopsis "Distributions for Generalized Additive Models for location scale and shape") (description "This package provides a set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} transformation, respectively.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) ;; This package includes JavaScript files, which are not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinyjs (package (name "r-shinyjs") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjs" version)) (sha256 (base32 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky")))) (build-system r-build-system) (propagated-inputs (list r-digest r-jsonlite r-shiny)) (native-inputs (list r-knitr)) (home-page "https://deanattali.com/shinyjs") (synopsis "Improve the user experience of your Shiny apps") (description "Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. Examples include: hiding an element, disabling an input, resetting an input back to its original value, delaying code execution by a few seconds, and many more useful functions for both the end user and the developer. Shinyjs can also be used to easily call your own custom JavaScript functions from R.") (license license:agpl3+))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-colourpicker (package (name "r-colourpicker") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "colourpicker" version)) (sha256 (base32 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" (let ((mapping `((,(assoc-ref inputs "js-salvattore") . "examples/colourInput/www/salvattore.min.js") (,(assoc-ref inputs "js-jquery") . "htmlwidgets/lib/jquery/jquery.min.js") ("www/shared/colourpicker/js/colourpicker.js" . "www/shared/colourpicker/js/colourpicker.min.js")))) (for-each (lambda (source target) (format #true "Processing ~a --> ~a~%" source target) (delete-file target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) (map car mapping) (map cdr mapping))))))))) (propagated-inputs (list r-ggplot2 r-htmltools r-htmlwidgets r-jsonlite r-miniui r-shiny r-shinyjs)) (native-inputs `(("esbuild" ,esbuild) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.11.3.js") (sha256 (base32 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90")))) ("js-salvattore" ,(origin (method url-fetch) (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js") (sha256 (base32 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5")))))) (home-page "https://github.com/daattali/colourpicker") (synopsis "Color picker tool for Shiny and for selecting colors in plots") (description "This package provides a color picker that can be used as an input in Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, custom color palettes, and many more options. A plot color helper tool is available as an RStudio Addin, which helps you pick colors to use in your plots. A more generic color picker RStudio Addin is also provided to let you select colors to use in your R code.") (license license:expat))) (define-public r-ggextra (package (name "r-ggextra") (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "ggExtra" version)) (sha256 (base32 "1rd3qv6ah3zphr1jicjhgxms73vi496mjnxnsrcgl7z8nyxmas6w")))) (properties `((upstream-name . "ggExtra"))) (build-system r-build-system) (propagated-inputs (list r-colourpicker r-ggplot2 r-gtable r-miniui r-r6 r-scales r-shiny r-shinyjs)) (native-inputs (list r-knitr)) (home-page "https://github.com/daattali/ggExtra") (synopsis "Marginal histograms for ggplot2 and other enhancements") (description "This package is a collection of functions and layers to enhance ggplot2. The flagship function is @code{ggMarginal()}, which can be used to add marginal histograms/boxplots/density plots to ggplot2 scatterplots.") (license license:expat))) (define-public r-minpack-lm (package (name "r-minpack-lm") (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/minpack.lm") (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") (description "The @code{nls.lm} function provides an R interface to @code{lmder} and @code{lmdif} from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via @code{nls}-like calls using the @code{nlsLM} function.") (license license:gpl3))) (define-public r-moments (package (name "r-moments") (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "moments" version)) (sha256 (base32 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/moments") (synopsis "Moments, cumulants, skewness, kurtosis and related tests") (description "This package provides functions to calculate: moments, Pearson's kurtosis, Geary's kurtosis and skewness; it also includes tests related to them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") (license license:gpl2+))) (define-public r-msir (package (name "r-msir") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "msir" version)) (sha256 (base32 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84")))) (build-system r-build-system) (propagated-inputs (list r-mclust)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/msir") (synopsis "Model-based sliced inverse regression") (description "This is an R package for dimension reduction based on finite Gaussian mixture modeling of inverse regression.") (license license:gpl2+))) (define-public r-pbivnorm (package (name "r-pbivnorm") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "pbivnorm" version)) (sha256 (base32 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://github.com/brentonk/pbivnorm") (synopsis "Vectorized bivariate normal CDF") (description "This package provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF.") (license license:gpl2+))) (define-public r-lavaan (package (name "r-lavaan") (version "0.6-11") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 "026k32paf51lpy6zxm9m81zg9szx14j37dxdip6nba334jw97h9c")))) (build-system r-build-system) (propagated-inputs (list r-mass r-mnormt r-numderiv r-pbivnorm)) (home-page "https://lavaan.ugent.be") (synopsis "Latent variable analysis") (description "This package provides tools to fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.") (license license:gpl2+))) (define-public r-nonnest2 (package (name "r-nonnest2") (version "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "nonnest2" version)) (sha256 (base32 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2")))) (build-system r-build-system) (propagated-inputs (list r-compquadform r-lavaan r-mvtnorm r-sandwich)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/nonnest2/") (synopsis "Tests of non-nested models") (description "This package allows for testing of non-nested models. It includes tests of model distinguishability and of model fit that can be applied to both nested and non-nested models. The package also includes functionality to obtain confidence intervals associated with AIC and BIC.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-penalized (package (name "r-penalized") (version "0.9-52") (source (origin (method url-fetch) (uri (cran-uri "penalized" version)) (sha256 (base32 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/penalized/") (synopsis "Penalized estimation in GLMs and in the Cox model") (description "This package provides tools for fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.") (license license:gpl2+))) (define-public r-zim (package (name "r-zim") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "ZIM" version)) (sha256 (base32 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) (properties `((upstream-name . "ZIM"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://github.com/biostatstudio/ZIM") (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") (description "Analyze count time series with excess zeros. Two types of statistical models are supported: Markov regression and state-space models. They are also known as observation-driven and parameter-driven models respectively in the time series literature. The functions used for Markov regression or observation-driven models can also be used to fit ordinary regression models with independent data under the zero-inflated Poisson (ZIP) or zero-inflated negative binomial (ZINB) assumption. The package also contains miscellaneous functions to compute density, distribution, quantile, and generate random numbers from ZIP and ZINB distributions.") (license license:gpl3))) (define-public r-nor1mix (package (name "r-nor1mix") (version "1.3-0") (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 "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "beanplot" version)) (sha256 (base32 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/beanplot/") (synopsis "Visualization via beanplots") (description "This package provides beanplots, an alternative to boxplot/stripchart/violin plots. It can be used to plot univariate comparison graphs.") (license license:gpl2))) (define-public r-pbdzmq (package (name "r-pbdzmq") (version "0.3-7") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 "020qy6fq8w8wq0j3bii14ahrlg8wzl0lrnndfr6scmrg9ghjnbfz")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs (list zeromq zlib)) (native-inputs (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "R interface to ZeroMQ") (description "ZeroMQ is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize ZeroMQ. The main focus is on interactive client/server programming frameworks. A few wrapper functions compatible with @code{rzmq} are also provided.") (license license:gpl3))) (define-public r-repr (package (name "r-repr") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-htmltools r-jsonlite r-pillar)) (home-page "https://cran.r-project.org/web/packages/repr/") (synopsis "Serializable representations") (description "This package provides string and binary representations of objects for several formats and MIME types.") (license license:gpl3))) (define-public r-irdisplay (package (name "r-irdisplay") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "IRdisplay" version)) (sha256 (base32 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3")))) (properties `((upstream-name . "IRdisplay"))) (build-system r-build-system) (propagated-inputs (list r-repr)) (home-page "https://cran.r-project.org/web/packages/IRdisplay/") (synopsis "Jupyter display machinery") (description "This package provides an interface to the rich display capabilities of Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a running IRkernel session.") (license license:expat))) (define-public r-irkernel (package (name "r-irkernel") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'install 'install-kernelspec (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (setenv "HOME" "/tmp") (invoke "jupyter" "kernelspec" "install" "--name" "ir" "--prefix" out (string-append out "/site-library/IRkernel/kernelspec")) ;; Record the absolute file name of the 'R' executable in ;; 'kernel.json'. (substitute* (string-append out "/share/jupyter" "/kernels/ir/kernel.json") (("\\[\"R\",") (string-append "[\"" (which "R") "\","))) #t)))))) (inputs (list jupyter)) (propagated-inputs (list r-crayon r-digest r-evaluate r-irdisplay r-jsonlite ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) r-minimal r-pbdzmq r-repr r-uuid)) (home-page "https://cran.r-project.org/web/packages/IRkernel/") (synopsis "Native R kernel for Jupyter") (description "The R kernel for the Jupyter environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.") (license license:expat))) (define-public r-gmodels (package (name "r-gmodels") (version "2.18.1.1") (source (origin (method url-fetch) (uri (cran-uri "gmodels" version)) (sha256 (base32 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs")))) (build-system r-build-system) (propagated-inputs (list r-gdata r-mass)) (home-page "https://cran.r-project.org/web/packages/gmodels/") (synopsis "Various R programming tools for model fitting") (description "This package provides various R programming tools for model fitting.") (license license:gpl2))) (define-public r-apcluster (package (name "r-apcluster") (version "1.4.9") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 "0wnbb3kj9m7rfq63xr43jjf6n8jxm1r2wvvx6g0qkss0wvipbb1s")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/apcluster/") (synopsis "Affinity propagation clustering") (description "This package implements affinity propagation clustering introduced by Frey and Dueck (2007). The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.") (license license:gpl2+))) (define-public r-rematch2 (package (name "r-rematch2") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "rematch2" version)) (sha256 (base32 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y")))) (build-system r-build-system) (propagated-inputs (list r-tibble)) (home-page "https://github.com/r-lib/rematch2") (synopsis "Tidy output from regular expression matching") (description "This package provides wrappers on @code{regexpr} and @code{gregexpr} to return the match results in tidy data frames.") (license license:expat))) (define-public r-picante (package (name "r-picante") (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "picante" version)) (sha256 (base32 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn")))) (build-system r-build-system) (propagated-inputs (list r-ape r-nlme r-vegan)) (home-page "https://cran.r-project.org/web/packages/picante/") (synopsis "Integrating phylogenies and ecology") (description "This package provides functions for phylocom integration, community analyses, null-models, traits and evolution. It implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010).") (license license:gpl2))) (define-public r-reinforcelearn (package (name "r-reinforcelearn") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "reinforcelearn" version)) (sha256 (base32 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-nnet r-purrr r-r6)) (home-page "https://markusdumke.github.io/reinforcelearn") (synopsis "Reinforcement learning") (description "This package implements reinforcement learning environments and algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm can be used with function approximation, eligibility traces (Singh & Sutton, 1996) and experience replay (Mnih et al., 2013).") (license license:expat))) (define-public r-lemon (package (name "r-lemon") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-gtable r-knitr r-lattice r-plyr r-rlang r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/stefanedwards/lemon") (synopsis "Freshen up your ggplot2 plots") (description "This package provides functions for working with legends and axis lines of ggplot2, facets that repeat axis lines on all panels, and some knitr extensions.") (license license:gpl3))) (define-public r-wgaim (package (name "r-wgaim") (version "2.0-1") (source (origin (method url-fetch) (uri (cran-uri "wgaim" version)) (sha256 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-qtl)) (home-page "https://cran.r-project.org/web/packages/wgaim") (synopsis "Whole genome average interval mapping for QTL detection") (description "This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.") (license license:gpl2+))) (define-public r-bedr (package (name "r-bedr") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "bedr" version)) (sha256 (base32 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-r-utils r-testthat r-venndiagram r-yaml bedops bedtools htslib)) ; for tabix (native-inputs (list r-knitr)) ; for vignettes (home-page "https://cran.r-project.org/web/packages/bedr") (synopsis "Genomic region processing") (description "This package is for genomic regions processing using command line tools such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. The bedr package's API enhances access to these tools as well as offers additional utilities for genomic regions processing.") (license license:gpl2))) (define-public r-sets (package (name "r-sets") (version "1.0-21") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp")))) (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 "1.9-22") (source (origin (method url-fetch) (uri (cran-uri "partitions" version)) (sha256 (base32 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns")))) (build-system r-build-system) (propagated-inputs (list r-gmp r-polynom r-sets)) (home-page "https://cran.r-project.org/web/packages/partitions") (synopsis "Additive partitions of integers") (description "This package provides tools to enumerates the partitions, unequal partitions, and restricted partitions of an integer; the three corresponding partition functions are also given.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-brobdingnag (package (name "r-brobdingnag") (version "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "Brobdingnag" version)) (sha256 (base32 "0hnp5nrpnscykvgrrbgp7987660hcbv92zc2q8lmpnin4ws399vk")))) (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 (list r-brobdingnag r-partitions r-polynom)) (home-page "https://github.com/RobinHankin/untb.git") (synopsis "Ecological drift under the UNTB") (description "This package provides numerical simulations, and visualizations, of Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).") (license license:gpl2+))) (define-public r-stepwise (package (name "r-stepwise") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "stepwise" version)) (sha256 (base32 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2")))) (build-system r-build-system) (home-page "https://stat.sfu.ca/statgen/research/stepwise.html") (synopsis "Stepwise detection of recombination breakpoints") (description "This package provides a stepwise approach to identifying recombination breakpoints in a genomic sequence alignment.") (license license:gpl2+))) (define-public r-snpmaxsel (package (name "r-snpmaxsel") (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "SNPmaxsel" version)) (sha256 (base32 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z")))) (properties `((upstream-name . "SNPmaxsel"))) (build-system r-build-system) (propagated-inputs (list r-combinat r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") (synopsis "Maximally selected statistics for SNP data") (description "This package implements asymptotic methods related to maximally selected statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP) data.") (license license:gpl2+))) (define-public r-acsnminer (package (name "r-acsnminer") (version "0.16.8.25") (source (origin (method url-fetch) (uri (cran-uri "ACSNMineR" version)) (sha256 (base32 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) (properties `((upstream-name . "ACSNMineR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra)) (home-page "https://cran.r-project.org/web/packages/ACSNMineR") (synopsis "Gene enrichment analysis") (description "This package provides tools to compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the @dfn{Atlas of Cancer Signalling Networks} (ACSN) or user imported maps. The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections. Visualization of data can be done either by barplots or heatmaps.") (license license:gpl2+))) (define-public r-seqinr (package (name "r-seqinr") (version "4.2-16") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-segmented)) (inputs (list 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 "0.8-0") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw")))) (build-system r-build-system) (inputs (list udunits)) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-quantities/units/") (synopsis "Measurement Units for R Vectors") (description "This package provides support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. It is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} classes.") (license license:gpl2))) (define-public r-udunits2 (package (name "r-udunits2") (version "0.13.2.1") (source (origin (method url-fetch) (uri (cran-uri "udunits2" version)) (sha256 (base32 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z")))) (properties `((upstream-name . "udunits2"))) (build-system r-build-system) (inputs (list udunits)) (home-page "https://cran.r-project.org/package=udunits2") (synopsis "Udunits-2 bindings for R") (description "This package provides simple bindings to Unidata's udunits library.") (license license:gpl2))) (define-public r-classint (package (name "r-classint") (version "0.4-3") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs (list r-class r-e1071 r-kernsmooth)) (native-inputs (list gfortran r-knitr)) (home-page "https://github.com/r-spatial/classInt/") (synopsis "Choose univariate class intervals") (description "This package provides selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.") (license license:gpl2+))) (define-public r-spdata (package (name "r-spdata") (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs (list r-raster r-sp)) (home-page "https://github.com/Nowosad/spData") (synopsis "Datasets for spatial analysis") (description "This a package containing diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some of the datasets are designed to illustrate specific analysis techniques. @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to illustrate point pattern analysis techniques.") (license license:cc0))) (define-public r-learnbayes (package (name "r-learnbayes") (version "2.15.1") (source (origin (method url-fetch) (uri (cran-uri "LearnBayes" version)) (sha256 (base32 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv")))) (properties `((upstream-name . "LearnBayes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/LearnBayes") (synopsis "Functions for learning Bayesian inference") (description "This package provides a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.") (license license:gpl2+))) (define-public r-deldir (package (name "r-deldir") (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/deldir") (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") (description "This package provides tools for calculating the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. It plots triangulations and tessellations in various ways, clips tessellations to sub-windows, calculates perimeters of tessellations, and summarizes information about the tiles of the tessellation.") (license license:gpl2+))) (define-public r-wk (package (name "r-wk") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) (home-page "https://paleolimbot.github.io/wk/") (synopsis "Lightweight well-known geometry parsing") (description "This package provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are only useful in R if the information they contain can be accessed in R, for which high-performance functions are provided here.") (license license:expat))) (define-public r-s2 (package (name "r-s2") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "s2" version)) (sha256 (base32 "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410")))) (properties `((upstream-name . "s2"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-wk)) (inputs (list openssl)) (native-inputs (list pkg-config)) (home-page "https://r-spatial.github.io/s2/") (synopsis "Spherical geometry operators using the S2 geometry library") (description "This package provides R bindings for Google's s2 library for geometric calculations on the sphere. High-performance constructors and exporters provide high compatibility with existing spatial packages, transformers construct new geometries from existing geometries, predicates provide a means to select geometries based on spatial relationships, and accessors extract information about geometries.") (license license:asl2.0))) (define-public r-sf (package (name "r-sf") (version "1.0-7") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 "0lsl4rh4lbv386hxlsnnwsjb5x1n9d3z0ckjmxakmmrqjjmiywyh")))) (build-system r-build-system) (inputs (list gdal geos proj sqlite zlib)) (propagated-inputs (list r-classint r-dbi r-magrittr r-rcpp r-s2 r-units)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-spatial/sf/") (synopsis "Simple features for R") (description "This package provides support for simple features, a standardized way to encode spatial vector data. It binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum transformations.") ;; Either of these licenses (license (list license:gpl2 license:expat)))) (define-public r-spdep (package (name "r-spdep") (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 "0xx6k3rsvsz1hwj0ny8aqfi9ca54x38f8pz8sfya5cggaspxbx59")) (snippet '(for-each delete-file '("inst/doc/CO69.html" "inst/doc/CO69.R" "inst/doc/nb.html" "inst/doc/nb.R" "inst/doc/nb_sf.html" "inst/doc/nb_sf.R" "inst/doc/nb_sf.Rmd" "inst/doc/sids.html" "inst/doc/sids.R"))))) (build-system r-build-system) (propagated-inputs (list r-boot r-deldir r-e1071 r-s2 r-sf r-sp r-spdata r-units)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-spatial/spdep/") (synopsis "Spatial dependence: weighting schemes, statistics and models") (description "This package provides a collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.") (license license:gpl2+))) (define-public r-adegenet (package (name "r-adegenet") (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 "0sx25p7bgz0h9mc3jsdnnjhvmb7sy8nb3r0z923vhk336d4xw8vq")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-boot r-dplyr r-ggplot2 r-igraph r-mass r-reshape2 r-seqinr r-shiny r-vegan)) (home-page "https://github.com/thibautjombart/adegenet") (synopsis "Exploratory analysis of genetic and genomic data") (description "This package provides a toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure (@code{genind} class), alleles counts by populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.") (license license:gpl2+))) (define-public r-pegas (package (name "r-pegas") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7")))) (build-system r-build-system) (propagated-inputs (list r-ape)) (home-page "http://ape-package.ird.fr/pegas.html") (synopsis "Population and evolutionary genetics analysis system") (description "This package provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.") (license license:gpl2+))) (define-public r-rmetasim (package (name "r-rmetasim") (version "3.1.14") (source (origin (method url-fetch) (uri (cran-uri "rmetasim" version)) (sha256 (base32 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-adegenet r-gtools 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 "1.3.8.1.3") (source (origin (method url-fetch) (uri (cran-uri "genetics" version)) (sha256 (base32 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy")))) (build-system r-build-system) (propagated-inputs (list r-combinat r-gdata r-gtools r-mass r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/genetics/") (synopsis "Population genetics") (description "This package provides classes and methods for handling genetic data. It includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...") ;; Any GPL version. (license license:gpl2+))) (define-public r-snp-plotter (package (name "r-snp-plotter") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "snp.plotter" version)) (sha256 (base32 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) (properties `((upstream-name . "snp.plotter"))) (build-system r-build-system) (propagated-inputs (list r-genetics)) (home-page "https://cran.r-project.org/web/packages/snp.plotter/") (synopsis "Plot p-values using single SNP and/or haplotype data") (description "This package helps you create plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple datasets simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either PDF/EPS files.") (license license:gpl2+))) (define-public r-polspline (package (name "r-polspline") (version "1.1.20") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") (synopsis "Polynomial spline routines") (description "This package provides routines for the polynomial spline fitting routines hazard regression, hazard estimation with flexible tails, logspline, lspec, polyclass, and polymars.") (license license:gpl2+))) (define-public r-rms (package (name "r-rms") (version "6.3-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-digest r-ggplot2 r-hmisc r-htmltable r-htmltools r-lattice r-mass r-multcomp r-nlme r-polspline r-quantreg r-rpart r-sparsem r-survival)) (native-inputs (list gfortran)) (home-page "http://biostat.mc.vanderbilt.edu/rms") (synopsis "Regression modeling strategies") (description "This is a package for regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. The rms package is a collection of functions that assist with and streamline modeling. It also contains functions for binary and ordinal logistic regression models, ordinal models for continuous Y with a variety of distribution families, and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. The package works with almost any regression model, but it was especially written to work with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.") (license license:gpl2+))) (define-public r-arsenal (package (name "r-arsenal") (version "3.6.3") (source (origin (method url-fetch) (uri (cran-uri "arsenal" version)) (sha256 (base32 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms")))) (properties `((upstream-name . "arsenal"))) (build-system r-build-system) (propagated-inputs (list r-knitr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mayoverse/arsenal") (synopsis "Functions for large-scale statistical summaries") (description "This package provides an arsenal of R functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in R and RStudio and which use formulas and versatile summary statistics for summary tables and models. The primary functions include @enumerate @item @code{tableby}, a Table-1-like summary of multiple variable types by the levels of one or more categorical variables; @item @code{paired}, a Table-1-like summary of multiple variable types paired across two time points; @item @code{modelsum}, which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); @item @code{freqlist}, a powerful frequency table across many categorical variables; @item @code{comparedf}, a function for comparing @code{data.frames}; and @item @code{write2}, a function to output tables to a document. @end enumerate ") (license license:gpl2+))) (define-public r-haplo-stats (package (name "r-haplo-stats") (version "1.8.7") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 "1q2zn72j92bwhcdswk4qqfgzch56p9pcy2xhkd3safvqp3l9rzpw")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs (list r-arsenal r-rms)) (native-inputs (list r-r-rsp)) ; for vignettes (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") (synopsis "Analysis of haplotypes when linkage phase is ambiguous") (description "This package provides routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()}, @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed examples in the vignette.") (license license:gpl2+))) (define-public r-bqtl (package (name "r-bqtl") (version "1.0-33") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") (synopsis "Bayesian QTL mapping toolkit") (description "This is a QTL mapping toolkit for inbred crosses and recombinant inbred lines. It includes maximum likelihood and Bayesian tools.") (license license:gpl2+))) (define-public r-ibdreg (package (name "r-ibdreg") (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "ibdreg" version)) (sha256 (base32 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g")))) (build-system r-build-system) (home-page "https://www.mayo.edu/research/labs/\ statistical-genetics-genetic-epidemiology/software") (synopsis "Regression methods for IBD linkage with covariates") (description "This package provides a method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree.") (license license:gpl2+))) (define-public r-dlmap (package (name "r-dlmap") (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "dlmap" version)) (sha256 (base32 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) (build-system r-build-system) (propagated-inputs (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim)) (home-page "https://cran.r-project.org/web/packages/dlmap/") (synopsis "Detection localization mapping for QTL") (description "This is package for QTL mapping in a mixed model framework with separate detection and localization stages. The first stage detects the number of QTL on each chromosome based on the genetic variation due to grouped markers on the chromosome; the second stage uses this information to determine the most likely QTL positions. The mixed model can accommodate general fixed and random effects, including spatial effects in field trials and pedigree effects. It is applicable to backcrosses, doubled haploids, recombinant inbred lines, F2 intercrosses, and association mapping populations.") (license license:gpl2))) (define-public r-hwde (package (name "r-hwde") (version "0.67") (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 (list r-rcurl r-xml)) (home-page "https://cran.r-project.org/web/packages/SPARQL") (synopsis "SPARQL client for R") (description "This package provides an interface to use SPARQL to pose SELECT or UPDATE queries to an end-point.") ;; The only license indication is found in the DESCRIPTION file, ;; which states GPL-3. So we cannot assume GPLv3+. (license license:gpl3))) (define-public r-bookdown (package (name "r-bookdown") (version "0.26") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 "11din9h2sgzvg44627xc5is4psbq2b34km5sbiaprskjrf474866")))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-jquerylib r-knitr r-rmarkdown r-tinytex r-xfun r-yaml pandoc)) ;; We cannot add knitr because this package depends on xfun, which is an ;; input to knitr. #; (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for authoring books and technical documents with R Markdown.") (license license:gpl3))) (define-public r-optparse (package (name "r-optparse") (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij")))) (build-system r-build-system) (propagated-inputs (list r-getopt)) (native-inputs (list r-knitr)) (home-page "https://github.com/trevorld/optparse") (synopsis "Command line option parser") (description "This package provides a command line parser inspired by Python's @code{optparse} library to be used with Rscript to write shebang scripts that accept short and long options.") (license license:gpl2+))) (define-public r-kernlab (package (name "r-kernlab") (version "0.9-30") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 "10gfb542nbl1d5pfy6r7gcg3j1ikra9l18r6xjv8lzp5ka1kmz28")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/kernlab") (synopsis "Kernel-based machine learning tools") (description "This package provides kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods @code{kernlab} includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.") (license license:gpl2))) (define-public r-hierfstat (package (name "r-hierfstat") (version "0.5-11") (source (origin (method url-fetch) (uri (cran-uri "hierfstat" version)) (sha256 (base32 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-adegenet r-gaston r-gtools)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/hierfstat/") (synopsis "Estimation and tests of hierarchical F-statistics") (description "This package allows the estimation of hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions are also given to test via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G.") (license license:gpl2+))) (define-public r-hapassoc (package (name "r-hapassoc") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "hapassoc" version)) (sha256 (base32 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6")))) (build-system r-build-system) (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html") (synopsis "Inference of trait associations with SNP haplotypes") (description "Hapassoc performs likelihood inference of trait associations with haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.") (license license:gpl2))) (define-public r-sampling (package (name "r-sampling") (version "2.9") (source (origin (method url-fetch) (uri (cran-uri "sampling" version)) (sha256 (base32 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz")))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-mass)) (home-page "https://cran.r-project.org/web/packages/sampling/") (synopsis "Survey sampling") (description "This package provides functions for drawing and calibrating samples.") (license license:gpl2+))) (define-public r-r2html (package (name "r-r2html") (version "2.3.3") (source (origin (method url-fetch) (uri (cran-uri "R2HTML" version)) (sha256 (base32 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja")))) (properties `((upstream-name . "R2HTML"))) (build-system r-build-system) (home-page "https://github.com/nalimilan/R2HTML") (synopsis "HTML export for R objects") (description "This package includes HTML functions and methods to write in an HTML file. Thus, making HTML reports is easy. It includes a function that allows redirection on the fly, which appears to be very useful for teaching purposes, as the student can keep a copy of the produced output to keep all that they did during the course. The package comes with a vignette describing how to write HTML reports for statistical analysis. Finally, a driver for Sweave parses HTML flat files containing R code and to automatically write the corresponding outputs (tables and graphs).") (license license:gpl2+))) (define-public r-rjava (package (name "r-rjava") (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472")))) (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") ("zlib" ,zlib))) (home-page "https://www.rforge.net/rJava/") (synopsis "Low-Level R to Java interface") (description "This package provides a low-level interface to the Java VM very much like .C/.Call and friends. It allows the creation of objects, calling methods and accessing fields.") (license license:gpl2))) (define-public r-svmisc (package (name "r-svmisc") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "svMisc" version)) (sha256 (base32 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d")))) (properties `((upstream-name . "svMisc"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/SciViews/svMisc") (synopsis "Miscellaneous functions for SciViews") (description "This package provides miscellaneous functions for SciViews or general use, including tools to manage a temporary environment attached to the search path for temporary variables you do not want to @code{save()} or @code{load()}; test the current platform; showing progress bars, etc.") (license license:gpl2))) (define-public r-xyz (package (name "r-xyz") (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "xyz" version)) (sha256 (base32 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/xyz/") (synopsis "Algorithm for fast interaction search in high-dimensional data") (description "High dimensional interaction search by brute force requires a quadratic computational cost in the number of variables. The xyz algorithm provably finds strong interactions in almost linear time. For details of the algorithm see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast interaction search in high-dimensional data.") ;; Any version of the GPL. (license license:gpl2+))) (define-public r-rttf2pt1 (package (name "r-rttf2pt1") (version "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "Rttf2pt1" version)) (sha256 (base32 "1fp1y0kxa5xg8w0dplm12wfm8h78az4k6ql1758wwhb3d17np241")))) (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 "0.18") (source (origin (method url-fetch) (uri (cran-uri "extrafont" version)) (sha256 (base32 "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4")))) (build-system r-build-system) (propagated-inputs (list r-extrafontdb r-rttf2pt1)) (home-page "https://github.com/wch/extrafont") (synopsis "Tools for using fonts in R") (description "The extrafont package makes it easier to use fonts other than the basic PostScript fonts that R uses. Fonts that are imported into extrafont can be used with PDF or PostScript output files. There are two hurdles for using fonts in PDF (or Postscript) output files: @enumerate @item Making R aware of the font and the dimensions of the characters. @item Embedding the fonts in the PDF file so that the PDF can be displayed properly on a device that doesn't have the font. This is usually needed if you want to print the PDF file or share it with others. @end enumerate The extrafont package makes both of these things easier.") (license license:gpl2))) (define-public r-xkcd (package (name "r-xkcd") (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "xkcd" version)) (sha256 (base32 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) (build-system r-build-system) (propagated-inputs (list r-extrafont r-ggplot2 r-hmisc)) (home-page "https://cran.r-project.org/web/packages/xkcd/") (synopsis "Plot ggplot2 graphics in the XKCD style") (description "This package provides the means to plot ggplot2 graphs in the style of the XKCD web comic.") (license license:gpl3))) (define-public r-babelgene (package (name "r-babelgene") (version "22.3") (source (origin (method url-fetch) (uri (cran-uri "babelgene" version)) (sha256 (base32 "1735h4s2vahv55pmq65zkgxq8d5x71i1is03rf17dric8yynjjhg")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-msigdbr (package (name "r-msigdbr") (version "7.5.1") (source (origin (method url-fetch) (uri (cran-uri "msigdbr" version)) (sha256 (base32 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w")))) (build-system r-build-system) (propagated-inputs (list r-babelgene r-dplyr r-magrittr r-rlang r-tibble r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://github.com/igordot/msigdbr") (synopsis "MSigDB gene sets for multiple organisms") (description "This package provides the @dfn{Molecular Signatures Database} (MSigDB) gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA) software in a standard R data frame with key-value pairs. Included are the original human gene symbols and Entrez IDs as well as the equivalents for various frequently studied model organisms such as mouse, rat, pig, fly, and yeast.") ;; The package is covered under the Expat license, but the upstream MSigDB ;; files are made available under the Creative Commons Attribution 4.0 ;; International license. (license (list license:expat license:cc-by4.0)))) (define-public r-gridgraphics (package (name "r-gridgraphics") (version "0.5-1") (source (origin (method url-fetch) (uri (cran-uri "gridGraphics" version)) (sha256 (base32 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219")))) (properties `((upstream-name . "gridGraphics"))) (build-system r-build-system) (home-page "https://github.com/pmur002/gridgraphics") (synopsis "Redraw base graphics using @code{grid} graphics") (description "This package provides functions to convert a page of plots drawn with the @code{graphics} package into identical output drawn with the @code{grid} package. The result looks like the original @code{graphics}-based plot, but consists of @code{grid} grobs and viewports that can then be manipulated with @code{grid} functions (e.g., edit grobs and revisit viewports).") (license license:gpl2+))) (define-public r-farver (package (name "r-farver") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "farver" version)) (sha256 (base32 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75")))) (build-system r-build-system) (home-page "https://github.com/thomasp85/farver") (synopsis "Vectorized color conversion and comparison") (description "The encoding of color can be handled in many different ways, using different color spaces. As different color spaces have different uses, efficient conversion between these representations are important. This package provides a set of functions that gives access to very fast color space conversion and comparisons implemented in C++, and offers 100-fold speed improvements over the @code{convertColor} function in the @code{grDevices} package.") (license license:expat))) (define-public r-yulab-utils (package (name "r-yulab-utils") (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=yulab.utils") (synopsis "Supporting functions for packages maintained by YuLab-SMU") (description "Miscellaneous functions commonly used by YuLab-SMU, such as @code{install_zip_gh} to install R packages from Github ZIP files.") (license license:artistic2.0))) (define-public r-ggplotify (package (name "r-ggplotify") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridgraphics r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/GuangchuangYu/ggplotify") (synopsis "Convert plots to @code{grob} or @code{ggplot} object") (description "This package provides tools to convert plot function calls (using expression or formula) to @code{grob} or @code{ggplot} objects that are compatible with the @code{grid} and @code{ggplot2} environment. With this package, we are able to e.g. use @code{cowplot} to align plots produced by @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by converting them to @code{ggplot} objects.") (license license:artistic2.0))) (define-public r-triebeard (package (name "r-triebeard") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "triebeard" version)) (sha256 (base32 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) (build-system r-build-system) (propagated-inputs (list 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 "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "tweenr" version)) (sha256 (base32 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q")))) (build-system r-build-system) (propagated-inputs (list r-farver r-magrittr r-rcpp 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 (list pkg-config)) (home-page "http://www.angusj.com/delphi/clipper.php") (synopsis "Polygon clipping") (description "This package provides an R port of the library Clipper. It performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. It computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. It computes the Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.") (license license:boost1.0))) (define-public r-urltools (package (name "r-urltools") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "urltools" version)) (sha256 (base32 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-triebeard)) (home-page "https://github.com/Ironholds/urltools/") (synopsis "Vectorized tools for URL handling and parsing") (description "This package provides a toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorized. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.") (license license:expat))) (define-public r-ggforce (package (name "r-ggforce") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "ggforce" version)) (sha256 (base32 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gtable r-mass r-polyclip r-rcpp r-rcppeigen r-rlang r-scales r-tidyselect r-tweenr r-withr)) (home-page "https://ggforce.data-imaginist.com") (synopsis "Accelerating ggplot2") (description "The aim of the ggplot2 package is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialized plots. This package aims to be a collection of mainly new statistics and geometries that fills this gap.") (license license:expat))) (define-public r-europepmc (package (name "r-europepmc") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "europepmc" version)) (sha256 (base32 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-httr r-jsonlite r-plyr r-progress r-purrr r-rlang r-tibble r-tidyr r-urltools r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/europepmc/") (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") (description "This package provides an R Client for the @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web Service}. It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible.") (license license:gpl3))) (define-public r-ggraph (package (name "r-ggraph") (version "2.0.5") (source (origin (method url-fetch) (uri (cran-uri "ggraph" version)) (sha256 (base32 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3")))) (build-system r-build-system) (propagated-inputs (list r-digest r-dplyr r-ggforce r-ggplot2 r-ggrepel r-graphlayouts r-gtable r-igraph r-mass r-rcpp r-rlang r-scales r-tidygraph r-viridis r-withr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ggraph/") (synopsis "Implementation of grammar of graphics for graphs and networks") (description "The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. The ggraph package is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.") (license license:gpl3))) (define-public r-gkmsvm (package (name "r-gkmsvm") (version "0.81.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs (list r-kernlab r-rcpp r-rocr r-seqinr)) (home-page "https://cran.r-project.org/web/packages/gkmSVM") (synopsis "Gapped-kmer support vector machine") (description "This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (license license:gpl2+))) (define-public r-varselrf (package (name "r-varselrf") (version "0.7-8") (source (origin (method url-fetch) (uri (cran-uri "varSelRF" version)) (sha256 (base32 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i")))) (properties `((upstream-name . "varSelRF"))) (build-system r-build-system) (propagated-inputs (list r-randomforest)) (home-page "https://www.ligarto.org/rdiaz/software/software") (synopsis "Variable selection using random forests") (description "This package provides tools for the variable selection from random forests using both backwards variable elimination (for the selection of small sets of non-redundant variables) and selection based on the importance spectrum (somewhat similar to scree plots; for the selection of large, potentially highly-correlated variables). The main applications are in high-dimensional data (e.g., microarray data, and other genomics and proteomics applications).") (license license:gpl2+))) (define-public r-pamr (package (name "r-pamr") (version "1.56.1") (source (origin (method url-fetch) (uri (cran-uri "pamr" version)) (sha256 (base32 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-survival)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pamr/") (synopsis "Prediction Analysis for Microarrays") (description "This package provides some functions for sample classification in microarrays.") 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"lintr"))) (build-system r-build-system) (propagated-inputs (list r-codetools r-crayon r-cyclocomp r-digest r-httr r-jsonlite r-knitr r-rex r-rstudioapi r-testthat r-xml2 r-xmlparsedata)) (home-page "https://github.com/jimhester/lintr") (synopsis "Linter for R code") (description "This package checks adherence to a given style, syntax errors and possible semantic issues. It supports on the fly checking of R code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (license license:expat))) (define-public r-sctransform (package (name "r-sctransform") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-future r-future-apply r-ggplot2 r-gridextra r-magrittr r-mass r-matrix r-matrixstats r-rcpp r-rcpparmadillo r-reshape2 r-rlang)) (home-page "https://github.com/ChristophH/sctransform") (synopsis "Variance stabilizing transformations for Single Cell UMI Data") (description "This package provides a normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction.") (license license:gpl3))) (define-public r-styler (package (name "r-styler") (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 "1ki260ga0jrmayhdlx2sl788yp5kkmi4wyl32nmvvyb55sng6j9y")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-cli r-magrittr r-purrr r-r-cache r-rematch2 r-rlang r-rprojroot r-tibble r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/styler") (synopsis "Non-invasive pretty printing of R code") (description "This is a package for pretty-printing R code without changing the user's formatting intent.") (license license:gpl3))) (define-public r-scrime (package (name "r-scrime") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "scrime" version)) (sha256 (base32 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/scrime/") (synopsis "Analysis of high-dimensional categorical data such as SNP data") (description "This package provides tools for the analysis of high-dimensional data developed/implemented at the group \"Statistical Complexity Reduction In Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of the functions can also be applied to other types of categorical data.") (license license:gpl2))) (define-public r-pbmcapply (package (name "r-pbmcapply") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "pbmcapply" version)) (sha256 (base32 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z")))) (build-system r-build-system) (home-page "https://github.com/kvnkuang/pbmcapply") (synopsis "Track the progress of apply procedures with a progress bar") (description "This light-weight package helps you track and visualize the progress of parallel versions of vectorized R functions of the @code{mc*apply} family.") (license license:expat))) (define-public r-blme (package (name "r-blme") (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "blme" version)) (sha256 (base32 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7")))) (build-system r-build-system) (propagated-inputs (list r-lme4)) (home-page "https://github.com/vdorie/blme") (synopsis "Bayesian linear mixed-effects models") (description "This package provides tools for maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting. It extends the lme4 package.") (license license:gpl2+))) (define-public r-batchtools (package (name "r-batchtools") (version "0.9.15") (source (origin (method url-fetch) (uri (cran-uri "batchtools" version)) (sha256 (base32 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52")))) (build-system r-build-system) (propagated-inputs (list r-backports r-base64url r-brew r-checkmate r-data-table r-digest r-fs r-progress r-r6 r-rappdirs r-stringi r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/mllg/batchtools") (synopsis "Tools for computation on batch systems") (description "As a successor of the packages BatchJobs and BatchExperiments, this package provides a parallel implementation of the Map function for high performance computing systems managed by various schedulers. A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.") (license license:lgpl3))) (define-public r-clue (package (name "r-clue") (version "0.3-61") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 "0cfw2k1kh4a8imdv7b5qw977xd6indampsabhfldj3rqrqb1ncbi")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") (synopsis "Tools for analyzing cluster ensembles") (description "Cluster ensembles are collections of individual solutions to a given clustering problem which are useful or necessary to consider in a wide range of applications. This R package provides an extensible computational environment for creating and analyzing cluster ensembles, with basic data structures for representing partitions and hierarchies, and facilities for computing on them, including methods for measuring proximity and obtaining consensus and secondary clusterings.") (license license:gpl2))) (define-public r-sitmo (package (name "r-sitmo") (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "sitmo" version)) (sha256 (base32 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/coatless/sitmo/") (synopsis "Parallel pseudo random number generator header files") (description "This package provides two high quality and fast PPRNGs that may be used in an OpenMP parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence.") (license license:expat))) (define-public r-dqrng (package (name "r-dqrng") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "dqrng" version)) (sha256 (base32 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb")))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp r-sitmo)) (native-inputs (list r-knitr)) (home-page "https://www.daqana.org/dqrng") (synopsis "Fast pseudo random number generators") (description "Several fast random number generators are provided as C++ header-only libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+. Additionally, fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a ;; whole is distributed under the terms of the AGPL 3. (license license:agpl3))) (define-public r-ingredients (package (name "r-ingredients") (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-scales)) (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/ingredients/") (synopsis "Effects and importances of model ingredients") (description "This is a collection of tools for assessment of feature importance and feature effects. Key functions are: @itemize @item @code{feature_importance()} for assessment of global level feature importance, @item @code{ceteris_paribus()} for calculation of the what-if plots, @item @code{partial_dependence()} for partial dependence plots, @item @code{conditional_dependence()} for conditional dependence plots, @item @code{accumulated_dependence()} for accumulated local effects plots, @item @code{aggregate_profiles()} and @code{cluster_profiles()} for aggregation of ceteris paribus profiles, @item generic @code{print()} and @code{plot()} for better usability of selected explainers, @item generic @code{plotD3()} for interactive, D3 based explanations, and @item generic @code{describe()} for explanations in natural language. @end itemize\n") (license license:gpl3))) (define-public r-ibreakdown (package (name "r-ibreakdown") (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "iBreakDown" version)) (sha256 (base32 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh")))) (properties `((upstream-name . "iBreakDown"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/iBreakDown/") (synopsis "Model agnostic instance level variable attributions") (description "This package provides a model agnostic tool for decomposition of predictions from black boxes. It supports additive attributions and attributions with interactions. The Break Down Table shows contributions of every variable to a final prediction. The Break Down Plot presents variable contributions in a concise graphical way. This package works for classification and regression models.") (license license:gpl3))) (define-public r-dae (package (name "r-dae") (version "3.2-13") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "http://chris.brien.name") (synopsis "Functions useful in the design and ANOVA of experiments") (description "This package provides functions useful in the design and ANOVA of experiments. The content falls into the following groupings: @enumerate @item data, @item factor manipulation functions, @item design functions, @item ANOVA functions, @item matrix functions, @item projector and canonical efficiency functions, and @item miscellaneous functions. @end enumerate There is a vignette called @code{DesignNotes} describing how to use the design functions for randomizing and assessing designs. The ANOVA functions facilitate the extraction of information when the @code{Error} function has been used in the call to @code{aov}.") (license license:gpl2))) (define-public r-dalex (package (name "r-dalex") (version "2.4.1") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 "0mcdd2bd8zlsz7x174g87dp8vy4wc06w58dyr27f6lgv9shzya8j")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ibreakdown r-ingredients)) (home-page "https://pbiecek.github.io/DALEX/") (synopsis "Descriptive machine learning explanations") (description "Machine Learning models are widely used and have various applications in classification or regression. Models created with boosting, bagging, stacking or similar techniques are often used due to their high performance, but such black-box models usually lack interpretability. The DALEX package contains various explainers that help to understand the link between input variables and model output.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-enrichr (package (name "r-enrichr") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "enrichR" version)) (sha256 (base32 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3")))) (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-httr r-rjson)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/enrichR/") (synopsis "R Interface to Enrichr database for analyzing gene sets") (description "This package provides an R interface to all Enrichr databases, a web-based tool for analyzing gene sets and returns any enrichment of common annotated biological functions.") (license license:gpl2+))) (define-public r-plot3d (package (name "r-plot3d") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs (list r-misc3d)) (home-page "https://cran.r-project.org/web/packages/plot3D") (synopsis "Plot multi-dimensional data") (description "This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.") (license license:gpl3+))) (define-public r-ggfortify (package (name "r-ggfortify") (version "0.4.14") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-gridextra r-scales r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/sinhrks/ggfortify") (synopsis "Data visualization tools for statistical analysis results") (description "This package provides unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using the @code{ggplot2} package.") (license license:gpl2))) (define-public r-refmanager (package (name "r-refmanager") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "RefManageR" version)) (sha256 (base32 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps")))) (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-lubridate r-plyr r-stringr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/RefManageR/") (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") (description "This package provides tools for importing and working with bibliographic references. It greatly enhances the @code{bibentry} class by providing a class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports UTF-8 encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read into R and converted to @code{BibEntry} objects.") ;; Any of these licenses may be picked. (license (list license:gpl2 license:gpl3 license:bsd-3)))) (define-public r-citr (package (name "r-citr") (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "citr" version)) (sha256 (base32 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-curl r-httr r-miniui r-refmanager r-rstudioapi r-shiny r-shinyjs r-yaml)) (home-page "https://github.com/crsh/citr") (synopsis "RStudio add-in to insert Markdown citations") (description "This package provides functions and an RStudio add-in that search a BibTeX or BibLaTeX file to create and insert formatted Markdown citations into the current document.") (license license:expat))) (define-public r-xgboost (package (name "r-xgboost") (version "1.6.0.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/dmlc/xgboost") (synopsis "Extreme gradient boosting") (description "This package provides an R interface to Extreme Gradient Boosting, which is an efficient implementation of the gradient boosting framework from Chen and Guestrin (2016). The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.") (license license:asl2.0))) (define-public r-umap (package (name "r-umap") (version "0.2.8.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 "0aiarnzc8gl932gi8fxd9f9rshaiwh9vj570l135fkiaja3q2wap")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra)) (native-inputs (list r-knitr)) (home-page "https://github.com/tkonopka/umap") (synopsis "Uniform manifold approximation and projection") (description "Uniform manifold approximation and projection is a technique for dimension reduction. This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R.") (license license:expat))) (define-public r-uwot (package (name "r-uwot") (version "0.1.11") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg")))) (build-system r-build-system) (propagated-inputs (list r-dqrng r-fnn r-irlba r-matrix r-rcpp r-rcppannoy r-rcppprogress 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 "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "kableExtra" version)) (sha256 (base32 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9")))) (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs (list r-digest r-glue r-htmltools r-knitr r-magrittr r-rmarkdown r-rstudioapi r-rvest r-scales r-stringr r-svglite r-viridislite r-webshot r-xml2)) (native-inputs (list r-knitr)) (home-page "https://haozhu233.github.io/kableExtra/") (synopsis "Construct complex tables with pipe syntax") (description "Build complex HTML or LaTeX tables using @code{kable()} from @code{knitr} and the piping syntax from @code{magrittr}. The function @code{kable()} is a light weight table generator coming from @code{knitr}. This package simplifies the way to manipulate the HTML or LaTeX codes generated by @code{kable()} and allows users to construct complex tables and customize styles using a readable syntax.") (license license:expat))) (define-public r-glasso (package (name "r-glasso") (version "1.11") (source (origin (method url-fetch) (uri (cran-uri "glasso" version)) (sha256 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/glasso/") (synopsis "Graphical Lasso: estimation of Gaussian graphical models") (description "This is a package for estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.") (license license:gpl2))) (define-public r-rhpcblasctl (package (name "r-rhpcblasctl") (version "0.21-247.1") (source (origin (method url-fetch) (uri (cran-uri "RhpcBLASctl" version)) (sha256 (base32 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav")))) (properties `((upstream-name . "RhpcBLASctl"))) (build-system r-build-system) (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/") (synopsis "Control the number of threads on BLAS") (description "This package allows you to control the number of threads the BLAS library uses. It is also possible to control the number of threads in OpenMP.") (license license:agpl3+))) (define-public r-lda (package (name "r-lda") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "lda" version)) (sha256 (base32 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lda/") (synopsis "Collapsed Gibbs sampling methods for topic models") (description "This package implements @dfn{latent Dirichlet allocation} (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is implemented via a fast collapsed Gibbs sampler written in C. Utility functions for reading/writing data typically used in topic models, as well as tools for examining posterior distributions are also included.") ;; Any version of the LGPL (license license:lgpl3+))) (define-public r-rann-l1 (package (name "r-rann-l1") (version "2.5.2") (source (origin (method url-fetch) (uri (cran-uri "RANN.L1" version)) (sha256 (base32 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44")))) (properties `((upstream-name . "RANN.L1"))) (build-system r-build-system) (home-page "https://github.com/jefferis/RANN/tree/master-L1") (synopsis "Fast nearest neighbour search using L1 metric") (description "This package provides tools to find the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. There is support for approximate as well as exact searches, fixed radius searches and @code{bd} as well as @code{kd} trees. The distance is computed using the L1 (Manhattan, taxicab) metric.") (license license:gpl3+))) (define-public r-leiden (package (name "r-leiden") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 "1gg24afwbz818041bhmswmdqgxv35zp5h1i1102p58aaiis8dkna")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-reticulate)) (native-inputs (list r-knitr)) (home-page "https://github.com/TomKellyGenetics/leiden") (synopsis "R implementation of Leiden clustering algorithm") (description "This package implements the Python @code{leidenalg} module to be called in R. It enables clustering using the Leiden algorithm for partitioning a graph into communities. See also Traag et al (2018) \"From Louvain to Leiden: guaranteeing well-connected communities.\" .") (license license:gpl3))) (define-public r-patchwork (package (name "r-patchwork") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gtable)) (native-inputs (list r-knitr)) (home-page "https://github.com/thomasp85/patchwork") (synopsis "Compose ggplot2 plots") (description "The @code{ggplot2} package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. Patchwork is a package that expands the API to allow for arbitrarily complex composition of plots by providing mathematical operators for combining multiple plots.") (license license:expat))) (define-public r-liger (package (name "r-liger") (version "0.4.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/MacoskoLab/liger") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx")) (modules '((guix build utils))) (snippet '(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 (list r-cowplot r-dosnow r-dplyr r-fnn r-foreach r-ggplot2 r-ggrepel r-hmisc r-ica r-irlba r-matrix r-mclust r-patchwork r-plyr r-rann-l1 r-rcpp r-rcpparmadillo r-riverplot r-rtsne r-snow)) (native-inputs `(("jdk" ,icedtea "jdk") ;; See https://github.com/MacoskoLab/liger/issues/96 ;; The optimizer is released under the Expat license. ("optimizer-src" ,(origin (method url-fetch) (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip") (sha256 (base32 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18")))) ("unzip" ,unzip) ("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 (package (name "r-harmony") (version "0.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/immunogenomics/harmony") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9")) (modules '((guix build utils))) (snippet '(begin (for-each delete-file '("config.status" "configure")) #t)))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-dplyr r-ggplot2 r-irlba r-matrix r-rcpp r-rcpparmadillo r-rcppprogress r-rlang r-tibble r-tidyr)) (native-inputs (list autoconf)) (home-page "https://github.com/immunogenomics/harmony") (synopsis "Integration of single cell sequencing data") (description "This package provides an implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al @url{doi.org/10.1101/461954}. The package includes a standalone Harmony function and interfaces to external frameworks.") (license license:gpl3))) (define-public r-covr (package (name "r-covr") (version "3.5.1") (source (origin (method url-fetch) (uri (cran-uri "covr" version)) (sha256 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55")))) (properties `((upstream-name . "covr"))) (build-system r-build-system) (propagated-inputs (list r-crayon r-digest r-httr r-jsonlite r-rex r-withr r-yaml)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/covr") (synopsis "Test coverage for R packages") (description "Thisp package enables you to track and report code coverage for your package and (optionally) upload the results to a coverage service. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.") (license license:gpl3))) (define-public r-systemfonts (package (name "r-systemfonts") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) (inputs (list fontconfig freetype zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/systemfonts") (synopsis "System native font finding") (description "This package provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries for finding font files that can then be used further by e.g. graphic devices.") (license license:expat))) (define-public r-graphlayouts (package (name "r-graphlayouts") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-rcpp 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 emphasize hidden group structures in networks or focus on specific nodes.") (license license:expat))) (define-public r-terra (package (name "r-terra") (version "1.5-21") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 "0gzl0ka19jjw0dmaghjk2sgwi78kkz4w3rlfkym62rdarhlfj7h9")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs (list gdal geos proj sqlite ; needed for proj zlib)) (propagated-inputs (list r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://rspatial.org/terra") (synopsis "Spatial data analysis") (description "This package provides methods for spatial data analysis, especially raster data. The included methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction. Processing of very large files is supported.") (license license:gpl3+))) (define-public r-tidygraph (package (name "r-tidygraph") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "tidygraph" version)) (sha256 (base32 "0dmdff3bkg53xn0c51xd6k2d9c7l250x1lhl5z3libf533dw5g9g")))) (properties `((upstream-name . "tidygraph"))) (build-system r-build-system) (propagated-inputs (list r-cli r-cpp11 r-dplyr r-igraph r-magrittr r-pillar r-r6 r-rlang r-tibble r-tidyr)) (home-page "https://github.com/thomasp85/tidygraph") (synopsis "Tidy API for graph manipulation") (description "This package provides a graph implementation that can be thought of as two tidy data frames describing node and edge data respectively. It provides an approach to manipulate these two virtual data frames using the API defined in the @code{dplyr} package, and it also provides tidy interfaces to a lot of common graph algorithms.") (license license:expat))) (define-public r-soupx (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8") (revision "1")) (package (name "r-soupx") (version (git-version "0.3.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/constantAmateur/SoupX") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99")))) (properties `((upstream-name . "SoupX"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-matrix r-seurat)) (home-page "https://github.com/constantAmateur/SoupX") (synopsis "Single cell mRNA Soup eXterminator") (description "This package provides a package for quantifying, profiling and removing cell free mRNA contamination (the \"soup\") from droplet based single cell RNA-seq experiments.") (license license:gpl2)))) (define-public r-assertr (package (name "r-assertr") (version "2.8") (source (origin (method url-fetch) (uri (cran-uri "assertr" version)) (sha256 (base32 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-mass r-rlang)) (native-inputs (list r-knitr)) ; needed for vignette (home-page "https://github.com/ropensci/assertr") (synopsis "Assertive programming for R analysis pipelines") (description "This package provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. It is similar to @code{stopifnot()} but more powerful, friendly, and easier for use in pipelines.") (license license:expat))) (define-public r-parameters (package (name "r-parameters") (version "0.18.1") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 "0zcypf3fi745pa18vpqgx3q9izhkkmpcvcv1gv8pxawyq9mw8ag9")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/parameters") (synopsis "Processing of model parameters") (description "This package provides utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models, this package implements features like standardization or bootstrapping of parameters and models, feature reduction (feature extraction and variable selection) as well as conversion between indices of effect size.") (license license:gpl3))) (define-public r-rgdal (package (name "r-rgdal") (version "1.5-32") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs (list gdal proj zlib)) (propagated-inputs (list r-sp)) (native-inputs (list pkg-config r-knitr)) (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 "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "insol" version)) (sha256 (base32 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3")))) (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs (list r-raster)) (native-inputs (list gfortran)) (home-page "https://meteoexploration.com/R/insol/index.html") (synopsis "Tools for calculating solar radiation") (description "This package provides functions to compute insolation on tilted surfaces, computes atmospheric transmittance and related parameters such as: Earth radius vector, declination, sunset and sunrise, daylength, equation of time, vector in the direction of the sun, vector normal to surface, and some atmospheric physics.") (license license:gpl2+))) (define-public r-lifecycle (package (name "r-lifecycle") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx")))) (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs (list r-glue r-rlang)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/lifecycle") (synopsis "Manage the life cycle of your package functions") (description "Manage the life cycle of your exported functions with shared conventions, documentation badges, and non-invasive deprecation warnings. The lifecycle package defines four development stages (experimental, maturing, stable, and questioning) and three deprecation stages (soft-deprecated, deprecated, and defunct). It makes it easy to insert badges corresponding to these stages in your documentation. Usage of deprecated functions are signalled with increasing levels of non-invasive verbosity.") (license license:gpl3))) (define-public r-assertable (package (name "r-assertable") (version "0.2.8") (source (origin (method url-fetch) (uri (cran-uri "assertable" version)) (sha256 (base32 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/assertable/") (synopsis "Verbose assertions for tabular data (data.frames and data.tables)") (description "This package provides simple, flexible assertions on data.frame or data.table objects with verbose output for vetting. While other assertion packages apply towards more general use-cases, @code{assertable} is tailored towards tabular data. It includes functions to check variable names and values, whether the dataset contains all combinations of a given set of unique identifiers, and whether it is a certain length. In addition, @code{assertable} includes utility functions to check the existence of target files and to efficiently import multiple tabular data files into one data.table.") (license license:gpl3))) (define-public r-quadprog (package (name "r-quadprog") (version "1.5-8") (source (origin (method url-fetch) (uri (cran-uri "quadprog" version)) (sha256 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/quadprog") (synopsis "Functions to solve quadratic programming problems") (description "This package contains routines and documentation for solving quadratic programming problems.") (license license:gpl3+))) (define-public r-desolve (package (name "r-desolve") (version "1.32") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 (base32 "1bfr4w760nr7mjhpmf32z39swr6isnn1665cld2d1pdgx8b0yrvl")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://desolve.r-forge.r-project.org/") (synopsis "Solvers for initial value problems of differential equations") (description "This package provides functions that solve initial value problems of a system of first-order @dfn{ordinary differential equations} (ODE), of @dfn{partial differential equations} (PDE), of @dfn{differential algebraic equations} (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations that have been converted to ODEs by numerical differencing.") (license license:gpl2+))) (define-public r-pmcmrplus (package (name "r-pmcmrplus") (version "1.9.4") (source (origin (method url-fetch) (uri (cran-uri "PMCMRplus" version)) (sha256 (base32 "16m1pdrzjq9vnx5v7zv56mz9r1205rkw92883cxaqbvdpds6dhqy")))) (properties `((upstream-name . "PMCMRplus"))) (build-system r-build-system) (inputs (list gmp)) (propagated-inputs (list r-bwstest r-gmp r-ksamples r-mass r-multcompview r-mvtnorm r-rmpfr r-suppdists)) (native-inputs (list gfortran r-knitr)) (home-page "https://cran.r-project.org/package=PMCMRplus") (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended") (description "This package provides multiple pairwise tests.") (license license:gpl3+))) (define-public r-pracma (package (name "r-pracma") (version "2.3.8") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 (base32 "0r17siivm37k4gp253v9mlg5m7cwqp85h9kk2hbp2wkf81ad80i3")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") (description "This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.") (license license:gpl3+))) (define-public r-subplex (package (name "r-subplex") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "subplex" version)) (sha256 (base32 "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/subplex") (synopsis "Unconstrained optimization using the subplex algorithm") (description "This package implements the Subplex optimization algorithm. It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy or are discontinuous at the solution.") (license license:gpl3+))) (define-public r-txtplot (package (name "r-txtplot") (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "txtplot" version)) (sha256 (base32 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/txtplot/") (synopsis "Text-based plotting") (description "This package provides functions to produce rudimentary ASCII graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.") (license license:lgpl3+))) (define-public r-bio3d (package (name "r-bio3d") (version "2.4-3") (source (origin (method url-fetch) (uri (cran-uri "bio3d" version)) (sha256 (base32 "0x3apqxbk4lvvcnvvdsyjd9f6qh9f9qgml3ih69hl9ikj06iy0y6")))) (properties `((upstream-name . "bio3d"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "http://thegrantlab.org/bio3d/") (synopsis "Biological structure analysis") (description "This package provides utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data.") (license license:gpl2+))) (define-public r-bios2cor (package (name "r-bios2cor") (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "Bios2cor" version)) (sha256 (base32 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w")))) (properties `((upstream-name . "Bios2cor"))) (build-system r-build-system) (propagated-inputs (list r-bigmemory r-bio3d r-circular r-igraph)) (home-page "https://cran.r-project.org/web/packages/Bios2cor/") (synopsis "From biological sequences and simulations to correlation analysis") (description "This package provides utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation.") (license license:gpl2+))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-networkd3 (package (name "r-networkd3") (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "networkD3" version)) (sha256 (base32 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k")) (snippet '(begin (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js") #t)))) (properties `((upstream-name . "networkD3"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "d3.v4.js") "d3-4.5.0/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (native-inputs `(("uglifyjs" ,node-uglify-js) ;; NOTE: Make sure that this version of d3 is still valid when ;; upgrading the package. ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) (propagated-inputs (list r-htmlwidgets r-igraph r-magrittr)) (home-page "https://cran.r-project.org/package=networkD3") (synopsis "D3 JavaScript network graphs from R") (description "This package creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.") (license license:gpl3+))) (define-public r-aasea (package (name "r-aasea") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "aaSEA" version)) (sha256 (base32 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h")))) (properties `((upstream-name . "aaSEA"))) (build-system r-build-system) (propagated-inputs (list r-bios2cor r-dt r-hmisc r-magrittr r-networkd3 r-plotly r-seqinr r-shiny r-shinydashboard)) (home-page "https://cran.r-project.org/web/packages/aaSEA/") (synopsis "Amino acid substitution effect analyzer") (description "Given a protein multiple sequence alignment, it is a daunting task to assess the effects of substitutions along sequence length. The aaSEA package is intended to help researchers to rapidly analyze property changes caused by single, multiple and correlated amino acid substitutions in proteins.") (license license:gpl3))) (define-public r-abacus (package (name "r-abacus") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ABACUS" version)) (sha256 (base32 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i")))) (properties `((upstream-name . "ABACUS"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-shiny)) (home-page "https://shiny.abdn.ac.uk/Stats/apps/") (synopsis "Apps-based activities for communicating and understanding statistics") (description "This package provides a set of Shiny apps for effective communication and understanding in statistics. The current version includes properties of normal distribution, properties of sampling distribution, one-sample z and t tests, two samples independent (unpaired) t test and analysis of variance.") (license license:gpl3))) (define-public r-abc-rap (package (name "r-abc-rap") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "ABC.RAP" version)) (sha256 (base32 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk")))) (properties `((upstream-name . 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(define-public r-rintrojs (package (name "r-rintrojs") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "rintrojs" version)) (sha256 (base32 "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw")) (snippet '(delete-file "inst/javascript/introjs/intro.min.js")))) (properties `((upstream-name . 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This package makes it easy to include step-by-step introductions, and clickable hints in a Shiny application. It supports both static introductions in the UI, and programmatic introductions from the server-side.") ;; The intro.js library is licensed under Expat. (license (list license:agpl3+ license:expat)))) (define-public r-sysfonts (package (name "r-sysfonts") (version "0.8.8") (source (origin (method url-fetch) (uri (cran-uri "sysfonts" version)) (sha256 (base32 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn")))) (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs (list freetype libpng zlib)) (native-inputs (list pkg-config)) (home-page "https://github.com/yixuan/sysfonts") (synopsis "Loading fonts into R") (description "This is a package to simplify loading of system fonts and Google Fonts into R, in order to support other packages.") 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Researchers need reliable tools to manage the accrual rate. This package provides an implementation of a Bayesian method that integrates researcher's experience on previous trials and data from the current study, providing reliable prediction on accrual rate for clinical studies. It provides functions for Bayesian accrual prediction which can be easily used by statisticians and clinical researchers.") (license license:gpl2))) (define-public r-accrued (package (name "r-accrued") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "accrued" version)) (sha256 (base32 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5")))) (properties `((upstream-name . "accrued"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/accrued/") (synopsis "Data quality visualization tools for partially accruing data") (description "This is a package for visualizing data quality of partially accruing data.") 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Various novel optimization approaches to this problem are implemented including @dfn{alternating direction method of multipliers} (ADMM), @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG). Functions for performing cross validation are also supplied along with basic prediction and plotting functions. @dfn{Sparse zero variance discriminant} (SZVD) analysis is also included in the package.") (license license:gpl2+))) (define-public r-ace2fastq (package (name "r-ace2fastq") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ace2fastq" version)) (sha256 (base32 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic")))) (properties `((upstream-name . "ace2fastq"))) (build-system r-build-system) (propagated-inputs (list r-stringr)) (home-page "https://github.com/c5sire/ace2fastq") (synopsis "ACE file to FASTQ converter") (description "The ACE file format is used in genomics to store contigs from sequencing machines. This tools converts it into FASTQ format. Both formats contain the sequence characters and their corresponding quality information. Unlike the FASTQ file, the ACE file stores the quality values numerically. The conversion algorithm uses the standard Sanger formula. The package facilitates insertion into pipelines, and content inspection.") (license license:gpl3))) (define-public r-rngwell (package (name "r-rngwell") (version "0.10-7") (source (origin (method url-fetch) (uri (cran-uri "rngWELL" version)) (sha256 (base32 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c")))) (properties `((upstream-name . "rngWELL"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rngWELL/") (synopsis "Toolbox for WELL random number generators") (description "This is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") (license license:bsd-3))) (define-public r-rnmf (package (name "r-rnmf") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "rNMF" version)) (sha256 (base32 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597")))) (build-system r-build-system) (propagated-inputs (list r-knitr r-nnls)) (home-page "https://cran.r-project.org/web/packages/rNMF/") (synopsis "Robust nonnegative matrix factorization") (description "This package provides an implementation of robust nonnegative matrix factorization (rNMF). The rNMF algorithm decomposes a nonnegative high dimension data matrix into the product of two low rank nonnegative matrices, while detecting and trimming outliers. The main function is @code{rnmf()}. The package also includes a visualization tool, @code{see()}, that arranges and prints vectorized images.") (license license:gpl2+))) (define-public r-randtoolbox (package (name "r-randtoolbox") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 "005x2igljc6vm0nsmkld9aqjqz1ccwapc8z3aw5c3ivh4n2bghf9")))) (properties `((upstream-name . 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(license license:bsd-3))) (define-public r-lhs (package (name "r-lhs") (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "lhs" version)) (sha256 (base32 "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/bertcarnell/lhs") (synopsis "Latin Hypercube Samples") (description "This package provides a number of methods for creating and augmenting Latin Hypercube Samples.") (license license:gpl3))) (define-public r-acebayes (package (name "r-acebayes") (version "1.10") (source (origin (method url-fetch) (uri (cran-uri "acebayes" version)) (sha256 (base32 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73")))) (properties `((upstream-name . "acebayes"))) (build-system r-build-system) (propagated-inputs (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/acebayes/") (synopsis "Optimal Bayesian experimental design using the ACE algorithm") (description "Finding an optimal Bayesian experimental design involves maximizing an objective function given by the expectation of some appropriately chosen utility function with respect to the joint distribution of unknown quantities (including responses). This objective function is usually not available in closed form and the design space can be continuous and of high dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE) to maximise an approximation to the expectation of the utility function.") (license license:gpl2))) (define-public r-acet (package (name "r-acet") (version "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "ACEt" version)) (sha256 (base32 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4")))) (properties `((upstream-name . "ACEt"))) (build-system r-build-system) (propagated-inputs (list r-bh r-mass r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/ACEt/") (synopsis "Estimating dynamic heritability and twin model comparison") (description "This package supports twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.") (license license:gpl2+))) (define-public r-acfmperiod (package (name "r-acfmperiod") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "acfMPeriod" version)) (sha256 (base32 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5")))) (properties `((upstream-name . "acfMPeriod"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") (synopsis "Estimation of the ACF from the M-periodogram") (description "This package support non-robust and robust computations of the sample autocovariance (ACOVF) and sample autocorrelation functions (ACF) of univariate and multivariate processes. The methodology consists in reversing the diagonalization procedure involving the periodogram or the cross-periodogram and the Fourier transform vectors, and, thus, obtaining the ACOVF or the ACF as discussed in Fuller (1995) @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting robust M-regressors to obtain the M-periodogram or M-cross-periodogram as discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") (license license:gpl2+))) (define-public r-gamlss-data (package (name "r-gamlss-data") (version "6.0-2") (source (origin (method url-fetch) (uri (cran-uri "gamlss.data" version)) (sha256 (base32 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv")))) (properties `((upstream-name . "gamlss.data"))) (build-system r-build-system) (home-page "http://www.gamlss.org/") (synopsis "GAMLSS data") (description "This package provides data used as examples to demonstrate GAMLSS models.") ;; Either version of the license (license (list license:gpl2 license:gpl3)))) (define-public r-gamlss (package (name "r-gamlss") (version "5.4-3") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival)) (home-page "http://www.gamlss.org/") (synopsis "Generalized additive models for location scale and shape") (description "This package provides functions for fitting the generalized additive models for location scale and shape introduced by Rigby and Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.") ;; Either version of the license (license (list license:gpl2 license:gpl3)))) (define-public r-acid (package (name "r-acid") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "acid" version)) (sha256 (base32 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd")))) (properties `((upstream-name . "acid"))) (build-system r-build-system) (propagated-inputs (list r-gamlss r-gamlss-dist r-hmisc)) (home-page "https://cran.r-project.org/web/packages/acid/") (synopsis "Analysing conditional income distributions") (description "This package provides functions for the analysis of income distributions for subgroups of the population as defined by a set of variables like age, gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture distribution as well as functions for moments, inequality measures, entropy measures and polarisation measures of income distributions. This package thus aides the analysis of income inequality by offering tools for the exploratory analysis of income distributions at the disaggregated level.") (license license:gpl3))) (define-public r-acm4r (package (name "r-acm4r") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "acm4r" version)) (sha256 (base32 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) (properties `((upstream-name . "acm4r"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acm4r/") (synopsis "Align-and-count method comparisons of RFLP data") (description "This is a package to compare sequence fragment lengths or molecular weights from pairs of lanes. The number of matching bands in the @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using the align-and-count method.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-filelock (package (name "r-filelock") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "filelock" version)) (sha256 (base32 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc")))) (properties `((upstream-name . "filelock"))) (build-system r-build-system) (home-page "https://github.com/r-lib/filelock") (synopsis "Portable file locking") (description "This library lets you place an exclusive or shared lock on a file using the appropriate system call provided by the underlying operating system.") (license license:expat))) (define-public r-filematrix (package (name "r-filematrix") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "filematrix" version)) (sha256 (base32 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b")))) (properties `((upstream-name . "filematrix"))) (build-system r-build-system) ;; These inputs are needed for vignettes (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/andreyshabalin/filematrix") (synopsis "File-backed matrix class with convenient read and write access") (description "This package provides an interface for working with large matrices stored in files, not in computer memory. It supports multiple non-character data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 byte real values). Access to parts of the matrix is done by indexing, exactly as with usual R matrices. It supports very large matrices; the package has been tested on multi-terabyte matrices. It allows for more than 2^32 rows or columns, ad allows for quick addition of extra columns to a filematrix.") (license license:lgpl3))) (define-public r-acmeeqtl (package (name "r-acmeeqtl") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "ACMEeqtl" version)) (sha256 (base32 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz")))) (properties `((upstream-name . "ACMEeqtl"))) (build-system r-build-system) (propagated-inputs (list r-filematrix)) (home-page "https://github.com/andreyshabalin/ACMEeqtl") (synopsis "Estimation of interpretable eQTL effect sizes") (description "This package provides a non-linear model, termed ACME, that reflects a parsimonious biological model for allelic contributions of cis-acting eQTLs. With non-linear least-squares algorithm the maximum likelihood parameters can be estimated. The ACME model provides interpretable effect size estimates and p-values with well controlled Type-I error.") (license license:lgpl3))) (define-public r-acmer (package (name "r-acmer") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "acmeR" version)) (sha256 (base32 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) (properties `((upstream-name . "acmeR"))) (build-system r-build-system) (propagated-inputs (list r-foreign)) (home-page "https://cran.r-project.org/web/packages/acmeR/") (synopsis "ACME estimator of bird and bat mortality by wind turbines") (description "This package provides an implementation of the ACME estimator, described in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran Mortality at Wind Turbines. Unlike most other models, this estimator supports decreasing-hazard Weibull model for persistence; decreasing search proficiency as carcasses age; variable bleed-through at successive searches; and interval mortality estimates. The package provides, based on search data, functions for estimating the mortality inflation factor in Frequentist and Bayesian settings.") (license license:expat))) (define-public r-r-huge (package (name "r-r-huge") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "R.huge" version)) (sha256 (base32 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi")))) (properties `((upstream-name . "R.huge"))) (build-system r-build-system) (propagated-inputs (list r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.huge") (synopsis "Methods for accessing huge amounts of data") (description "This is a deprecated package for accessing huge amounts of data. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside the @code{aroma.affymetrix} package.") (license license:lgpl2.1+))) (define-public r-r-filesets (package (name "r-r-filesets") (version "2.14.0") (source (origin (method url-fetch) (uri (cran-uri "R.filesets" version)) (sha256 (base32 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh")))) (properties `((upstream-name . "R.filesets"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.filesets") (synopsis "Easy handling of and access to files") (description "This package provides classes and methods to locate, setup, subset, navigate and iterate file sets, i.e. sets of files located in one or more directories on the file system. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files.") (license license:lgpl2.1+))) (define-public r-r-devices (package (name "r-r-devices") (version "2.17.0") (source (origin (method url-fetch) (uri (cran-uri "R.devices" version)) (sha256 (base32 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62")))) (properties `((upstream-name . "R.devices"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.devices") (synopsis "Unified handling of graphics devices") (description "This package provides functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.") (license license:lgpl2.1+))) (define-public r-acnr (package (name "r-acnr") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "acnr" version)) (sha256 (base32 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym")))) (properties `((upstream-name . "acnr"))) (build-system r-build-system) (home-page "https://github.com/mpierrejean/acnr") (synopsis "Annotated copy-number regions") (description "This package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.") (license license:lgpl2.1+))) (define-public r-acopula (package (name "r-acopula") (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "acopula" version)) (sha256 (base32 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln")))) (properties `((upstream-name . "acopula"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/acopula/") (synopsis "Modelling dependence with multivariate Archimax copulas") (description "Archimax copulas are a mixture of Archimedean and EV copulas. This package provides definitions of several parametric families of generator and dependence function, computes CDF and PDF, estimates parameters, tests for goodness of fit, generates random sample and checks copula properties for custom constructs. In the 2-dimensional case explicit formulas for density are used, contrary to higher dimensions when all derivatives are linearly approximated. Several non-archimax families (normal, FGM, Plackett) are provided as well.") (license license:gpl2))) (define-public r-tuner (package (name "r-tuner") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 "1sd0drxzbdy71bh35fccg9ajhpdhdpy0m9nja2lw82p1pzhyl7jn")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs (list r-signal)) (home-page "https://cran.r-project.org/web/packages/tuneR/") (synopsis "Analysis of music and speech") (description "This is a package for the analysis of music and speech. Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read MP3, read MIDI, perform steps of a transcription, ...") ;; Either of these versions. (license (list license:gpl2 license:gpl3)))) (define-public r-seewave (package (name "r-seewave") (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "seewave" version)) (sha256 (base32 "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl")))) (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs (list libsndfile)) (propagated-inputs (list r-tuner)) (home-page "http://rug.mnhn.fr/seewave") (synopsis "Sound analysis and synthesis") (description "This package provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.") (license license:gpl2+))) (define-public r-acousticndlcoder (package (name "r-acousticndlcoder") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "AcousticNDLCodeR" version)) (sha256 (base32 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb")))) (properties `((upstream-name . "AcousticNDLCodeR"))) (build-system r-build-system) (propagated-inputs (list r-seewave r-tuner r-zoo)) (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") (synopsis "Coding sound files for use with NDL") (description "Make acoustic cues to use with the R package @code{ndl}. The package implements functions used in the PLoS ONE paper \"Words from spontaneous conversational speech can be recognized with human-like accuracy by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit.\" @url{doi:10.1371/journal.pone.0174623}") (license license:gpl2+))) (define-public r-acp (package (name "r-acp") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "acp" version)) (sha256 (base32 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn")))) (properties `((upstream-name . "acp"))) (build-system r-build-system) (propagated-inputs (list r-quantmod r-tseries)) (home-page "https://cran.r-project.org/web/packages/acp/") (synopsis "Autoregressive conditional Poisson") (description "This package supports the analysis of count data exhibiting autoregressive properties, using the @dfn{Autoregressive Conditional Poisson} model (ACP(p,q)) proposed by Heinen (2003).") (license license:gpl2))) (define-public r-ada (package (name "r-ada") (version "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "ada" version)) (sha256 (base32 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) (properties `((upstream-name . "ada"))) (build-system r-build-system) (propagated-inputs (list r-rpart)) (home-page "https://cran.r-project.org/web/packages/ada/") (synopsis "Stochastic boosting") (description "This package provides a straightforward, well-documented, and broad boosting routine for classification, ideally suited for small to moderate-sized data sets. It performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-genalg (package (name "r-genalg") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "genalg" version)) (sha256 (base32 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna")))) (properties `((upstream-name . "genalg"))) (build-system r-build-system) (home-page "https://github.com/egonw/genalg") (synopsis "R based genetic algorithm") (description "This package provides an R based genetic algorithm for binary and floating point chromosomes.") (license license:gpl2))) (define-public r-kernelfactory (package (name "r-kernelfactory") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "kernelFactory" version)) (sha256 (base32 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j")))) (properties `((upstream-name . "kernelFactory"))) (build-system r-build-system) (propagated-inputs (list r-auc r-genalg r-kernlab r-randomforest)) (home-page "https://cran.r-project.org/web/packages/kernelFactory/") (synopsis "Ensemble of kernel machines") (description "Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.") (license license:gpl2+))) (define-public r-dummies (package (name "r-dummies") (version "1.5.6") (source (origin (method url-fetch) (uri (cran-uri "dummies" version)) (sha256 (base32 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm")))) (properties `((upstream-name . "dummies"))) (build-system r-build-system) (home-page "https://decisionpatterns.com") (synopsis "Create dummy/indicator variables flexibly and efficiently") (description "This package lets you expand factors, characters and other eligible classes into dummy/indicator variables.") (license license:gpl2+))) (define-public r-acrm (package (name "r-acrm") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "aCRM" version)) (sha256 (base32 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v")))) (properties `((upstream-name . "aCRM"))) (build-system r-build-system) (propagated-inputs (list r-ada r-dummies r-kernelfactory r-randomforest)) (home-page "https://cran.r-project.org/web/packages/aCRM/") (synopsis "Convenience functions for analytical customer relationship management") (description "This package provides convenience functions for data preparation and modeling often used in @dfn{analytical customer relationship management} (aCRM).") (license license:gpl2+))) (define-public r-tree (package (name "r-tree") (version "1.0-42") (source (origin (method url-fetch) (uri (cran-uri "tree" version)) (sha256 (base32 "1q3jgkhl5d4d8c396cyvkw60094p0z0a3x7xwhdbi8gl4c2c65ss")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tree/") (synopsis "Classification and regression trees") (description "This package provides procedures to work with classification and regression trees.") (license license:gpl2+))) (define-public r-treeclust (package (name "r-treeclust") (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "treeClust" version)) (sha256 (base32 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z")))) (properties `((upstream-name . "treeClust"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-rpart)) (home-page "https://cran.r-project.org/web/packages/treeClust/") (synopsis "Cluster distances through trees") (description "This package provides tools to create a measure of inter-point dissimilarity useful for clustering mixed data, and, optionally, perform the clustering.") (license license:gpl2+))) (define-public r-acrosstic (package (name "r-acrosstic") (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "AcrossTic" version)) (sha256 (base32 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0")))) (properties `((upstream-name . "AcrossTic"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-treeclust)) (home-page "https://cran.r-project.org/web/packages/AcrossTic/") (synopsis "Cost-minimal regular spanning subgraph with TreeClust") (description "This is a package for constructing minimum-cost regular spanning subgraph as part of a non-parametric two-sample test for equality of distribution.") (license license:gpl2+))) (define-public r-acrt (package (name "r-acrt") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "acrt" version)) (sha256 (base32 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s")))) (properties `((upstream-name . "acrt"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen r-sandwich)) (home-page "https://cran.r-project.org/web/packages/acrt/") (synopsis "Autocorrelation robust testing") (description "This package provides functions for testing affine hypotheses on the regression coefficient vector in regression models with autocorrelated errors.") (license license:gpl2))) (define-public r-acs (package (name "r-acs") (version "2.1.4") (source (origin (method url-fetch) (uri (cran-uri "acs" version)) (sha256 (base32 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5")))) (properties `((upstream-name . "acs"))) (build-system r-build-system) (propagated-inputs (list r-httr r-plyr r-rcpp r-stringr r-xml)) (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn") (synopsis "Work with data from the US Census") (description "This package provides a general toolkit for downloading, managing, analyzing, and presenting data from the @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census}, including SF1 (Decennial short-form), SF3 (Decennial long-form), and the American Community Survey (ACS). Confidence intervals provided with ACS data are converted to standard errors to be bundled with estimates in complex @code{acs} objects. The package provides new methods to conduct standard operations on @code{acs} objects and present/plot data in statistically appropriate ways.") (license license:gpl3))) (define-public r-acss-data (package (name "r-acss-data") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "acss.data" version)) (sha256 (base32 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv")))) (properties `((upstream-name . "acss.data"))) (build-system r-build-system) (home-page "http://complexitycalculator.com/methodology.html") (synopsis "Data for algorithmic complexity of short strings") (description "This is a data only package providing the algorithmic complexity of short strings, computed using the coding theorem method. For a given set of symbols in a string, all possible or a large number of random samples of Turing machines with a given number of states (e.g., 5) and number of symbols corresponding to the number of symbols in the strings were simulated until they reached a halting state or failed to end. This package contains data on 4.5 million strings from length 1 to 12 simulated on Turing machines with 2, 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the distribution of the halting states.") (license license:gpl2+))) (define-public r-acss (package (name "r-acss") (version "0.2-5") (source (origin (method url-fetch) (uri (cran-uri "acss" version)) (sha256 (base32 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk")))) (properties `((upstream-name . "acss"))) (build-system r-build-system) (propagated-inputs (list r-acss-data r-zoo)) (home-page "http://complexitycalculator.com/methodology.html") (synopsis "Algorithmic complexity for short strings") (description "The main purpose of this package is to provide the algorithmic complexity for short strings, an approximation of the Kolmogorov Complexity of a short string using the coding theorem method. While the database containing the complexity is provided in the data only package @code{acss.data}, this package provides functions accessing the data such as @code{prob_random} returning the posterior probability that a given string was produced by a random process. In addition, two traditional (but problematic) measures of complexity are also provided: entropy and change complexity.") (license license:gpl2+))) (define-public r-acswr (package (name "r-acswr") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ACSWR" version)) (sha256 (base32 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n")))) (properties `((upstream-name . "ACSWR"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ACSWR/") (synopsis "Companion package for the book \"A Course in Statistics with R\"") (description "This is a companion package for the book \"A Course in Statistics with R\" (ISBN 978-1-119-15272-9.)") (license license:gpl2))) (define-public r-alabama (package (name "r-alabama") (version "2022.4-1") (source (origin (method url-fetch) (uri (cran-uri "alabama" version)) (sha256 (base32 "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8")))) (properties `((upstream-name . "alabama"))) (build-system r-build-system) (propagated-inputs (list r-numderiv)) (home-page "https://cran.r-project.org/web/packages/alabama/") (synopsis "Constrained nonlinear optimization") (description "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization Algorithm; it is used for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed.") (license license:gpl2+))) (define-public r-gdina (package (name "r-gdina") (version "2.8.8") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs (list r-alabama r-ggplot2 r-mass r-numderiv r-rcpp r-rcpparmadillo r-rsolnp r-shiny r-shinydashboard)) (native-inputs (list r-knitr)) (home-page "https://github.com/Wenchao-Ma/GDINA") (synopsis "Generalized DINA model framework") (description "This package provides a set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7} and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.") (license license:gpl3))) (define-public r-actcd (package (name "r-actcd") (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "ACTCD" version)) (sha256 (base32 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p")))) (properties `((upstream-name . "ACTCD"))) (build-system r-build-system) (propagated-inputs (list r-gdina r-r-methodss3)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ACTCD/") (synopsis "Asymptotic classification theory for cognitive diagnosis") (description "This is a package supporting cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of sum-scores, cluster analysis techniques can be used to classify examinees into latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.") (license license:gpl2+))) (define-public r-ineq (package (name "r-ineq") (version "0.2-13") (source (origin (method url-fetch) (uri (cran-uri "ineq" version)) (sha256 (base32 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0")))) (properties `((upstream-name . "ineq"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ineq/") (synopsis "Measuring inequality, concentration, and poverty") (description "This package provides tools for measuring inequality, concentration, and poverty measures. It provides both empirical and theoretical Lorenz curves.") ;; Either of these two versions. (license (list license:gpl2 license:gpl3)))) (define-public r-actfrag (package (name "r-actfrag") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "ActFrag" version)) (sha256 (base32 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1")))) (properties `((upstream-name . "ActFrag"))) (build-system r-build-system) (propagated-inputs (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr)) (home-page "https://github.com/junruidi/ActFrag") (synopsis "Activity fragmentation metrics extraction") (description "This package provides functions to extract commonly used fragmentation metrics to quantify time accumulation strategies based on minute level actigraphy-measured activity counts data.") (license license:gpl3))) (define-public r-ash (package (name "r-ash") (version "1.0-15") (source (origin (method url-fetch) (uri (cran-uri "ash" version)) (sha256 (base32 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb")))) (properties `((upstream-name . "ash"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ash/") (synopsis "David Scott's ASH routines") (description "This package provides David Scott's ASH routines ported from S-PLUS to R.") (license license:gpl2+))) (define-public r-hdrcde (package (name "r-hdrcde") (version "3.4") (source (origin (method url-fetch) (uri (cran-uri "hdrcde" version)) (sha256 (base32 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3")))) (properties `((upstream-name . "hdrcde"))) (build-system r-build-system) (propagated-inputs (list r-ash r-ggplot2 r-kernsmooth r-ks r-locfit r-rcolorbrewer)) (native-inputs (list gfortran)) (home-page "http://pkg.robjhyndman.com/hdrcde") (synopsis "Highest density regions and conditional density estimation") (description "This is a package for the computation of highest density regions in one and two dimensions, kernel estimation of univariate density functions conditional on one covariate, and multimodal regression.") (license license:gpl3))) (define-public r-rainbow (package (name "r-rainbow") (version "3.6") (source (origin (method url-fetch) (uri (cran-uri "rainbow" version)) (sha256 (base32 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3")))) (properties `((upstream-name . "rainbow"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-colorspace r-hdrcde r-ks r-mass r-pcapp)) (home-page "https://cran.r-project.org/web/packages/rainbow/") (synopsis "Bagplots, boxplots and rainbow plots for functional data") (description "This is a package for visualizing functional data and identifying functional outliers with bagplots, boxplots and rainbow plots.") (license license:gpl3))) (define-public r-fds (package (name "r-fds") (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "fds" version)) (sha256 (base32 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0")))) (properties `((upstream-name . "fds"))) (build-system r-build-system) (propagated-inputs (list r-rainbow r-rcurl)) (home-page "https://cran.r-project.org/web/packages/fds/") (synopsis "Functional data sets") (description "This package contains a list of functional time series, sliced functional time series, and functional data sets. Functional time series is a special type of functional data observed over time. Sliced functional time series is a special type of functional time series with a time variable observed over time.") (license license:gpl2+))) (define-public r-fda (package (name "r-fda") (version "6.0.3") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 "1lvp4i4hqz650k27sa5flbdlkalihc79xy9128hfhr16h6wi8n10")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs (list r-desolve r-fds)) (native-inputs (list r-knitr)) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description "These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. The package includes data sets and script files working many examples.") (license license:gpl2+))) (define-public r-actigraphy (package (name "r-actigraphy") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "Actigraphy" version)) (sha256 (base32 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20")))) (properties `((upstream-name . "Actigraphy"))) (build-system r-build-system) (propagated-inputs (list r-fda)) (home-page "https://cran.r-project.org/web/packages/Actigraphy/") (synopsis "Actigraphy data analysis") (description "This package provides tools for functional linear modeling and analysis of actigraphy data.") (license license:asl2.0))) (define-public r-activedriver (package (name "r-activedriver") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriver" version)) (sha256 (base32 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa")))) (properties `((upstream-name . "ActiveDriver"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") (synopsis "Tools for finding cancer driver proteins") (description "This package provides a mutation analysis tool that discovers cancer driver genes with frequent mutations in protein signalling sites such as post-translational modifications (phosphorylation, ubiquitination, etc). The Poisson generalized linear regression model identifies genes where cancer mutations in signalling sites are more frequent than expected from the sequence of the entire gene. Integration of mutations with signalling information helps find new driver genes and propose candidate mechanisms to known drivers.") (license license:gpl2+))) (define-public r-activitycounts (package (name "r-activitycounts") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "activityCounts" version)) (sha256 (base32 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz")))) (properties `((upstream-name . "activityCounts"))) (build-system r-build-system) (propagated-inputs (list r-lubridate r-magrittr r-seewave r-signal r-tibble)) (home-page "https://github.com/walkabillylab/activityCounts") (synopsis "Generate ActiLife counts") (description "ActiLife generates activity counts from data collected by Actigraph accelerometers. Actigraph is one of the most common research-grade accelerometers. There is considerable research validating and developing algorithms for human activity using ActiLife counts. Unfortunately, ActiLife counts are proprietary and difficult to implement if researchers use different accelerometer brands. The code creates ActiLife counts from raw acceleration data for different accelerometer brands.") (license license:gpl3))) (define-public r-activityindex (package (name "r-activityindex") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "ActivityIndex" version)) (sha256 (base32 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5")))) (properties `((upstream-name . "ActivityIndex"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-matrixstats r-r-utils)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") (synopsis "Activity Index calculation using raw accelerometry data") (description "This is a package to read raw accelerometry from GT3X+ accelerometry data and plain table data to calculate the Activity Index from Bai et al. (2016) @url{doi:10.1371/journal.pone.0160644}.") (license license:gpl3))) (define-public r-activpal (package (name "r-activpal") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "activPAL" version)) (sha256 (base32 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na")))) (properties `((upstream-name . "activPAL"))) (build-system r-build-system) (propagated-inputs (list r-devtools r-dplyr r-ggplot2 r-lubridate r-magrittr r-tidyr)) (home-page "https://cran.r-project.org/web/packages/activPAL") (synopsis "Processing and chart generation from activPAL events files") (description "This package contains functions to generate pre-defined summary statistics from activPAL events files. The package also contains functions to produce informative graphics that visualize physical activity behaviour and trends. This includes generating graphs that align physical activity behaviour with additional time based observations described by other data sets, such as sleep diaries and continuous glucose monitoring data.") (license license:gpl3))) (define-public r-activpalprocessing (package (name "r-activpalprocessing") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "activpalProcessing" version)) (sha256 (base32 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1")))) (properties `((upstream-name . "activpalProcessing"))) (build-system r-build-system) (propagated-inputs (list r-chron)) (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") (synopsis "Process activPAL events files") (description "This package performs estimation of physical activity and sedentary behavior variables from activPAL events files.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-actogrammr (package (name "r-actogrammr") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "actogrammr" version)) (sha256 (base32 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa")))) (properties `((upstream-name . "actogrammr"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr)) (home-page "https://cran.r-project.org/web/packages/actogrammr/") (synopsis "Read in activity data and plot actograms") (description "Read in activity measurements from standard file formats used by circadian rhythm researchers, currently only ClockLab format, and process and plot the data. The central type of plot is the actogram, as first described in \"Activity and distribution of certain wild mice in relation to biotic communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") (license license:gpl3))) (define-public r-expint (package (name "r-expint") (version "0.1-7") (source (origin (method url-fetch) (uri (cran-uri "expint" version)) (sha256 (base32 "01d0a7pc4qx7044a0cymnv5ld88r90vdvlqjbnzg9qlfbizdgyvw")))) (properties `((upstream-name . "expint"))) (build-system r-build-system) (home-page "https://gitlab.com/vigou3/expint") (synopsis "Exponential integral and incomplete Gamma function") (description "This package provides the exponential integrals @code{E_1(x)}, @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma function @code{G(a, x)} defined for negative values of its first argument. The package also gives easy access to the underlying C routines through an API; see the package vignette for details.") (license license:gpl2+))) (define-public r-actuar (package (name "r-actuar") (version "3.2-2") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 "0dhpaivyga0jwvw1csagbx74biy9jfkw4a8sa871579njxl1x7p1")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs (list r-expint)) (home-page "https://gitlab.com/vigou3/actuar") (synopsis "Actuarial functions and heavy tailed distributions") (description "This package provides functions and data sets for actuarial science: modeling of loss distributions; risk theory and ruin theory; simulation of compound models, discrete mixtures and compound hierarchical models; credibility theory. It boasts support for many additional probability distributions to model insurance loss amounts and loss frequency: 19 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete distribution; zero-truncated and zero-modified extensions of the standard discrete distributions. It also supports phase-type distributions commonly used to compute ruin probabilities.") (license license:gpl2+))) (define-public r-bmp (package (name "r-bmp") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "bmp" version)) (sha256 (base32 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx")))) (properties `((upstream-name . "bmp"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bmp/") (synopsis "Read Bitmap (BMP) images") (description "This package provides pure R tools to read BMP format images. It is currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") (license license:gpl2+))) (define-public r-readbitmap (package (name "r-readbitmap") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "readbitmap" version)) (sha256 (base32 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk")))) (properties `((upstream-name . "readbitmap"))) (build-system r-build-system) (inputs (list libjpeg-turbo libpng)) (propagated-inputs (list r-bmp r-jpeg r-png r-tiff)) (home-page "https://github.com/jefferis/readbitmap") (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") (description "This package provides tools to identify and read BMP, JPEG, PNG, and TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than the file extension.") (license license:gpl2+))) (define-public r-imager (package (name "r-imager") (version "0.42.13") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs (list fftw libtiff libx11 zlib)) (propagated-inputs (list r-downloader r-igraph r-jpeg r-magrittr r-png r-purrr r-rcpp r-readbitmap r-stringr)) (native-inputs (list pkg-config r-knitr)) (home-page "https://dahtah.github.io/imager/") (synopsis "Image processing library") (description "This is a package for fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one color dimension). It provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a simple, modern C++ library for image processing.") (license license:lgpl3))) (define-public r-acuityview (package (name "r-acuityview") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "AcuityView" version)) (sha256 (base32 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l")))) (properties `((upstream-name . "AcuityView"))) (build-system r-build-system) (propagated-inputs (list r-fftwtools r-imager r-plotrix)) (home-page "https://cran.r-project.org/web/packages/AcuityView/") (synopsis "Display scenes as seen by an animal with less acute vision") (description "This package provides a simple method for representing a visual scene as it may be seen by an animal with less acute vision.") (license license:gpl2+))) (define-public r-caret (package (name "r-caret") (version "6.0-92") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 "048mp325ndfl83a8p4dkd1b6zh5bws4gg9kxka5ss8qsj8m4m08x")))) (build-system r-build-system) (propagated-inputs (list r-e1071 r-foreach r-ggplot2 r-lattice r-modelmetrics r-nlme r-plyr r-proc r-recipes r-reshape2 r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/topepo/caret") (synopsis "Classification and regression training") (description "This package provides miscellaneous functions for training and plotting classification and regression models.") (license license:gpl2+))) (define-public r-adabag (package (name "r-adabag") (version "4.2") (source (origin (method url-fetch) (uri (cran-uri "adabag" version)) (sha256 (base32 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7")))) (properties `((upstream-name . "adabag"))) (build-system r-build-system) (propagated-inputs (list r-caret r-doparallel r-foreach r-rpart)) (home-page "https://cran.r-project.org/web/packages/adabag/") (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") (description "This package implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation estimation of the error can be done.") (license license:gpl2+))) (define-public r-adagio (package (name "r-adagio") (version "0.8.4") (source (origin (method url-fetch) (uri (cran-uri "adagio" version)) (sha256 (base32 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl")))) (properties `((upstream-name . "adagio"))) (build-system r-build-system) (propagated-inputs (list r-lpsolve)) (home-page "https://cran.r-project.org/web/packages/adagio/") (synopsis "Discrete and global optimization routines") (description "This package provides methods and algorithms for discrete optimization, e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and Hooke-Jeeves minimization, and some (evolutionary) global optimization functions.") (license license:gpl3+))) (define-public r-univoutl (package (name "r-univoutl") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "univOutl" version)) (sha256 (base32 "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp")))) (properties `((upstream-name . 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Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. Among several built-in similarity/distance measures, computation of correlation, cosine similarity and Euclidean distance is particularly fast.") (license license:gpl3))) (define-public r-isocodes (package (name "r-isocodes") (version "2022.01.10") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") (synopsis "Selected ISO codes") (description "This package provides ISO language, territory, currency, script and character codes. It provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 character codes as well as the UN M.49 area codes.") (license license:gpl2))) (define-public r-stopwords (package (name "r-stopwords") (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "stopwords" version)) (sha256 (base32 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65")))) (properties `((upstream-name . "stopwords"))) (build-system r-build-system) (propagated-inputs (list r-isocodes)) (home-page "https://github.com/quanteda/stopwords") (synopsis "Multilingual stopword lists") (description "This package provides multiple sources of stopwords, for use in text analysis and natural language processing.") (license license:expat))) (define-public r-spacyr (package (name "r-spacyr") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "spacyr" version)) (sha256 (base32 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-stanheaders (package (name "r-stanheaders") (version "2.21.0-7") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-rcppeigen r-rcppparallel)) (native-inputs (list gfortran r-knitr)) ; for vignettes (home-page "https://mc-stan.org/") (synopsis "C++ header files for Stan") (description "The C++ header files of the Stan project are provided by this package. There is a shared object containing part of the @code{CVODES} library, but it is not accessible from R. @code{r-stanheaders} is only useful for developers who want to utilize the @code{LinkingTo} directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan} package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.") (license license:bsd-3))) (define-public r-rpf (package (name "r-rpf") (version "1.0.11") (source (origin (method url-fetch) (uri (cran-uri "rpf" version)) (sha256 (base32 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1")))) (properties `((upstream-name . 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The primary goals of the package are to: @enumerate @item Efficiently convert between many different useful formats of draws (samples) from posterior or prior distributions. @item Provide consistent methods for operations commonly performed on draws, for example, subsetting, binding, or mutating draws. @item Provide various summaries of draws in convenient formats. @item Provide lightweight implementations of state of the art posterior inference diagnostics. @end enumerate ") (license license:bsd-3))) (define-public r-brms (package (name "r-brms") (version "2.17.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94")))) (properties `((upstream-name . 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For more information, see @enumerate @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, @url{https://doi.org/10.18637/jss.v001.i04}; @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital Library, @url{https://doi.org/10.1145/1772690.1772862}; @item \"Armadillo: a template-based C++ library for linear algebra\" by Sanderson et al (2016), The Journal of Open Source Software, @url{https://doi.org/10.21105/joss.00026}; @item \"Clustering by Passing Messages Between Data Points\" by Brendan J. 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The methods can also be used for univariate censored data (see data set @code{cosmesis}), and for censored data with competing risks (see data set @code{menopause}). The package also provides functions to visualize the observed data and the MLE.") (license license:gpl2+))) (define-public r-metafor (package (name "r-metafor") (version "2.4-0") (source (origin (method url-fetch) (uri (cran-uri "metafor" version)) (sha256 (base32 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn")))) (properties `((upstream-name . "metafor"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-nlme)) (home-page "https://cran.r-project.org/web/packages/metafor/") (synopsis "Meta-analysis package for R") (description "This package provides a comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e. mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g. due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g. due to phylogenetic relatedness) can also be conducted.") (license license:gpl2+))) (define-public r-altmeta (package (name "r-altmeta") (version "4.0") (source (origin (method url-fetch) (uri (cran-uri "altmeta" version)) (sha256 (base32 "17cyiydf4n5j64izj7jph2v43h4x9kfd5b0x6m0ik5ci2aw8xzr5")))) (properties `((upstream-name . 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It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs). Using a hidden Markov model, R/qtl estimates genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.") (license license:gpl3))) (define-public r-qtl2 (package (name "r-qtl2") (version "0.28") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-rcpp r-rcppeigen r-rsqlite r-yaml)) (home-page "https://kbroman.org/qtl2/") (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") (description "This package provides a set of tools to perform @dfn{Quantitative Trait Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the @code{R/qtl} package to better handle high-dimensional data and complex cross designs. Broman et al. (2018) .") 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It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.") (license license:gpl3))) (define-public r-seuratdisk (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610") (revision "1")) (package (name "r-seuratdisk") (version (git-version "0.0.0.9019" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mojaveazure/seurat-disk") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw")))) (properties `((upstream-name . 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(add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-cli r-crayon r-rappdirs)) (home-page "https://github.com/satijalab/seurat-data") (synopsis "Install and manage Seurat datasets") (description "Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages.") (license license:gpl3)))) (define-public r-phangorn (package (name "r-phangorn") (version "2.8.1") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd")))) (build-system r-build-system) (propagated-inputs (list r-ape r-fastmatch r-igraph r-matrix r-quadprog r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/KlausVigo/phangorn") (synopsis "Phylogenetic analysis in R") (description "Phangorn is a package for phylogenetic analysis in R. It supports estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.") (license license:gpl2+))) (define-public r-diversitree (package (name "r-diversitree") (version "0.9-16") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc")))) (build-system r-build-system) (native-inputs (list gfortran)) (inputs (list fftw gsl)) (propagated-inputs (list r-ape r-desolve r-rcpp r-subplex)) (home-page "https://www.zoology.ubc.ca/prog/diversitree") (synopsis "Comparative 'phylogenetic' analyses of diversification") (description "This package contains a number of comparative \"phylogenetic\" methods, mostly focusing on analysing diversification and character evolution. Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) (define-public r-calculus (package (name "r-calculus") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 "1fhvr0l2mqik3d95v0vanafxmiab147g5a87q956g2i945wc5f22")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/eguidotti/calculus") (synopsis "High dimensional numerical and symbolic calculus") (description "Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, accurate high-order derivatives, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.") (license license:gpl3))) (define-public r-decon (package (name "r-decon") (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "decon" version)) (sha256 (base32 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs")))) (properties `((upstream-name . 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Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.") (license license:gpl3+))) (define-public r-densestbayes (package (name "r-densestbayes") (version "1.0-2.1") (source (origin (method url-fetch) (uri (cran-uri "densEstBayes" version)) (sha256 (base32 "1pzmgn65lv91zg1588qhwczy9f2zgciknlc4l072mvh2i7hncw2b")))) (properties `((upstream-name . 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(license license:lgpl3))) (define-public r-mlr3misc (package (name "r-mlr3misc") (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-r6)) (home-page "https://mlr3misc.mlr-org.com/") (synopsis "Helper functions for mlr3") (description "@code{mlr3misc} provides frequently used helper functions and assertions used in @code{mlr3} and its companion packages. It comes with helper functions for functional programming, for printing, to work with @code{data.table}, as well as some generally useful @code{R6} classes. This package also supersedes the package @code{BBmisc}.") (license license:lgpl3))) (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-lgr r-mlr3 r-mlr3misc r-paradox r-r6 r-withr)) (home-page "https://mlr3pipelines.mlr-org.com/") (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}") (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse set of pipelining operators (PipeOps) that can be composed into graphs. Operations exist for data preprocessing, model fitting, and ensemble learning. Graphs can themselves be treated as @code{mlr3} Learners and can therefore be resampled, benchmarked, and tuned.") (license license:lgpl3))) (define-public r-mlr3ordinal (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44") (revision "0")) (package (name "r-mlr3ordinal") (version (git-version "0.1.0-9000" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mlr-org/mlr3ordinal") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-mlr3 r-mlr3misc r-mlr3pipelines r-nloptr r-ordinal r-paradox r-r6)) (home-page "https://mlr3ordinal.mlr-org.com/") (synopsis "Ordinal Regression for mlr3") (description "This package extends @code{mlr3} with support for performing ordinal regression.") (license license:expat)))) (define-public r-paradox (package (name "r-paradox") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 "0fzq59903fklgj3kblnpzasy13a82s72c1qjsy7d1m0fyj28ahdw")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) (home-page "https://paradox.mlr-org.com/") (synopsis "Define and work with parameter spaces for complex algorithms") (description "With this package it is possible to define parameter spaces, constraints and dependencies for arbitrary algorithms, and to program on such spaces. It also includes statistical designs and random samplers. Objects are implemented as @code{R6} classes.") (license license:lgpl3))) (define-public r-mlr3 (package (name "r-mlr3") (version "0.13.3") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 "010kl51zsgpc0qv63g1fg9kiw9m0wzqskcr14f1j8b9zi1lwi0bf")))) (build-system r-build-system) (propagated-inputs (list r-r6 r-backports r-checkmate r-data-table r-evaluate r-future r-future-apply r-lgr r-mlbench r-mlr3measures r-mlr3misc r-palmerpenguins r-paradox r-parallelly r-uuid)) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") (description "@code{mlr3} enables efficient, object-oriented programming on the building blocks of machine learning. It provides @code{R6} objects for tasks, learners, resamplings, and measures. The package is geared towards scalability and larger datasets by supporting parallelization and out-of-memory data-backends like databases. While @code{mlr3} focuses on the core computational operations, add-on packages provide additional functionality.") (license license:lgpl3))) (define-public r-mlr3learners (package (name "r-mlr3learners") (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 "088i2piv7sgxsvc7jyr6mq53vqf8yjdlrysgqphsryq6k50i00zd")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-mlr3 r-mlr3misc r-paradox r-r6)) (home-page "https://mlr3learners.mlr-org.com/") (synopsis "Recommended Learners for @code{mlr3}") (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba} with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.") (license license:lgpl3))) (define-public r-bbotk (package (name "r-bbotk") (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 "13qj8qysqismv9k9rfw770r7w8jdaw82n71k7sp3wsrlhxjxw734")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table r-lgr r-mlr3misc r-paradox r-r6)) (native-inputs (list r-knitr)) (home-page "https://bbotk.mlr-org.com") (synopsis "Black-Box Optimization Toolkit") (description "This package provides a common framework for optimization of black-box functions for other packages, e.g. @code{mlr3}. It offers various optimization methods e.g. grid search, random search and generalized simulated annealing.") (license license:lgpl3))) (define-public r-mlr3tuning (package (name "r-mlr3tuning") (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 "0jfslx6pwk408ydn69grrvsp22jd7gsjmwvss0a1j0zav3q1pvks")))) (build-system r-build-system) (propagated-inputs (list r-bbotk r-checkmate r-data-table r-lgr r-mlr3 r-mlr3misc r-paradox r-r6)) (home-page "https://mlr3tuning.mlr-org.com/") (synopsis "Tuning for @code{mlr3}") (description "@code{mlr3tuning} implements methods for hyperparameter tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various termination criteria can be set and combined. The class @code{AutoTuner} provides a convenient way to perform nested resampling in combination with @code{mlr3}.") (license license:lgpl3))) (define-public r-fontliberation (package (name "r-fontliberation") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "fontLiberation" version)) (sha256 (base32 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc")))) (properties `((upstream-name . "fontLiberation"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fontLiberation") (synopsis "Liberation fonts") (description "This package provides a placeholder for the Liberation fontset intended for the fontquiver package. This fontset covers the 12 combinations of families (sans, serif, mono) and faces (plain, bold, italic, bold italic) supported in R graphics devices.") (license license:silofl1.1))) (define-public r-fontbitstreamvera (package (name "r-fontbitstreamvera") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "fontBitstreamVera" version)) (sha256 (base32 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j")))) (properties `((upstream-name . "fontBitstreamVera"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fontBitstreamVera") (synopsis "Fonts for fontquiver") (description "This package is a placeholder for the Bitstream Vera font. It is intended for the fontquiver package.") (license (license:fsdg-compatible "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts" "The Font Software may be sold as part of a larger software package but no copy of one or more of the Font Software typefaces may be sold by itself.")))) (define-public r-fontquiver (package (name "r-fontquiver") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "fontquiver" version)) (sha256 (base32 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm")))) (properties `((upstream-name . "fontquiver"))) (build-system r-build-system) (propagated-inputs (list r-fontbitstreamvera r-fontliberation)) (home-page "https://cran.r-project.org/package=fontquiver") (synopsis "Set of installed fonts") (description "This package provides a set of fonts. This is useful when you want to avoid system fonts to make sure your outputs are reproducible.") (license license:gpl3))) (define-public r-freetypeharfbuzz (package (name "r-freetypeharfbuzz") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "freetypeharfbuzz" version)) (sha256 (base32 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7")))) (properties `((upstream-name . "freetypeharfbuzz"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'prepare-static-libraries (lambda* (#:key inputs #:allow-other-keys) (mkdir-p "src/target/include") (let ((freetype (assoc-ref inputs "static-freetype")) (harfbuzz (assoc-ref inputs "static-harfbuzz"))) (substitute* "src/Makevars.in" (("include @MK_FILE@") "") ; do not build static libs (("^HB_STATIC_LIB =.*") (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n")) (("^FT_STATIC_LIB =.*") (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n"))) (copy-recursively (string-append freetype "/include") "src/target/include") (copy-recursively (string-append harfbuzz "/include") "src/target/include"))))))) (propagated-inputs (list r-fontquiver)) ;; This may defeat the purpose of this package as our versions of freetype ;; and harfbuzz obviously differ from the tarballs offered by this ;; project. On the other hand, Guix arguably does a better job at ;; "ensur[ing] deterministic computation". (native-inputs `(("static-freetype" ,(package (inherit (static-package freetype)) (arguments `(#:configure-flags (list "--enable-static=yes" "--with-pic=yes" "--without-zlib" "--without-bzip2" "--without-png" "--without-harfbuzz"))))) ("static-harfbuzz" ,(package (inherit (static-package harfbuzz)) (arguments `(#:tests? #false ; fail because shared library is disabled #:configure-flags (list "--enable-static=yes" "--enable-shared=no" "--with-pic=yes" "--with-freetype=yes" "--without-icu" "--without-cairo" "--without-fontconfig" "--without-glib"))))))) (inputs (list zlib)) (home-page "https://cran.r-project.org/package=freetypeharfbuzz") (synopsis "Deterministic computation of text box metrics") (description "Unlike other tools that dynamically link to the Cairo stack, freetypeharfbuzz is statically linked to specific versions of the FreeType and harfbuzz libraries. This ensures deterministic computation of text box extents for situations where reproducible results are crucial (for instance unit tests of graphics).") (license license:gpl3))) (define-public r-vdiffr (package (name "r-vdiffr") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "vdiffr" version)) (sha256 (base32 "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy")))) (properties `((upstream-name . "vdiffr"))) (build-system r-build-system) (inputs (list libpng zlib)) (propagated-inputs (list r-cpp11 r-diffobj r-glue r-htmltools r-lifecycle r-rlang r-testthat r-xml2)) (home-page "https://github.com/r-lib/vdiffr") (synopsis "Visual regression testing and graphical diffing") (description "This package is an extension to the testthat package that makes it easy to add graphical unit tests. It provides a Shiny application to manage the test cases.") (license license:gpl3))) (define-public r-highlight (package (name "r-highlight") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "highlight" version)) (sha256 (base32 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf")))) (properties `((upstream-name . "highlight"))) (build-system r-build-system) (home-page "https://github.com/hadley/highlight") (synopsis "Syntax highlighter for R code") (description "This package provides a syntax highlighter for R code based on the results of the R parser. It supports rendering in HTML and LaTeX markup. It includes a custom Sweave driver performing syntax highlighting of R code chunks.") (license license:gpl3+))) (define-public r-clustree (package (name "r-clustree") (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "clustree" version)) (sha256 (base32 "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs")))) (properties `((upstream-name . "clustree"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-dplyr r-ggplot2 r-ggraph r-ggrepel r-igraph r-rlang r-tidygraph r-viridis)) (native-inputs (list r-knitr)) (home-page "https://github.com/lazappi/clustree") (synopsis "Visualize clusterings at different resolutions") (description "Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualization for interrogating clusterings as resolution increases.") (license license:gpl3))) (define-public r-textshaping (package (name "r-textshaping") (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs (list freetype fribidi harfbuzz zlib)) (propagated-inputs (list r-cpp11 r-systemfonts)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/textshaping") (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping") (description "This package provides access to the text shaping functionality in the HarfBuzz library and the bidirectional algorithm in the Fribidi library. This is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the @code{systemfonts} package.") (license license:expat))) (define-public r-ragg (package (name "r-ragg") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 "1q43pwmljsqgrikkh2g1n7bpz9c8py5dnj44cfg3y2br7b4m2q9v")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs (list freetype libjpeg-turbo libpng libtiff zlib)) (propagated-inputs (list r-systemfonts r-textshaping)) (native-inputs (list pkg-config)) (home-page "https://ragg.r-lib.org") (synopsis "Graphic devices based on AGG") (description "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The ragg package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the @code{grDevices} package.") (license license:expat))) (define-public r-downlit (package (name "r-downlit") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "downlit" version)) (sha256 (base32 "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl")))) (properties `((upstream-name . "downlit"))) (build-system r-build-system) (propagated-inputs (list r-brio r-desc r-digest r-evaluate r-fansi r-memoise r-rlang r-vctrs r-yaml)) (home-page "https://downlit.r-lib.org/") (synopsis "Syntax highlighting and automatic linking") (description "This package provides syntax highlighting of R code, specifically designed for the needs of RMarkdown packages like @code{pkgdown}, @code{hugodown}, and @code{bookdown}. It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.") (license license:expat))) (define-public r-pkgdown (package (name "r-pkgdown") (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 "0wqga9bcl7wmvkwpkkmf5hx1cl7rjq5ddvqmxhl4p1dczys3adnr")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-bslib r-callr r-crayon r-desc r-digest r-downlit r-fs r-httr r-jsonlite r-magrittr r-memoise r-purrr r-ragg r-rlang r-rmarkdown r-tibble r-whisker r-withr r-xml2 r-yaml)) (native-inputs (list r-knitr)) (home-page "https://pkgdown.r-lib.org") (synopsis "Make static HTML documentation for an R package") (description "The goal of this package is to generate an attractive and useful website from a source package. @code{pkgdown} converts your documentation, vignettes, README file, and more to HTML making it easy to share information about your package online.") (license license:expat))) (define-public r-prereg (package (name "r-prereg") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "prereg" version)) (sha256 (base32 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw")))) (properties `((upstream-name . "prereg"))) (build-system r-build-system) (propagated-inputs (list r-rmarkdown ;; The package provides a custom LaTex template in ;; inst/rmd/prereg_form.tex, which depends on these packages: texlive-amsmath texlive-booktabs texlive-etoolbox texlive-generic-iftex texlive-latex-fancyhdr texlive-latex-fancyvrb texlive-latex-geometry texlive-latex-graphics texlive-latex-threeparttable texlive-latex-titlesec texlive-latex-upquote texlive-listings texlive-polyglossia texlive-titling texlive-tools texlive-ulem (texlive-updmap.cfg (list texlive-amsfonts texlive-lm)))) (home-page "https://github.com/crsh/prereg") (synopsis "R Markdown Templates to preregister Scientific Studies") (description "This package provides a collection of templates to author preregistration documents for scientific studies in PDF format.") (license license:gpl3))) (define-public r-ez (package (name "r-ez") (version "4.4-0") (source (origin (method url-fetch) (uri (cran-uri "ez" version)) (sha256 (base32 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq")))) (properties `((upstream-name . "ez"))) (build-system r-build-system) (propagated-inputs (list r-car r-ggplot2 r-lme4 r-mass r-matrix r-mgcv r-plyr r-reshape2 r-scales r-stringr)) (home-page "https://github.com/mike-lawrence/ez") (synopsis "Easy Analysis and Visualization of Factorial Experiments") (description "Facilitates easy analysis of factorial experiments, including purely within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs, and mixed within-and-between-Ss designs. The functions in this package aim to provide simple, intuitive and consistent specification of data analysis and visualization. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Finally, this package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. The bootstrap function obtains predictions either by cell means or by more advanced/powerful mixed effects models, yielding predictions and confidence intervals that may be easily visualized at any level of the experiment's design.") (license license:gpl2+))) (define-public r-qdapregex (package (name "r-qdapregex") (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "qdapRegex" version)) (sha256 (base32 "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb")))) (properties `((upstream-name . "qdapRegex"))) (build-system r-build-system) (propagated-inputs (list r-stringi)) (home-page "https://trinker.github.com/qdapRegex/") (synopsis "Regular Expression Removal, Extraction, and Replacement Tools") (description "This package provides a collection of regular expression tools associated with the @code{qdap} package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, citations, person tags, phone numbers, times, and zip codes.") (license license:gpl2))) (define-public r-mgsub (package (name "r-mgsub") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "mgsub" version)) (sha256 (base32 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9")))) (properties `((upstream-name . "mgsub"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=mgsub") (synopsis "Safe, Multiple, Simultaneous String Substitution") (description "Designed to enable simultaneous substitution in strings in a safe fashion. Safe means it does not rely on placeholders (which can cause errors in same length matches).") (license license:expat))) (define-public r-textshape (package (name "r-textshape") (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "textshape" version)) (sha256 (base32 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds")))) (properties `((upstream-name . "textshape"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-slam r-stringi)) (home-page "https://github.com/trinker/textshape") (synopsis "Tools for Reshaping Text") (description "Tools that can be used to reshape and restructure text data.") (license license:gpl2))) (define-public r-syuzhet (package (name "r-syuzhet") (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "syuzhet" version)) (sha256 (base32 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv")))) (properties `((upstream-name . "syuzhet"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-dtt r-nlp r-rlang r-textshape r-tidyr r-zoo)) (native-inputs (list r-knitr)) (home-page "https://github.com/mjockers/syuzhet") (synopsis "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text") (description "Extracts sentiment and sentiment-derived plot arcs from text using a variety of sentiment dictionaries conveniently packaged for consumption by R users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing} developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif M. and Turney, Peter D. Applicable references are available in @file{README.md} and in the documentation for the @code{get_sentiment} function. The package also provides a hack for implementing Stanford's coreNLP sentiment parser. The package provides several methods for plot arc normalization.") (license license:gpl3))) (define-public r-lexicon (package (name "r-lexicon") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "lexicon" version)) (sha256 (base32 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c")))) (properties `((upstream-name . "lexicon"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-syuzhet)) (home-page "https://github.com/trinker/lexicon") (synopsis "Lexicons for Text Analysis") (description "This package provides a collection of lexical hash tables, dictionaries, and word lists.") (license license:gpl3))) (define-public r-english (package (name "r-english") (version "1.2-6") (source (origin (method url-fetch) (uri (cran-uri "english" version)) (sha256 (base32 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9")))) (properties `((upstream-name . "english"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=english") (synopsis "Translate Integers into English") (description "Allow numbers to be presented in an English language version, one, two, three, ... Ordinals are also available, first, second, third, ... and indefinite article choice, \"a\" or \"an\".") (license license:gpl2))) (define-public r-textclean (package (name "r-textclean") (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "textclean" version)) (sha256 (base32 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz")))) (properties `((upstream-name . "textclean"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-english r-glue r-lexicon r-mgsub r-qdapregex r-stringi r-textshape)) (home-page "https://github.com/trinker/textclean") (synopsis "Text Cleaning Tools") (description "Tools to clean and process text. Tools are geared at checking for substrings that are not optimal for analysis and replacing or removing them (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or extracting them into new variables. For example, emoticons are often used in text but not always easily handled by analysis algorithms. The @code{replace_emoticon()} function replaces emoticons with word equivalents.") (license license:gpl2))) (define-public r-striprtf (package (name "r-striprtf") (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "striprtf" version)) (sha256 (base32 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316")))) (properties `((upstream-name . "striprtf"))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-rcpp r-stringr)) (home-page "https://github.com/kota7/striprtf") (synopsis "Extract Text from RTF File") (description "Extracts plain text from @dfn{Rich Text Format} (RTF) file.") (license license:expat))) (define-public r-ndjson (package (name "r-ndjson") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ndjson" version)) (sha256 (base32 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812")) (modules '((guix build utils))) (snippet '(begin ;; unvendor gzstream (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h")) #t)))) (properties `((upstream-name . "ndjson"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-gzstream (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Makevars" (("PKG_LIBS = " all) (string-append all "-lgzstream "))) #t))))) (inputs (list zlib gzstream)) (propagated-inputs (list r-data-table r-rcpp r-tibble)) (home-page "https://gitlab.com/hrbrmstr/ndjson") (synopsis "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader") (description "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many modern ndjson files contain large numbers of records. These constructs may not be columnar in nature, but it is often useful to read in these files and \"flatten\" the structure out to enable working with the data in an R @code{data.frame}-like context. Functions are provided that make it possible to read in plain ndjson files or compressed (@code{gz}) ndjson files and either validate the format of the records or create \"flat\" @code{data.table} structures from them.") (license license:expat))) (define-public r-streamr (package (name "r-streamr") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "streamR" version)) (sha256 (base32 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix")))) (properties `((upstream-name . "streamR"))) (build-system r-build-system) (propagated-inputs (list r-ndjson r-rcurl r-rjson)) (home-page "https://cran.r-project.org/package=streamR") (synopsis "Access to Twitter Streaming API via R") (description "This package provides functions to access Twitter's filter, sample, and user streams, and to parse the output into data frames.") (license license:gpl2))) (define-public r-readods (package (name "r-readods") (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "readODS" version)) (sha256 (base32 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n")))) (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-readr r-stringi r-xml2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=readODS") (synopsis "Read and Write ODS Files") (description "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame. Also support writing data frame into ODS file.") (license license:gpl3))) (define-public r-qpdf (package (name "r-qpdf") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "qpdf" version)) (sha256 (base32 "1a1d7zad2l94z068mic6dg9wr9bq8mlmqszrj8vxps1441mb6gfh")) (modules '((guix build utils))) (snippet '(begin ;; unvendor libqpdf (delete-file-recursively "src/libqpdf") (delete-file-recursively "src/include/qpdf"))))) (properties `((upstream-name . "qpdf"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'configure (lambda _ (setenv "EXTERNAL_QPDF" "1")))))) (inputs (list libjpeg-turbo qpdf zlib)) (propagated-inputs (list r-askpass r-curl r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://github.com/ropensci/qpdf") (synopsis "Split, Combine and Compress PDF Files") (description "Content-preserving transformations transformations of PDF files such as split, combine, and compress. This package interfaces directly to the @code{qpdf} C++ API and does not require any command line utilities. Note that @code{qpdf} does not read actual content from PDF files: to extract text and data you need the @code{pdftools} package.") (license license:asl2.0))) (define-public r-pdftools (package (name "r-pdftools") (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 "1b9ppdndvlf8nl0i3xy1rx4f9j0j8ic6q9n0c4zn3rv6jdy8zqfi")))) (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs (list zlib poppler)) (propagated-inputs (list r-qpdf r-rcpp)) (native-inputs (list pkg-config)) (home-page "https://docs.ropensci.org/pdftools/") (synopsis "Text Extraction, Rendering and Converting of PDF Documents") (description "This package provides utilities based on @code{libpoppler} for extracting text, fonts, attachments and metadata from a PDF file. It also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.") (license license:expat))) (define-public r-antiword (package (name "r-antiword") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "antiword" version)) (sha256 (base32 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2")) (modules '((guix build utils))) (snippet '(begin ;; unvendor libantiword (delete-file-recursively "src") #t)))) (properties `((upstream-name . "antiword"))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-antiword (lambda* (#:key inputs #:allow-other-keys) (substitute* "R/antiword.R" (("system.file\\(\"bin\", package = \"antiword\"\\)") (string-append "\"" (assoc-ref inputs "antiword") "/bin\""))) #t))))) (inputs (list antiword)) (propagated-inputs (list r-sys)) (home-page "https://github.com/ropensci/antiword#readme") (synopsis "Extract Text from Microsoft Word Documents") (description "Wraps the @code{AntiWord} utility to extract text from Microsoft Word documents. The utility only supports the old @code{doc} format, not the new xml based @code{docx} format. Use the @code{xml2} package to read the latter.") (license license:gpl2))) (define-public r-readtext (package (name "r-readtext") (version "0.81") (source (origin (method url-fetch) (uri (cran-uri "readtext" version)) (sha256 (base32 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c")))) (properties `((upstream-name . "readtext"))) (build-system r-build-system) (propagated-inputs (list r-antiword r-data-table r-digest r-httr r-jsonlite r-pdftools r-readods r-readxl r-streamr r-stringi r-striprtf r-tibble r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/quanteda/readtext") (synopsis "Import and Handling for Plain and Formatted Text Files") (description "This package provides functions for importing and handling text files and formatted text files with additional meta-data, such including @code{.csv}, @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc}, @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.") (license license:gpl3))) (define-public r-packcircles (package (name "r-packcircles") (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "packcircles" version)) (sha256 (base32 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk")))) (properties `((upstream-name . "packcircles"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/mbedward/packcircles") (synopsis "Circle Packing") (description "Algorithms to find arrangements of non-overlapping circles.") (license license:expat))) ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on ;; its own. (define-public r-lwgeom (package (name "r-lwgeom") (version "0.2-8") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl")))) (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs (list geos proj sqlite zlib)) (propagated-inputs (list r-rcpp r-sf r-units)) (native-inputs (list pkg-config)) (home-page "https://github.com/r-spatial/lwgeom/") (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features") (description "Access to selected functions found in @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (license license:gpl2))) (define-public r-stars (package (name "r-stars") (version "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 "0hcbzr8c7wk30qjwrvx6bflzwkjpms79pavaxawnq1h8kry5fngk")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs (list r-abind r-classint r-lwgeom r-rlang r-sf r-units)) (native-inputs (list r-knitr)) (home-page "https://r-spatial.github.io/stars/") (synopsis "Spatiotemporal Arrays, Raster and Vector Data Cubes") (description "Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.") (license license:asl2.0))) (define-public r-tmaptools (package (name "r-tmaptools") (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "tmaptools" version)) (sha256 (base32 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx")))) (properties `((upstream-name . "tmaptools"))) (build-system r-build-system) (propagated-inputs (list r-dichromat r-lwgeom r-magrittr r-rcolorbrewer r-sf r-stars r-units r-viridislite r-xml)) (home-page "https://github.com/mtennekes/tmaptools") (synopsis "Thematic Map Tools") (description "Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates @code{tmap}, the package for visualizing thematic maps.") (license license:gpl3))) (define-public r-rworldmap (package (name "r-rworldmap") (version "1.3-6") (source (origin (method url-fetch) (uri (cran-uri "rworldmap" version)) (sha256 (base32 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk")))) (properties `((upstream-name . "rworldmap"))) (build-system r-build-system) (propagated-inputs (list r-fields r-maptools r-sp)) (home-page "https://github.com/AndySouth/rworldmap/") (synopsis "Mapping Global Data") (description "Enables mapping of country level and gridded user datasets.") (license license:gpl2+))) (define-public r-rtweet (package (name "r-rtweet") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "rtweet" version)) (sha256 (base32 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n")))) (properties `((upstream-name . "rtweet"))) (build-system r-build-system) (propagated-inputs (list r-httpuv r-httr r-jsonlite r-magrittr r-progress r-rcpp r-tibble)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/rtweet/") (synopsis "Collecting Twitter Data") (description "An implementation of calls designed to collect and organize Twitter data via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream Application Program Interfaces (API)}.") (license license:expat))) (define-public r-intervals (package (name "r-intervals") (version "0.15.2") (source (origin (method url-fetch) (uri (cran-uri "intervals" version)) (sha256 (base32 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb")))) (properties `((upstream-name . "intervals"))) (build-system r-build-system) (home-page "https://github.com/edzer/intervals") (synopsis "Tools for Working with Points and Intervals") (description "Tools for working with and comparing sets of points and intervals.") (license license:artistic2.0))) (define-public r-eyelinker (package (name "r-eyelinker") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "eyelinker" version)) (sha256 (base32 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71")))) (properties `((upstream-name . "eyelinker"))) (build-system r-build-system) (propagated-inputs (list r-intervals r-readr r-stringi r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/a-hurst/eyelinker") (synopsis "Import ASC Files from EyeLink Eye Trackers") (description "Imports plain-text ASC data files from EyeLink eye trackers into (relatively) tidy data frames for analysis and visualization.") (license license:gpl3))) (define-public r-btm (package (name "r-btm") (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "BTM" version)) (sha256 (base32 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr")))) (properties `((upstream-name . "BTM"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/bnosac/BTM") (synopsis "Biterm Topic Models for Short Text") (description "Biterm Topic Models find topics in collections of short texts. It is a word co-occurrence based topic model that learns topics by modeling word-word co-occurrences patterns which are called biterms. This in contrast to traditional topic models like Latent Dirichlet Allocation and Probabilistic Latent Semantic Analysis which are word-document co-occurrence topic models. A biterm consists of two words co-occurring in the same short text window. This context window can for example be a twitter message, a short answer on a survey, a sentence of a text or a document identifier. The techniques are explained in detail in the paper 'A Biterm Topic Model For Short Text' by Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\ BTM-WWW13.pdf}.") (license license:asl2.0))) (define-public r-delaporte (package (name "r-delaporte") (version "8.0.2") (source (origin (method url-fetch) (uri (cran-uri "Delaporte" version)) (sha256 (base32 "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5")))) (properties `((upstream-name . "Delaporte"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://github.com/aadler/Delaporte") (synopsis "Statistical functions for the Delaporte distribution") (description "This package provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution with parameterization based on Vose (2008). The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.") (license license:bsd-2))) (define-public r-rjsonio (package (name "r-rjsonio") (version "1.3-1.6") (source (origin (method url-fetch) (uri (cran-uri "RJSONIO" version)) (sha256 (base32 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2")))) (properties `((upstream-name . "RJSONIO"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=RJSONIO") (synopsis "Serialize R objects to JSON") (description "This is a package that allows conversion to and from data in JavaScript Object Notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to the @code{rjson} package.") (license license:bsd-3))) (define-public r-revgeo (package (name "r-revgeo") (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "revgeo" version)) (sha256 (base32 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55")))) (properties `((upstream-name . "revgeo"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) (home-page "https://cran.r-project.org/package=revgeo") (synopsis "Reverse geocoding") (description "The @code{revgeo} procedure allows you to use the Photon geocoder for OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with minimal hassle.") (license license:gpl3+))) (define-public r-qpcr (package (name "r-qpcr") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "qpcR" version)) (sha256 (base32 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv")))) (properties `((upstream-name . "qpcR"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase)) (home-page "https://cran.r-project.org/package=qpcR") (synopsis "Modelling and analysis of real-time PCR data") (description "This is a package for model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).") (license license:gpl2+))) (define-public r-textplot (package (name "r-textplot") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "textplot" version)) (sha256 (base32 "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl")))) (properties `((upstream-name . "textplot"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-lattice r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/bnosac/textplot") (synopsis "Text Plots") (description "Visualise complex relations in texts. This is done by providing functionalities for displaying text co-occurrence networks, text correlation networks, dependency relationships as well as text clustering. Feel free to join the effort of providing interesting text visualisations.") (license license:gpl2))) (define-public r-gsa (package (name "r-gsa") (version "1.03.2") (source (origin (method url-fetch) (uri (cran-uri "GSA" version)) (sha256 (base32 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p")))) (properties `((upstream-name . "GSA"))) (build-system r-build-system) (home-page "https://statweb.stanford.edu/~tibs/GSA/") (synopsis "Gene set analysis") (description "This package lets you determine the significance of pre-defined sets of genes with respect to an outcome variable, such as a group indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) (define-public r-gsalib (package (name "r-gsalib") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "gsalib" version)) (sha256 (base32 "1k3zjdydzb0dfh1ihih08d4cw6rdamgb97cdqna9mf0qdjc3pcp1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gsalib") (synopsis "Utility functions for GATK") (description "This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.") (license license:expat))) (define-public r-randomforestsrc (package (name "r-randomforestsrc") (version "2.9.3") (source (origin (method url-fetch) (uri (cran-uri "randomForestSRC" version)) (sha256 (base32 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw")))) (properties `((upstream-name . "randomForestSRC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/randomForestSRC/") (synopsis "Random forests for survival, regression, and classification") (description "This package implements fast OpenMP parallel computing of Breiman's random forests for survival, competing risks, regression and classification based on Ishwaran and Kogalur's popular random survival forests (RSF) package. It handles missing data and now includes multivariate, unsupervised forests, quantile regression and solutions for class imbalanced data. It provides a fast interface using subsampling and confidence regions for variable importance.") (license license:gpl3+))) (define-public r-contfrac (package (name "r-contfrac") (version "1.1-12") (source (origin (method url-fetch) (uri (cran-uri "contfrac" version)) (sha256 (base32 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm")))) (properties `((upstream-name . "contfrac"))) (build-system r-build-system) (home-page "https://github.com/RobinHankin/contfrac") (synopsis "Continued Fractions") (description "Various utilities for evaluating continued fractions.") (license license:gpl2))) (define-public r-elliptic (package (name "r-elliptic") (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "elliptic" version)) (sha256 (base32 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn")))) (properties `((upstream-name . "elliptic"))) (build-system r-build-system) (inputs (list pari-gp)) (propagated-inputs (list r-mass)) (home-page "https://github.com/RobinHankin/elliptic") (synopsis "Weierstrass and Jacobi Elliptic Functions") (description "A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.") (license license:gpl2))) (define-public r-hypergeo (package (name "r-hypergeo") (version "1.2-13") (source (origin (method url-fetch) (uri (cran-uri "hypergeo" version)) (sha256 (base32 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd")))) (properties `((upstream-name . "hypergeo"))) (build-system r-build-system) (propagated-inputs (list r-contfrac r-desolve r-elliptic)) (home-page "https://cran.r-project.org/web/packages/hypergeo/") (synopsis "The Gauss Hypergeometric Function") (description "The Gaussian hypergeometric function for complex numbers.") (license license:gpl2))) (define-public r-gganimate (package (name "r-gganimate") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "gganimate" version)) (sha256 (base32 "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f")))) (properties `((upstream-name . "gganimate"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'absolute-paths (lambda* (#:key inputs #:allow-other-keys) (substitute* "R/renderers.R" (("'ffmpeg'") (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'")))))))) (inputs ;; For video output. (list ffmpeg)) (propagated-inputs (list r-ggplot2 r-glue r-plyr r-progress r-rlang r-scales r-stringi r-tweenr ;; For GIF/SVG output. gifski is faster, but depends on Rust. r-magick ;; For HTML output. r-base64enc r-htmltools)) (native-inputs (list r-knitr)) (home-page "https://gganimate.com") (synopsis "Grammar of Animated Graphics") (description "This package extends the grammar of graphics as implemented by @code{ggplot2} to include the description of animation. It does this by providing a range of new grammar classes that can be added to the plot object in order to customise how it should change with time.") (license license:expat))) ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle ;; it, because its C++ libtz.so is built with different compiler flags than ;; ours. (define-public r-tzdb (package (name "r-tzdb") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "tzdb" version)) (sha256 (base32 "0f3h4zaf9f4l371k6nc1mq6z2f9aj1vaf2inni8jnsds3zng16b0")))) (properties `((upstream-name . "tzdb"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) (home-page "https://github.com/r-lib/tzdb") (synopsis "Time Zone Database Information") (description "This package provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the @code{date} library. @code{date} provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.") (license license:expat))) (define-public r-vroom (package (name "r-vroom") (version "1.5.7") (source (origin (method url-fetch) (uri (cran-uri "vroom" version)) (sha256 (base32 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh")))) (properties `((upstream-name . "vroom"))) (build-system r-build-system) (propagated-inputs (list r-bit64 r-cli r-cpp11 r-crayon r-glue r-hms r-lifecycle r-progress r-rlang r-tibble r-tidyselect r-tzdb r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://vroom.r-lib.org") (synopsis "Read and Write Rectangular Text Data") (description "This package reads and writes data files like @acronym{CSV}, @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing step, then reads the values lazily, so only the data you actually use needs to be read. 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(license license:asl2.0))) (define-public r-paws-compute (package (name "r-paws-compute") (version "0.1.12") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services compute services") (description "This package provides an interface to Amazon Web Services compute services, including Elastic Compute Cloud (EC2), Lambda functions-as-a-service, containers, batch processing, and more.") (license license:asl2.0))) (define-public r-paws (package (name "r-paws") (version "0.1.12") (source (origin (method url-fetch) (uri (cran-uri "paws" version)) (sha256 (base32 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6")))) (properties `((upstream-name . 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Log ratios are used to compare the relative (rather than the absolute) dimensions of animals from archaeological contexts. The zoolog package is also able to seamlessly integrate data and references with heterogeneous nomenclature, which is internally managed by a zoolog thesaurus.") (license license:gpl3))) (define-public r-filehash (package (name "r-filehash") (version "2.4-3") (source (origin (method url-fetch) (uri (cran-uri "filehash" version)) (sha256 (base32 "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k")))) (properties `((upstream-name . "filehash"))) (build-system r-build-system) (home-page "http://github.com/rdpeng/filehash") (synopsis "Simple key-value database") (description "This package implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow filehash databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets.") (license license:gpl2+))) (define-public r-mlearning (package (name "r-mlearning") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "mlearning" version)) (sha256 (base32 "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3")))) (properties `((upstream-name . "mlearning"))) (build-system r-build-system) (propagated-inputs (list r-class r-e1071 r-ipred r-mass r-nnet r-randomforest)) (home-page "http://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description "This package provides a unified interface to various machine learning algorithms. Confusion matrices are provided too.") (license license:gpl2+))) (define-public r-zooimage (package (name "r-zooimage") (version "5.5.2") (source (origin (method url-fetch) (uri (cran-uri "zooimage" version)) (sha256 (base32 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8")))) (properties `((upstream-name . "zooimage"))) (build-system r-build-system) (propagated-inputs (list r-digest r-dt r-filehash r-jpeg r-mass r-mda r-mlearning r-png r-shiny r-svdialogs r-svmisc r-tiff)) (home-page "http://www.sciviews.org/zooimage") (synopsis "Analysis of numerical plankton images") (description "This package provides a solution for analyzing digital images of plankton. In combination with ImageJ, an image analysis system, it processes digital images, measures individuals, trains for automatic classification of taxa, and finally, measures plankton samples (abundances, total and partial size spectra or biomasses, etc.).") (license license:gpl2+))) (define-public r-zooarch (package (name "r-zooarch") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "zooaRch" version)) (sha256 (base32 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc")))) (properties `((upstream-name . "zooaRch"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zooaRch") (synopsis "Analytical Tools for Zooarchaeological Data") (description "The analysis and inference of faunal remains recovered from archaeological sites concerns the field of zooarchaeology. The zooaRch package provides analytical tools to make inferences on zooarchaeological data. Functions in this package allow users to read, manipulate, visualize, and analyze zooarchaeological data.") (license license:gpl2+))) (define-public r-zonebuilder (package (name "r-zonebuilder") (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "zonebuilder" version)) (sha256 (base32 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn")))) (properties `((upstream-name . "zonebuilder"))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-sf)) (native-inputs (list r-knitr)) (home-page "https://github.com/zonebuilders/zonebuilder") (synopsis "Create and explore geographic zoning systems") (description "This package provides functions, documentation and example data to help divide geographic space into discrete polygons (zones). The functions are motivated by research into the merits of different zoning systems. A flexible @code{ClockBoard} zoning system is provided, which breaks-up space by concentric rings and radial lines emanating from a central point.") (license license:gpl3))) (define-public r-zonator (package (name "r-zonator") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "zonator" version)) (sha256 (base32 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k")))) (properties `((upstream-name . "zonator"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal)) (native-inputs (list r-knitr)) (home-page "https://cbig.github.io/zonator/") (synopsis "Utilities for Zonation spatial conservation prioritization") (description "Create new analysis setups and deal with results of Zonation conservation prioritization software.") (license license:bsd-2))) (define-public r-mmwrweek (package (name "r-mmwrweek") (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "MMWRweek" version)) (sha256 (base32 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s")))) (properties `((upstream-name . 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(native-inputs `(("esbuild" ,esbuild) ("js-bokeh-widgets" ,(origin (method url-fetch) (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js") (sha256 (base32 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy")))) ("js-bokeh" ,(origin (method url-fetch) (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js") (sha256 (base32 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q")))) ("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/rbokeh/") (synopsis "R interface for the Bokeh visualization library") (description "This package provides a native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.") 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(license license:expat))) (define-public r-iotools (package (name "r-iotools") (version "0.3-2") (source (origin (method url-fetch) (uri (cran-uri "iotools" version)) (sha256 (base32 "07q0z0kszm1xx5hfhisfliyrcsxd8dc5mx0a2bwwnv5l1xzmix17")))) (properties `((upstream-name . "iotools"))) (build-system r-build-system) (home-page "https://www.rforge.net/iotools") (synopsis "I/O tools for streaming") (description "This package provides basic I/O tools for streaming and data parsing.") ;; GPL 2 or GPL 3. (license license:gpl3))) (define-public r-wordspace (package (name "r-wordspace") (version "0.2-7") (source (origin (method url-fetch) (uri (cran-uri "wordspace" version)) (sha256 (base32 "0hrjv5mag7gwl4wj7np248sdyns5i623wl37b11hlgalhbmlypyf")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-zoib (package (name "r-zoib") (version "1.5.5") (source (origin (method url-fetch) (uri (cran-uri "zoib" version)) (sha256 (base32 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f")))) (properties `((upstream-name . "zoib"))) (build-system r-build-system) (propagated-inputs (list r-abind r-coda r-formula r-rjags)) (home-page "https://www.r-project.org") (synopsis "Bayesian inference for beta regression") (description "This package lets you fit beta regression and zero-or-one inflated beta regression and obtain Bayesian inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.") (license license:gpl3+))) (define-public r-logger (package (name "r-logger") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "logger" version)) (sha256 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg")))) (properties `((upstream-name . 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(license license:gpl2+)))