;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2016, 2017 Ben Woodcroft ;;; Copyright © 2016, 2017, 2018, 2020 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 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 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 Lars-Dominik Braun ;;; Copyright © 2020 Vinicius Monego ;;; Copyright © 2020 Antoine Côté ;;; Copyright © 2020 Arun Isaac ;;; Copyright © 2020 Magali Lemes ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . (define-module (gnu packages cran) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system r) #:use-module (gnu packages) #: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 curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages libevent) #:use-module (gnu packages lisp-xyz) #: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 perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile #: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 tls) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) (define-public r-rticles (package (name "r-rticles") (version "0.16") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 "1ca3k5sdy9mnm6frcimqwf5k18j14wn69x5iagjnjwhq711l8dv0")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-clipr (package (name "r-clipr") (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903")))) (build-system r-build-system) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") (description "This package provides simple utility functions to read from and write to the system clipboards.") 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(license license:gpl2+))) (define-public r-scales (package (name "r-scales") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0")))) (build-system r-build-system) (propagated-inputs `(("r-farver" ,r-farver) ("r-labeling" ,r-labeling) ("r-lifecycle" ,r-lifecycle) ("r-munsell" ,r-munsell) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-r6" ,r-r6) ("r-viridislite" ,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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(license license:gpl3))) (define-public r-grr (package (name "r-grr") (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "grr" version)) (sha256 (base32 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/grr") (synopsis "Alternative implementations of base R functions") (description "This package provides alternative implementations of some base R functions, including @code{sort}, @code{order}, and @code{match}. The functions are simplified but can be faster or have other advantages.") (license license:gpl3))) (define-public r-matrix-utils (package (name "r-matrix-utils") (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "Matrix.utils" version)) (sha256 (base32 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-sys (package (name "r-sys") (version "3.4") (source (origin (method url-fetch) (uri (cran-uri "sys" version)) (sha256 (base32 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p")))) (build-system r-build-system) (home-page "https://github.com/jeroen/sys") (synopsis "Powerful and reliable tools for running system commands in R") (description "This package provides drop-in replacements for the base @code{system2()} function with fine control and consistent behavior across platforms. It supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. The package also provides functions for evaluating expressions inside a temporary fork. Such evaluations have no side effects on the main R process, and support reliable interrupts and timeouts. This provides the basis for a sandboxing mechanism.") 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(license license:bsd-3))) (define-public r-reprex (package (name "r-reprex") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-clipr" ,r-clipr) ("r-fs" ,r-fs) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-whisker" ,r-whisker) ("r-withr" ,r-withr))) (home-page "https://github.com/tidyverse/reprex") (synopsis "Prepare reproducible R code examples for sharing") (description "This package provides a convenience wrapper that uses the @code{rmarkdown} package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites or email. @code{reprex} also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.") (license license:expat))) (define-public r-reordercluster (package (name "r-reordercluster") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ReorderCluster" version)) (sha256 (base32 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58")))) (build-system r-build-system) (propagated-inputs `(("r-gplots" ,r-gplots) ("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/ReorderCluster") (synopsis "Reordering the dendrogram according to the class labels") (description "This package provides tools for performing the leaf reordering for the dendrogram that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together.") (license license:gpl3+))) (define-public r-callr (package (name "r-callr") (version "3.4.4") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 "1hgc4mfwv83104fh93v8g2srpwzjayq7krgzi9r0apq784r61642")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) ("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") (description "It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This package does exactly that.") (license license:expat))) (define-public r-readxl (package (name "r-readxl") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) ("r-progress" ,r-progress) ("r-rcpp" ,r-rcpp) ("r-tibble" ,r-tibble))) (home-page "https://readxl.tidyverse.org") (synopsis "Read Excel files") (description "This package lets you import Excel files into R. It supports @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via the embedded @code{RapidXML} C++ library.") ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and ;; 'rapidxml' which is Boost. (license (list license:gpl3 license:bsd-2 license:boost1.0)))) (define-public r-modelr (package (name "r-modelr") (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "modelr" version)) (sha256 (base32 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-tidyselect" ,r-tidyselect) ("r-vctrs" ,r-vctrs))) (home-page "https://github.com/tidyverse/modelr") (synopsis "Helper functions for modelling in pipelines") (description "Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.") (license license:gpl3))) (define-public r-httpuv (package (name "r-httpuv") (version "1.5.4") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm")) ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv ;; only contains fixes for building on Solaris. (patches (search-patches "r-httpuv-1.5.4-unvendor-libuv.patch")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1))) (snippet `(begin (delete-file-recursively "src/libuv") ;; Cannot unbundle http-parser, because it contains local ;; modifications. #t)))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'unbundle-libuv (lambda* (#:key outputs #:allow-other-keys) (substitute* (find-files "src" "\\.cpp$|\\.h$") (("\"libuv/include/uv\\.h\"") "")) ;; Fix https://github.com/rstudio/httpuv/issues/282 (substitute* "src/http.cpp" (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);") "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")) #t))))) (inputs `(("libuv" ,libuv))) (propagated-inputs `(("r-bh" ,r-bh) ("r-later" ,r-later) ("r-promises" ,r-promises) ("r-r6" ,r-r6) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/rstudio/httpuv") (synopsis "HTTP and WebSocket server library for R") (description "The httpuv package provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone.") ;; This package includes third-party code that was originally released ;; under various non-copyleft licenses. Full licensing information can be ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE (license license:gpl3+))) (define-public r-jsonlite (package (name "r-jsonlite") (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") (description "The jsonlite package provides a fast JSON parser and generator optimized for statistical data and the web. It offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. In addition to converting JSON data from/to R objects, jsonlite contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.") (license license:expat))) (define-public r-servr (package (name "r-servr") (version "0.18") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 "0xfbf1a1w34hbsx4jrdr4rqf22v7gf1p37ngknglv1dyxih7ipja")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) ("r-jsonlite" ,r-jsonlite) ("r-mime" ,r-mime) ("r-xfun" ,r-xfun))) (home-page "https://github.com/yihui/servr") (synopsis "Simple HTTP server to serve static files or dynamic documents") (description "Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.") (license license:expat))) (define-public r-htmltools (package (name "r-htmltools") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-digest" ,r-digest) ("r-rlang" ,r-rlang))) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description "This package provides tools for HTML generation and output in R.") (license license:expat))) (define-public r-htmlwidgets (package (name "r-htmlwidgets") (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 "0072wlkl58lav3qszzqw6pmx8qra4784r0yb6rx4lg7rbrik6335")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-yaml" ,r-yaml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ramnathv/htmlwidgets") (synopsis "HTML Widgets for R") (description "HTML widgets is a framework for creating HTML widgets that render in various contexts including the R console, R Markdown documents, and Shiny web applications.") (license license:expat))) (define-public r-htmltable (package (name "r-htmltable") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) ("r-rstudioapi" ,r-rstudioapi) ("r-stringr" ,r-stringr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://gforge.se/packages/") (synopsis "Advanced tables for Markdown/HTML") (description "This package provides functions to build tables with advanced layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying CSS-structure is simple in order to maximize compatibility with word processors such as LibreOffice. The package also contains a few text formatting functions that help outputting text compatible with HTML or LaTeX.") (license license:gpl3+))) (define-public r-curl (package (name "r-curl") (version "4.3") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases ;; The environment variable CURL_CA_BUNDLE is only respected when ;; running Windows, so we disable the platform checks. ;; This can be removed once the libcurl has been patched. (add-after 'unpack 'allow-CURL_CA_BUNDLE (lambda _ (substitute* "R/onload.R" (("if \\(!grepl\\(\"mingw\".*") "if (FALSE)\n")) (substitute* "src/handle.c" (("/\\* Only set" m) (string-append "\ const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\"); if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); } " m))) #t))))) (inputs `(("libcurl" ,curl) ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://github.com/jeroenooms/curl") (synopsis "HTTP client for R") (description "The @code{curl()} and @code{curl_download()} functions provide highly configurable drop-in replacements for base @code{url()} and @code{download.file()} with better performance, support for encryption, gzip compression, authentication, and other @code{libcurl} goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces.") (license license:expat))) (define-public r-hwriter (package (name "r-hwriter") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "hwriter" version)) (sha256 (base32 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/hwriter") (synopsis "Output R objects in HTML format") (description "This package provides easy-to-use and versatile functions to output R objects in HTML format.") (license license:lgpl2.1+))) (define-public r-rjson (package (name "r-rjson") (version "0.2.20") (source (origin (method url-fetch) (uri (cran-uri "rjson" version)) (sha256 (base32 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rjson") (synopsis "JSON library for R") (description "This package provides functions to convert R objects into JSON objects and vice-versa.") (license license:gpl2+))) (define-public r-fastmap (package (name "r-fastmap") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "fastmap" version)) (sha256 (base32 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27")))) (properties `((upstream-name . "fastmap"))) (build-system r-build-system) (home-page "https://r-lib.github.io/fastmap/") (synopsis "Fast implementation of a key-value store") (description "This package provides a fast implementation of a key-value store. Environments are commonly used as key-value stores, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.") (license license:expat))) (define-public r-shiny (package (name "r-shiny") (version "1.4.0.2") (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 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs")))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) (guix build minify-build-system) (guix build utils) (ice-9 match)) #:imported-modules (,@%r-build-system-modules (guix build minify-build-system)) #:phases (modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda* (#:key inputs #:allow-other-keys) (let ((replace-file (lambda (old new) (format #t "replacing ~a with ~a\n" old new) (delete-file old) (symlink new old)))) ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ ;; contain just data. They are not minified code, so we don't ;; replace them. (with-directory-excursion "inst/www/shared" (replace-file "bootstrap/shim/respond.min.js" (string-append (assoc-ref inputs "js-respond") "/share/javascript/respond.min.js")) (replace-file "bootstrap/shim/html5shiv.min.js" (string-append (assoc-ref inputs "js-html5shiv") "/share/javascript/html5shiv.min.js")) (replace-file "json2-min.js" (string-append (assoc-ref inputs "js-json2") "/share/javascript/json2-min.js")) (replace-file "strftime/strftime-min.js" (string-append (assoc-ref inputs "js-strftime") "/share/javascript/strftime.min.js")) (replace-file "highlight/highlight.pack.js" (string-append (assoc-ref inputs "js-highlight") "/share/javascript/highlight.min.js")) (replace-file "datatables/js/jquery.dataTables.min.js" (string-append (assoc-ref inputs "js-datatables") "/share/javascript/jquery.dataTables.min.js")) (replace-file "selectize/js/selectize.min.js" (string-append (assoc-ref inputs "js-selectize") "/share/javascript/selectize.min.js")) (replace-file "selectize/js/es5-shim.min.js" (string-append (assoc-ref inputs "js-es5-shim") "/share/javascript/es5-shim.min.js")) (for-each (match-lambda ((source . target) (delete-file target) (minify source #:target target))) '(("jqueryui/jquery-ui.js" . "jqueryui/jquery-ui.min.js") ("datepicker/js/bootstrap-datepicker.js" . "datepicker/js/bootstrap-datepicker.min.js") ("ionrangeslider/js/ion.rangeSlider.js" . "ionrangeslider/js/ion.rangeSlider.min.js") ("bootstrap/js/bootstrap.js" . "bootstrap/js/bootstrap.min.js") ("shiny.js" . "shiny.min.js") ("jquery.js" . "jquery.min.js") ("legacy/jquery.js" . "legacy/jquery.min.js") ("showdown/src/showdown.js" . "showdown/compressed/showdown.js"))))) #t))))) (propagated-inputs `(("r-crayon" ,r-crayon) ("r-digest" ,r-digest) ("r-fastmap" ,r-fastmap) ("r-htmltools" ,r-htmltools) ("r-httpuv" ,r-httpuv) ("r-jsonlite" ,r-jsonlite) ("r-later" ,r-later) ("r-mime" ,r-mime) ("r-promises" ,r-promises) ("r-r6" ,r-r6) ("r-rlang" ,r-rlang) ("r-sourcetools" ,r-sourcetools) ("r-withr" ,r-withr) ("r-xtable" ,r-xtable))) (inputs `(("js-datatables" ,js-datatables) ("js-html5shiv" ,js-html5shiv) ("js-json2" ,js-json2) ("js-respond" ,js-respond) ("js-selectize" ,js-selectize) ("js-strftime" ,js-strftime) ("js-highlight" ,js-highlight) ("js-es5-shim" ,js-es5-shim))) (native-inputs `(("uglify-js" ,uglify-js) ("gfortran" ,gfortran))) (home-page "http://shiny.rstudio.com") (synopsis "Easy interactive web applications with R") (description "Makes it incredibly easy to build interactive web applications with R. Automatic \"reactive\" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.") (license license:artistic2.0))) ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-shinytree (package (name "r-shinytree") (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "shinyTree" version)) (sha256 (base32 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3")) (modules '((guix build utils))) (snippet '(begin ;; Delete minified JavaScript (for-each delete-file '("inst/www/jsTree-3.3.7/libs/require.js" "inst/www/jsTree-3.3.7/libs/jquery.js" "inst/www/jsTree-3.3.7/jstree.min.js")) #t)))) (properties `((upstream-name . "shinyTree"))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'replace-minified-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/jsTree-3.3.7/" (symlink (string-append (assoc-ref inputs "js-requirejs") "/share/javascript/require.min.js") "libs/require.js") (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-jquery") "libs/jquery.js") ("jstree.js" "jstree.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs `(("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-promises" ,r-promises) ("r-shiny" ,r-shiny) ("r-stringr" ,r-stringr))) (inputs `(("js-requirejs" ,js-requirejs))) (native-inputs `(("uglify-js" ,uglify-js) ("js-jquery" ,(origin (method url-fetch) (uri "https://code.jquery.com/jquery-3.3.1.js") (sha256 (base32 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))))) (home-page "https://cran.r-project.org/web/packages/shinyTree/") (synopsis "jsTree bindings for Shiny") (description "This package exposes R bindings to jsTree, a JavaScript library that supports interactive trees, to enable rich, editable trees in Shiny.") (license license:expat))) (define-public r-shinydashboard (package (name "r-shinydashboard") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. (arguments `(#:modules ((guix build utils) (guix build r-build-system) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'generate-minified-javascript (lambda _ (with-directory-excursion "inst/AdminLTE" (delete-file "app.min.js") (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js"))) (call-with-output-file "app.min.js" (lambda (port) (dump-port minified port)))))))))) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-promises" ,r-promises) ("r-shiny" ,r-shiny))) (native-inputs `(("uglify-js" ,uglify-js))) (home-page "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 "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs `(("r-fs" ,r-fs) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-shiny" ,r-shiny) ("r-tibble" ,r-tibble))) (home-page "https://github.com/thomasp85/shinyFiles") (synopsis "Server-side file system viewer for Shiny") (description "This package provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to \"download\" files to a temporary location. Both file and folder selection as well as file saving is available.") (license license:gpl2+))) (define-public r-shinythemes (package (name "r-shinythemes") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "shinythemes" version)) (sha256 (base32 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf")))) (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) (propagated-inputs `(("r-shiny" ,r-shiny))) (home-page "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 "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y")))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (ice-9 popen)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/d3/" (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "d3.v3.js") "v3/dist/d3.min.js") (,(assoc-ref inputs "d3.v4.js") "v4/dist/d3.min.js") (,(assoc-ref inputs "d3.v5.js") "v5/dist/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-htmltools" ,r-htmltools) ("r-rlang" ,r-rlang) ("r-tidyr" ,r-tidyr))) (native-inputs `(("uglify-js" ,uglify-js) ("d3.v3.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v3.js") (sha256 (base32 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))) ("d3.v5.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v5.js") (sha256 (base32 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description "This package provides a suite of functions to help ease the use of the d3.js visualization library in R. These helpers include @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame} R objects into the JSON format that the d3.js library expects.") (license license:bsd-3))) ;; We use the latest commit here because the last release was in 2016 while ;; the latest commit was in 2018. (define-public r-sankeyd3 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc") (revision "1")) (package (name "r-sankeyd3") (version (git-version "0.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/fbreitwieser/sankeyD3") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) (build-system r-build-system) (propagated-inputs `(("r-d3r" ,r-d3r) ("r-htmlwidgets" ,r-htmlwidgets) ("r-shiny" ,r-shiny) ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/fbreitwieser/sankeyD3") (synopsis "Sankey network graphs from R") (description "This package provides an R library to generate Sankey network graphs in R and Shiny via the D3 visualization library.") ;; The R code is licensed under GPLv3+. It includes the non-minified ;; JavaScript source code of d3-sankey, which is released under the ;; 3-clause BSD license. (license (list license:gpl3+ license:bsd-3))))) (define-public r-crosstalk (package (name "r-crosstalk") (version "1.1.0.1") (source (origin (method url-fetch) (uri (cran-uri "crosstalk" version)) (sha256 (base32 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-lazyeval" ,r-lazyeval) ("r-r6" ,r-r6))) (home-page "https://rstudio.github.io/crosstalk/") (synopsis "Inter-widget interactivity for HTML widgets") (description "This package provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static @code{.html} files). It currently supports linked brushing and filtering.") (license license:expat))) (define-public r-rook (package (name "r-rook") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "Rook" version)) (sha256 (base32 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) (properties `((upstream-name . "Rook"))) (build-system r-build-system) (propagated-inputs `(("r-brew" ,r-brew))) (home-page "https://cran.r-project.org/web/packages/Rook") (synopsis "Web server interface for R") (description "This package contains the Rook specification and convenience software for building and running Rook applications. A Rook application is an R reference class object that implements a @code{call} method or an R closure that takes exactly one argument, an environment, and returns a list with three named elements: the @code{status}, the @code{headers}, and the @code{body}.") (license license:gpl2))) (define-public r-miniui (package (name "r-miniui") (version "0.1.1.1") (source (origin (method url-fetch) (uri (cran-uri "miniUI" version)) (sha256 (base32 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) (properties `((upstream-name . "miniUI"))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-shiny" ,r-shiny))) (home-page "https://cran.r-project.org/web/packages/miniUI/") (synopsis "Shiny UI widgets for small screens") (description "This package provides UI widget and layout functions for writing Shiny apps that work well on small screens.") (license license:gpl3))) (define-public r-feather (package (name "r-feather") (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "feather" version)) (sha256 (base32 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh")))) (build-system r-build-system) (propagated-inputs `(("r-hms" ,r-hms) ("r-rcpp" ,r-rcpp) ("r-tibble" ,r-tibble))) (home-page "https://github.com/wesm/feather") (synopsis "R Bindings to the Feather API") (description "Read and write feather files, a lightweight binary columnar data store designed for maximum speed.") (license license:asl2.0))) (define-public r-maps (package (name "r-maps") (version "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "maps" version)) (sha256 (base32 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/maps") (synopsis "Draw geographical maps") (description "This package provides an R module for display of maps. Projection code and larger maps are in separate packages (@code{mapproj} and @code{mapdata}).") (license license:gpl2))) (define-public r-mapproj (package (name "r-mapproj") (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,r-maps))) (home-page "https://cran.r-project.org/web/packages/mapproj") (synopsis "Map projection in R") (description "This package converts latitude/longitude into projected coordinates.") (license (list license:gpl2 ; The R interface (license:non-copyleft ; The C code "https://www.gnu.org/licenses/license-list.en.html#lucent102" "Lucent Public License Version 1.02"))))) (define-public r-rgooglemaps (package (name "r-rgooglemaps") (version "1.4.5.3") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs `(("r-png" ,r-png) ("r-sp" ,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. This requires proper coordinate scaling. @end enumerate\n") (license license:gpl2+))) (define-public r-geosphere (package (name "r-geosphere") (version "1.5-10") (source (origin (method url-fetch) (uri (cran-uri "geosphere" version)) (sha256 (base32 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan")))) (build-system r-build-system) (propagated-inputs `(("r-sp" ,r-sp))) (home-page "https://cran.r-project.org/web/packages/geosphere") (synopsis "Spherical trigonometry") (description "This package computes spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.") (license license:gpl3+))) (define-public r-jpeg (package (name "r-jpeg") (version "0.1-8.1") (source (origin (method url-fetch) (uri (cran-uri "jpeg" version)) (sha256 (base32 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x")))) (build-system r-build-system) (inputs `(("libjpeg" ,libjpeg-turbo))) (home-page "https://www.rforge.net/jpeg/") (synopsis "Read and write JPEG images with R") (description "This package provides a way to read, write and display bitmap images stored in the JPEG format with R. It can read and write both files and in-memory raw vectors.") (license license:gpl2+))) (define-public r-ggmap (package (name "r-ggmap") (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggmap" version)) (sha256 (base32 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) (build-system r-build-system) (propagated-inputs `(("r-bitops" ,r-bitops) ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jpeg" ,r-jpeg) ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) ("r-png" ,r-png) ("r-purrr" ,r-purrr) ("r-rgooglemaps" ,r-rgooglemaps) ("r-rjson" ,r-rjson) ("r-scales" ,r-scales) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/dkahle/ggmap") (synopsis "Spatial visualization with ggplot2") (description "This package provides a collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.") (license license:gpl2))) (define-public r-haven (package (name "r-haven") (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs `(("r-forcats" ,r-forcats) ("r-hms" ,r-hms) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-readr" ,r-readr) ("r-tibble" ,r-tibble) ("r-tidyselect" ,r-tidyselect) ("r-vctrs" ,r-vctrs))) (home-page "https://haven.tidyverse.org") (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files") (description "This package lets you mport foreign statistical formats into R via the embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (license license:expat))) (define-public r-amap (package (name "r-amap") (version "0.8-18") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") (synopsis "Another multidimensional analysis package") (description "This package provides tools for clustering and principal component analysis (with robust methods, and parallelized functions).") (license license:gpl2+))) (define-public r-ape (package (name "r-ape") (version "5.4-1") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-nlme" ,r-nlme) ("r-rcpp" ,r-rcpp))) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description "This package provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, and several other tools.") (license license:gpl2+))) (define-public r-abbyyr (package (name "r-abbyyr") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "abbyyR" version)) (sha256 (base32 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r")))) (properties `((upstream-name . "abbyyR"))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-httr" ,r-httr) ("r-plyr" ,r-plyr) ("r-progress" ,r-progress) ("r-readr" ,r-readr) ("r-xml" ,r-xml))) (home-page "https://github.com/soodoku/abbyyR") (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") (description "This package provides tools to get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily OCR images, barcodes, forms, documents with machine readable zones, e.g. passports and get the results in a variety of formats including plain text and XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (license license:expat))) (define-public r-colorspace (package (name "r-colorspace") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") (description "This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.") (license license:bsd-3))) (define-public r-glue (package (name "r-glue") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz")))) (build-system r-build-system) ;; knitr depends on glue, so we can't add knitr here to build the ;; vignettes. #; (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidyverse/glue") (synopsis "Interpreted string literals") (description "This package provides an implementation of interpreted string literals, inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (license license:expat))) (define-public r-pastecs (package (name "r-pastecs") (version "1.3.21") (source (origin (method url-fetch) (uri (cran-uri "pastecs" version)) (sha256 (base32 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot))) (home-page "http://www.sciviews.org/pastecs") (synopsis "Analysis of space-time ecological series") (description "This package provides functions for regulation, decomposition and analysis of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER initiative to bring PASSTEC 2000 functionalities to R.") (license license:gpl2+))) (define-public r-partykit (package (name "r-partykit") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 "18nc6vvj1cy8ly2hqixg544sbg8vbpzwsr1cdlzrqfykd0pzgkvf")))) (build-system r-build-system) (propagated-inputs `(("r-formula" ,r-formula) ("r-inum" ,r-inum) ("r-libcoin" ,r-libcoin) ("r-mvtnorm" ,r-mvtnorm) ("r-rpart" ,r-rpart) ("r-survival" ,r-survival))) (home-page "http://partykit.R-Forge.R-project.org/partykit") (synopsis "Toolkit for recursive partytioning") (description "This package provides a toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models.") (license license:gpl2+))) (define-public r-plogr (package (name "r-plogr") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "plogr" version)) (sha256 (base32 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/plogr") (synopsis "R bindings for the plog C++ logging library") (description "This package provides the header files for a stripped-down version of the plog header-only C++ logging library, and a method to log to R's standard error stream.") (license license:expat))) (define-public r-pls (package (name "r-pls") (version "2.7-3") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg")))) (build-system r-build-system) (home-page "https://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") (description "The pls package implements multivariate regression methods: Partial Least Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports: @itemize @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd} @item multi-response models (or @dfn{PLS2}) @item flexible cross-validation @item Jackknife variance estimates of regression coefficients @item extensive and flexible plots: scores, loadings, predictions, coefficients, (R)MSEP, R², and correlation loadings @item formula interface, modelled after @code{lm()}, with methods for predict, print, summary, plot, update, etc. @item extraction functions for coefficients, scores, and loadings @item MSEP, RMSEP, and R² estimates @item multiplicative scatter correction (@dfn{MSC}) @end itemize\n") (license license:gpl2))) (define-public r-ps (package (name "r-ps") (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 (base32 "1cxfhnff22fbsr9vynhql0rhhrqfxvkb6kv11h2m740r9scwcs44")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") (description "The ps package implements an API to list, query, and manipulate system processes. Most of its code is based on the @code{psutil} Python package.") (license license:bsd-3))) (define-public r-pkgbuild (package (name "r-pkgbuild") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-desc" ,r-desc) ("r-prettyunits" ,r-prettyunits) ("r-r6" ,r-r6) ("r-rprojroot" ,r-rprojroot) ("r-withr" ,r-withr))) (home-page "https://github.com/r-pkgs/pkgbuild") (synopsis "Find tools needed to build R packages") (description "This package provides functions used to build R packages. It locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.") (license license:gpl3))) (define-public r-pkgload (package (name "r-pkgload") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-desc" ,r-desc) ("r-pkgbuild" ,r-pkgbuild) ("r-rlang" ,r-rlang) ("r-rprojroot" ,r-rprojroot) ("r-rstudioapi" ,r-rstudioapi) ("r-withr" ,r-withr))) (home-page "https://github.com/r-lib/pkgload") (synopsis "Simulate package installation and attach") (description "This package simulates the process of installing a package and then attaching it. This is a key part of the @code{devtools} package as it allows you to rapidly iterate while developing a package.") (license license:gpl3))) (define-public r-rcpp (package (name "r-rcpp") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") (description "The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the @code{Rcpp Gallery} site at , the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) (define-public r-bindr (package (name "r-bindr") (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "bindr" version)) (sha256 (base32 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/bindr") (synopsis "Parametrized active bindings") (description "This package provides a simple interface for creating active bindings where the bound function accepts additional arguments.") (license license:expat))) (define-public r-bindrcpp (package (name "r-bindrcpp") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "bindrcpp" version)) (sha256 (base32 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) (build-system r-build-system) (propagated-inputs `(("r-bindr" ,r-bindr) ("r-plogr" ,r-plogr) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/krlmlr/bindrcpp") (synopsis "Rcpp interface to active bindings") (description "This package provides an easy way to fill an environment with active bindings that call a C++ function.") (license license:expat))) (define-public r-bisquerna (package (name "r-bisquerna") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "BisqueRNA" version)) (sha256 (base32 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-limsolve" ,r-limsolve))) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples.") (license license:gpl3))) (define-public r-auc (package (name "r-auc") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "AUC" version)) (sha256 (base32 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7")))) (properties `((upstream-name . "AUC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AUC") (synopsis "Compute the area under the curve of selected measures") (description "This package includes functions to compute the area under the curve of selected measures: the area under the sensitivity curve (AUSEC), the area under the specificity curve (AUSPC), the area under the accuracy curve (AUACC), and the area under the receiver operating characteristic curve (AUROC). The curves can also be visualized. Support for partial areas is provided.") (license license:gpl2+))) (define-public r-calibrate (package (name "r-calibrate") (version "1.7.7") (source (origin (method url-fetch) (uri (cran-uri "calibrate" version)) (sha256 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (home-page "https://cran.r-project.org/web/packages/calibrate") (synopsis "Calibration of scatterplot and biplot axes") (description "This is a package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots.") (license license:gpl2))) (define-public r-shape (package (name "r-shape") (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9")))) (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 `(("r-knitr" ,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 "0.4.10") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) ("r-globaloptions" ,r-globaloptions) ("r-shape" ,r-shape))) (native-inputs `(("r-knitr" ,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 `(("r-pracma" ,r-pracma))) (native-inputs `(("r-knitr" ,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 "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,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 "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 "142gi3ifpcz1rhqrbw4wh326jn2q61s659wkzf92ys4dybs43dky")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs `(("perl" ,perl))) (propagated-inputs `(("r-crayon" ,r-crayon) ("r-globaloptions" ,r-globaloptions) ("r-rjson" ,r-rjson))) (native-inputs `(("r-knitr" ,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 "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "fastmatch" version)) (sha256 (base32 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) (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 "4.0.2") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 "1qbfmhk4v76q145yalqaiaffklvkfs615b5m0imxyjyjcvx1nbn0")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) (home-page "http://ff.r-forge.r-project.org/") (synopsis "Memory-efficient storage of large data on disk and access functions") (description "This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.") ;; error Architecture not supported. (supported-systems (delete "aarch64-linux" %supported-systems)) (license license:gpl2))) (define-public r-ffbase (package (name "r-ffbase") (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit) ("r-fastmatch" ,r-fastmatch) ("r-ff" ,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.") (license license:expat))) (define-public r-reshape (package (name "r-reshape") (version "0.8.8") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp))) (home-page "http://had.co.nz/reshape") (synopsis "Flexibly reshape data") (description "Flexibly restructure and aggregate data using just two functions: @code{melt} and @code{cast}. This package provides them.") (license license:expat))) (define-public r-progress (package (name "r-progress") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "progress" version)) (sha256 (base32 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l")))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon) ("r-hms" ,r-hms) ("r-prettyunits" ,r-prettyunits) ("r-r6" ,r-r6))) (home-page "https://github.com/gaborcsardi/progress") (synopsis "Terminal progress bars") (description "This package provides configurable progress bars. They may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The package also provides a C++ API, that works with or without Rcpp.") (license license:expat))) (define-public r-ggally (package (name "r-ggally") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-lifecycle" ,r-lifecycle) ("r-plyr" ,r-plyr) ("r-progress" ,r-progress) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape" ,r-reshape) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description "The R package ggplot2 is a plotting system based on the grammar of graphics. GGally extends ggplot2 by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.") (license license:gpl2+))) (define-public r-proxy (package (name "r-proxy") (version "0.4-24") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc")))) (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 "1.4-2") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) (home-page "https://cran.r-project.org/web/packages/sp") (synopsis "Classes and methods for spatial data") (description "This package provides classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.") (license license:gpl2+))) (define-public r-laplacesdemon (package (name "r-laplacesdemon") (version "16.1.4") (source (origin (method url-fetch) (uri (cran-uri "LaplacesDemon" version)) (sha256 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1")))) (properties `((upstream-name . "LaplacesDemon"))) (build-system r-build-system) (home-page "https://github.com/LaplacesDemonR/LaplacesDemon") (synopsis "Complete environment for Bayesian inference") (description "This package provides a complete environment for Bayesian inference using a variety of different samplers.") (license license:expat))) (define-public r-rmtstat (package (name "r-rmtstat") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "RMTstat" version)) (sha256 (base32 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1")))) (properties `((upstream-name . "RMTstat"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RMTstat") (synopsis "Distributions, statistics and tests derived from random matrix theory") (description "This package provides functions for working with the Tracy-Widom laws and other distributions related to the eigenvalues of large Wishart matrices.") (license license:bsd-3))) (define-public r-rmpi (package (name "r-rmpi") (version "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"") #:phases (modify-phases %standard-phases (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs `(("openmpi" ,openmpi))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") (synopsis "R interface to message-passing interface (MPI)") (description "This package provides an interface (wrapper) to MPI APIs. It also provides an interactive R manager and worker environment.") (license license:gpl2+))) (define-public r-lmoments (package (name "r-lmoments") (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "Lmoments" version)) (sha256 (base32 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw")))) (properties `((upstream-name . "Lmoments"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo))) (home-page "http://www.tilastotiede.fi/juha_karvanen.html") (synopsis "L-moments and quantile mixtures") (description "This package contains functions to estimate L-moments and trimmed L-moments from the data. It also contains functions to estimate the parameters of the normal polynomial quantile mixture and the Cauchy polynomial quantile mixture from L-moments and trimmed L-moments.") (license license:gpl2))) (define-public r-distillery (package (name "r-distillery") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh")))) (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-extremes (package (name "r-extremes") (version "2.0-12") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs `(("r-distillery" ,r-distillery) ("r-lmoments" ,r-lmoments))) (home-page "https://www.assessment.ucar.edu/toolkit/") (synopsis "Extreme value analysis") (description "ExtRemes is a suite of functions for carrying out analyses on the extreme values of a process of interest; be they block maxima over long blocks or excesses over a high threshold.") (license license:gpl2+))) (define-public r-lmtest (package (name "r-lmtest") (version "0.9-38") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/lmtest") (synopsis "Testing linear regression models") (description "This package provides a collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.") ;; Either version is okay (license (list license:gpl2 license:gpl3)))) (define-public r-idr (package (name "r-idr") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "idr" version)) (sha256 (base32 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/idr/") (synopsis "Irreproducible discovery rate") (description "This is a package for estimating the copula mixture model and plotting correspondence curves in \"Measuring reproducibility of high-throughput experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel") (license license:gpl2+))) (define-public r-inline (package (name "r-inline") (version "0.3.16") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj")))) (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 "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "inum" version)) (sha256 (base32 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,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-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 "1.0.23.1") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0")))) (build-system r-build-system) (propagated-inputs `(("r-bdsmatrix" ,r-bdsmatrix) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-mvtnorm" ,r-mvtnorm) ("r-numderiv" ,r-numderiv))) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description "This package provides methods and functions for fitting maximum likelihood models in R. This package modifies and extends the @code{mle} classes in the @code{stats4} package.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-emdbook (package (name "r-emdbook") (version "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6")))) (build-system r-build-system) (propagated-inputs `(("r-bbmle" ,r-bbmle) ("r-coda" ,r-coda) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-plyr" ,r-plyr))) (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 `(("r-lpsolve" ,r-lpsolve) ("r-mass" ,r-mass) ("r-quadprog" ,r-quadprog))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/limSolve") (synopsis "Solving linear inverse models") (description "This package provides functions that: @enumerate @item find the minimum/maximum of a linear or quadratic function, @item sample an underdetermined or overdetermined system, @item solve a linear system Ax=B for the unknown x. @end enumerate It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.") ;; Any GPL version. (license (list license:gpl2+ license:gpl3+)))) (define-public r-fitdistrplus (package (name "r-fitdistrplus") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-survival" ,r-survival))) (native-inputs `(("r-knitr" ,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 "1.7-7") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/energy") (synopsis "Multivariate inference via the energy of data") (description "This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.") (license license:gpl2+))) (define-public r-suppdists (package (name "r-suppdists") (version "1.1-9.5") (source (origin (method url-fetch) (uri (cran-uri "SuppDists" version)) (sha256 (base32 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak")))) (properties `((upstream-name . "SuppDists"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/SuppDists") (synopsis "Supplementary distributions") (description "This package provides ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. In addition two random number generators of George Marsaglia are included.") (license license:gpl2+))) (define-public r-ksamples (package (name "r-ksamples") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "kSamples" version)) (sha256 (base32 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms")))) (properties `((upstream-name . "kSamples"))) (build-system r-build-system) (propagated-inputs `(("r-suppdists" ,r-suppdists))) (home-page "https://cran.r-project.org/web/packages/kSamples") (synopsis "K-Sample rank tests and their combinations") (description "This package provides tools to compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples.") (license license:gpl2+))) (define-public r-cvst (package (name "r-cvst") (version "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "CVST" version)) (sha256 (base32 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5")))) (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs `(("r-kernlab" ,r-kernlab) ("r-matrix" ,r-matrix))) (home-page "https://cran.r-project.org/web/packages/CVST") (synopsis "Fast cross-validation via sequential testing") (description "This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.") (license license:gpl2+))) (define-public r-squarem (package (name "r-squarem") (version "2020.4") (source (origin (method url-fetch) (uri (cran-uri "SQUAREM" version)) (sha256 (base32 "1r2yxfiqbpwy5ccg94r7f6sz7lh5aq0xjpf632s42wgmml1dvlzb")))) (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-lava (package (name "r-lava") (version "1.6.8") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 "0jdmjjs894mfncswmzz7sa6cy7hqbqii5fcvl3zqkmzpbadb2za2")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) ("r-squarem" ,r-squarem) ("r-survival" ,r-survival))) (native-inputs `(("r-knitr" ,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 `(("r-kernsmooth" ,r-kernsmooth) ("r-lava" ,r-lava) ("r-rcpp" ,r-rcpp) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/prodlim") (synopsis "Product-limit estimation for censored event history analysis") (description "This package provides a fast and user-friendly implementation of nonparametric estimators for censored event history (survival) analysis with the Kaplan-Meier and Aalen-Johansen methods.") (license license:gpl2+))) (define-public r-dimred (package (name "r-dimred") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs `(("r-drr" ,r-drr) ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description "This package provides a collection of dimensionality reduction techniques from R packages and provides a common interface for calling the methods.") (license license:gpl3))) (define-public r-timedate (package (name "r-timedate") (version "3043.102") (source (origin (method url-fetch) (uri (cran-uri "timeDate" version)) (sha256 (base32 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p")))) (properties `((upstream-name . "timeDate"))) (build-system r-build-system) (home-page "https://www.rmetrics.org") (synopsis "Chronological and calendar objects") (description "This package provides an environment for teaching \"Financial Engineering and Computational Finance\" and for managing chronological and calendar objects.") (license license:gpl2+))) (define-public r-magic (package (name "r-magic") (version "1.5-9") (source (origin (method url-fetch) (uri (cran-uri "magic" version)) (sha256 (base32 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind))) (home-page "https://github.com/RobinHankin/magic.git") (synopsis "Create and investigate magic squares") (description "This package provides a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.") (license license:gpl2))) (define-public r-rmysql (package (name "r-rmysql") (version "0.10.20") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs `(("mariadb" ,mariadb "lib") ("mariadb-dev" ,mariadb "dev") ("zlib" ,zlib))) (propagated-inputs `(("r-dbi" ,r-dbi))) (home-page "https://github.com/r-dbi/RMySQL") (synopsis "Database interface and MySQL driver for R") (description "This package provides a DBI interface to MySQL / MariaDB. The RMySQL package contains an old implementation based on legacy code from S-PLUS which is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.") (license license:gpl2))) (define-public r-rpostgresql (package (name "r-rpostgresql") (version "0.6-2") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) (properties `((upstream-name . "RPostgreSQL"))) (build-system r-build-system) (inputs `(("postgresql" ,postgresql))) (propagated-inputs `(("r-dbi" ,r-dbi))) (home-page "https://github.com/tomoakin/RPostgreSQL") (synopsis "R interface to the PostgreSQL database system") (description "This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems.") ;; The whole package is released under GPL version 2. It includes code ;; under the PostgreSQL license. (license license:gpl2))) (define-public r-linprog (package (name "r-linprog") (version "0.9-2") (source (origin (method url-fetch) (uri (cran-uri "linprog" version)) (sha256 (base32 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9")))) (build-system r-build-system) (propagated-inputs `(("r-lpsolve" ,r-lpsolve))) (home-page "http://linprog.r-forge.r-project.org/") (synopsis "Linear programming and optimization") (description "This package can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm.") (license license:gpl2+))) (define-public r-geometry (package (name "r-geometry") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg")))) (build-system r-build-system) (propagated-inputs `(("r-magic" ,r-magic) ("r-linprog" ,r-linprog) ("r-lpsolve" ,r-lpsolve) ("r-rcpp" ,r-rcpp) ("r-rcppprogress" ,r-rcppprogress))) (home-page "http://geometry.r-forge.r-project.org/") (synopsis "Mesh generator and surface tessellator") (description "This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this. Currently the package only gives access to Delaunay triangulation and convex hull computation.") ;; The Qhull sources are included and are distributed under a custom ;; non-copyleft license. The R sources are released under GPL version 2. (license (list license:gpl2 (license:non-copyleft "http://www.qhull.org/COPYING.txt"))))) (define-public r-ddalpha (package (name "r-ddalpha") (version "1.3.11") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-class" ,r-class) ("r-geometry" ,r-geometry) ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-robustbase" ,r-robustbase) ("r-sfsmisc" ,r-sfsmisc))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/ddalpha") (synopsis "Depth-Based classification and calculation of data depth") (description "This package contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.") (license license:gpl2))) (define-public r-gower (package (name "r-gower") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "gower" version)) (sha256 (base32 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/gower") (synopsis "Gower's distance") (description "This package provides tools to compute Gower's distance (or similarity) coefficient between records, and to compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.") (license license:gpl3))) (define-public r-rcpproll (package (name "r-rcpproll") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppRoll" version)) (sha256 (base32 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) (properties `((upstream-name . "RcppRoll"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/RcppRoll") (synopsis "Efficient rolling and windowed operations") (description "This package provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.") (license license:gpl2+))) (define-public r-ipred (package (name "r-ipred") (version "0.9-9") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) ("r-mass" ,r-mass) ("r-nnet" ,r-nnet) ("r-prodlim" ,r-prodlim) ("r-rpart" ,r-rpart) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/ipred") (synopsis "Improved predictors") (description "This package provides improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.") (license license:gpl2+))) (define-public r-psych (package (name "r-psych") (version "2.0.9") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 "0wdh580a0psbdil28n0d85hnp42wmn11hcbnihjq8r7h54drgzpn")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-mnormt" ,r-mnormt) ("r-nlme" ,r-nlme))) (home-page "https://cran.r-project.org/web/packages/psych/") (synopsis "Procedures for psychological, psychometric, and personality research") (description "This package provides a general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics.") 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(license license:gpl2))) (define-public r-broom (package (name "r-broom") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 "12xnpmm1cyhksv4gwcrwgrpw7c0xf1c7chlpng9lk8arifbfvqpg")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-dplyr" ,r-dplyr) ("r-ellipsis" ,r-ellipsis) ("r-generics" ,r-generics) ("r-glue" ,r-glue) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,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 "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) ("r-glue" ,r-glue) ("r-gower" ,r-gower) ("r-ipred" ,r-ipred) ("r-lifecycle" ,r-lifecycle) ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-tidyselect" ,r-tidyselect) ("r-timedate" ,r-timedate) ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,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") (source (origin (method url-fetch) (uri (cran-uri "pdist" version)) (sha256 (base32 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd")))) (build-system r-build-system) (home-page "https://github.com/jeffwong/pdist") (synopsis "Partitioned distance function") (description "Pdist computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling @code{dist}, but this creates unnecessary computation by computing the distances between a row of X and another row of X, and likewise for Y. Pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.") (license license:gpl3+))) (define-public r-ggrepel (package (name "r-ggrepel") (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-rcpp" ,r-rcpp) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,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-corrplot (package (name "r-corrplot") (version "0.84") (source (origin (method url-fetch) (uri (cran-uri "corrplot" version)) (sha256 (base32 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd")))) (build-system r-build-system) (home-page "https://github.com/taiyun/corrplot") (synopsis "Visualization of a correlation matrix") (description "This package provides a graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including choosing color, text labels, color labels, layout, etc.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-stringdist (package (name "r-stringdist") (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 "0nb3iwpl4f3xxirns1frwvarpyrl4i5f74h8r6h80cg0a4mpdgcb")))) (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 `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/ucminf/") (synopsis "General-purpose unconstrained non-linear optimization") (description "This package provides an implementation of an algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of @code{ucminf} is designed for easy interchange with the package @code{optim}.") (license license:gpl2+))) (define-public r-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 `(("r-assertthat" ,r-assertthat) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) ("r-plyr" ,r-plyr) ("r-purrr" ,r-purrr) ("r-scales" ,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 `(("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-numderiv" ,r-numderiv) ("r-ucminf" ,r-ucminf))) (home-page "https://github.com/runehaubo/ordinal") (synopsis "Regression models for ordinal data") (description "This package provides an implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered models. Estimation is via maximum likelihood and mixed models are fitted with the Laplace approximation and adaptive Gauss-Hermite quadrature.") (license license:gpl2+))) (define-public r-jomo (package (name "r-jomo") (version "2.7-2") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-ordinal" ,r-ordinal) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/jomo/") (synopsis "Multilevel Joint Modelling Multiple Imputation") (description "Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation @url{Carpenter and Kenward (2013), http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.") (license license:gpl2))) (define-public r-pan (package (name "r-pan") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/pan/") (synopsis "Multiple imputation for multivariate panel or clustered data") (description "This package implements multiple imputation for multivariate panel or clustered data.") (license license:gpl3))) (define-public r-mitml (package (name "r-mitml") (version "0.3-7") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) ("r-jomo" ,r-jomo) ("r-pan" ,r-pan))) (home-page "https://cran.r-project.org/web/packages/mitml/") (synopsis "Tools for multiple imputation in multilevel modeling") (description "This package provides tools for multiple imputation of missing data in multilevel modeling. It includes a user-friendly interface to the packages pan and jomo, and several functions for visualization, data management and the analysis of multiply imputed data sets.") (license license:gpl2+))) (define-public r-mice (package (name "r-mice") (version "3.11.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) ("r-lattice" ,r-lattice) ("r-rcpp" ,r-rcpp) ("r-tidyr" ,r-tidyr))) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") (description "Multiple imputation using @dfn{Fully Conditional Specification} (FCS) implemented by the MICE algorithm as described in @url{Van Buuren and Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.") ;; Any of these two versions. (license (list license:gpl2 license:gpl3)))) (define-public r-truncnorm (package (name "r-truncnorm") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "truncnorm" version)) (sha256 (base32 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/truncnorm/") (synopsis "Truncated normal distribution") (description "This package provides functions for the truncated normal distribution with mean equal to @code{mean} and standard deviation equal to @code{sd}. It includes density, distribution, quantile, and expected value functions, as well as a random generation function.") (license license:gpl2))) (define-public r-rsolnp (package (name "r-rsolnp") (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "Rsolnp" version)) (sha256 (base32 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii")))) (properties `((upstream-name . "Rsolnp"))) (build-system r-build-system) (propagated-inputs `(("r-truncnorm" ,r-truncnorm))) (home-page "https://cran.r-project.org/web/packages/Rsolnp/") (synopsis "General non-linear optimization") (description "The Rsolnp package implements a general non-linear augmented Lagrange multiplier method solver, a @dfn{sequential quadratic programming} (SQP) based solver).") ;; Any version of the GPL. (license license:gpl2+))) (define-public r-hardyweinberg (package (name "r-hardyweinberg") (version "1.6.8") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 "0b6j1mkpr7ck2nr9fmpnsjdv29jc6vg4b91cg50skmcgky1j0zi7")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs `(("r-mice" ,r-mice) ("r-rcpp" ,r-rcpp) ("r-rsolnp" ,r-rsolnp))) (home-page "https://cran.r-project.org/package=HardyWeinberg") (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") (description "This package contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of diallelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.") (license license:gpl2+))) (define-public r-sm (package (name "r-sm") (version "2.2-5.6") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") (synopsis "Smoothing methods for nonparametric regression and density estimation") (description "This is software accompanying the book 'Applied Smoothing Techniques for Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford University Press. It provides smoothing methods for nonparametric regression and density estimation") (license license:gpl2+))) (define-public r-venndiagram (package (name "r-venndiagram") (version "1.6.20") (source (origin (method url-fetch) (uri (cran-uri "VennDiagram" version)) (sha256 (base32 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775")))) (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs `(("r-futile-logger" ,r-futile-logger))) (home-page "https://cran.r-project.org/web/packages/VennDiagram/") (synopsis "Generate High-Resolution Venn and Euler Plots") (description "This package provides a set of functions to generate high-resolution Venn and Euler plots. It includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.") (license license:gpl2+))) (define-public r-vioplot (package (name "r-vioplot") (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v")))) (build-system r-build-system) (propagated-inputs `(("r-sm" ,r-sm) ("r-zoo" ,r-zoo))) (native-inputs `(("r-knitr" ,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 `(("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") (synopsis "Port of sofia-ml to R") (description "This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.") (license license:asl2.0))) (define-public r-xts (package (name "r-xts") (version "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (home-page "https://github.com/joshuaulrich/xts") (synopsis "Extensible time series") (description "This package provides for uniform handling of R's different time-based data classes by extending @code{zoo}, maximizing native format information preservation and allowing for user-level customization and extension, while simplifying cross-class interoperability.") (license license:gpl2+))) (define-public r-performanceanalytics (package (name "r-performanceanalytics") (version "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 `(("r-quadprog" ,r-quadprog) ("r-xts" ,r-xts) ("r-zoo" ,r-zoo))) (home-page "https://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.") ;; Either version may be picked. (license (list license:gpl2 license:gpl3)))) (define-public r-laeken (package (name "r-laeken") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-mass" ,r-mass))) (home-page "https://cran.r-project.org/web/packages/laeken/") (synopsis "Estimation of indicators on social exclusion and poverty") (description "This package provides tools for the estimation of indicators on social exclusion and poverty, as well as an implementation of Pareto tail modeling for empirical income distributions.") (license license:gpl2+))) (define-public r-vcd (package (name "r-vcd") (version "1.4-8") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass))) (home-page "https://cran.r-project.org/web/packages/vcd/") (synopsis "Visualizing categorical data") (description "This package provides visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was originally inspired by the book \"Visualizing Categorical Data\" by Michael Friendly and is now the main support package for a new book, \"Discrete Data Analysis with R\" by Michael Friendly and David Meyer (2015).") (license license:gpl2))) (define-public r-ica (package (name "r-ica") (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "ica" version)) (sha256 (base32 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ica/") (synopsis "Independent component analysis") (description "This package provides tools for @dfn{Independent Component Analysis} (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization of Eigenmatrices} (JADE).") (license license:gpl2+))) (define-public r-dtw (package (name "r-dtw") (version "1.22-3") (source (origin (method url-fetch) (uri (cran-uri "dtw" version)) (sha256 (base32 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z")))) (build-system r-build-system) (propagated-inputs `(("r-proxy" ,r-proxy))) (home-page "http://dtw.r-forge.r-project.org/") (synopsis "Dynamic Time Warping Algorithms") (description "This package provides a comprehensive implementation of @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on.") (license license:gpl2+))) (define-public r-sdmtools (package (name "r-sdmtools") (version "1.1-221.2") (source (origin (method url-fetch) (uri (cran-uri "SDMTools" version)) (sha256 (base32 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh")))) (properties `((upstream-name . "SDMTools"))) (build-system r-build-system) (propagated-inputs `(("r-r-utils" ,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 "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-scales" ,r-scales) ("r-withr" ,r-withr))) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description "Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) (define-public r-ggjoy (package (name "r-ggjoy") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggjoy" version)) (sha256 (base32 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges))) (home-page "https://github.com/clauswilke/ggjoy") (synopsis "Joyplots in ggplot2") (description "Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) (define-public r-cli (package (name "r-cli") (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-crayon" ,r-crayon) ("r-fansi" ,r-fansi) ("r-glue" ,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 "0.6") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") (description "This package provides a cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script.") (license license:gpl3+))) (define-public r-debugme (package (name "r-debugme") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "debugme" version)) (sha256 (base32 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon))) (home-page "https://github.com/r-lib/debugme#readme") (synopsis "Debug R packages") (description "This package allows the user to specify debug messages as special string constants, and control debugging of packages via environment variables.") (license license:expat))) (define-public r-processx (package (name "r-processx") (version "3.4.4") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) ("r-r6" ,r-r6))) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description "This package provides portable tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes and their children; restart processes. It can read the standard output and error of the processes, using non-blocking connections. @code{processx} can poll a process for standard output or error, with a timeout. It can also poll several processes at once.") (license license:expat))) (define-public r-tsp (package (name "r-tsp") (version "1.1-10") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach))) (home-page "https://cran.r-project.org/web/packages/TSP/") (synopsis "Traveling salesperson problem (TSP)") (description "This package provides basic infrastructure and some algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the traveling salesman problem).") (license license:gpl3))) (define-public r-qap (package (name "r-qap") (version "0.1-1") (source (origin (method url-fetch) (uri (cran-uri "qap" version)) (sha256 (base32 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic assignment problem} (QAP). Currently only a simulated annealing heuristic is available.") (license license:gpl3))) (define-public r-gclus (package (name "r-gclus") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "gclus" version)) (sha256 (base32 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/gclus/") (synopsis "Clustering graphics") (description "This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices of merit, ordering functions, and enhanced versions of @code{pairs} and @code{parcoord} which color panels according to their merit level.") (license license:gpl2+))) (define-public r-webshot (package (name "r-webshot") (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description "Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and screenshot static as well as interactive R Markdown documents.") (license license:gpl2))) (define-public r-seriation (package (name "r-seriation") (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-colorspace" ,r-colorspace) ("r-dendextend" ,r-dendextend) ("r-gclus" ,r-gclus) ("r-gplots" ,r-gplots) ("r-mass" ,r-mass) ("r-qap" ,r-qap) ("r-registry" ,r-registry) ("r-tsp" ,r-tsp))) (native-inputs `(("gfortran" ,gfortran))) (home-page "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 "0.18") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 "0iqh9b0a5wlc4lmqf7r169h4m2xji5l1viwwi47qf094rl5r3ddr")))) (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 "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) (build-system r-build-system) (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description "This package provides tools to process and print UTF-8 encoded international text (Unicode). Input, validate, normalize, encode, format, and display.") (license license:asl2.0))) (define-public r-zeallot (package (name "r-zeallot") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "zeallot" version)) (sha256 (base32 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3")))) (build-system r-build-system) (home-page "https://github.com/nteetor/zeallot") (synopsis "Multiple, unpacking, and destructuring assignment") (description "This package provides a @code{%<-%} operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.") (license license:expat))) (define-public r-vctrs (package (name "r-vctrs") (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-ellipsis" ,r-ellipsis) ("r-glue" ,r-glue) ("r-rlang" ,r-rlang))) (native-inputs `(("r-knitr" ,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 "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-ellipsis" ,r-ellipsis) ("r-fansi" ,r-fansi) ("r-lifecycle" ,r-lifecycle) ("r-rlang" ,r-rlang) ("r-utf8" ,r-utf8) ("r-vctrs" ,r-vctrs))) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description "This package provides a @code{pillar} generic designed for formatting columns of data using the full range of colours provided by modern terminals.") (license license:gpl3))) (define-public r-uuid (package (name "r-uuid") (version "0.1-4") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q")))) (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 "0.26") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 "02b0v8ydbfspma3rgsdpkf2cm6jl9qm3l9jsrl0xng482b06bb0q")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description "This package provides helper functions to install and maintain the LaTeX distribution named TinyTeX, a lightweight, cross-platform, portable, and easy-to-maintain version of TeX Live. This package also contains helper functions to compile LaTeX documents, and install missing LaTeX packages automatically.") (license license:expat))) (define-public r-network (package (name "r-network") (version "1.16.0") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) ("r-tibble" ,r-tibble))) (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description "This package provides tools to create and modify network objects. The @code{network} class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) (define-public r-stabs (package (name "r-stabs") (version "0.6-3") (source (origin (method url-fetch) (uri (cran-uri "stabs" version)) (sha256 (base32 "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9")))) (build-system r-build-system) (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 "4.4.1") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) (propagated-inputs `(("r-coda" ,r-coda) ("r-rle" ,r-rle))) (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 `(("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-rmarkdown" ,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 "2.5") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k")))) (build-system r-build-system) (propagated-inputs `(("r-network" ,r-network) ("r-statnet-common" ,r-statnet-common))) (home-page "https://statnet.org") (synopsis "Tools for social network analysis") (description "This package provides a range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.") (license license:gpl2+))) (define-public r-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 `(("r-matrix" ,r-matrix) ("r-mvtnorm" ,r-mvtnorm) ("r-sn" ,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 "0.24.2") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-xts" ,r-xts) ("r-zoo" ,r-zoo))) (home-page "https://github.com/joshuaulrich/TTR") (synopsis "Technical trading rules") (description "This package provides functions and data to construct technical trading rules with R.") (license license:gpl2))) (define-public r-leaps (package (name "r-leaps") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "leaps" version)) (sha256 (base32 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/leaps/") (synopsis "Regression subset selection") (description "This package provides tools for regression subset selection, including exhaustive search.") (license license:gpl2+))) (define-public r-splus2r (package (name "r-splus2r") (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "splus2R" version)) (sha256 (base32 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz")))) (properties `((upstream-name . "splus2R"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/splus2R/") (synopsis "Supplemental S-PLUS functionality in R") (description "Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.") (license license:gpl2))) (define-public r-ifultools (package (name "r-ifultools") (version "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "ifultools" version)) (sha256 (base32 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-splus2r" ,r-splus2r))) (home-page "https://cran.r-project.org/web/packages/ifultools/") (synopsis "Insightful research tools") (description "This package provides C code used by the wmtsa, fractal, and sapa R packages.") (license license:gpl2))) (define-public r-sapa (package (name "r-sapa") (version "2.0-2") (source (origin (method url-fetch) (uri (cran-uri "sapa" version)) (sha256 (base32 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds")))) (build-system r-build-system) (propagated-inputs `(("r-ifultools" ,r-ifultools) ("r-splus2r" ,r-splus2r))) (home-page "https://cran.r-project.org/web/packages/sapa/") (synopsis "Spectral analysis for physical applications") (description "This package provides software for the book Spectral Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.") (license license:gpl2))) (define-public r-aggregation (package (name "r-aggregation") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "aggregation" version)) (sha256 (base32 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/aggregation/") (synopsis "Methods for p-value aggregation") (description "This package contains functionality for performing the following methods of p-value aggregation: Fisher's method, the Lancaster method (weighted Fisher's method), and Sidak correction.") (license license:gpl3))) (define-public r-quantmod (package (name "r-quantmod") (version "0.4.17") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-ttr" ,r-ttr) ("r-xts" ,r-xts) ("r-zoo" ,r-zoo))) (home-page "https://cran.r-project.org/web/packages/quantmod/") (synopsis "Quantitative financial modelling framework") (description "This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.") (license license:gpl3))) (define-public r-tseries (package (name "r-tseries") (version "0.10-47") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog) ("r-quantmod" ,r-quantmod) ("r-zoo" ,r-zoo))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/tseries/") (synopsis "Time series analysis and computational finance") (description "This package provides functions relating to time series analysis and computational finance.") (license license:gpl2))) (define-public r-wmtsa (package (name "r-wmtsa") (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "wmtsa" version)) (sha256 (base32 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) (build-system r-build-system) (propagated-inputs `(("r-ifultools" ,r-ifultools) ("r-mass" ,r-mass) ("r-splus2r" ,r-splus2r))) (home-page "https://cran.r-project.org/web/packages/wmtsa/") (synopsis "Wavelet methods for time series analysis") (description "This package provides software to accompany the book \"Wavelet Methods for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge University Press, 2000.") (license license:gpl2))) (define-public r-tsa (package (name "r-tsa") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb")))) (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs `(("r-leaps" ,r-leaps) ("r-locfit" ,r-locfit) ("r-mgcv" ,r-mgcv) ("r-tseries" ,r-tseries))) (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description "This package contains R functions and datasets detailed in the book \"Time Series Analysis with Applications in R (second edition)\" by Jonathan Cryer and Kung-Sik Chan.") (license license:gpl2+))) (define-public r-extradistr (package (name "r-extradistr") (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/twolodzko/extraDistr") (synopsis "Additional univariate and multivariate distributions") (description "This package implements density, distribution functions, quantile functions and random generation functions for a large number of univariate and multivariate distributions.") (license license:gpl2))) (define-public r-fractal (package (name "r-fractal") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "fractal" version)) (sha256 (base32 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) (build-system r-build-system) (propagated-inputs `(("r-ifultools" ,r-ifultools) ("r-mass" ,r-mass) ("r-sapa" ,r-sapa) ("r-scatterplot3d" ,r-scatterplot3d) ("r-splus2r" ,r-splus2r) ("r-wmtsa" ,r-wmtsa))) (home-page "https://cran.r-project.org/web/packages/fractal/") (synopsis "Fractal time series modeling and analysis") (description "This package provides tools for stochastic fractal and deterministic chaotic time series analysis.") (license license:gpl2))) (define-public r-urca (package (name "r-urca") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "urca" version)) (sha256 (base32 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732")))) (build-system r-build-system) (propagated-inputs `(("r-nlme" ,r-nlme))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/urca/") (synopsis "Unit root and cointegration tests for time series data") (description "This package provides unit root and cointegration tests encountered in applied econometric analysis.") (license license:gpl2+))) (define-public r-cubature (package (name "r-cubature") (version "2.0.4.1") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,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 `(("r-extradistr" ,r-extradistr))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/trend/") (synopsis "Non-parametric trend tests and change-point detection") (description "The analysis of environmental data often requires the detection of trends and change-points. This package includes tests for trend detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman correlation trend test), change-point detection (Lanzante's test procedures, Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two sample Robust Rank-Order Distributional Test.") (license license:gpl3))) (define-public r-expm (package (name "r-expm") (version "0.999-5") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://r-forge.r-project.org/projects/expm/") (synopsis "Tools for matrix exponentials and related quantities") (description "This package provides tools for the computation of the matrix exponential, logarithm, square root, and related quantities.") (license license:gpl2+))) (define-public r-complexplus (package (name "r-complexplus") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "complexplus" version)) (sha256 (base32 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) (build-system r-build-system) (propagated-inputs `(("r-expm" ,r-expm) ("r-matrix" ,r-matrix))) (home-page "https://cran.r-project.org/web/packages/complexplus/") (synopsis "Functions of complex or real variables") (description "This package extends several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.") (license license:gpl2))) (define-public r-phontools (package (name "r-phontools") (version "0.2-2.1") (source (origin (method url-fetch) (uri (cran-uri "phonTools" version)) (sha256 (base32 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7")))) (properties `((upstream-name . "phonTools"))) (build-system r-build-system) (home-page "http://www.santiagobarreda.com/rscripts.html") (synopsis "Tools for phonetic and acoustic analyses") (description "This package contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.") (license license:bsd-2))) (define-public r-np (package (name "r-np") (version "0.60-10") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-cubature" ,r-cubature) ("r-quadprog" ,r-quadprog) ("r-quantreg" ,r-quantreg))) (home-page "https://github.com/JeffreyRacine/R-Package-np") (synopsis "Non-parametric kernel smoothing methods for mixed data types") (description "This package provides non-parametric (and semi-parametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-powerplus (package (name "r-powerplus") (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "powerplus" version)) (sha256 (base32 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) (build-system r-build-system) (propagated-inputs `(("r-complexplus" ,r-complexplus) ("r-expm" ,r-expm) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-phontools" ,r-phontools))) (home-page "https://cran.r-project.org/web/packages/powerplus/") (synopsis "Exponentiation operations") (description "This package provides tools for the computation of matrix and scalar exponentiation.") (license license:gpl2))) (define-public r-egg (package (name "r-egg") (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "egg" version)) (sha256 (base32 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m")))) (properties `((upstream-name . "egg"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtable" ,r-gtable))) (home-page "https://cran.r-project.org/web/packages/egg") (synopsis "Extensions for ggplot2") (description "This package provides miscellaneous functions to help customize ggplot2 objects. High-level functions are provided to post-process ggplot2 layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. Other functions include a custom @code{geom}, and helper functions to enforce symmetric scales or add tags to facetted plots.") (license license:gpl3))) (define-public r-heatmaply (package (name "r-heatmaply") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-colorspace" ,r-colorspace) ("r-dendextend" ,r-dendextend) ("r-egg" ,r-egg) ("r-ggplot2" ,r-ggplot2) ("r-htmlwidgets" ,r-htmlwidgets) ("r-magrittr" ,r-magrittr) ("r-plotly" ,r-plotly) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-scales" ,r-scales) ("r-seriation" ,r-seriation) ("r-viridis" ,r-viridis) ("r-webshot" ,r-webshot))) (native-inputs `(("r-knitr" ,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 `(("zlib" ,zlib) ("hdf5" ,hdf5))) (native-inputs `(("which" ,which))) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/mannau/h5") (synopsis "Interface to the HDF5 Library") (description "This package provides an S4 interface to the HDF5 library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The HDF5 format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.") (license license:bsd-2))) (define-public r-cgdsr (package (name "r-cgdsr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "cgdsr" version)) (sha256 (base32 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) ("r-r-methodss3" ,r-r-methodss3) ("r-r-oo" ,r-r-oo))) (home-page "https://github.com/cBioPortal/cgdsr") (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") (description "This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).") (license license:lgpl3))) (define-public r-import (package (name "r-import") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "import" version)) (sha256 (base32 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/smbache/import") (synopsis "Import mechanism for R") (description "This is an alternative mechanism for importing objects from packages. The syntax allows for importing multiple objects from a package with a single command in an expressive way. The import package bridges some of the gap between using @code{library} (or @code{require}) and direct (single-object) imports. Furthermore the imported objects are not placed in the current environment. It is also possible to import objects from stand-alone @code{.R} files.") (license license:expat))) (define-public r-shinyace (package (name "r-shinyace") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs `(("r-shiny" ,r-shiny) ("r-jsonlite" ,r-jsonlite))) (home-page "https://cran.r-project.org/web/packages/shinyAce/") (synopsis "Ace editor bindings for Shiny") (description "This package provides Ace editor bindings to enable a rich text editing environment within Shiny.") (license license:expat))) (define-public r-randomizr (package (name "r-randomizr") (version "0.20.0") (source (origin (method url-fetch) (uri (cran-uri "randomizr" version)) (sha256 (base32 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h")))) (properties `((upstream-name . "randomizr"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://declaredesign.org/r/randomizr/") (synopsis "Tools for common forms of random assignment and sampling") (description "This package provides tools for generating random assignments for common experimental designs and random samples for common sampling designs.") (license license:expat))) (define-public r-base64url (package (name "r-base64url") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "base64url" version)) (sha256 (base32 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports))) (home-page "https://github.com/mllg/base64url") (synopsis "Fast and URL-safe base64 encoder and decoder") (description "This package provides a URL-safe base64 encoder and decoder. In contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-}, the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the encoder does not fill the string with trailing @code{=}. The resulting encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]} and thus are safe to use in URLs or for file names. The package also comes with a simple base32 encoder/decoder suited for case insensitive file systems.") (license license:gpl3))) (define-public r-radiant-data (package (name "r-radiant-data") (version "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c")) (modules '((guix build utils))) (snippet '(begin ;; Delete files that are under CC-NC-SA. (delete-file-recursively "inst/app/tools/help") #t)))) (properties `((upstream-name . "radiant.data"))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-broom" ,r-broom) ("r-car" ,r-car) ("r-curl" ,r-curl) ("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) ("r-import" ,r-import) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-markdown" ,r-markdown) ("r-mass" ,r-mass) ("r-patchwork" ,r-patchwork) ("r-plotly" ,r-plotly) ("r-psych" ,r-psych) ("r-randomizr" ,r-randomizr) ("r-readr" ,r-readr) ("r-readxl" ,r-readxl) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-rstudioapi" ,r-rstudioapi) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-shinyfiles" ,r-shinyfiles) ("r-shinyace" ,r-shinyace) ("r-stringi" ,r-stringi) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-writexl" ,r-writexl))) (home-page "https://github.com/radiant-rstats/radiant.data") (synopsis "Data menu for Radiant: business analytics using R and Shiny") (description "The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.") (license license:agpl3))) (define-public r-algdesign (package (name "r-algdesign") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "AlgDesign" version)) (sha256 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz")))) (properties `((upstream-name . "AlgDesign"))) (build-system r-build-system) (home-page "https://github.com/jvbraun/AlgDesign") (synopsis "Algorithmic experimental design") (description "This package provides tools to calculate exact and approximate theory experimental designs for D, A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.") (license license:gpl2+))) (define-public r-signal (package (name "r-signal") (version "0.7-6") (source (origin (method url-fetch) (uri (cran-uri "signal" version)) (sha256 (base32 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/signal/") (synopsis "Signal processing") (description "This package provides a set of signal processing functions originally written for Matlab and GNU Octave. It includes filter generation utilities, filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.") (license license:gpl2))) (define-public r-gsubfn (package (name "r-gsubfn") (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "gsubfn" version)) (sha256 (base32 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) (build-system r-build-system) (propagated-inputs `(("r-proto" ,r-proto))) (home-page "https://code.google.com/archive/p/gsubfn/") (synopsis "Utilities for strings and function arguments.") (description "This package provides @code{gsubfn} which is like @code{gsub} but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. @code{gsubfn} can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions.") (license license:gpl2+))) (define-public r-sqldf (package (name "r-sqldf") (version "0.4-11") (source (origin (method url-fetch) (uri (cran-uri "sqldf" version)) (sha256 (base32 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff")))) (build-system r-build-system) (propagated-inputs `(("r-chron" ,r-chron) ("r-dbi" ,r-dbi) ("r-gsubfn" ,r-gsubfn) ("r-proto" ,r-proto) ("r-rsqlite" ,r-rsqlite))) (home-page "https://github.com/ggrothendieck/sqldf") (synopsis "Manipulate R data frames using SQL") (description "The @code{sqldf} function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. @code{sqldf} transparently sets up a database, imports the data frames into that database, performs the SQL statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be used to read filtered files into R even if the original files are larger than R itself can handle.") (license license:gpl2))) (define-public r-abind (package (name "r-abind") (version "1.4-5") (source (origin (method url-fetch) (uri (cran-uri "abind" version)) (sha256 (base32 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abind/") (synopsis "Combine multidimensional arrays") (description "This package provides tools to combine multidimensional arrays into a single array. This is a generalization of @code{cbind} and @code{rbind}. It works with vectors, matrices, and higher-dimensional arrays. It also provides the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating, extracting and replacing data in arrays.") (license license:lgpl2.0+))) (define-public r-prroc (package (name "r-prroc") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "PRROC" version)) (sha256 (base32 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7")))) (properties `((upstream-name . "PRROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PRROC/") (synopsis "Precision-Recall and ROC curves for weighted and unweighted data") (description "This package computes the areas under the @dfn{precision-recall} (PR) and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.") (license license:gpl3))) (define-public r-vim (package (name "r-vim") (version "6.0.0") (source (origin (method url-fetch) (uri (cran-uri "VIM" version)) (sha256 (base32 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv")))) (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) ("r-colorspace" ,r-colorspace) ("r-data-table" ,r-data-table) ("r-e1071" ,r-e1071) ("r-laeken" ,r-laeken) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-nnet" ,r-nnet) ("r-ranger" ,r-ranger) ("r-rcpp" ,r-rcpp) ("r-robustbase" ,r-robustbase) ("r-sp" ,r-sp) ("r-vcd" ,r-vcd))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/alexkowa/VIM") (synopsis "Visualization and imputation of missing values") (description "This package provides tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods.") (license license:gpl2+))) (define-public r-fnn (package (name "r-fnn") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") (synopsis "Fast nearest neighbor search algorithms and applications") (description "This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms. Related applications including KNN classification, regression and information measures are implemented.") ;; The DESCRIPTION file erroneously states that GPL version 2.1 or ;; later can be used. (license license:gpl2+))) (define-public r-smoother (package (name "r-smoother") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "smoother" version)) (sha256 (base32 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci")))) (build-system r-build-system) (propagated-inputs `(("r-ttr" ,r-ttr))) (home-page "https://cran.r-project.org/web/packages/smoother") (synopsis "Functions relating to the smoothing of numerical data") (description "This package provides a collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.") (license license:gpl2))) (define-public r-riverplot (package (name "r-riverplot") (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "riverplot" version)) (sha256 (base32 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z")))) (build-system r-build-system) (home-page "https://logfc.wordpress.com") (synopsis "Sankey or ribbon plots") (description "Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For example, they can be used to compare different clusterings. This package provides an implementation of Sankey plots for R.") (license license:gpl2+))) (define-public r-dyn (package (name "r-dyn") (version "0.2-9.6") (source (origin (method url-fetch) (uri (cran-uri "dyn" version)) (sha256 (base32 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (home-page "https://cran.r-project.org/web/packages/dyn") (synopsis "Time series regression") (description "This package provides the dyn class interfaces @code{ts}, @code{irts}, @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm}, @code{loess}, @code{quantreg::rq}, @code{MASS::rlm}, @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()}, @code{randomForest::randomForest()} and other regression functions, allowing those functions to be used with time series including specifications that may contain lags, diffs and missing values.") ;; Any GPL version. (license license:gpl2+))) (define-public r-catdap (package (name "r-catdap") (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "catdap" version)) (sha256 (base32 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/catdap/") (synopsis "Tools for categorical data analysis") (description "This package provides functions for analyzing multivariate data. Dependencies of the distribution of the specified variable (response variable) to other variables (explanatory variables) are derived and evaluated by the @dfn{Akaike Information Criterion} (AIC).") 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(license license:gpl3+))) (define-public r-abc (package (name "r-abc") (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "abc" version)) (sha256 (base32 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) (build-system r-build-system) (propagated-inputs `(("r-abc-data" ,r-abc-data) ("r-locfit" ,r-locfit) ("r-mass" ,r-mass) ("r-nnet" ,r-nnet) ("r-quantreg" ,r-quantreg))) (home-page "https://cran.r-project.org/web/packages/abc/") (synopsis "Tools for Approximate Bayesian Computation (ABC)") (description "This package implements several @dfn{Approximate Bayesian Computation} (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.") 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(license license:cc0))) (define-public r-openxlsx (package (name "r-openxlsx") (version "4.2.2") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 "12sjarcmbdww6jmkcqy8c6id94zv3lwmm15ns1y0xj3ipr8qmphb")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-stringi" ,r-stringi) ("r-zip" ,r-zip))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/awalker89/openxlsx") (synopsis "Read, write and edit XLSX files") (description "This package simplifies the creation of Excel @code{.xlsx} files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the @code{xlsx} and @code{XLConnect} packages with the added benefit of removing the dependency on Java.") (license license:gpl3))) (define-public r-rio (package (name "r-rio") (version "0.5.16") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-data-table" ,r-data-table) ("r-foreign" ,r-foreign) ("r-haven" ,r-haven) ("r-openxlsx" ,r-openxlsx) ("r-readxl" ,r-readxl) ("r-tibble" ,r-tibble))) (home-page "https://github.com/leeper/rio") (synopsis "Swiss-army knife for data I/O") (description "This package provides streamlined data import and export infrastructure by making assumptions that the user is probably willing to make: @code{import} and @code{export} determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., @code{stringsAsFactors=FALSE}), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate. An additional convenience function, @code{convert}, provides a simple method for converting between file types.") (license license:gpl2))) (define-public r-maptools (package (name "r-maptools") (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) ("r-lattice" ,r-lattice) ("r-sp" ,r-sp))) (home-page "https://r-forge.r-project.org/projects/maptools/") (synopsis "Tools for reading and handling spatial objects") (description "This package provides a set of tools for manipulating and reading geographic data, in particular ESRI Shapefiles. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with other R packages.") ;; The C source files from shapelib are released under the Expat license. ;; The R code is released under GPL version 2 or later. (license (list license:gpl2+ license:expat)))) (define-public r-later (package (name "r-later") (version "1.1.0.1") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/later") (synopsis "Utilities for delaying function execution") (description "This package provides tools to execute arbitrary R or C functions some time after the current time, after the R execution stack has emptied.") 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(license license:expat))) (define-public r-dosnow (package (name "r-dosnow") (version "1.0.18") (source (origin (method url-fetch) (uri (cran-uri "doSNOW" version)) (sha256 (base32 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh")))) (properties `((upstream-name . "doSNOW"))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach) ("r-iterators" ,r-iterators) ("r-snow" ,r-snow))) (home-page "https://cran.r-project.org/web/packages/doSNOW") (synopsis "Foreach parallel adaptor for the snow package") (description "This package provides a parallel backend for the @code{%dopar%} function using the @code{snow} package.") (license license:gpl2))) (define-public r-snowfall (package (name "r-snowfall") (version "1.84-6.1") (source (origin (method url-fetch) (uri (cran-uri "snowfall" version)) (sha256 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) (build-system r-build-system) (propagated-inputs `(("r-snow" ,r-snow))) (home-page "https://cran.r-project.org/web/packages/snowfall/") (synopsis "Easier cluster computing") (description "This package is a usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. The package is also designed as connector to the cluster management tool @code{sfCluster}, but can also used without it.") (license license:gpl2+))) (define-public r-rappdirs (package (name "r-rappdirs") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "rappdirs" version)) (sha256 (base32 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rappdirs/") (synopsis "Determine where to save data, caches, and logs") (description "This package provides an easy way to determine which directories on the user's computer should be used to save data, caches and logs. It is a port of Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (license license:expat))) (define-public r-renv (package (name "r-renv") (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-learnr (package (name "r-learnr") (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "learnr" version)) (sha256 (base32 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31")))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-ellipsis" ,r-ellipsis) ("r-evaluate" ,r-evaluate) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-markdown" ,r-markdown) ("r-rappdirs" ,r-rappdirs) ("r-renv" ,r-renv) ("r-rmarkdown" ,r-rmarkdown) ("r-rprojroot" ,r-rprojroot) ("r-shiny" ,r-shiny) ("r-withr" ,r-withr))) (home-page "https://rstudio.github.io/learnr/") (synopsis "Interactive tutorials for R") (description "This package provides tools to create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.") (license license:asl2.0))) (define-public r-analytics (package (name "r-analytics") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "analytics" version)) (sha256 (base32 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) ("r-cluster" ,r-cluster) ("r-fractal" ,r-fractal) ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-np" ,r-np) ("r-powerplus" ,r-powerplus) ("r-robust" ,r-robust) ("r-trend" ,r-trend) ("r-tsa" ,r-tsa) ("r-urca" ,r-urca) ("r-vim" ,r-vim))) (home-page "https://cran.r-project.org/web/packages/analytics/") (synopsis "Collection of data analysis tools") (description "This package is a collection of data analysis tools. It includes tools for regression outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.") (license license:gpl2))) (define-public r-reticulate (package (name "r-reticulate") (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs `(("r-rappdirs" ,r-rappdirs) ("r-jsonlite" ,r-jsonlite) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rstudio/reticulate") (synopsis "R interface to Python") (description "This package provides an interface from R to Python modules, classes, and functions. When calling into Python, R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types.") (license license:asl2.0))) (define-public r-bibtex (package (name "r-bibtex") (version "0.4.2.3") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) (home-page "https://github.com/romainfrancois/bibtex") (synopsis "Bibtex parser") (description "This package provides a utility for R to parse a bibtex file.") 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(license license:lgpl3+))) (define-public r-ggsci (package (name "r-ggsci") (version "2.9") (source (origin (method url-fetch) (uri (cran-uri "ggsci" version)) (sha256 (base32 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-scales" ,r-scales))) (home-page "https://nanx.me/ggsci/") (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") (description "This package provides a collection of ggplot2 color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.") 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(license license:gpl3))) (define-public r-rstatix (package (name "r-rstatix") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-car" ,r-car) ("r-corrplot" ,r-corrplot) ("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-tidyselect" ,r-tidyselect))) (home-page "https://rpkgs.datanovia.com/rstatix/") (synopsis "Pipe-friendly framework for basic statistical tests") (description "This package provides a simple and intuitive pipe-friendly framework, coherent with the @code{tidyverse} design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.") (license license:gpl2))) (define-public r-ggpubr (package (name "r-ggpubr") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-ggsci" ,r-ggsci) ("r-ggsignif" ,r-ggsignif) ("r-glue" ,r-glue) ("r-gridextra" ,r-gridextra) ("r-magrittr" ,r-magrittr) ("r-polynom" ,r-polynom) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-rstatix" ,r-rstatix) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (home-page "http://www.sthda.com/english/rpkgs/ggpubr") (synopsis "ggplot2-based publication-ready plots") (description "The ggplot2 package is an excellent and flexible package for elegant data visualization in R. However the default generated plots require some formatting before we can send them for publication. The ggpubr package provides some easy-to-use functions for creating and customizing ggplot2-based publication-ready plots.") (license license:gpl2))) (define-public r-ellipse (package (name "r-ellipse") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "ellipse" version)) (sha256 (base32 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ellipse/") (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") (description "This package contains various routines for drawing ellipses and ellipse-like confidence regions, implementing the plots described in Murdoch and Chow (1996), A graphical display of large correlation matrices, The American Statistician 50, 178-180. There are also routines implementing the profile plots described in Bates and Watts (1988), Nonlinear Regression Analysis and its Applications.") 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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 `(("r-abind" ,r-abind) ("r-cluster" ,r-cluster) ("r-dendextend" ,r-dendextend) ("r-factominer" ,r-factominer) ("r-ggplot2" ,r-ggplot2) ("r-ggpubr" ,r-ggpubr) ("r-ggrepel" ,r-ggrepel) ("r-reshape2" ,r-reshape2) ("r-tidyr" ,r-tidyr))) (home-page "http://www.sthda.com/english/rpkgs/factoextra") (synopsis "Extract and visualize the results of multivariate data analyses") (description "This package provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.") (license license:gpl2))) (define-public r-fansi (package (name "r-fansi") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/brodieG/fansi") (synopsis "ANSI control sequence aware string functions") (description "This package provides counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.") (license license:gpl2+))) (define-public r-nbclust (package (name "r-nbclust") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "NbClust" version)) (sha256 (base32 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c")))) (properties `((upstream-name . 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This package provides a nearly feature complete, object oriented wrapper for the HDF5 API using R6 classes. Additionally, functionality is added so that HDF5 objects behave very similar to their corresponding R counterparts.") (license license:asl2.0))) (define-public r-itertools (package (name "r-itertools") (version "0.1-3") (source (origin (method url-fetch) (uri (cran-uri "itertools" version)) (sha256 (base32 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn")))) (build-system r-build-system) (propagated-inputs `(("r-iterators" ,r-iterators))) (home-page "https://cran.r-project.org/web/packages/itertools/") (synopsis "Iterator tools") (description "This package provides various tools for creating iterators, many patterned after functions in the Python @code{itertools} module, and others patterned after functions in the snow package.") (license license:gpl2))) (define-public r-polynom (package (name "r-polynom") (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "polynom" version)) (sha256 (base32 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/polynom/") (synopsis "Functions for univariate polynomial manipulations") (description "This package provides a collection of functions to implement a class for univariate polynomial manipulations.") (license license:gpl2))) (define-public r-gbrd (package (name "r-gbrd") (version "0.4-11") (source (origin (method url-fetch) (uri (cran-uri "gbRd" version)) (sha256 (base32 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82")))) (properties `((upstream-name . 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It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (license license:gpl2))) (define-public r-rdpack (package (name "r-rdpack") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-officer (package (name "r-officer") (version "0.3.14") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) ("r-r6" ,r-r6) ("r-uuid" ,r-uuid) ("r-xml2" ,r-xml2) ("r-zip" ,r-zip))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "profileModel" version)) (sha256 (base32 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8")))) (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. 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These procedures return estimates with improved frequentist properties (bias, mean squared error) that are always finite even in cases where the maximum likelihood estimates are infinite (data separation). Fitting takes place by fitting generalized linear models on iteratively updated pseudo-data. The interface is essentially the same as @code{glm}. More flexibility is provided by the fact that custom pseudo-data representations can be specified and used for model fitting. Functions are provided for the construction of confidence intervals for the reduced-bias estimates.") (license license:gpl2+))) (define-public r-entropy (package (name "r-entropy") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "entropy" version)) (sha256 (base32 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-abn (package (name "r-abn") (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) (propagated-inputs `(("r-boot" ,r-boot) ("r-brglm" ,r-brglm) ("r-entropy" ,r-entropy) ("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-moments" ,r-moments) ("r-nnet" ,r-nnet) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rjags" ,r-rjags))) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description "Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a @dfn{generalized linear model} (GLM). Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. This package provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data.") (license license:gpl2+))) (define-public r-acd (package (name "r-acd") (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "ACD" version)) (sha256 (base32 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6")))) (properties `((upstream-name . "ACD"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACD/") (synopsis "Categorical data analysis with complete or missing responses") (description "This package provides tools for categorical data analysis with complete or missing responses.") (license license:gpl2+))) (define-public r-acdm (package (name "r-acdm") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "ACDm" version)) (sha256 (base32 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil")))) (properties `((upstream-name . "ACDm"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-rsolnp" ,r-rsolnp) ("r-zoo" ,r-zoo))) (home-page "https://cran.r-project.org/web/packages/ACDm/") (synopsis "Tools for Autoregressive Conditional Duration Models") (description "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. It creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.") (license license:gpl2+))) (define-public r-overlap (package (name "r-overlap") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "overlap" version)) (sha256 (base32 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/overlap/") (synopsis "Estimates of coefficient of overlapping for animal activity patterns") (description "This package provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.") 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(license license:expat))) (define-public r-insight (package (name "r-insight") (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 "15mws316qfbq3nn6gb7s0m0a6jk2zi056g43yqiw4gp2ar92wd0h")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://easystats.github.io/insight/") (synopsis "Easy access to model information for various model objects") (description "This package provides a tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. The package mainly revolves around two types of functions: Functions that find (the names of) information, starting with @code{find_}, and functions that get the underlying data, starting with @code{get_}. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.") (license license:gpl3))) (define-public r-sjlabelled (package (name "r-sjlabelled") (version "1.1.7") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description "This package provides a collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.") (license license:gpl3))) (define-public r-sjmisc (package (name "r-sjmisc") (version "2.8.5") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-insight" ,r-insight) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-sjlabelled" ,r-sjlabelled) ("r-tidyselect" ,r-tidyselect))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/strengejacke/sjmisc") (synopsis "Data and variable transformation functions") (description "This package is a collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a tidyverse workflow.") (license license:gpl3))) (define-public r-nortest (package (name "r-nortest") (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "nortest" version)) (sha256 (base32 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/nortest/") (synopsis "Tests for normality") (description "This package provides five omnibus tests for testing the composite hypothesis of normality.") (license license:gpl2+))) (define-public r-moonbook (package (name "r-moonbook") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "moonBook" version)) (sha256 (base32 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-flextable (package (name "r-flextable") (version "0.5.11") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-data-table" ,r-data-table) ("r-gdtools" ,r-gdtools) ("r-htmltools" ,r-htmltools) ("r-knitr" ,r-knitr) ("r-officer" ,r-officer) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-uuid" ,r-uuid) ("r-xml2" ,r-xml2))) (home-page "https://davidgohel.github.io/flextable") (synopsis "Functions for tabular reporting") (description "This package provides tools to create pretty tables for HTML documents and other formats. Functions are provided to let users create tables, modify and format their content. It extends the @code{officer} package and can be used within R markdown documents when rendering to HTML and to Word documents.") (license license:gpl3))) (define-public r-writexl (package (name "r-writexl") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/ropensci/writexl") (synopsis "Export data frames to xlsx format") (description "This package provides a data frame to xlsx exporter based on libxlsxwriter.") (license license:bsd-2))) (define-public r-biasedurn (package (name "r-biasedurn") (version "1.07") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) (properties `((upstream-name . 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Many users will prefer to use the packages @code{optparse} or @code{argparse} which add extra features like automatically generated help options and usage texts, support for default values, positional argument support, etc.") (license license:gpl2+))) (define-public r-findpython (package (name "r-findpython") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy")))) (build-system r-build-system) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") (description "This package was designed to find an acceptable Python binary that matches version and feature constraints.") (license license:expat))) ;; This in not the same as "r-argparser" (define-public r-argparse (package (name "r-argparse") (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs `(("r-findpython" ,r-findpython) ("r-jsonlite" ,r-jsonlite) ("r-r6" ,r-r6))) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description "This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.") 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(license license:gpl2))) (define-public r-deriv (package (name "r-deriv") (version "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 "1n5d10g9qv4fvl8q0q6yc0mzdbba10jniid6k3br3bfqvdp2a4pq")))) (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 "4.6.7") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk")))) (properties `((upstream-name . 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"BASIX"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BASIX/") (synopsis "Efficient C/C++ toolset for R") (description "BASIX provides some efficient C/C++ implementations of native R procedures to speed up calculations in R.") (license license:gpl2))) (define-public r-blockfest (package (name "r-blockfest") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs `(("r-basix" ,r-basix))) (home-page "https://cran.r-project.org/web/packages/BlockFeST/") (synopsis "Bayesian calculation of region-specific fixation index") (description "This package provides an R implementation of an extension of the BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.") (license license:gpl2))) (define-public r-proc (package (name "r-proc") (version "1.16.2") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) ("r-rcpp" ,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 "1.8.2.1") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/rootSolve/") (synopsis "Tools for the analysis of ordinary differential equations") (description "This package provides routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of @dfn{ordinary differential equations} (ODE). It includes routines that: @enumerate @item generate gradient and jacobian matrices (full and banded), @item find roots of non-linear equations by the Newton-Raphson method, @item estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running, @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). @end enumerate\n") (license license:gpl2+))) (define-public r-abcanalysis (package (name "r-abcanalysis") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ABCanalysis" version)) (sha256 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) (properties `((upstream-name . "ABCanalysis"))) (build-system r-build-system) (propagated-inputs `(("r-plotrix" ,r-plotrix))) (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") (synopsis "Computed ABC Analysis") (description "Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to the perception of losing information from a data set. This package provides tools to calculate these limits on the basis of the mathematical properties of the distribution of the analyzed items.") 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"manipulateWidget"))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-codetools" ,r-codetools) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-knitr" ,r-knitr) ("r-miniui" ,r-miniui) ("r-shiny" ,r-shiny) ("r-webshot" ,r-webshot))) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description "This package lets you create in just a few lines of R code a nice user interface to modify the data or the graphical parameters of one or multiple interactive charts. It is useful to quickly explore visually some data or for package developers to generate user interfaces easy to maintain.") (license license:gpl2+))) (define-public r-a3 (package (name "r-a3") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "A3" version)) (sha256 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) (properties `((upstream-name . "A3"))) (build-system r-build-system) (propagated-inputs `(("r-pbapply" ,r-pbapply) ("r-xtable" ,r-xtable))) (home-page "https://cran.r-project.org/web/packages/A3/") (synopsis "Error metrics for predictive models") (description "This package supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward.") (license license:gpl2+))) (define-public r-infotheo (package (name "r-infotheo") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "infotheo" version)) (sha256 (base32 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv")))) (build-system r-build-system) (home-page "http://homepage.meyerp.com/software") (synopsis "Information-theoretic measures") (description "This package implements various measures of information theory based on several entropy estimators.") (license license:gpl3+))) (define-public r-abcoptim (package (name "r-abcoptim") (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "ABCoptim" version)) (sha256 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) (properties `((upstream-name . "ABCoptim"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/gvegayon/ABCoptim/") (synopsis "Optimization of Artificial Bee Colony algorithm") (description "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms, and uses only common control parameters such as colony size and maximum cycle number. The @code{r-abcoptim} implements the Artificial bee colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. This version is a work-in-progress and is written in R code.") (license license:expat))) (define-public r-abcp2 (package (name "r-abcp2") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "ABCp2" version)) (sha256 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) (properties `((upstream-name . "ABCp2"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (home-page "https://cran.r-project.org/web/packages/ABCp2/") (synopsis "Approximate Bayesian Computational Model for Estimating P2") (description "This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.") (license license:gpl2))) (define-public r-abcrf (package (name "r-abcrf") (version "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "abcrf" version)) (sha256 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27")))) (build-system r-build-system) (propagated-inputs `(("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-ranger" ,r-ranger) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-readr" ,r-readr) ("r-stringr" ,r-stringr))) (home-page "https://cran.r-project.org/web/packages/abcrf/") (synopsis "Approximate bayesian computation via random forests") (description "This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.") (license license:gpl2+))) (define-public r-abctools (package (name "r-abctools") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "abctools" version)) (sha256 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) (build-system r-build-system) (propagated-inputs `(("r-abc" ,r-abc) ("r-abind" ,r-abind) ("r-hmisc" ,r-hmisc) ("r-plyr" ,r-plyr))) (home-page "https://github.com/dennisprangle/abctools/") (synopsis "Tools for ABC analyses") (description "This @code{r-abctools} package provides tools for approximate Bayesian computation including summary statistic selection and assessing coverage. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods to tune the choice of threshold.") (license license:gpl2+))) (define-public r-ggstance (package (name "r-ggstance") (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "ggstance" version)) (sha256 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-rlang" ,r-rlang) ("r-withr" ,r-withr))) (home-page "https://cran.r-project.org/web/packages/ggstance/") (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") (description "This package is a @code{r-ggplot2} extension that provides flipped components: @enumerate @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms; @item vertical versions of @code{r-ggplot2} positions. @end enumerate") (license license:gpl3))) (define-public r-mosaiccore (package (name "r-mosaiccore") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "mosaicCore" version)) (sha256 (base32 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-ggformula (package (name "r-ggformula") (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "ggformula" version)) (sha256 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f")))) (build-system r-build-system) (propagated-inputs `(("r-ggforce" ,r-ggforce) ("r-ggplot2" ,r-ggplot2) ("r-ggstance" ,r-ggstance) ("r-magrittr" ,r-magrittr) ("r-mosaiccore" ,r-mosaiccore) ("r-rlang" ,r-rlang) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble))) (home-page "https://github.com/ProjectMOSAIC/ggformula/") (synopsis "Formula interface for the @code{r-ggplot2}") (description "The @code{r-ggformula} introduces a family of graphics functions, gf_point(), gf_density(), and so on, bring the formula interface to ggplot(). This captures and extends the excellent simplicity of the lattice-graphics formula interface, while providing the intuitive capabilities of @code{r-ggplot2}.") (license license:expat))) (define-public r-mosaicdata (package (name "r-mosaicdata") (version "0.20.1") (source (origin (method url-fetch) (uri (cran-uri "mosaicData" version)) (sha256 (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji")))) (properties `((upstream-name . "mosaicData"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mosaicData/") (synopsis "Data sets for project Mosaic") (description "This package provides data sets from project Mosaic @url{http://mosaic-web.org} used to teach mathematics, statistics, computation and modeling.") 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(license license:gpl2))) (define-public r-svgui (package (name "r-svgui") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "svGUI" version)) (sha256 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc")))) (properties `((upstream-name . "svGUI"))) (build-system r-build-system) (home-page "https://github.com/SciViews/svGUI/") (synopsis "Functions for managing GUI clients in R") (description "The SciViews @code{svGUI} package eases the management of Graphical User Interfaces (GUI) in R. It is independent from any particular GUI widgets. It centralizes info about GUI elements currently used, and it dispatches GUI calls to the particular toolkits in use in function of the context.") (license license:gpl2))) (define-public r-svdialogs (package (name "r-svdialogs") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "svDialogs" version)) (sha256 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97")))) (properties `((upstream-name . "svDialogs"))) (build-system r-build-system) (inputs `(("yad" ,yad) ("zenity" ,zenity))) (propagated-inputs `(("r-rstudioapi" ,r-rstudioapi) ("r-svgui" ,r-svgui))) (home-page "https://github.com/SciViews/svDialogs/") (synopsis "Portable dialog boxes") (description "This package helps to construct standard dialog boxes for your GUI, including message boxes, input boxes, list, file or directory selection, and others. In case R cannot display GUI dialog boxes, a simpler command line version of these interactive elements is also provided as a fallback solution.") (license license:gpl2))) (define-public r-abe (package (name "r-abe") (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "abe" version)) (sha256 (base32 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abe/") (synopsis "Augmented backward elimination") (description "This package performs augmented backward elimination and checks the stability of the obtained model. Augmented backward elimination combines significance or information based criteria with the change in estimate to either select the optimal model for prediction purposes or to serve as a tool to obtain a practically sound, highly interpretable model.") (license license:gpl2+))) (define-public r-abf2 (package (name "r-abf2") (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "abf2" version)) (sha256 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abf2/") (synopsis "Load gap-free axon @code{r-abf2} files") (description "This package loads electrophysiology data from ABF2 files, as created by Axon Instruments/Molecular Devices software. Only files recorded in gap-free mode are currently supported.") (license license:artistic2.0))) (define-public r-abhgenotyper (package (name "r-abhgenotyper") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ABHgenotypeR" version)) (sha256 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l")))) (properties `((upstream-name . "ABHgenotypeR"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,r-reshape2))) (home-page "https://github.com/StefanReuscher/ABHgenotypeR/") (synopsis "Visualize and manipulate ABH genotypes") (description "The @code{r-abhgenotyper} package provides simple imputation, error-correction and plotting capacities for genotype data. The package is supposed to serve as an intermediate but independent analysis tool between the TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities not found in either TASSEL or @code{r-qtl} in addition to visualization of genotypes as \"graphical genotypes\".") (license license:gpl3))) (define-public r-furrr (package (name "r-furrr") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx")))) (build-system r-build-system) (propagated-inputs `(("r-future" ,r-future) ("r-globals" ,r-globals) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang))) (home-page "https://github.com/DavisVaughan/furrr") (synopsis "Apply mapping functions in parallel using futures") (description "This package provides implementations of the family of @code{map()} functions from the @code{purrr} package that can be resolved using any @code{future}-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.") (license license:lgpl2.1+))) (define-public r-abjutils (package (name "r-abjutils") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "abjutils" version)) (sha256 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-rstudioapi" ,r-rstudioapi) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/abjur/abjutils/") (synopsis "Collection of tools for jurimetrical analysis") (description "This package implements general purpose tools, such as functions for sampling and basic manipulation of Brazilian lawsuits identification number. It also implements functions for text cleaning, such as accentuation removal.") (license license:expat))) (define-public r-abnormality (package (name "r-abnormality") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "abnormality" version)) (sha256 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-matrix" ,r-matrix))) (home-page "https://cran.r-project.org/web/packages/abnormality/") (synopsis "Measure a subject's abnormality with respect to a reference population") (description "This package contains functions to implement the methodology and considerations laid out by Marks et al. in the article \"Measuring abnormality in high dimensional spaces: applications in biomechanical gait analysis\". Using high-dimensional datasets to measure a subject's overall level of abnormality as compared to a reference population is often needed in outcomes research.") (license license:expat))) (define-public r-abodoutlier (package (name "r-abodoutlier") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "abodOutlier" version)) (sha256 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj")))) (properties `((upstream-name . "abodOutlier"))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/abodOutlier/") (synopsis "Angle-based outlier detection") (description "This package performs angle-based outlier detection on a given data frame. It offers three methods to process data: @enumerate @item full but slow implementation using all the data that has cubic complexity; @item a fully randomized method; @item a method using k-nearest neighbours. @end enumerate These algorithms are well suited for high dimensional data outlier detection.") (license license:expat))) (define-public r-abps (package (name "r-abps") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ABPS" version)) (sha256 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) (properties `((upstream-name . "ABPS"))) (build-system r-build-system) (propagated-inputs `(("r-kernlab" ,r-kernlab))) (home-page "https://cran.r-project.org/web/packages/ABPS/") (synopsis "Abnormal blood profile score to detect blood doping") (description "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS). The ABPS is a part of the Athlete biological passport program of the World anti-doping agency, which combines several blood parameters into a single score in order to detect blood doping. The package also contains functions to calculate other scores used in anti-doping programs, such as the ratio of hemoglobin to reticulocytes (OFF-score), as well as example data.") (license license:gpl2+))) (define-public r-parmigene (package (name "r-parmigene") (version "1.1.0") (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 `(("r-mass" ,r-mass))) (home-page "https://github.com/atahk/pscl/") (synopsis "Political science computational laboratory") (description "The @code{pscl} is an R package providing classes and methods for: @enumerate @item Bayesian analysis of roll call data (item-response models); @item elementary Bayesian statistics; @item maximum likelihood estimation of zero-inflated and hurdle models for count data; @item utility functions. @end enumerate") (license license:gpl2))) (define-public r-accelmissing (package (name "r-accelmissing") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "accelmissing" version)) (sha256 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) (build-system r-build-system) (propagated-inputs `(("r-mice" ,r-mice) ("r-pscl" ,r-pscl))) (home-page "https://cran.r-project.org/web/packages/accelmissing/") (synopsis "Missing value imputation for accelerometer data") (description "This package provides a statistical method to impute the missing values in accelerometer data. The methodology includes both parametric and semi-parametric multiple imputations under the zero-inflated Poisson lognormal model. It also provides multiple functions to preprocess the accelerometer data previous to the missing data imputation. These include detecting the wearing and the non-wearing time, selecting valid days and subjects, and creating plots.") (license license:gpl2+))) (define-public r-mhsmm (package (name "r-mhsmm") (version "0.4.16") (source (origin (method url-fetch) (uri (cran-uri "mhsmm" version)) (sha256 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) (home-page "https://github.com/jaredo/mhsmm/") (synopsis "Inference for hidden Markov and semi-Markov models") (description "The @code{r-mhsmm} package implements estimation and prediction methods for hidden Markov and semi-Markov models for multiple observation sequences. Such techniques are of interest when observed data is thought to be dependent on some unobserved (or hidden) state. Also, this package is suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.") (license license:gpl2+))) (define-public r-nleqslv (package (name "r-nleqslv") (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "nleqslv" version)) (sha256 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/nleqslv/") (synopsis "Solve systems of nonlinear equations") (description "The @code{r-nleqslv} package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.") (license license:gpl2+))) (define-public r-physicalactivity (package (name "r-physicalactivity") (version "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "PhysicalActivity" version)) (sha256 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln")))) (properties `((upstream-name . "PhysicalActivity"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") (synopsis "Procesing accelerometer data for physical activity measurement") (description "This @code{r-physicalactivity} package provides a function @code{wearingMarking} for classification of monitor wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plots of accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. The revised package version 0.2-1 improved the functions regarding speed, robustness and add better support for time zones and daylight saving. In addition, several functions were added: @enumerate @item the @code{markDelivery} can classify days for ActiGraph delivery by mail; @item the @code{markPAI} can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. @end enumerate It also supports importing ActiGraph (AGD) files with @code{readActigraph} and @code{queryActigraph} functions.") (license license:gpl3+))) (define-public r-acc (package (name "r-acc") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "acc" version)) (sha256 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) ("r-dbi" ,r-dbi) ("r-ggplot2" ,r-ggplot2) ("r-iterators" ,r-iterators) ("r-mhsmm" ,r-mhsmm) ("r-nleqslv" ,r-nleqslv) ("r-physicalactivity" ,r-physicalactivity) ("r-plyr" ,r-plyr) ("r-r-utils" ,r-r-utils) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rsqlite" ,r-rsqlite) ("r-zoo" ,r-zoo))) (home-page "https://cran.r-project.org/web/packages/acc/") (synopsis "Exploring accelerometer data") (description "This package processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also, includes functions to plot, analyze, and simulate accelerometer data.") (license license:gpl2+))) (define-public r-rbenchmark (package (name "r-rbenchmark") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rbenchmark" version)) (sha256 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rbenchmark/") (synopsis "Benchmarking routine for R") (description "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.") (license license:gpl2+))) (define-public r-mitools (package (name "r-mitools") (version "2.4") (source (origin (method url-fetch) (uri (cran-uri "mitools" version)) (sha256 (base32 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j")))) (build-system r-build-system) (propagated-inputs `(("r-dbi" ,r-dbi))) (home-page "https://cran.r-project.org/web/packages/mitools/") (synopsis "Tools for multiple imputation of missing data") (description "This package provides tools to perform analyses and combine results from multiple-imputation datasets.") (license license:gpl2))) (define-public r-magick (package (name "r-magick") (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) ("zlib" ,zlib))) (propagated-inputs `(("r-curl" ,r-curl) ("r-magrittr" ,r-magrittr) ("r-rcpp" ,r-rcpp))) (native-inputs `(("pkg-config" ,pkg-config) ("r-knitr" ,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 "4.0") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-matrix" ,r-matrix) ("r-minqa" ,r-minqa) ("r-mitools" ,r-mitools) ("r-numderiv" ,r-numderiv) ("r-survival" ,r-survival))) (home-page "http://r-survey.r-forge.r-project.org/survey/") (synopsis "Analysis of complex survey samples") (description "This package provides tools for the analysis of complex survey samples. The provided features include: summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples; variances by Taylor series linearisation or replicate weights; post-stratification, calibration, and raking; two-phase subsampling designs; graphics; PPS sampling without replacement; principal components, and factor analysis.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-gee (package (name "r-gee") (version "4.13-20") (source (origin (method url-fetch) (uri (cran-uri "gee" version)) (sha256 (base32 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak")))) (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 "4.1.1") (source (origin (method url-fetch) (uri (cran-uri "tab" version)) (sha256 (base32 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm")))) (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-gee" ,r-gee) ("r-knitr" ,r-knitr) ("r-mass" ,r-mass) ("r-survey" ,r-survey) ("r-survival" ,r-survival) ("r-xtable" ,r-xtable))) (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 `(("r-cubature" ,r-cubature) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-mass" ,r-mass) ("r-mvtnorm" ,r-mvtnorm) ("r-pracma" ,r-pracma) ("r-rbenchmark" ,r-rbenchmark) ("r-rcpp" ,r-rcpp) ("r-survey" ,r-survey) ("r-tab" ,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 `(("r-dvmisc" ,r-dvmisc) ("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/accelerometry/") (synopsis "Functions for processing accelerometer data") (description "This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented.") (license license:gpl3))) (define-public r-absim (package (name "r-absim") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "AbSim" version)) (sha256 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) (properties `((upstream-name . "AbSim"))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) ("r-powerlaw" ,r-powerlaw))) (home-page "https://cran.r-project.org/web/packages/AbSim/") (synopsis "Time resolved simulations of antibody repertoires") (description "This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins with an initial V-D-J recombination event, starting the first phylogenetic tree. Upon completion, the main loop of the algorithm begins, with each iteration representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.") (license license:gpl2))) (define-public r-quic (package (name "r-quic") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "QUIC" version)) (sha256 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) (properties `((upstream-name . "QUIC"))) (build-system r-build-system) (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") (synopsis "Regularized sparse inverse covariance matrix estimation") (description "This package implements the regularized Gaussian maximum likelihood estimation of the inverse of a covariance matrix. It uses Newton's method and coordinate descent to solve the regularized inverse covariance matrix estimation problem.") ;; The project home page states that the release is under GPLv3 or later. ;; The CRAN page only says GPL-3. (license license:gpl3+))) (define-public r-abundant (package (name "r-abundant") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "abundant" version)) (sha256 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) (build-system r-build-system) (propagated-inputs `(("r-quic" ,r-quic))) (home-page "https://cran.r-project.org/web/packages/abundant/") (synopsis "Abundant regression and high-dimensional principal fitted components") (description "This package provides tools to fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) @url{doi:10.1214/11-AOS962}.") ;; The DESCRIPTION file states GPL-2, but since it directly depends on a ;; GPLv3+ package (QUIC) this likely means GPLv2+. (license license:gpl2+))) (define-public r-ac3net (package (name "r-ac3net") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "Ac3net" version)) (sha256 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) (properties `((upstream-name . "Ac3net"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table))) (home-page "https://cran.r-project.org/web/packages/Ac3net/") (synopsis "Inferring directional conservative causal core gene networks") (description "This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.") (license license:gpl3+))) (define-public r-aca (package (name "r-aca") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "ACA" version)) (sha256 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) (properties `((upstream-name . "ACA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACA/") (synopsis "Abrupt change-point or aberration detection in point series") (description "This package offers an interactive function for the detection of breakpoints in series.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-acceptancesampling (package (name "r-acceptancesampling") (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9")))) (properties `((upstream-name . "AcceptanceSampling"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") (synopsis "Creation and evaluation of acceptance sampling plans") (description "This @code{r-acceptancesampling} provides functionality for creating and evaluating acceptance sampling plans. Acceptance sampling is a methodology commonly used in quality control and improvement. International standards of acceptance sampling provide sampling plans for specific circumstances. The aim of this package is to provide an easy-to-use interface to visualize single, double or multiple sampling plans. In addition, methods have been provided to enable the user to assess sampling plans against pre-specified levels of performance, as measured by the probability of acceptance for a given level of quality in the lot.") (license license:gpl3+))) (define-public r-acclma (package (name "r-acclma") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ACCLMA" version)) (sha256 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) (properties `((upstream-name . "ACCLMA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACCLMA/") (synopsis "ACC & LMA graph plotting") (description "This package contains a function that imports data from a @acronym{CSV, Comma-Separated Values} file, or uses manually entered data from the format (x, y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration Curve} vs @acronym{LOI, Line of Independence} graph and @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main function is @code{plotLMA} (source file, header) that takes a data set and plots the appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a string) was passed, a manual data entry window is opened. The header parameter indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has a header row or not. The dataset should contain only one independent variable (x) and one dependent variable (y) and can contain a weight for each observation.") (license license:gpl2))) (define-public r-aspi (package (name "r-aspi") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "aspi" version)) (sha256 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/aspi/") (synopsis "Analysis of symmetry of parasitic infections") (description "This package provides tools for the analysis and visualization of bilateral asymmetry in parasitic infections.") (license license:gpl3+))) (define-public r-sandwich (package (name "r-sandwich") (version "3.0-0") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (home-page "https://cran.r-project.org/web/packages/sandwich/") (synopsis "Robust Covariance Matrix Estimators") (description "This package provides model-robust standard error estimators for cross-sectional, time series, clustered, panel, and longitudinal data.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-th-data (package (name "r-th-data") (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/TH.data/") (synopsis "Shared data sets") (description "This package contains supporting data sets that are used in other packages maintained by Torsten Hothorn.") (license license:gpl3))) (define-public r-multcomp (package (name "r-multcomp") (version "1.4-14") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 "14a55isy1sp745s109nirlk5fryy144cri6dl8y9d9wjhfxz336a")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-mvtnorm" ,r-mvtnorm) ("r-sandwich" ,r-sandwich) ("r-survival" ,r-survival) ("r-th-data" ,r-th-data))) (home-page "https://cran.r-project.org/web/packages/multcomp/") (synopsis "Simultaneous inference in general parametric models") (description "Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, Hothorn, Westfall, 2010, CRC Press).") (license license:gpl2))) (define-public r-emmeans (package (name "r-emmeans") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 "05z3vvykn56g50zhzsphdhfjzdw8g8xfindcas08hbhv5y7izhs8")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) ("r-mvtnorm" ,r-mvtnorm) ("r-numderiv" ,r-numderiv) ("r-plyr" ,r-plyr) ("r-xtable" ,r-xtable))) (native-inputs `(("r-knitr" ,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 `(("r-knitr" ,r-knitr))) (home-page "https://github.com/heliosdrm/pwr") (synopsis "Basic functions for power analysis") (description "This package provides power analysis functions along the lines of Cohen (1988).") (license license:gpl3+))) (define-public r-libcoin (package (name "r-libcoin") (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) (home-page "https://cran.r-project.org/web/packages/libcoin") (synopsis "Linear test statistics for permutation inference") (description "This package provides basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999).") (license license:gpl2))) (define-public r-coin (package (name "r-coin") (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,r-libcoin) ("r-matrixstats" ,r-matrixstats) ("r-modeltools" ,r-modeltools) ("r-multcomp" ,r-multcomp) ("r-mvtnorm" ,r-mvtnorm) ("r-survival" ,r-survival))) (home-page "http://coin.r-forge.r-project.org") (synopsis "Conditional inference procedures in a permutation test framework") (description "This package provides conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.") (license license:gpl2))) (define-public r-bayesplot (package (name "r-bayesplot") (version "1.7.2") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl")))) (build-system r-build-system) (inputs `(("pandoc" ,pandoc) ("pandoc-citeproc" ,pandoc-citeproc))) (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges) ("r-glue" ,r-glue) ("r-reshape2" ,r-reshape2) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyselect" ,r-tidyselect))) (home-page "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 "1.7.18") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) ("r-rcppeigen" ,r-rcppeigen))) (home-page "http://tmb-project.org") (synopsis "Template model builder: a general random effect tool") (description "With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through BLAS and parallel user templates.") (license license:gpl2))) (define-public r-sjstats (package (name "r-sjstats") (version "0.18.0") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-effectsize" ,r-effectsize) ("r-emmeans" ,r-emmeans) ("r-insight" ,r-insight) ("r-lme4" ,r-lme4) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-modelr" ,r-modelr) ("r-parameters" ,r-parameters) ("r-performance" ,r-performance) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-sjlabelled" ,r-sjlabelled) ("r-sjmisc" ,r-sjmisc) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/strengejacke/sjstats") (synopsis "Functions for common statistical computations") (description "This package provides a collection of convenient functions for common statistical computations, which are not directly provided by R's @code{base} or @code{stats} packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort. Second, these shortcut functions are generic, and can be applied not only to vectors, but also to other objects as well. The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models, mixed effects models and Bayesian models.") (license license:gpl3))) (define-public r-glmmtmb (package (name "r-glmmtmb") (version "1.0.2.1") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) ("r-matrix" ,r-matrix) ("r-nlme" ,r-nlme) ("r-rcppeigen" ,r-rcppeigen) ("r-tmb" ,r-tmb))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description "Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via the Template Model Builder. Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.") (license license:agpl3+))) (define-public r-bayestestr (package (name "r-bayestestr") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 "1c82bpxg2ha93rna4sy9pdp422dnk6b378dcg8x04clfg0y0lsi2")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight))) (native-inputs `(("r-knitr" ,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 "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 "01csmn52d6rhlmcj7gi6ckc6v6a8pymnrpx9l729h13igxsnaf28")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-insight" ,r-insight))) (home-page "https://easystats.github.io/performance/") (synopsis "Assessment of regression models performance") (description "This package provides utilities for computing measures to assess model quality, which are not directly provided by R's @code{base} or @code{stats} packages. These include e.g. measures like r-squared, intraclass correlation coefficient, root mean squared error or functions to check models for overdispersion, singularity or zero-inflation and more. Functions apply to a large variety of regression models, including generalized linear models, mixed effects models and Bayesian models.") (license license:gpl3))) (define-public r-ggeffects (package (name "r-ggeffects") (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) ("r-mass" ,r-mass) ("r-sjlabelled" ,r-sjlabelled))) (native-inputs `(("r-knitr" ,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 "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 "00c9j6lc58ls1vrwlpzk3h1lgvxpkcrh7b4ym6kmy4fg4f08izp7")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-insight" ,r-insight) ("r-parameters" ,r-parameters))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/easystats/effectsize") (synopsis "Indices of effect size and standardized parameters") (description "This package provides utilities to work with indices of effect size and standardized parameters for a wide variety of models, allowing computation and conversion of indices such as Cohen's d, r, odds, etc.") (license license:gpl3))) (define-public r-sjplot (package (name "r-sjplot") (version "2.8.5") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 "07fwa6ga9430irk68g9wcfpn9g24pf8qc2i127nrydm865y7ri24")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) ("r-dplyr" ,r-dplyr) ("r-effectsize" ,r-effectsize) ("r-ggeffects" ,r-ggeffects) ("r-ggplot2" ,r-ggplot2) ("r-insight" ,r-insight) ("r-knitr" ,r-knitr) ("r-mass" ,r-mass) ("r-parameters" ,r-parameters) ("r-performance" ,r-performance) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-sjlabelled" ,r-sjlabelled) ("r-sjmisc" ,r-sjmisc) ("r-sjstats" ,r-sjstats) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://strengejacke.github.io/sjPlot/") (synopsis "Data visualization for statistics in social science") (description "This package represents a collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.") (license license:gpl3))) (define-public r-ini (package (name "r-ini") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "ini" version)) (sha256 (base32 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) (build-system r-build-system) (home-page "https://github.com/dvdscripter/ini") (synopsis "Read and write configuration files") (description "This package provides tools to parse simple @code{.ini} configuration files to an structured list. Users can manipulate this resulting list with @code{lapply()} functions. This same structured list can be used to write back to file after modifications.") (license license:gpl3))) (define-public r-gh (package (name "r-gh") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-httr" ,r-httr) ("r-ini" ,r-ini) ("r-jsonlite" ,r-jsonlite))) (home-page "https://github.com/r-lib/gh#readme") (synopsis "Access the GitHub API via R") (description "This package provides a minimal R client to access the GitHub API.") (license license:expat))) (define-public r-fs (package (name "r-fs") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://fs.r-lib.org") (synopsis "Cross-platform file system operations based on libuv") (description "This package provides a cross-platform interface to file system operations, built on top of the libuv C library.") (license license:gpl3))) (define-public r-clisymbols (package (name "r-clisymbols") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "clisymbols" version)) (sha256 (base32 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/clisymbols") (synopsis "Unicode symbols at the R prompt") (description "This package provides a small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode.") (license license:expat))) (define-public r-usethis (package (name "r-usethis") (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 "09lk04kycvf5x9ggrb6pwc7bx5mzqxwialm2w9vn1a0w0gh2gcfc")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-clipr" ,r-clipr) ("r-crayon" ,r-crayon) ("r-curl" ,r-curl) ("r-desc" ,r-desc) ("r-fs" ,r-fs) ("r-gh" ,r-gh) ("r-git2r" ,r-git2r) ("r-glue" ,r-glue) ("r-purrr" ,r-purrr) ("r-rematch2" ,r-rematch2) ("r-rlang" ,r-rlang) ("r-rprojroot" ,r-rprojroot) ("r-rstudioapi" ,r-rstudioapi) ("r-whisker" ,r-whisker) ("r-withr" ,r-withr) ("r-yaml" ,r-yaml))) (home-page "https://github.com/r-lib/usethis") (synopsis "Automate R package and project setup") (description "This package helps you to automate R package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, GitHub integration, licenses, Rcpp, RStudio projects, and more.") (license license:gpl3))) (define-public r-sessioninfo (package (name "r-sessioninfo") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "sessioninfo" version)) (sha256 (base32 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-withr" ,r-withr))) (home-page "https://github.com/r-lib/sessioninfo#readme") (synopsis "R session information") (description "This package provides tools to query and print information about the current R session. It is similar to @code{utils::sessionInfo()}, but includes more information about packages, and where they were installed from.") (license license:gpl2))) (define-public r-remotes (package (name "r-remotes") (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") (description "Download and install R packages stored in GitHub, BitBucket, or plain subversion or git repositories. This package is a lightweight replacement of the @code{install_*} functions in the @code{devtools} package. Indeed most of the code was copied over from @code{devtools}.") (license license:gpl2+))) (define-public r-xopen (package (name "r-xopen") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "xopen" version)) (sha256 (base32 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) (build-system r-build-system) (propagated-inputs `(("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/xopen#readme") (synopsis "Open system files, URLs, anything") (description "This package provides a cross-platform solution to open files, directories or URLs with their associated programs.") (license license:expat))) (define-public r-rcmdcheck (package (name "r-rcmdcheck") (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-desc" ,r-desc) ("r-digest" ,r-digest) ("r-pkgbuild" ,r-pkgbuild) ("r-prettyunits" ,r-prettyunits) ("r-r6" ,r-r6) ("r-rprojroot" ,r-rprojroot) ("r-sessioninfo" ,r-sessioninfo) ("r-withr" ,r-withr) ("r-xopen" ,r-xopen))) (home-page "https://github.com/r-Lib/rcmdcheck#readme") (synopsis "Run R CMD check from R and capture results") (description "Run @code{R CMD check} from R programmatically, and capture the results of the individual checks.") (license license:expat))) (define-public r-rapportools (package (name "r-rapportools") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "rapportools" version)) (sha256 (base32 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) (build-system r-build-system) (propagated-inputs `(("r-pander" ,r-pander) ("r-plyr" ,r-plyr) ("r-reshape" ,r-reshape))) (home-page "https://cran.r-project.org/web/packages/rapportools/") (synopsis "Miscellaneous helper functions with sane defaults for reporting") (description "This package provides helper functions that act as wrappers to more advanced statistical methods with the advantage of having sane defaults for quick reporting.") (license license:agpl3+))) (define-public r-pander (package (name "r-pander") (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "pander" version)) (sha256 (base32 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-rcpp" ,r-rcpp))) (home-page "https://rapporter.github.io/pander") (synopsis "Render R objects into Pandoc's markdown") (description "The main aim of the pander R package is to provide a minimal and easy tool for rendering R objects into Pandoc's markdown. The package is also capable of exporting/converting complex Pandoc documents (reports) in various ways.") ;; This package is licensed under either the AGPLv3+ or the very rarely ;; used OSL 3.0. (license license:agpl3+))) (define-public r-summarytools (package (name "r-summarytools") (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-checkmate" ,r-checkmate) ("r-dplyr" ,r-dplyr) ("r-htmltools" ,r-htmltools) ("r-lubridate" ,r-lubridate) ("r-magick" ,r-magick) ("r-matrixstats" ,r-matrixstats) ("r-pander" ,r-pander) ("r-pryr" ,r-pryr) ("r-rapportools" ,r-rapportools) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/dcomtois/summarytools") (synopsis "Tools to quickly and neatly summarize data") (description "This package provides tools for data frame summaries, cross-tabulations, weight-enabled frequency tables and common univariate statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.") (license license:gpl2))) (define-public r-lsei (package (name "r-lsei") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "lsei" version)) (sha256 (base32 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Solve regression problems under equality/inequality constraints") (description "It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving quadratic programming problems are also available, which transform such problems into least squares ones first.") (license license:gpl2+))) (define-public r-npsurv (package (name "r-npsurv") (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "npsurv" version)) (sha256 (base32 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw")))) (build-system r-build-system) (propagated-inputs `(("r-lsei" ,r-lsei))) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Nonparametric survival analysis") (description "This package contains functions for non-parametric survival analysis of exact and interval-censored observations.") (license license:gpl2+))) (define-public r-clusteval (package (name "r-clusteval") (version "0.1") (source (origin (method url-fetch) (uri (cran-uri "clusteval" version)) (sha256 (base32 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm) ("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/clusteval/") (synopsis "Evaluation of clustering algorithms") (description "This R package provides a suite of tools to evaluate clustering algorithms, clusterings, and individual clusters.") (license license:expat))) (define-public r-tweedie (package (name "r-tweedie") (version "2.3.2") (source (origin (method url-fetch) (uri (cran-uri "tweedie" version)) (sha256 (base32 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/tweedie/") (synopsis "Evaluation of Tweedie exponential family models") (description "Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; ) and the Fourier inversion (Dunn and Smyth, 2008; ), and related methods.") (license license:gpl2+))) (define-public r-rcppgsl (package (name "r-rcppgsl") (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-mvabund (package (name "r-mvabund") (version "4.1.3") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-rcppgsl" ,r-rcppgsl) ("r-statmod" ,r-statmod) ("r-tweedie" ,r-tweedie))) (home-page "https://cran.r-project.org/web/packages/mvabund/") (synopsis "Statistical methods for analysing multivariate abundance data") (description "This package provides a set of tools for displaying, modeling and analysing multivariate abundance data in community ecology.") (license license:lgpl2.1+))) (define-public r-afex (package (name "r-afex") (version "0.28-0") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 "0c47bq2llzw2b4avhkxyhmf1m2zjh9jsjiw2kww9n1bhwqsyr4ci")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) ("r-lme4" ,r-lme4) ("r-lmertest" ,r-lmertest) ("r-pbkrtest" ,r-pbkrtest) ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://afex.singmann.science/") (synopsis "Analysis of factorial experiments") (description "This package provides convenience functions for analyzing factorial experiments using ANOVA or mixed models.") (license license:gpl2+))) (define-public r-lmertest (package (name "r-lmertest") (version "3.1-2") (source (origin (method url-fetch) (uri (cran-uri "lmerTest" version)) (sha256 (base32 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-r2glmm (package (name "r-r2glmm") (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "r2glmm" version)) (sha256 (base32 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) (build-system r-build-system) (propagated-inputs `(("r-afex" ,r-afex) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-lmertest" ,r-lmertest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-mgcv" ,r-mgcv) ("r-pbkrtest" ,r-pbkrtest))) (home-page "https://github.com/bcjaeger/r2glmm") (synopsis "Compute R squared for mixed (multilevel) models") (description "This package computes model and semi partial R squared with confidence limits for the linear and generalized linear mixed model (LMM and GLMM). The R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et al. (2016)).") (license license:gpl2))) (define-public r-weights (package (name "r-weights") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "weights" version)) (sha256 (base32 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5")))) (build-system r-build-system) (propagated-inputs `(("r-gdata" ,r-gdata) ("r-hmisc" ,r-hmisc) ("r-mice" ,r-mice))) (home-page "https://cran.r-project.org/web/packages/weights/") (synopsis "Weighting and weighted statistics") (description "This package Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial correlations, Chi-Squared statistics, histograms, and t-tests. Also now includes some software for quickly recoding survey data and plotting point estimates from interaction terms in regressions (and multiply imputed regressions). NOTE: Weighted partial correlation calculations pulled to address a bug.") (license license:gpl2+))) (define-public r-rcppannoy (package (name "r-rcppannoy") (version "0.0.16") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") (description "Annoy is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from and save to disk. This package provides an R interface.") ;; Annoy is released under ASL 2.0, but this wrapper is released under ;; GPLv2+. (license (list license:gpl2+ license:asl2.0)))) (define-public r-rcpphnsw (package (name "r-rcpphnsw") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppHNSW" version)) (sha256 (base32 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") (description "Hnswlib is a C++ library for approximate nearest neighbors. This package provides a minimal R interface by relying on the Rcpp package.") ;; hnswlib is released under Version 2.0 of the Apache License. (license (list license:gpl3 license:asl2.0)))) (define-public r-rcppparallel (package (name "r-rcppparallel") (version "5.0.2") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc")))) (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.") (license license:gpl2))) (define-public r-ncdf4 (package (name "r-ncdf4") (version "1.17") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv")))) (build-system r-build-system) (inputs `(("netcdf" ,netcdf) ("zlib" ,zlib))) (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") (synopsis "R interface to Unidata netCDF format data files") (description "This package provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files.") (license license:gpl3+))) (define-public r-biocmanager (package (name "r-biocmanager") (version "1.30.10") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiocManager/") (synopsis "Access the Bioconductor project package repository") (description "This package provides a convenient tool to install and update Bioconductor packages.") (license license:artistic2.0))) (define-public r-rgl (package (name "r-rgl") (version "0.100.54") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("freetype" ,freetype) ("libpng" ,libpng) ("glu" ,glu) ("libx11" ,libx11) ("pandoc" ,pandoc) ("zlib" ,zlib))) (propagated-inputs `(("r-crosstalk" ,r-crosstalk) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) ("r-manipulatewidget" ,r-manipulatewidget) ("r-shiny" ,r-shiny))) (home-page "https://r-forge.r-project.org/projects/rgl/") (synopsis "3D visualization using OpenGL") (description "This package provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (@code{plot3d()}, etc.) as well as functions for constructing representations of geometric objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-multicool (package (name "r-multicool") (version "0.1-11") (source (origin (method url-fetch) (uri (cran-uri "multicool" version)) (sha256 (base32 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/multicool/") (synopsis "Permutations of multisets in cool-lex order") (description "This package provides a set of tools to permute multisets without loops or hash tables and to generate integer partitions. Cool-lex order is similar to colexicographical order.") (license license:gpl2))) (define-public r-misc3d (package (name "r-misc3d") (version "0.9-0") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/misc3d/") (synopsis "Miscellaneous 3D Plots") (description "This package provides a collection of miscellaneous 3d plots, including isosurfaces.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-ks (package (name "r-ks") (version "1.11.7") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba")))) (build-system r-build-system) (propagated-inputs `(("r-fnn" ,r-fnn) ("r-kernlab" ,r-kernlab) ("r-kernsmooth" ,r-kernsmooth) ("r-matrix" ,r-matrix) ("r-mclust" ,r-mclust) ("r-mgcv" ,r-mgcv) ("r-multicool" ,r-multicool) ("r-mvtnorm" ,r-mvtnorm))) (home-page "http://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description "This package provides kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-feature (package (name "r-feature") (version "1.2.13") (source (origin (method url-fetch) (uri (cran-uri "feature" version)) (sha256 (base32 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra")))) (build-system r-build-system) (propagated-inputs `(("r-ks" ,r-ks) ("r-misc3d" ,r-misc3d) ("r-rgl" ,r-rgl))) (home-page "http://www.mvstat.net/tduong/") (synopsis "Inferential feature significance for kernel density estimation") (description "The feature package contains functions to display and compute kernel density estimates, significant gradient and significant curvature regions. Significant gradient and/or curvature regions often correspond to significant features (e.g. local modes).") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-arm (package (name "r-arm") (version "1.11-2") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-coda" ,r-coda) ("r-hmisc" ,r-hmisc) ("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-nlme" ,r-nlme))) (home-page "https://cran.r-project.org/web/packages/arm/") (synopsis "Data analysis using regression and multilevel/hierarchical models") (description "This package provides functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.") (license license:gpl3+))) (define-public r-circular (package (name "r-circular") (version "0.4-93") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-mvtnorm" ,r-mvtnorm))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/circular/") (synopsis "Circular statistics") (description "This package provides tools for circular statistics, from \"Topics in circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.") (license license:gpl2+))) (define-public r-activity (package (name "r-activity") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92")))) (build-system r-build-system) (propagated-inputs `(("r-circular" ,r-circular) ("r-insol" ,r-insol) ("r-pbapply" ,r-pbapply))) (home-page "https://cran.r-project.org/web/packages/activity/") (synopsis "Animal activity statistics") (description "This package provides functions to fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; and evaluate variation in linear variables with time (or other circular variables).") (license license:gpl3))) (define-public r-ouch (package (name "r-ouch") (version "2.14-1") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b")))) (build-system r-build-system) (propagated-inputs `(("r-subplex" ,r-subplex))) (home-page "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 "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45")))) (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.") (license license:gpl2+))) (define-public r-gsl (package (name "r-gsl") (version "2.1-6") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) (home-page "https://cran.r-project.org/web/packages/gsl") (synopsis "Wrapper for the GNU Scientific Library") (description "This package provides an R wrapper for the special functions and quasi random number generators of the GNU Scientific Library.") (license license:gpl2+))) (define-public r-adgoftest (package (name "r-adgoftest") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ADGofTest" version)) (sha256 (base32 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) (properties `((upstream-name . "ADGofTest"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ADGofTest") (synopsis "Anderson-Darling GoF test") (description "This package provides an implementation of the Anderson-Darling GoF test with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the Anderson-Darling Distribution\".") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-softimpute (package (name "r-softimpute") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "softImpute" version)) (sha256 (base32 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq")))) (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/softImpute") (synopsis "Matrix completion via iterative soft-thresholded SVD") (description "This package provides iterative methods for matrix completion that use nuclear-norm regularization. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank @dfn{single value decompositions} (SVDs) on large sparse centered matrices (i.e. principal components).") (license license:gpl2))) (define-public r-fftwtools (package (name "r-fftwtools") (version "0.9-9") (source (origin (method url-fetch) (uri (cran-uri "fftwtools" version)) (sha256 (base32 "0h8lyl2i6zq16ir7xnfj9dhyivxvwikm8lml19s8s8jx95z3n9x9")))) (build-system r-build-system) (inputs `(("fftw" ,fftw))) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description "This package provides a wrapper for several FFTW functions. It provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using the FFTW3 library. The package includes the functions @code{fftw()} and @code{mvfftw()} which are designed to mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. The FFT functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.") (license license:gpl2+))) (define-public r-tiff (package (name "r-tiff") (version "0.1-5") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) (build-system r-build-system) (inputs `(("libtiff" ,libtiff) ("libjpeg" ,libjpeg-turbo) ("zlib" ,zlib))) (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 "0.2-0") (source (origin (method url-fetch) (uri (cran-uri "NLP" version)) (sha256 (base32 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w")))) (properties `((upstream-name . "NLP"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/NLP/") (synopsis "Natural language processing infrastructure") (description "This package provides basic classes and methods for Natural Language Processing.") (license license:gpl3))) (define-public r-tm (package (name "r-tm") (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-nlp" ,r-nlp) ("r-rcpp" ,r-rcpp) ("r-slam" ,r-slam) ("r-xml2" ,r-xml2))) (home-page "http://tm.r-forge.r-project.org/") (synopsis "Text mining package") (description "This package provides a framework for text mining applications within R.") (license license:gpl3))) (define-public r-waveslim (package (name "r-waveslim") (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "waveslim" version)) (sha256 (base32 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://waveslim.blogspot.com") (synopsis "Basic wavelet routines for signal processing") (description "This package provides basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).") (license license:bsd-3))) (define-public r-wordcloud (package (name "r-wordcloud") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "wordcloud" version)) (sha256 (base32 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) (build-system r-build-system) (propagated-inputs `(("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ;; The "tm" package is only "suggested" according to CRAN, but the ;; wordcloud package cannot be loaded without it. ("r-tm" ,r-tm))) (home-page "https://cran.r-project.org/web/packages/wordcloud") (synopsis "Word clouds") (description "This package provides functionality to create pretty word clouds, visualize differences and similarity between documents, and avoid over-plotting in scatter plots with text.") (license license:lgpl2.1))) (define-public r-colorramps (package (name "r-colorramps") (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "colorRamps" version)) (sha256 (base32 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z")))) (properties `((upstream-name . "colorRamps"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/colorRamps") (synopsis "Build color tables") (description "This package provides features to build gradient color maps.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-tidytree (package (name "r-tidytree") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) ("r-dplyr" ,r-dplyr) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/tidytree") (synopsis "Tidy tool for phylogenetic tree data manipulation") (description "Phylogenetic trees generally contain multiple components including nodes, edges, branches and associated data. This package provides an approach to convert tree objects to tidy data frames. It also provides tidy interfaces to manipulate tree data.") (license license:artistic2.0))) (define-public r-rvcheck (package (name "r-rvcheck") (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac")))) (build-system r-build-system) (propagated-inputs `(("r-biocmanager" ,r-biocmanager) ("r-rlang" ,r-rlang))) (home-page "https://cran.r-project.org/web/packages/rvcheck") (synopsis "R package version check") (description "This package provides tools to check the latest release version of R and R packages (on CRAN, Bioconductor or Github).") (license license:artistic2.0))) (define-public r-docopt (package (name "r-docopt") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "docopt" version)) (sha256 (base32 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz")))) (build-system r-build-system) (home-page "https://github.com/docopt/docopt.R") (synopsis "Command-line interface specification language") (description "This package enables you to define a command-line interface by just giving it a description in the specific format.") (license license:expat))) (define-public r-sparsesvd (package (name "r-sparsesvd") (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "sparsesvd" version)) (sha256 (base32 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") (synopsis "Sparse truncated singular value decomposition") (description "This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported.") ;; SVDLIBC is released under BSD-2. The R interface is released under ;; BSD-3. (license (list license:bsd-3 license:bsd-2)))) (define-public r-speedglm (package (name "r-speedglm") (version "0.3-2") (source (origin (method url-fetch) (uri (cran-uri "speedglm" version)) (sha256 (base32 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-matrix" ,r-matrix))) (home-page "https://cran.r-project.org/web/packages/speedglm") (synopsis "Fit linear and generalized linear models to large data sets") (description "This package provides tools for fitting linear models and generalized linear models to large data sets by updating algorithms.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-densityclust (package (name "r-densityclust") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "densityClust" version)) (sha256 (base32 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13")))) (properties `((upstream-name . "densityClust"))) (build-system r-build-system) (propagated-inputs `(("r-fnn" ,r-fnn) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gridextra" ,r-gridextra) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rtsne" ,r-rtsne))) (home-page "https://cran.r-project.org/web/packages/densityClust") (synopsis "Clustering by fast search and find of density peaks") (description "This package provides an improved implementation (based on k-nearest neighbors) of the density peak clustering algorithm, originally described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle large datasets (> 100,000 samples) very efficiently.") (license license:gpl2+))) (define-public r-combinat (package (name "r-combinat") (version "0.0-8") (source (origin (method url-fetch) (uri (cran-uri "combinat" version)) (sha256 (base32 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/combinat") (synopsis "Combinatorics utilities") (description "This package provides assorted routines for combinatorics.") (license license:gpl2))) (define-public r-qlcmatrix (package (name "r-qlcmatrix") (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "qlcMatrix" version)) (sha256 (base32 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) (properties `((upstream-name . "qlcMatrix"))) (build-system r-build-system) (propagated-inputs `(("r-docopt" ,r-docopt) ("r-matrix" ,r-matrix) ("r-slam" ,r-slam) ("r-sparsesvd" ,r-sparsesvd))) (home-page "https://cran.r-project.org/web/packages/qlcMatrix") (synopsis "Sparse matrix functions for quantitative language comparison") (description "This package provides an extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for the special data format used for @dfn{quantitative language comparison} (QLC).") (license license:gpl3))) (define-public r-ddrtree (package (name "r-ddrtree") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "DDRTree" version)) (sha256 (base32 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) (properties `((upstream-name . "DDRTree"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-irlba" ,r-irlba) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen))) (home-page "https://cran.r-project.org/web/packages/DDRTree") (synopsis "Learning principal graphs with DDRTree") (description "This package provides an implementation of the framework of @dfn{reversed graph embedding} (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of the data simultaneously. DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the ordering as well as the intrinsic structure of single cell genomics data. In general, it could be used to reconstruct the temporal progression as well as the bifurcation structure of any data type.") (license license:asl2.0))) (define-public r-corpcor (package (name "r-corpcor") (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "corpcor" version)) (sha256 (base32 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf")))) (build-system r-build-system) (home-page "http://strimmerlab.org/software/corpcor/") (synopsis "Efficient estimation of covariance and (partial) correlation") (description "This package implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.") (license license:gpl3+))) (define-public r-rspectra (package (name "r-rspectra") (version "0.16-0") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen))) (home-page "https://github.com/yixuan/RSpectra") (synopsis "Solvers for large-scale Eigenvalue and SVD problems") (description "This package provides an R interface to the Spectra library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than @code{eigen()} if k << n.") ;; MPL 2 or later. (license license:mpl2.0))) (define-public r-vbsr (package (name "r-vbsr") (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "vbsr" version)) (sha256 (base32 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/vbsr") (synopsis "Variational Bayes spike regression regularized linear models") (description "This package provides an efficient algorithm for solving ultra-sparse regularized regression models using a variational Bayes algorithm with a spike prior. The algorithm is solved on a path, with coordinate updates, and is capable of generating very sparse models. Very general model diagnostics for controlling type-1 errors are also provided.") (license license:gpl2))) (define-public r-flare (package (name "r-flare") (version "1.6.0.2") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix))) (home-page "https://cran.r-project.org/web/packages/flare") (synopsis "Family of Lasso regression implementations") (description "This package provides implementations of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear models.") (license license:gpl2))) (define-public r-lassopv (package (name "r-lassopv") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "lassopv" version)) (sha256 (base32 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) (build-system r-build-system) (propagated-inputs `(("r-lars" ,r-lars))) (home-page "https://github.com/lingfeiwang/lassopv") (synopsis "Non-parametric p-value estimation for predictors in Lasso") (description "This package enables you to estimate the p-values for predictors x against target variable y in Lasso regression, using the regularization strength when each predictor enters the active set of regularization path for the first time as the statistic.") (license license:gpl3))) (define-public r-splitstackshape (package (name "r-splitstackshape") (version "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "splitstackshape" version)) (sha256 (base32 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table))) (home-page "https://github.com/mrdwab/splitstackshape") (synopsis "Stack and reshape datasets after splitting concatenated values") (description "Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The @code{concat.split} (cSplit) family of functions provided by this package splits such data into separate cells. This package also includes functions to stack groups of columns and to reshape wide data, even when the data are \"unbalanced\"---something which @code{reshape} (from base R) does not handle, and which @code{melt} and @code{dcast} from @code{reshape2} do not easily handle.") (license license:gpl3))) (define-public r-tfmpvalue (package (name "r-tfmpvalue") (version "0.0.8") (source (origin (method url-fetch) (uri (cran-uri "TFMPvalue" version)) (sha256 (base32 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/ge11232002/TFMPvalue") (synopsis "P-value computation for position weight matrices") (description "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match scores. TFMPvalue provides the accurate calculation of a p-value with a score threshold for position weight matrices, or the score with a given p-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) (define-public r-rnifti (package (name "r-rnifti") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 "0h837jdspy071ckij8szqd8149bm113jpqwbclg87is4brsm5jzg")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/jonclayden/RNifti") (synopsis "Fast R and C++ access to NIfTI images") (description "This package provides very fast read and write access to images stored in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. It also provides a C/C++ API that can be used by other packages.") (license license:gpl2))) (define-public r-shades (package (name "r-shades") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "shades" version)) (sha256 (base32 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/shades") (synopsis "Simple color manipulation") (description "This package provides functions for easily manipulating colors, creating color scales and calculating color distances.") (license license:bsd-3))) (define-public r-ore (package (name "r-ore") (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") (description "This package provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.") (license license:bsd-3))) (define-public r-reportr (package (name "r-reportr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "reportr" version)) (sha256 (base32 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) (build-system r-build-system) (propagated-inputs `(("r-ore" ,r-ore))) (home-page "https://github.com/jonclayden/reportr") (synopsis "General message and error reporting system") (description "This package provides a system for reporting messages, which offers certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current \"output level\".") (license license:gpl2))) (define-public r-tractor-base (package (name "r-tractor-base") (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i")))) (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs `(("r-ore" ,r-ore) ("r-reportr" ,r-reportr) ("r-rnifti" ,r-rnifti) ("r-shades" ,r-shades))) (home-page "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 "0.9-3") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs `(("ghostscript" ,ghostscript))) (propagated-inputs `(("r-xml" ,r-xml))) (home-page "https://cran.r-project.org/web/packages/grImport") (synopsis "Convert, import, and draw PostScript pictures") (description "This package provides functions for converting, importing, and drawing PostScript pictures in R plots.") (license license:gpl2+))) (define-public r-grimport2 (package (name "r-grimport2") (version "0.2-0") (source (origin (method url-fetch) (uri (cran-uri "grImport2" version)) (sha256 (base32 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1")))) (properties `((upstream-name . "grImport2"))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-jpeg" ,r-jpeg) ("r-png" ,r-png) ("r-xml" ,r-xml))) (home-page "https://cran.r-project.org/web/packages/grImport2/") (synopsis "Import SVG graphics") (description "This package provides functions for importing external vector images and drawing them as part of R plots. This package is different from the @code{grImport} package because, where that package imports PostScript format images, this package imports SVG format images. Furthermore, this package imports a specific subset of SVG, so external images must be preprocessed using a package like @code{rsvg} to produce SVG that this package can import. SVG features that are not supported by R graphics, such as gradient fills, can be imported and then exported via the @code{gridSVG} package.") (license license:gpl2+))) (define-public r-kohonen (package (name "r-kohonen") (version "3.0.10") (source (origin (method url-fetch) (uri (cran-uri "kohonen" version)) (sha256 (base32 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/kohonen") (synopsis "Supervised and unsupervised self-organising maps") (description "This package provides functions to train @dfn{self-organising maps} (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.") (license license:gpl2+))) (define-public r-nnls (package (name "r-nnls") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/nnls") (synopsis "Lawson-Hanson algorithm for non-negative least squares") (description "This package provides an R interface to the Lawson-Hanson implementation of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows the combination of non-negative and non-positive constraints.") (license license:gpl2+))) (define-public r-iso (package (name "r-iso") (version "0.0-18.1") (source (origin (method url-fetch) (uri (cran-uri "Iso" version)) (sha256 (base32 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g")))) (properties `((upstream-name . "Iso"))) (build-system r-build-system) (native-inputs `(("gfortran" ,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 `(("r-devtools" ,r-devtools) ("r-kohonen" ,r-kohonen) ("r-mass" ,r-mass) ("r-pls" ,r-pls))) (home-page "https://github.com/rwehrens/CWR") (synopsis "Chemometrics with R") (description "This package provides functions and scripts used in the book \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences\" by Ron Wehrens, Springer (2011).") (license license:gpl2+))) (define-public r-als (package (name "r-als") (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "ALS" version)) (sha256 (base32 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) (properties `((upstream-name . "ALS"))) (build-system r-build-system) (propagated-inputs `(("r-iso" ,r-iso) ("r-nnls" ,r-nnls))) (home-page "https://cran.r-project.org/web/packages/ALS") (synopsis "Multivariate curve resolution alternating least squares") (description "Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. This package provides an implementation of @dfn{multivariate curve resolution alternating least squares} (MCR-ALS). Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.") (license license:gpl2+))) (define-public r-strucchange (package (name "r-strucchange") (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "strucchange" version)) (sha256 (base32 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x")))) (build-system r-build-system) (propagated-inputs `(("r-sandwich" ,r-sandwich) ("r-zoo" ,r-zoo))) (home-page "https://cran.r-project.org/web/packages/strucchange") (synopsis "Testing, monitoring, and dating structural changes") (description "This package provides tools for testing, monitoring and dating structural changes in (linear) regression models. It features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F statistics, respectively. It is possible to monitor incoming data online using fluctuation processes. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data.") ;; Either of these two GPL versions (license (list license:gpl2 license:gpl3)))) (define-public r-pixmap (package (name "r-pixmap") (version "0.4-11") (source (origin (method url-fetch) (uri (cran-uri "pixmap" version)) (sha256 (base32 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pixmap") (synopsis "Tools for bitmap images") (description "This package provides functions for importing, exporting, plotting and other manipulations of bitmapped images.") (license license:gpl2))) (define-public r-rapidjsonr (package (name "r-rapidjsonr") (version "1.2.0") (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 "2.5") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ontologyIndex") (synopsis "Functions for processing ontologies in R") (description "This package provides functions for reading ontologies into R as lists and manipulating sets of ontological terms.") (license license:gpl2+))) (define-public r-gargle (package (name "r-gargle") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n")))) (build-system r-build-system) (propagated-inputs `(("r-fs" ,r-fs) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-rlang" ,r-rlang) ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://gargle.r-lib.org") (synopsis "Utilities for working with Google APIs") (description "This package provides utilities for working with Google APIs. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.") (license license:expat))) (define-public r-bigrquery (package (name "r-bigrquery") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "bigrquery" version)) (sha256 (base32 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-bit64" ,r-bit64) ("r-curl" ,r-curl) ("r-dbi" ,r-dbi) ("r-gargle" ,r-gargle) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-prettyunits" ,r-prettyunits) ("r-progress" ,r-progress) ("r-rapidjsonr" ,r-rapidjsonr) ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble))) (home-page "https://github.com/rstats-db/bigrquery") (synopsis "R interface to Google's BigQuery API") (description "This package provides an R interface to Google's BigQuery database.") (license license:gpl3))) (define-public r-gmp (package (name "r-gmp") (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 "11rl7qmfrpp1974f0vzsi3zjyx147wlb82ydxak2b60khfvhrn90")))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-CC (lambda _ (setenv "CC" "gcc") #t))))) (inputs `(("gmp" ,gmp))) (home-page "https://cran.r-project.org/web/packages/gmp") (synopsis "Multiple precision arithmetic") (description "This package supports multiple precision arithmetic (big integers and rationals, prime number tests, matrix computation), \"arithmetic without limitations\" using the GNU Multiple Precision library.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-rmpfr (package (name "r-rmpfr") (version "0.8-1") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs `(("mpfr" ,mpfr) ("gmp" ,gmp))) (propagated-inputs `(("r-gmp" ,r-gmp))) (native-inputs `(("pkg-config" ,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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"assertive.properties"))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,r-assertive-base))) (home-page "https://bitbucket.org/richierocks/assertive.properties") (synopsis "Assertions to check properties of variables") (description "This package provides a set of predicates and assertions for checking the properties of variables, such as length, names and attributes. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-numbers (package (name "r-assertive-numbers") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.numbers" version)) (sha256 (base32 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds")))) (properties `((upstream-name . 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"assertive.sets"))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,r-assertive-base))) (home-page "https://bitbucket.org/richierocks/assertive.sets") (synopsis "Assertions to check properties of sets") (description "This package provides a set of predicates and assertions for checking the properties of sets. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-matrices (package (name "r-assertive-matrices") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.matrices" version)) (sha256 (base32 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil")))) (properties `((upstream-name . "assertive.matrices"))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,r-assertive-base))) (home-page "https://bitbucket.org/richierocks/assertive.matrices") (synopsis "Assertions to check properties of matrices") (description "This package provides a set of predicates and assertions for checking the properties of matrices. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-models (package (name "r-assertive-models") (version "0.0-2") (source (origin (method url-fetch) (uri (cran-uri "assertive.models" version)) (sha256 (base32 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr")))) (properties `((upstream-name . 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"assertive.datetimes"))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,r-assertive-base) ("r-assertive-types" ,r-assertive-types))) (home-page "https://bitbucket.org/richierocks/assertive.datetimes") (synopsis "Assertions to check properties of dates and times") (description "This package provides a set of predicates and assertions for checking the properties of dates and times. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) (define-public r-assertive-strings (package (name "r-assertive-strings") (version "0.0-3") (source (origin (method url-fetch) (uri (cran-uri "assertive.strings" version)) (sha256 (base32 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-timeseries (package (name "r-timeseries") (version "4032.109") (source (origin (method url-fetch) (uri (cran-uri "timeSeries" version)) (sha256 (base32 "07vkppp9azbrn0lv1xhi4s3vpy4mglhysp7d250fl08b9rc4f32y")))) (properties `((upstream-name . "timeSeries"))) (build-system r-build-system) (propagated-inputs (list r-timedate)) (home-page "https://r-forge.r-project.org/scm/viewvc.php/pkg/timeSeries/?root=rmetrics") (synopsis "Metrics for financial time series objects") (description "This package implements S4 classes and various tools for financial time series. Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions are provided.") (license license:gpl2+))) (define-public r-tsp (package (name "r-tsp") (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 "1263ay3dar2mzm89nf31gl7n8d983qjiy4qwz7sgv8vwkbz0pg9h")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) (home-page "https://cran.r-project.org/web/packages/TSP/") (synopsis "Traveling salesperson problem (TSP)") (description "This package provides basic infrastructure and some algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the traveling salesman problem).") (license license:gpl3))) (define-public r-qap (package (name "r-qap") (version "0.1-2") (source (origin (method url-fetch) (uri (cran-uri "qap" version)) (sha256 (base32 "19adb1bw46pcnmmhqz2jklr0vmma3llxajqp0j9mqfksmsisv927")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic assignment problem} (QAP). Currently only a simulated annealing heuristic is available.") (license license:gpl3))) (define-public r-gclus (package (name "r-gclus") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "gclus" version)) (sha256 (base32 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/gclus/") (synopsis "Clustering graphics") (description "This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices of merit, ordering functions, and enhanced versions of @code{pairs} and @code{parcoord} which color panels according to their merit level.") (license license:gpl2+))) (define-public r-webchem (package (name "r-webchem") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "webchem" version)) (sha256 (base32 "06b9i9jipg564zyw4gkgiidz7501rlp40hxm4z3k5mzy148lr5vq")))) (properties `((upstream-name . "webchem"))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-data-tree r-dplyr r-httr r-jsonlite r-purrr r-rlang r-rvest r-stringr r-tibble r-xml2)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/webchem/") (synopsis "Chemical information from the web") (description "This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.") (license license:expat))) (define-public r-webshot (package (name "r-webshot") (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 "04xrrf72323sgzsdkbl05p2fdsi486i9avrrxvw0l3n8r8y92xfn")))) (build-system r-build-system) (propagated-inputs (list r-callr r-jsonlite r-magrittr)) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description "Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and screenshot static as well as interactive R Markdown documents.") (license license:gpl2))) (define-public r-seriation (package (name "r-seriation") (version "1.5.6") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 "1a69sxzy6m5kykdr6gcmjqdh50ld0mbl94hi2gb9jcggp3g0d1yz")))) (build-system r-build-system) (propagated-inputs (list r-ca r-cluster r-colorspace r-foreach r-gclus r-mass r-qap r-registry r-tsp r-vegan)) (native-inputs (list gfortran)) (home-page "https://s2.smu.edu/IDA/seriation/") (synopsis "Infrastructure for ordering objects using seriation") (description "This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).") (license license:gpl3))) (define-public r-xfun (package (name "r-xfun") (version "0.47") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 "0jrc4g799nhyra8n202107mx7h42yzz4n4yblf3fdwjdpzyp964r")))) (build-system r-build-system) (properties ;; knitr itself depends on xfun '((updater-ignored-native-inputs . ("r-knitr")))) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") (description "This package provides miscellaneous functions commonly used in other packages maintained by Yihui Xie.") (license license:expat))) (define-public r-utf8 (package (name "r-utf8") (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 "0zbv2s5dkzxim3ydyk12479m28f68mak9m50v396in4wpm5q53s1")))) (build-system r-build-system) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description "This package provides tools to process and print UTF-8 encoded international text (Unicode). Input, validate, normalize, encode, format, and display.") (license license:asl2.0))) (define-public r-zeallot (package (name "r-zeallot") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "zeallot" version)) (sha256 (base32 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3")))) (build-system r-build-system) (home-page "https://github.com/nteetor/zeallot") (synopsis "Multiple, unpacking, and destructuring assignment") (description "This package provides a @code{%<-%} operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.") (license license:expat))) (define-public r-zlog (package (name "r-zlog") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "zlog" version)) (sha256 (base32 "0fi9aqrmikdg5ibwhn82kslj4lxih03vm27jmi14m73h09yy4in5")))) (properties `((upstream-name . "zlog"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zlog") (synopsis "Transformation for laboratory easurements") (description "The @code{zlog} package offers functions to transform laboratory measurements into standardised z or @math{z(log)-values}. Therefore the lower and upper reference limits are needed. If these are not known they could be estimated from a given sample.") (license license:gpl3+))) (define-public r-vctrs (package (name "r-vctrs") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 "00p4r1z4xc05m25y0qa7svr67lbypcfqyp2b0ja9asgx90i7s5j3")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) (properties ;; We can't have r-knitr among the inputs here, because r-vctrs ends up ;; being an eventual input to r-knitr. '((updater-ignored-native-inputs . ("r-knitr")))) (home-page "https://github.com/r-lib/vctrs") (synopsis "Vector helpers") (description "There are three main goals to the @code{vctrs} package: @enumerate @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to @code{length()} and @code{class()}. These definitions are paired with a framework for type-coercion and size-recycling. @item To define type- and size-stability as desirable function properties, use them to analyse existing base function, and to propose better alternatives. This work has been particularly motivated by thinking about the ideal properties of @code{c()}, @code{ifelse()}, and @code{rbind()}. @item To provide a new @code{vctr} base class that makes it easy to create new S3 vectors. @code{vctrs} provides methods for many base generics in terms of a few new @code{vctrs} generics, making implementation considerably simpler and more robust. @end enumerate\n") (license license:gpl3))) (define-public r-pillar (package (name "r-pillar") (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 "1k3sp37dpn46d2xbq621alpvzgnm06x5qb87nk169y47q23b8gpj")))) (build-system r-build-system) (propagated-inputs (list r-cli r-fansi r-glue r-lifecycle r-rlang r-utf8 r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description "This package provides a @code{pillar} generic designed for formatting columns of data using the full range of colours provided by modern terminals.") (license license:gpl3))) (define-public r-pinfsc50 (package (name "r-pinfsc50") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "pinfsc50" version)) (sha256 (base32 "1gs9x328qqvqwx3k4z9jgzq5zb6g8kdz4430n96v7zb78p7jf5lp")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pinfsc50/") (synopsis "Genomic data for the plant pathogen Phytophthora infestans") (description "This package contains genomic data for the plant pathogen Phytophthora infestans. It includes a variant file, a sequence file and an annotation file. This package is intended to be used as example data for packages that work with genomic data.") (license license:gpl2+))) (define-public r-piton (package (name "r-piton") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "piton" version)) (sha256 (base32 "1krf6zi238m275nxjlpyayv8y2drbgs2kg19dpkqm0lmlz5y5ar8")))) (properties `((upstream-name . "piton"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/Ironholds/piton") (synopsis "Parsing expression grammars in Rcpp") (description "This package provides a wrapper around the Parsing Expression Grammar Template Library, a C++11 library for generating parsing expression grammars, that makes it accessible within Rcpp. With this, developers can implement their own grammars and easily expose them in R packages.") (license license:expat))) (define-public r-uuid (package (name "r-uuid") (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 "15jbzj0i4qphakbi8s9yk55lm8z9s2vhgp5bj77sfvkx7mrlj3pr")))) (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-tinylabels (package (name "r-tinylabels") (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "tinylabels" version)) (sha256 (base32 "01pvnirma3wzfqnnz8zvyqajjyysjm3sd6813bgdhz199lcg7hhz")))) (properties `((upstream-name . "tinylabels"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/mariusbarth/tinylabels") (synopsis "Lightweight variable labels") (description "This package lets you assign, extract, or remove variable labels from R vectors.") (license license:expat))) (define-public r-tinytex (package (name "r-tinytex") (version "0.52") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 "0fji3yca7qpxpzdd8hy55v0g40jny41qvhz8d64gwlnxkwxp2alk")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description "This package provides helper functions to install and maintain the LaTeX distribution named TinyTeX, a lightweight, cross-platform, portable, and easy-to-maintain version of TeX Live. This package also contains helper functions to compile LaTeX documents, and install missing LaTeX packages automatically.") (license license:expat))) (define-public r-tinytest (package (name "r-tinytest") (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "tinytest" version)) (sha256 (base32 "0x0w1fiqd98vmpz8yrp9ig0ry1wfr16g6bkjzd2a8sq9gn417z7n")))) (properties `((upstream-name . "tinytest"))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/tinytest") (synopsis "Lightweight unit testing framework") (description "This package provides a lightweight unit testing framework. Main features: @enumerate @item install tests with the package; @item test results are treated as data that can be stored and manipulated; @item test files are R scripts interspersed with test commands, that can be programmed over; @item fully automated build-install-test sequence for packages; @item skip tests when not run locally (e.g. on CRAN); @item flexible and configurable output printing; @item compare computed output with output stored with the package; @item run tests in parallel; @item extensible by other packages; @item report side effects. @end enumerate ") (license license:gpl3))) (define-public r-n2r (package (name "r-n2r") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "N2R" version)) (sha256 (base32 "0bbxl0y36bmsxwi4rs4f6jwhf9bhag2rkvvzcg5669vgm2p4scjr")))) (properties `((upstream-name . 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"nestedcv"))) (build-system r-build-system) (propagated-inputs (list r-caret r-data-table r-doparallel r-foreach r-ggplot2 r-glmnet r-matrixstats r-matrixtests r-proc r-rfast r-rhpcblasctl r-rlang r-rocr)) (native-inputs (list r-knitr)) (home-page "https://github.com/myles-lewis/nestedcv") (synopsis "Nested cross-validation with glmnet and caret") (description "This package implements nested cross-validation applied to the @code{glmnet} and @code{caret} packages. With glmnet this includes cross-validation of elastic net alpha parameter. A number of feature selection filter functions (t-test, Wilcoxon test, ANOVA, Pearson/Spearman correlation, random forest, ReliefF) for feature selection are provided and can be embedded within the outer loop of the nested CV. Nested CV can be also be performed with the @code{caret} package giving access to the large number of prediction methods available in @code{caret}.") (license license:expat))) (define-public r-network (package (name "r-network") (version "1.18.2") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 "0yx20v3izm7037cx5swc19966z97w7q9xw4p2p6skfyap4nqjcxz")))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-statnet-common r-tibble)) (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description "This package provides tools to create and modify network objects. The @code{network} class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) (define-public r-nistunits (package (name "r-nistunits") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "NISTunits" version)) (sha256 (base32 "0km9l3k9p35sb1qrhrz4ijjsdihvsp6j7cz5kh46lgf7nn6xdk7a")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-stabs (package (name "r-stabs") (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "stabs" version)) (sha256 (base32 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/hofnerb/stabs") (synopsis "Stability selection with error control") (description "This package provides resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting. Both, standard stability selection (Meinshausen & Buhlmann, 2010) and complementary pairs stability selection with improved error bounds (Shah & Samworth, 2013) are implemented. The package can be combined with arbitrary user specified variable selection approaches.") (license license:gpl2))) (define-public r-rle (package (name "r-rle") (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "rle" version)) (sha256 (base32 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40")))) (properties `((upstream-name . "rle"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rle/") (synopsis "Common functions for run-length encoded vectors") (description "This package provides common @code{base} and @code{stats} methods for @code{rle} objects, aiming to make it possible to treat them transparently as vectors.") (license license:gpl3))) (define-public r-statnet-common (package (name "r-statnet-common") (version "4.9.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 "1mrdzhxxrr6a0hwxczs40f8ppkdimlki1gbg6f3kv69s6rpdr1d4")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-statcheck (package (name "r-statcheck") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "statcheck" version)) (sha256 (base32 "0gsr068if5k8124x1cbm48720l9qvnfmdg6rmh7rwh6jvxxgknd7")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr r-rlang r-rmarkdown r-stringi)) (home-page "https://cran.r-project.org/web/packages/statcheck/") (synopsis "Extract statistics from articles and recompute p-values") (description "This package can automatically extract statistical null-hypothesis significant testing (NHST) results from articles and recompute the p-values based on the reported test statistic and degrees of freedom to detect possible inconsistencies.") (license license:gpl2))) (define-public r-sna (package (name "r-sna") (version "2.7-2") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 "1kd7qxdc8wy8d385yddj6rs0xc6lkn8hpra3wy4r7svzjqk4c8bv")))) (build-system r-build-system) (propagated-inputs (list r-network r-statnet-common)) (home-page "https://statnet.org") (synopsis "Tools for social network analysis") (description "This package provides a range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.") (license license:gpl2+))) (define-public r-tfisher (package (name "r-tfisher") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "TFisher" version)) (sha256 (base32 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx")))) (properties `((upstream-name . 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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 "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 "1crdm7avxv3zx59byz2fqbcw95728crwf9cckjb9gal1065xv95c")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-colorspace r-dendextend r-egg r-ggplot2 r-htmlwidgets r-magrittr r-plotly r-rcolorbrewer r-reshape2 r-scales r-seriation r-viridis r-webshot)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=heatmaply") (synopsis "Interactive cluster heat maps using plotly") (description "This package enables you to create interactive cluster heatmaps that can be saved as a stand-alone HTML file, embedded in R Markdown documents or in a Shiny app, and made available in the RStudio viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A heatmap is a popular graphical method for visualizing high-dimensional data, in which a table of numbers is encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by dendrograms.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-h5 (package (name "r-h5") (version "0.9.9") (source (origin (method url-fetch) (uri (cran-uri "h5" version)) (sha256 (base32 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs (list zlib hdf5)) (native-inputs (list which)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/mannau/h5") (synopsis "Interface to the HDF5 Library") (description "This package provides an S4 interface to the HDF5 library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The HDF5 format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.") (license license:bsd-2))) (define-public r-cgdsr (package (name "r-cgdsr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "cgdsr" version)) (sha256 (base32 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) (build-system r-build-system) (propagated-inputs (list r-httr r-r-methodss3 r-r-oo)) (home-page "https://github.com/cBioPortal/cgdsr") (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") (description "This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).") (license license:lgpl3))) (define-public r-cqrreg (package (name "r-cqrreg") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "cqrReg" version)) (sha256 (base32 "1788hnm1qd5mv5bcizz2h170jg6954sfggjnfqcwfwg167px0df2")))) (properties `((upstream-name . "cqrReg"))) (build-system r-build-system) (propagated-inputs (list r-quantreg r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/package=cqrReg") (synopsis "Quantile, composite quantile regression and regularized versions") (description "Estimate @dfn{quantile regression} (QR) and @dfn{composite quantile regression} (cqr) and with adaptive lasso penalty using @dfn{interior point} (IP), @dfn{majorize and minimize} (MM), @dfn{coordinate descent} (CD), and @dfn{alternating direction method of multipliers algorithms} (ADMM).") (license license:gpl2+))) (define-public r-imifa (package (name "r-imifa") (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "IMIFA" version)) (sha256 (base32 "08h53w1axvmvnd4z1nf5bsps5sr6g8a77q6pvg39ss7jcfqm800v")))) (properties `((upstream-name . "IMIFA"))) (build-system r-build-system) (propagated-inputs (list r-matrixstats r-mvnfast r-mclust r-rfast r-slam r-viridislite)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=IMIFA") (synopsis "Infinite mixtures of infinite factor analysers and related models") (description "This package provides flexible Bayesian estimation of @acronym{IMIFA, infinite mixtures of infinite factor analysers} and related models, for nonparametrically clustering high-dimensional data. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.") (license license:gpl3+))) (define-public r-import (package (name "r-import") (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "import" version)) (sha256 (base32 "0ngakg8jqn76c05hrglp4hmmwvm5a9ldc9s1i83a9rc8lni6nb1j")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/smbache/import") (synopsis "Import mechanism for R") (description "This is an alternative mechanism for importing objects from packages. The syntax allows for importing multiple objects from a package with a single command in an expressive way. The import package bridges some of the gap between using @code{library} (or @code{require}) and direct (single-object) imports. Furthermore the imported objects are not placed in the current environment. It is also possible to import objects from stand-alone @code{.R} files.") (license license:expat))) (define-public r-shinyace (package (name "r-shinyace") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs (list r-shiny r-jsonlite)) (home-page "https://cran.r-project.org/web/packages/shinyAce/") (synopsis "Ace editor bindings for Shiny") (description "This package provides Ace editor bindings to enable a rich text editing environment within Shiny.") (license license:expat))) (define-public r-rafalib (package (name "r-rafalib") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rafalib" version)) (sha256 (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k")))) (properties `((upstream-name . "rafalib"))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer)) (home-page "https://cran.r-project.org/package=rafalib") (synopsis "Convenience functions for routine data exploration") (description "This package provides a series of shortcuts for routine tasks to facilitate data exploration.") (license license:artistic2.0))) (define-public r-randomizr (package (name "r-randomizr") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "randomizr" version)) (sha256 (base32 "0r7yawh4dnxawinnlz09f57kgdwa08rpwxq3y35jam3x2q48qijn")))) (properties `((upstream-name . "randomizr"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://declaredesign.org/r/randomizr/") (synopsis "Tools for common forms of random assignment and sampling") (description "This package provides tools for generating random assignments for common experimental designs and random samples for common sampling designs.") (license license:expat))) (define-public r-roi (package (name "r-roi") (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "ROI" version)) (sha256 (base32 "05hnj9fskfm2klz7zv97lb0r60akjq4a1cay8p62whpi0hri9zyl")))) (properties `((upstream-name . "ROI"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-registry r-slam)) (home-page "https://roi.r-forge.r-project.org/") (synopsis "R optimization infrastructure") (description "The @acronym{ROI, R Optimization Infrastructure} is a framework for handling optimization problems in R.") (license license:gpl3))) (define-public r-roptim (package (name "r-roptim") (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "roptim" version)) (sha256 (base32 "11h6qdi0rsv0bpps6nxkzzapan284q0gldzkmgx3ww5kvnic5w3y")))) (properties `((upstream-name . "roptim"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) (home-page "https://github.com/ypan1988/roptim/") (synopsis "General purpose optimization in R using C++") (description "This package performs optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms (Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying @code{optim()}.") (license license:gpl2+))) (define-public r-base64url (package (name "r-base64url") (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "base64url" version)) (sha256 (base32 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x")))) (build-system r-build-system) (propagated-inputs (list r-backports)) (home-page "https://github.com/mllg/base64url") (synopsis "Fast and URL-safe base64 encoder and decoder") (description "This package provides a URL-safe base64 encoder and decoder. In contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-}, the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the encoder does not fill the string with trailing @code{=}. The resulting encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]} and thus are safe to use in URLs or for file names. The package also comes with a simple base32 encoder/decoder suited for case insensitive file systems.") (license license:gpl3))) (define-public r-baseline (package (name "r-baseline") (version "1.3-5") (source (origin (method url-fetch) (uri (cran-uri "baseline" version)) (sha256 (base32 "0l0llb3pi89ixkpvfg5vbvwwv3gzldf0g98rrd3vkm7q26rqmmd2")))) (properties `((upstream-name . "baseline"))) (build-system r-build-system) (propagated-inputs (list r-gwidgets2tcltk ;for GUI r-limsolve r-sparsem)) (home-page "https://github.com/khliland/baseline/") (synopsis "Baseline correction of spectra") (description "This package is a collection of baseline correction algorithms. Beside those it provides a framework and a Tcl/Tk enabled GUI for optimizing baseline algorithm parameters. Typical use is the removal of the background effects from spectra, which are originating from various types of spectroscopy and spectrometry. Also, there is a possibility of optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.") (license license:gpl2))) (define-public r-radiant-data (package (name "r-radiant-data") (version "1.6.6") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 "09cbd21bvj4a3n5r1ch638y5dgi7xmmg1y62i6ixcjhbr8wypjmn")) (modules '((guix build utils))) (snippet '(delete-file "inst/assets/html2canvas/html2canvas.min.js")))) (properties `((upstream-name . "radiant.data"))) (build-system r-build-system) (arguments (list #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils)) #:imported-modules `(,@%r-build-system-modules (guix build minify-build-system)) #:phases #~(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/assets/html2canvas/" (minify (assoc-ref inputs "_") #:target "html2canvas.min.js"))))))) (propagated-inputs (list r-arrow r-base64enc r-broom r-bslib r-car r-curl r-dplyr r-dt r-ggplot2 r-glue r-import r-jsonlite r-knitr r-lubridate r-magrittr r-markdown r-mass r-patchwork r-plotly r-png r-psych r-randomizr r-readr r-readxl r-rlang r-rmarkdown r-rstudioapi r-scales r-shiny r-shinyace r-shinyfiles r-stringi r-tibble r-tidyr r-writexl)) (native-inputs (list esbuild (origin (method url-fetch) (uri "https://web.archive.org/web/20230428182027id_/\ https://html2canvas.hertzen.com/dist/html2canvas.js") (sha256 (base32 "0svkfnzzsydbsrwi7ky91rjqj97x5rfic69hbr9pwhm0zxlb9i81"))))) (home-page "https://github.com/radiant-rstats/radiant.data") (synopsis "Data menu for Radiant: business analytics using R and Shiny") (description "The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.") (license license:agpl3))) (define-public r-algdesign (package (name "r-algdesign") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "AlgDesign" version)) (sha256 (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar")))) (properties `((upstream-name . "AlgDesign"))) (build-system r-build-system) (home-page "https://github.com/jvbraun/AlgDesign") (synopsis "Algorithmic experimental design") (description "This package provides tools to calculate exact and approximate theory experimental designs for D, A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.") (license license:gpl2+))) (define-public r-alluvial (package (name "r-alluvial") (version "0.1-2") (source (origin (method url-fetch) (uri (cran-uri "alluvial" version)) (sha256 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp")))) (properties `((upstream-name . "alluvial"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/mbojan/alluvial") (synopsis "Create parallel sets plots (Alluvial Diagrams)") (description "This package creates alluvial diagrams (also known as parallel sets plots) for multivariate and time series-like data.") (license license:expat))) (define-public r-signal (package (name "r-signal") (version "1.8-1") (source (origin (method url-fetch) (uri (cran-uri "signal" version)) (sha256 (base32 "1c7fw5akdm8f44zgdafsgz2fpn6kfwifaw29yakl7zykq89vq8m3")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/signal/") (synopsis "Signal processing") (description "This package provides a set of signal processing functions originally written for Matlab and GNU Octave. It includes filter generation utilities, filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.") (license license:gpl2))) (define-public r-simplermarkdown (package (name "r-simplermarkdown") (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "simplermarkdown" version)) (sha256 (base32 "0lffwsrhsdqcqhklh24v0y0x6w4vq9jch93m330kfdv2amab1l06")))) (properties `((upstream-name . "simplermarkdown"))) (build-system r-build-system) (propagated-inputs ;; We cannot patch references to pandoc because the patched files are ;; compiled to an opaque rdb/rdx pair. "guix gc" would not be able to ;; find the patched references in those files. (list pandoc r-rjson)) (home-page "https://github.com/djvanderlaan/simplermarkdown") (synopsis "Simple engine for generating reports using R") (description "This package runs R-code present in a pandoc markdown file and includes the resulting output in the resulting markdown file. This file can then be converted into any of the output formats supported by pandoc. The package can also be used as an engine for writing package vignettes.") (license license:gpl3+))) (define-public r-sitar (package (name "r-sitar") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "sitar" version)) (sha256 (base32 "14qc5qy21qyj4gml0gwfn8izbsmzwy30ddc7mazhszi487jrcrp0")))) (properties `((upstream-name . "sitar"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-forcats r-ggplot2 r-glue r-magrittr r-nlme r-purrr r-rlang r-rsample r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/statist7/sitar") (synopsis "Super imposition by translation and rotation growth curve analysis") (description "This package provides functions for fitting and plotting @acronym{SITAR, Super Imposition by Translation And Rotation} growth curve models. SITAR is a shape- invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.") (license license:gpl2+))) (define-public r-gsubfn (package (name "r-gsubfn") (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "gsubfn" version)) (sha256 (base32 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) (build-system r-build-system) (propagated-inputs (list r-proto)) (home-page "https://code.google.com/archive/p/gsubfn/") (synopsis "Utilities for strings and function arguments") (description "This package provides @code{gsubfn} which is like @code{gsub} but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. @code{gsubfn} can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions.") (license license:gpl2+))) (define-public r-sqldf (package (name "r-sqldf") (version "0.4-11") (source (origin (method url-fetch) (uri (cran-uri "sqldf" version)) (sha256 (base32 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff")))) (build-system r-build-system) (propagated-inputs (list r-chron r-dbi r-gsubfn r-proto r-rsqlite)) (home-page "https://github.com/ggrothendieck/sqldf") (synopsis "Manipulate R data frames using SQL") (description "The @code{sqldf} function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. @code{sqldf} transparently sets up a database, imports the data frames into that database, performs the SQL statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be used to read filtered files into R even if the original files are larger than R itself can handle.") (license license:gpl2))) (define-public r-abind (package (name "r-abind") (version "1.4-5") (source (origin (method url-fetch) (uri (cran-uri "abind" version)) (sha256 (base32 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abind/") (synopsis "Combine multidimensional arrays") (description "This package provides tools to combine multidimensional arrays into a single array. This is a generalization of @code{cbind} and @code{rbind}. It works with vectors, matrices, and higher-dimensional arrays. It also provides the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating, extracting and replacing data in arrays.") (license license:lgpl2.0+))) (define-public r-prroc (package (name "r-prroc") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "PRROC" version)) (sha256 (base32 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7")))) (properties `((upstream-name . "PRROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PRROC/") (synopsis "Precision-Recall and ROC curves for weighted and unweighted data") (description "This package computes the areas under the @dfn{precision-recall} (PR) and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.") (license license:gpl3))) (define-public r-vim (package (name "r-vim") (version "6.2.2") (source (origin (method url-fetch) (uri (cran-uri "VIM" version)) (sha256 (base32 "1r0myxcx8y1a3fkf9ssk882f09snn2j6zilsygpld32hahn4k9xg")))) (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs (list r-car r-colorspace r-data-table r-e1071 r-laeken r-magrittr r-mass r-nnet r-ranger r-rcpp r-robustbase r-sp r-vcd)) (native-inputs (list r-knitr)) (home-page "https://github.com/alexkowa/VIM") (synopsis "Visualization and imputation of missing values") (description "This package provides tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods.") (license license:gpl2+))) (define-public r-fnn (package (name "r-fnn") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 "09zwlblkb7wkyk6azq2iizv3kj2wdqmjhg0r8zjiy1f692ivakfv")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") (synopsis "Fast nearest neighbor search algorithms and applications") (description "This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms. Related applications including KNN classification, regression and information measures are implemented.") ;; The DESCRIPTION file erroneously states that GPL version 2.1 or ;; later can be used. (license license:gpl2+))) (define-public r-smoother (package (name "r-smoother") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "smoother" version)) (sha256 (base32 "0xw28qv8f5i05ajx32njnql6hql5njqyc47wcq6c75cxiv44ppz8")))) (build-system r-build-system) (propagated-inputs (list r-ttr)) (home-page "https://cran.r-project.org/web/packages/smoother") (synopsis "Functions relating to the smoothing of numerical data") (description "This package provides a collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.") (license license:gpl2))) (define-public r-riverplot (package (name "r-riverplot") (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "riverplot" version)) (sha256 (base32 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://logfc.wordpress.com") (synopsis "Sankey or ribbon plots") (description "Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For example, they can be used to compare different clusterings. This package provides an implementation of Sankey plots for R.") 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Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame.") (license license:gpl3+))) (define-public r-rapiclient (package (name "r-rapiclient") (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "rapiclient" version)) (sha256 (base32 "0kw09zgqz25xkiyl74qsi4l3shci6a0jpvqb6qr1fgzm6h97zdxj")))) (properties `((upstream-name . "rapiclient"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-yaml)) (home-page "https://github.com/bergant/rapiclient") (synopsis "Dynamic OpenAPI/Swagger client") (description "This package lets you access services specified in OpenAPI (formerly Swagger) format. It is not a code generator. The client is generated dynamically as a list of R functions.") (license license:expat))) (define-public r-rappdirs (package (name "r-rappdirs") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "rappdirs" version)) (sha256 (base32 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rappdirs/") (synopsis "Determine where to save data, caches, and logs") (description "This package provides an easy way to determine which directories on the user's computer should be used to save data, caches and logs. It is a port of Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (license license:expat))) (define-public r-rastervis (package (name "r-rastervis") (version "0.51.6") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 "12cl201gwah0bn14ji4nbygayd77w5fck9zkcikhrda5s0chvgb1")))) (properties `((upstream-name . 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"rentrez"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-xml)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/rentrez/") (synopsis "Entrez in R") (description "This package provides an R interface to the NCBI's EUtils API, allowing users to search databases like GenBank PubMed, process the results of those searches and pull data into their R sessions.") (license license:expat))) (define-public r-renv (package (name "r-renv") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 "01s5g4w96s0jz9xa1gdj8y4pfvz8cf3gg0kz2smh6f3l4f5baq3v")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://rstudio.github.io/renv") (synopsis "Project environments") (description "This package provides a dependency management toolkit for R. Using renv, you can create and manage project-local R libraries, save the state of these libraries to a lockfile, and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.") (license license:expat))) ;; TODO: esbuild (define-public r-learnr (package (name "r-learnr") (version "0.11.5") (source (origin (method url-fetch) (uri (cran-uri "learnr" version)) (sha256 (base32 "01xig6ijsjnkwdjh03zdp86mqm5pjlqp9br34pn644rf98qg8k2y")))) (build-system r-build-system) (native-inputs (list esbuild r-knitr)) (propagated-inputs (list r-checkmate r-digest r-ellipsis r-evaluate r-htmltools r-htmlwidgets r-jsonlite r-knitr r-lifecycle r-markdown r-promises r-rappdirs r-renv r-rlang r-rmarkdown r-rprojroot r-shiny r-withr)) (home-page "https://rstudio.github.io/learnr/") (synopsis "Interactive tutorials for R") (description "This package provides tools to create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.") (license license:asl2.0))) (define-public r-analytics (package (name "r-analytics") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "analytics" version)) (sha256 (base32 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) (build-system r-build-system) (propagated-inputs (list r-car r-cluster r-fractal r-lmtest r-mass r-np r-powerplus r-robust r-trend r-tsa r-urca r-vim)) (home-page "https://cran.r-project.org/web/packages/analytics/") (synopsis "Collection of data analysis tools") (description "This package is a collection of data analysis tools. It includes tools for regression outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.") (license license:gpl2))) (define-public r-here (package (name "r-here") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "here" version)) (sha256 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88")))) (properties `((upstream-name . "here"))) (build-system r-build-system) (propagated-inputs (list r-rprojroot)) (native-inputs (list r-knitr)) (home-page "https://here.r-lib.org/") (synopsis "Simpler way to find files") (description "This package lets you construct paths to your project's files. Use the @code{here} function as a drop-in replacement for @code{file.path}, it will always locate the files relative to your project root.") (license license:expat))) (define-public r-reticulate (package (name "r-reticulate") (version "1.38.0") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 "13favs31kzzff7ii0fxsdwvwb3iijasn2mg57ghcv8si4cz32byb")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'build-reproducibly (lambda _ (setenv "PYTHONHASHSEED" "0") (setenv "PYTHONDONTWRITEBYTECODE" "1")))))) (inputs (list python)) (propagated-inputs (list r-here r-jsonlite r-matrix r-png r-rappdirs r-rcpp r-rcpptoml r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/reticulate") (synopsis "R interface to Python") (description "This package provides an interface from R to Python modules, classes, and functions. When calling into Python, R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types.") (license license:asl2.0))) (define-public r-bibtex (package (name "r-bibtex") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 "1l9y945qmpla68rx6dnaxc83vmvkw26cw4zzfgfsvi36wsja1hgk")))) (build-system r-build-system) (propagated-inputs (list r-backports)) (home-page "https://github.com/romainfrancois/bibtex") (synopsis "Bibtex parser") (description "This package provides a utility for R to parse a bibtex file.") (license license:gpl2+))) (define-public r-billboarder (package (name "r-billboarder") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "billboarder" version)) (sha256 (base32 "0byj1ilwnmq9n9gswsnj17r8pzhm4fp6567nbz1xfmlvl3402qkn")) (snippet '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js")))) (properties `((upstream-name . 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("js-billboard" ,(origin (method url-fetch) (uri "https://unpkg.com/billboard.js@3.6.3/dist/billboard.js") (sha256 (base32 "1lyj4yl95qgh06iygb2y2mdg1zxijzxi5h85z7kp8ngm825z6rpi")))))) (home-page "https://github.com/dreamRs/billboarder") (synopsis "Create interactive charts with the JavaScript Billboard library") (description "This package provides an @code{htmlwidgets} interface to billboard.js, a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in shiny apps.") (license license:expat))) (define-public r-ggseqlogo (package (name "r-ggseqlogo") (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "ggseqlogo" version)) (sha256 (base32 "1drncw73950dzjx3lyyfqrxm3rdbrp44n27sl4b17m9d0crdbgqw")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://github.com/omarwagih/ggseqlogo") (synopsis "ggplot2 extension for drawing genetic sequence logos") (description "The range of functions provided by this package makes it possible to draw highly versatile genomic sequence logos. Features include, but are not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other ggplot2 plots.") ;; Unspecified version of the LGPL. (license license:lgpl3+))) (define-public r-ggsci (package (name "r-ggsci") (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "ggsci" version)) (sha256 (base32 "0jiwkk2ij1qnsaqr6354wihj057ia1arrfpjpll00x63056fvn21")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales)) (native-inputs (list r-knitr)) (home-page "https://nanx.me/ggsci/") (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") (description "This package provides a collection of ggplot2 color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.") (license license:gpl3))) (define-public r-ggsignif (package (name "r-ggsignif") (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 "02mjailzyqkdnzky60dgampw2sq6mnn7s66fk0lhy32s8apm280i")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-ggplot2)) (home-page "https://github.com/const-ae/ggsignif") (synopsis "Significance brackets for ggplot2") (description "Enrich your ggplots with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance. The package provides a single layer that takes the groups for comparison and the test as arguments and adds the annotation to the plot.") (license license:gpl3))) (define-public r-rstatix (package (name "r-rstatix") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 "1891a976k2qjrh1vkzfg8icxblxa978wbazg7mqq8pcw3nmzbip0")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs (list r-broom r-car r-corrplot r-dplyr r-generics r-magrittr r-purrr r-rlang r-tibble r-tidyr r-tidyselect)) (home-page "https://rpkgs.datanovia.com/rstatix/") (synopsis "Pipe-friendly framework for basic statistical tests") (description "This package provides a simple and intuitive pipe-friendly framework, coherent with the @code{tidyverse} design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.") (license license:gpl2))) (define-public r-ggpubr (package (name "r-ggpubr") (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 "0x7p3lbh0xv5qk0shsrj1fjx382zak7mj8l3z1zd348r2pccavif")))) (build-system r-build-system) (propagated-inputs (list r-cowplot r-dplyr r-ggplot2 r-ggrepel r-ggsci r-ggsignif r-glue r-gridextra r-magrittr r-polynom r-purrr r-rlang r-scales r-rstatix r-tibble r-tidyr)) (home-page "http://www.sthda.com/english/rpkgs/ggpubr") (synopsis "ggplot2-based publication-ready plots") (description "The ggplot2 package is an excellent and flexible package for elegant data visualization in R. However the default generated plots require some formatting before we can send them for publication. The ggpubr package provides some easy-to-use functions for creating and customizing ggplot2-based publication-ready plots.") (license license:gpl2))) (define-public r-ellipse (package (name "r-ellipse") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ellipse" version)) (sha256 (base32 "1wy25kw3055zxzidzzkif6c8bmch73qkv2ri4i1w0b6ffcwmbs6d")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ellipse/") (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") (description "This package contains various routines for drawing ellipses and ellipse-like confidence regions, implementing the plots described in Murdoch and Chow (1996), A graphical display of large correlation matrices, The American Statistician 50, 178-180. There are also routines implementing the profile plots described in Bates and Watts (1988), Nonlinear Regression Analysis and its Applications.") (license license:gpl2+))) (define-public r-flashclust (package (name "r-flashclust") (version "1.01-2") (source (origin (method url-fetch) (uri (cran-uri "flashClust" version)) (sha256 (base32 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) (properties `((upstream-name . "flashClust"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/flashClust/") (synopsis "Implementation of optimal hierarchical clustering") (description "This package provides a fast implementation of hierarchical clustering.") (license license:gpl2+))) (define-public r-factominer (package (name "r-factominer") (version "2.11") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 "0qzhfjcz0kahqf214g4xs7gfpqx05xbfiwa5r2ldgn2drd16phij")))) (properties `((upstream-name . 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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-fancova (package (name "r-fancova") (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "fANCOVA" version)) (sha256 (base32 "04mw0blgpwdk6wdg8llrig43psgc0vb42cbimvzbnym8v503dsn3")))) (properties `((upstream-name . "fANCOVA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=fANCOVA") (synopsis "Nonparametric analysis of covariance") (description "This package provides a collection of R functions to perform nonparametric analysis of covariance for regression curves or surfaces. Testing the equality or parallelism of nonparametric curves or surfaces is equivalent to analysis of variance (ANOVA) or analysis of covariance (ANCOVA) for one-sample functional data. Three different testing methods are available in the package, including one based on L-2 distance, one based on an ANOVA statistic, and one based on variance estimators.") (license license:gpl3))) (define-public r-fansi (package (name "r-fansi") (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 "0qqq8gz6sfr5yib4qmvk458qa0ypaz0n7f2ygjnpy2p5vy8cd7ga")))) (build-system r-build-system) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/brodieG/fansi") (synopsis "ANSI control sequence aware string functions") (description "This package provides counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.") 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The interface is essentially the same as @code{glm}. More flexibility is provided by the fact that custom pseudo-data representations can be specified and used for model fitting. Functions are provided for the construction of confidence intervals for the reduced-bias estimates.") (license license:gpl2+))) (define-public r-entropy (package (name "r-entropy") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "entropy" version)) (sha256 (base32 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg")))) (properties `((upstream-name . "entropy"))) (build-system r-build-system) (home-page "https://www.strimmerlab.org/software/entropy/") (synopsis "Estimation of entropy, mutual information and related quantities") (description "This package implements various estimators of entropy, such as the shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen estimator. 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The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.") (license license:gpl3))) (define-public r-sjlabelled (package (name "r-sjlabelled") (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 "1va86q5wddyvqgdpy8d0an2c7v1qbb4hpn0ai6y1v5v1ff87w73k")))) (build-system r-build-system) (propagated-inputs (list r-datawizard r-insight)) (native-inputs (list r-knitr)) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description "This package provides a collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.") 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(license license:expat))) ;; This in not the same as "r-argparser" (define-public r-argparse (package (name "r-argparse") (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 "0x16zp6jh9asyval1kwkxzavwjhx3a47xzlc593kw1hz4bhw8355")))) (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.") 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(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 "4.6.22") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 "038b1gs039br4xzv6axij2fzdzahmk718qm4akg77bwqvqvf59ra")))) (properties `((upstream-name . 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"BASIX"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BASIX/") (synopsis "Efficient C/C++ toolset for R") (description "BASIX provides some efficient C/C++ implementations of native R procedures to speed up calculations in R.") (license license:gpl2))) (define-public r-blockfest (package (name "r-blockfest") (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs (list r-basix)) (home-page "https://cran.r-project.org/web/packages/BlockFeST/") (synopsis "Bayesian calculation of region-specific fixation index") (description "This package provides an R implementation of an extension of the BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.") (license license:gpl2))) (define-public r-proc (package (name "r-proc") (version "1.18.5") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 "129cnh3kh9sr42nc7n9f14kr9svi3501834x40njynnzlr0wi4sm")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs (list r-plyr r-rcpp)) (home-page "https://web.expasy.org/pROC/") (synopsis "Display and analyze ROC curves") (description "This package provides tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). The area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") 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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 . 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(license license:gpl3))) (define-public r-slam (package (name "r-slam") (version "0.1-52") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 (base32 "09j1k63nw1m1vgblnla6s52v2337ixs958jmlzkjjz1xb01yd0y3")))) (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-slanter (package (name "r-slanter") (version "0.2-0") (source (origin (method url-fetch) (uri (cran-uri "slanter" version)) (sha256 (base32 "024dkman0r5qzc215gw0ds932vdaz8krrhv64fjw9pni37ixc3mf")))) (properties `((upstream-name . "slanter"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-pheatmap r-pracma)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=slanter") (synopsis "Slanted matrices and ordered clustering") (description "This is a package for slanted matrices and ordered clustering for better visualization of similarity data.") (license license:expat))) (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 . 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"A3"))) (build-system r-build-system) (propagated-inputs (list r-pbapply r-xtable)) (home-page "https://cran.r-project.org/web/packages/A3/") (synopsis "Error metrics for predictive models") (description "This package supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward.") (license license:gpl2+))) (define-public r-infotheo (package (name "r-infotheo") (version "1.2.0.1") (source (origin (method url-fetch) (uri (cran-uri "infotheo" version)) (sha256 (base32 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0")))) (build-system r-build-system) (home-page "http://homepage.meyerp.com/software") (synopsis "Information-theoretic measures") (description "This package implements various measures of information theory based on several entropy estimators.") (license license:gpl3+))) (define-public r-nsprcomp (package (name "r-nsprcomp") (version "0.5.1-2") (source (origin (method url-fetch) (uri (cran-uri "nsprcomp" version)) (sha256 (base32 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f")))) (properties `((upstream-name . "nsprcomp"))) (build-system r-build-system) (home-page "https://sigg-iten.ch/research/") (synopsis "Non-negative and sparse PCA") (description "This package implements two methods for performing a constrained principal component analysis (PCA), where non-negativity and/or sparsity constraints are enforced on the principal axes (PAs). The function @code{nsprcomp} computes one principal component (PC) after the other. Each PA is optimized such that the corresponding PC has maximum additional variance not explained by the previous components. In contrast, the function @code{nscumcomp} jointly computes all PCs such that the cumulative variance is maximal. Both functions have the same interface as the @code{prcomp} function from the @code{stats} package (plus some extra parameters).") (license license:gpl2+))) (define-public r-cmplot (package (name "r-cmplot") (version "4.5.1") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 "0ml6n1wjxrnq13042jihpjlmm6vmkaiks9n49qp7v7rg47gn2ik8")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") (synopsis "Circle Manhattan plot") (description "Circle Manhattan Plot is an R package that can lay out genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.") (license license:gpl2+))) (define-public r-precrec (package (name "r-precrec") (version "0.14.4") (source (origin (method url-fetch) (uri (cran-uri "precrec" version)) (sha256 (base32 "03hvp5h7fz4v2aswxim0mqgj9rdrhnk5xqz212161kpcrw6m67z8")))) (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-data-table r-ggplot2 r-gridextra r-rcpp r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://evalclass.github.io/precrec/") (synopsis "Calculate accurate precision-recall and ROC curves") (description "This package provides tools for accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.") (license license:gpl3))) (define-public r-netrep (package (name "r-netrep") (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "NetRep" version)) (sha256 (base32 "02ss45giv30pi31b5rysa36bn5c4fs5x58g4vb0arz9cnicznv97")))) (properties `((upstream-name . "NetRep"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bh r-foreach r-rcolorbrewer r-rcpp r-rcpparmadillo r-rhpcblasctl r-statmod)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=NetRep") (synopsis "Permutation testing network module preservation across datasets") (description "This package provides functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing.") (license license:gpl2))) (define-public r-intergraph (package (name "r-intergraph") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "intergraph" version)) (sha256 (base32 "1jarzhrgm5g8z2h10h8x7jk9q2al6rx5kgnwvwi2199am6gjypsq")))) (properties `((upstream-name . "intergraph"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-network)) (native-inputs (list r-knitr)) (home-page "https://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description "Functions implemented in this package allow coercing (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages @code{network} and @code{igraph}.") (license license:gpl3))) (define-public r-interp (package (name "r-interp") (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "interp" version)) (sha256 (base32 "0d6ddvm94113d9bjhghjsfbhgz44q0lkjc2l809dzv1lad708x1n")))) (properties `((upstream-name . "interp"))) (build-system r-build-system) (propagated-inputs (list r-deldir r-rcpp r-rcppeigen)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=interp") (synopsis "Interpolation methods") (description "Bivariate data interpolation on regular and irregular grids, either linear or using splines are the main part of this package. It is intended to provide replacement functions for the ACM licensed @code{akima::interp} and @code{tripack::tri.mesh} functions.") (license license:gpl2+))) (define-public r-abcoptim (package (name "r-abcoptim") (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "ABCoptim" version)) (sha256 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) (properties `((upstream-name . "ABCoptim"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/gvegayon/ABCoptim/") (synopsis "Optimization of Artificial Bee Colony algorithm") (description "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms, and uses only common control parameters such as colony size and maximum cycle number. The @code{r-abcoptim} implements the Artificial bee colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. This version is a work-in-progress and is written in R code.") (license license:expat))) (define-public r-abcp2 (package (name "r-abcp2") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "ABCp2" version)) (sha256 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) (properties `((upstream-name . "ABCp2"))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ABCp2/") (synopsis "Approximate Bayesian Computational Model for Estimating P2") (description "This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.") (license license:gpl2))) (define-public r-abcrf (package (name "r-abcrf") (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "abcrf" version)) (sha256 (base32 "08mh1a6gxp0mfx6qnp1qzcrfx7xp64qj9kad4ziyswfx22ykdsxi")))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-mass r-matrixstats r-ranger r-rcpp r-rcpparmadillo r-readr r-stringr)) (home-page "https://cran.r-project.org/web/packages/abcrf/") (synopsis "Approximate bayesian computation via random forests") (description "This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.") 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(license license:gpl3))) (define-public r-furrr (package (name "r-furrr") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 "12z4q0fn7asxis17hisi82bvfabl5if1338lmfqmkrwv5rg7748d")))) (build-system r-build-system) (propagated-inputs (list r-future r-globals r-lifecycle r-purrr r-rlang r-vctrs)) (home-page "https://github.com/DavisVaughan/furrr") (synopsis "Apply mapping functions in parallel using futures") (description "This package provides implementations of the family of @code{map()} functions from the @code{purrr} package that can be resolved using any @code{future}-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.") 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The methodology includes both parametric and semi-parametric multiple imputations under the zero-inflated Poisson lognormal model. It also provides multiple functions to preprocess the accelerometer data previous to the missing data imputation. These include detecting the wearing and the non-wearing time, selecting valid days and subjects, and creating plots.") (license license:gpl2+))) (define-public r-mhsmm (package (name "r-mhsmm") (version "0.4.21") (source (origin (method url-fetch) (uri (cran-uri "mhsmm" version)) (sha256 (base32 "1fibgpl65bl3rwlf9dhlams3gxbjqgwcd26gb0flp4wln6pl8d99")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://github.com/jaredo/mhsmm/") (synopsis "Inference for hidden Markov and semi-Markov models") (description "The @code{r-mhsmm} package implements estimation and prediction methods for hidden Markov and semi-Markov models for multiple observation sequences. Such techniques are of interest when observed data is thought to be dependent on some unobserved (or hidden) state. Also, this package is suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.") (license license:gpl2+))) (define-public r-nleqslv (package (name "r-nleqslv") (version "3.3.5") (source (origin (method url-fetch) (uri (cran-uri "nleqslv" version)) (sha256 (base32 "0fjby0qva2lp2i7x752wva0z15xqys9fgrrcfimqszg65wnig60j")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nleqslv/") (synopsis "Solve systems of nonlinear equations") (description "The @code{r-nleqslv} package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. 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The package @code{phyclust} provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in @code{C} for performance and interfaced with @code{R} for visualization.") (license license:gpl2+))) (define-public r-physicalactivity (package (name "r-physicalactivity") (version "0.2-4") (source (origin (method url-fetch) (uri (cran-uri "PhysicalActivity" version)) (sha256 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40")))) (properties `((upstream-name . 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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.") 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"mixsqp"))) (build-system r-build-system) (propagated-inputs (list r-irlba r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/stephenslab/mixsqp") (synopsis "Sequential quadratic programming for maximum-likelihood estimation") (description "This package provides an optimization method based on sequential quadratic programming for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithm is expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver, and they are expected to arrive at solutions more quickly when the number of samples is large and the number of mixture components is not too large.") (license license:expat))) (define-public r-magick (package (name "r-magick") (version "2.8.4") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 "02pa6kkymj4idawnffqk2fn6zgkw33ib6541vclvg5hd1wvh7j25")))) (properties '((updater-extra-inputs . ("imagemagick")))) (build-system r-build-system) (inputs (list imagemagick pcre2 zlib)) (propagated-inputs (list r-curl r-magrittr r-rcpp)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/ropensci/magick") (synopsis "Advanced graphics and image-processing in R") (description "This package provides bindings to ImageMagick, a comprehensive image processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio, images are automatically previewed when printed to the console, resulting in an interactive editing environment.") (license license:expat))) (define-public r-survey (package (name "r-survey") (version "4.4-2") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 "1ggisal5g16p3n03bch7ymawd4hig3fmm02nhxy1z5zh48qhyjla")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-matrix r-minqa r-mitools r-numderiv r-rcpp r-rcpparmadillo r-survival)) (native-inputs (list r-r-rsp)) (home-page "https://r-survey.r-forge.r-project.org/survey/") (synopsis "Analysis of complex survey samples") (description "This package provides tools for the analysis of complex survey samples. The provided features include: summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples; variances by Taylor series linearisation or replicate weights; post-stratification, calibration, and raking; two-phase subsampling designs; graphics; PPS sampling without replacement; principal components, and factor analysis.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-gee (package (name "r-gee") (version "4.13-27") (source (origin (method url-fetch) (uri (cran-uri "gee" version)) (sha256 (base32 "1754173msjxhkpl95v6z8c73vhz7ivfil0xfs25smrlgslzpgd1z")))) (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/gee/") (synopsis "Generalized estimation equation solver") (description "This package provides a solver for generalized estimation equations.") (license license:gpl2))) (define-public r-tab (package (name "r-tab") (version "5.1.1") (source (origin (method url-fetch) (uri (cran-uri "tab" version)) (sha256 (base32 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv")))) (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-kableextra r-knitr r-mass r-survey)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tab/") (synopsis "Create summary tables for statistical reports") (description "This package contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards models. Functions are available to handle data from simple random samples as well as complex surveys.") (license license:gpl3+))) (define-public r-tarchetypes (package (name "r-tarchetypes") (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 "0lb5y3rlm369szabmamhq8rrjh7ybngmd3av0jisi84bwdvrwhxk")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-fs r-rlang r-secretbase r-targets r-tibble r-tidyselect r-vctrs r-withr)) (home-page "https://docs.ropensci.org/tarchetypes/") (synopsis "Archetypes for Targets") (description "Function-oriented Make-like declarative pipelines for statistics and data science are supported in the targets R package. As an extension to targets, the tarchetypes package provides convenient user-side functions to make targets easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the drake R package by Will Landau (2018) <doi:10.21105/joss.00550>.") (license license:expat))) (define-public r-targets (package (name "r-targets") (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 "1r4pg990nhmyg4i15qgqafvqas4vh5rvcki3iaff2hyrfdcmy6vy")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url r-callr r-cli r-codetools r-data-table r-igraph r-knitr r-ps r-r6 r-rlang r-secretbase r-tibble r-tidyselect r-vctrs r-yaml)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/targets/") (synopsis "Dynamic function-oriented Make-like declarative pipelines") (description "This package provides a pipeline toolkit for statistics and data science in R; the @code{targets} package brings function-oriented programming to Make-like declarative pipelines. It orchestrates a pipeline as a graph of dependencies, skips steps that are already up to date, runs the necessary computation with optional parallel workers, abstracts files as R objects, and provides tangible evidence that the results are reproducible given the underlying code and data. The methodology in this package borrows from GNU Make (2015, ISBN:978-9881443519) and drake (2018, <doi:10.21105/joss.00550>).") (license license:expat))) (define-public r-tidygeocoder (package (name "r-tidygeocoder") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "tidygeocoder" version)) (sha256 (base32 "1ffj8ka5miv3jnds7fdrkcqdc3m2w1ab724z9m10biky213skqka")))) (properties `((upstream-name . "tidygeocoder"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-httr r-jsonlite r-lifecycle r-progress r-tibble)) (native-inputs (list r-knitr)) (home-page "https://jessecambon.github.io/tidygeocoder/") (synopsis "Intuitive interface for getting data from geocoding services") (description "Tidygeocoder makes getting data from geocoding services easy. A unified high-level interface is provided for a selection of supported geocoding services and results are returned in tibble format.") (license license:expat))) (define-public r-dvmisc (package (name "r-dvmisc") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dvmisc" version)) (sha256 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs (list r-cubature r-data-table r-dplyr r-ggplot2 r-mass r-mvtnorm r-pracma r-rbenchmark r-rcpp r-survey r-tab)) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description "This package implements faster versions of base R functions (e.g. mean, standard deviation, covariance, weighted mean), mostly written in C++, along with miscellaneous functions for various purposes (e.g. create the histogram with fitted probability density function or probability mass function curve, create the body mass index groups, assess the linearity assumption in logistic regression).") (license license:gpl2))) (define-public r-accelerometry (package (name "r-accelerometry") (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "accelerometry" version)) (sha256 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) (build-system r-build-system) (propagated-inputs (list r-dvmisc r-rcpp)) (home-page "https://cran.r-project.org/web/packages/accelerometry/") (synopsis "Functions for processing accelerometer data") (description "This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented.") (license license:gpl3))) (define-public r-absim (package (name "r-absim") (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "AbSim" version)) (sha256 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) (properties `((upstream-name . "AbSim"))) (build-system r-build-system) (propagated-inputs (list r-ape r-powerlaw)) (home-page "https://cran.r-project.org/web/packages/AbSim/") (synopsis "Time resolved simulations of antibody repertoires") (description "This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins with an initial V-D-J recombination event, starting the first phylogenetic tree. Upon completion, the main loop of the algorithm begins, with each iteration representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.") (license license:gpl2))) (define-public r-quic (package (name "r-quic") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "QUIC" version)) (sha256 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) (properties `((upstream-name . "QUIC"))) (build-system r-build-system) (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") (synopsis "Regularized sparse inverse covariance matrix estimation") (description "This package implements the regularized Gaussian maximum likelihood estimation of the inverse of a covariance matrix. It uses Newton's method and coordinate descent to solve the regularized inverse covariance matrix estimation problem.") ;; The project home page states that the release is under GPLv3 or later. ;; The CRAN page only says GPL-3. (license license:gpl3+))) (define-public r-quickjsr (package (name "r-quickjsr") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "QuickJSR" version)) (sha256 (base32 "1lcg437b93yvbk4q63m2sh8ih4p2b6505invmjbyqf58hip9sm8h")))) (properties `((upstream-name . "QuickJSR"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=QuickJSR") (synopsis "Interface for the QuickJS lightweight JavaScript engine") (description "This package provides an R interface to the @code{QuickJS} portable @code{JavaScript} engine. The engine is bundled entirely within the package, requiring no external system dependencies beyond a C compiler.") (license license:expat))) (define-public r-abundant (package (name "r-abundant") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "abundant" version)) (sha256 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd")))) (build-system r-build-system) (propagated-inputs (list r-glasso)) (home-page "https://cran.r-project.org/web/packages/abundant/") (synopsis "Abundant regression and high-dimensional principal fitted components") (description "This package provides tools to fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) @url{doi:10.1214/11-AOS962}.") ;; The DESCRIPTION file states GPL-2, but since it directly depends on a ;; GPLv3+ package (QUIC) this likely means GPLv2+. (license license:gpl2+))) (define-public r-ac3net (package (name "r-ac3net") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "Ac3net" version)) (sha256 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) (properties `((upstream-name . "Ac3net"))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/Ac3net/") (synopsis "Inferring directional conservative causal core gene networks") (description "This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.") (license license:gpl3+))) (define-public r-aca (package (name "r-aca") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "ACA" version)) (sha256 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) (properties `((upstream-name . "ACA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACA/") (synopsis "Abrupt change-point or aberration detection in point series") (description "This package offers an interactive function for the detection of breakpoints in series.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-acceptancesampling (package (name "r-acceptancesampling") (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 (base32 "1sbv2yrvnn0zgdmqvjlmz2vllsg6r9nlmxdgadhymhm9s51gfx65")))) (properties `((upstream-name . "AcceptanceSampling"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") (synopsis "Creation and evaluation of acceptance sampling plans") (description "This @code{r-acceptancesampling} provides functionality for creating and evaluating acceptance sampling plans. Acceptance sampling is a methodology commonly used in quality control and improvement. International standards of acceptance sampling provide sampling plans for specific circumstances. The aim of this package is to provide an easy-to-use interface to visualize single, double or multiple sampling plans. In addition, methods have been provided to enable the user to assess sampling plans against pre-specified levels of performance, as measured by the probability of acceptance for a given level of quality in the lot.") (license license:gpl3+))) (define-public r-acclma (package (name "r-acclma") (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "ACCLMA" version)) (sha256 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) (properties `((upstream-name . "ACCLMA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ACCLMA/") (synopsis "ACC & LMA graph plotting") (description "This package contains a function that imports data from a @acronym{CSV, Comma-Separated Values} file, or uses manually entered data from the format (x, y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration Curve} vs @acronym{LOI, Line of Independence} graph and @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main function is @code{plotLMA} (source file, header) that takes a data set and plots the appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a string) was passed, a manual data entry window is opened. The header parameter indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has a header row or not. The dataset should contain only one independent variable (x) and one dependent variable (y) and can contain a weight for each observation.") (license license:gpl2))) (define-public r-aspi (package (name "r-aspi") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "aspi" version)) (sha256 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/aspi/") (synopsis "Analysis of symmetry of parasitic infections") (description "This package provides tools for the analysis and visualization of bilateral asymmetry in parasitic infections.") (license license:gpl3+))) (define-public r-sandwich (package (name "r-sandwich") (version "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 "1yi3l2q63j0vlaqqh1x3bxb0i7v6lrmmbsc6s8gilfahxq2y3c4n")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/doc" ;; These files are generated from Rnw files. (for-each delete-file (list "sandwich-OOP.pdf" "sandwich-OOP.R" "sandwich-OOP.Rnw" "sandwich-CL.R" "sandwich-CL.Rnw" "sandwich-CL.pdf" "sim-CL.rda" "sim-CL.R" "sandwich.pdf" "sandwich.R")))))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/sandwich/") (synopsis "Robust Covariance Matrix Estimators") (description "This package provides model-robust standard error estimators for cross-sectional, time series, clustered, panel, and longitudinal data.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-th-data (package (name "r-th-data") (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 "0wyyvm6l6yvqvfnd1c4l9ff5445zaq9lr0ihz8pg9kkggfslxya7")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-multcomp (package (name "r-multcomp") (version "1.4-26") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 "1v3979my2yzpqc5lrx7fy72765j2cw1giv4xlpwrr2zvmzgvn051")))) (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 "0.1-10") (source (origin (method url-fetch) (uri (cran-uri "multcompView" version)) (sha256 (base32 "12mdk12xciq1d3zn94rixahhcah2qq41lvb5n4kzgjaq4yr4kwiq")))) (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 "1.10.4") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 "1hywpa7kz6i77w2f9fq7gxbrx0ivrzb131hs92x9jkwqqlikcrb6")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") (synopsis "Estimated marginal means, aka least-squares means") (description "This package provides tools to obtain @dfn{estimated marginal means} (EMMs) for many linear, generalized linear, and mixed models. It can be used to compute contrasts or linear functions of EMMs, trends, and comparisons of slopes.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) (define-public r-pwr (package (name "r-pwr") (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "pwr" version)) (sha256 (base32 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/heliosdrm/pwr") (synopsis "Basic functions for power analysis") (description "This package provides power analysis functions along the lines of Cohen (1988).") (license license:gpl3+))) (define-public r-libcoin (package (name "r-libcoin") (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 (base32 "1bvysrq2s3951vr5ab1jzbz4hyx5j04yzh04vxdpd287bm4y08rh")))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/libcoin") (synopsis "Linear test statistics for permutation inference") (description "This package provides basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999).") 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(license license:gpl2))) (define-public r-sjstats (package (name "r-sjstats") (version "0.19.0") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 "07qv32gnrhrl21zgj1xp1gqdqjn6ax1nf40s11nmpag8r0xgvqnk")))) (build-system r-build-system) (propagated-inputs (list r-datawizard r-effectsize r-insight r-parameters r-performance)) (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 "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 "0qw9ww3l506vivs6k8v5cdiv6lf9a32f0d1iq6bizxxh0ywsdmck")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-matrix r-mgcv r-nlme r-numderiv r-rcppeigen r-tmb)) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description "Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via the Template Model Builder. 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These data frames are ready to use with the @code{ggplot2} package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are @code{ggpredict()} and @code{ggeffect()}. There is a generic @code{plot()} method to plot the results using @code{ggplot2}.") (license license:gpl3))) (define-public r-effectsize (package (name "r-effectsize") (version "0.8.9") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 "12qzz3zl5yn28ybmmryhmi29zwzwrfgqhb6wm7aqg78id463bjz9")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-lisreltor (package (name "r-lisreltor") (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "lisrelToR" version)) (sha256 (base32 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5")))) (properties `((upstream-name . "lisrelToR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=lisrelToR") (synopsis "Import output from LISREL into R") (description "This is an unofficial package aimed at automating the import of LISREL output in R.") (license license:gpl2))) (define-public r-bdgraph (package (name "r-bdgraph") (version "2.63") (source (origin (method url-fetch) (uri (cran-uri "BDgraph" version)) (sha256 (base32 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc")))) (properties `((upstream-name . 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"d3Network"))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) ("r-rjson" ,r-rjson) ("r-whisker" ,r-whisker))) (home-page "http://christophergandrud.github.io/d3Network/") (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs") (description "This package is intended to make it easy to create D3 JavaScript network, tree, dendrogram, and Sankey graphs from R using data frames.") (license license:gpl3+))) (define-public r-qgraph (package (name "r-qgraph") (version "1.6.5") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-bdgraph" ,r-bdgraph) ("r-colorspace" ,r-colorspace) ("r-corpcor" ,r-corpcor) ("r-d3network" ,r-d3network) ("r-dplyr" ,r-dplyr) ("r-fdrtool" ,r-fdrtool) ("r-ggplot2" ,r-ggplot2) ("r-ggraph" ,r-ggraph) ("r-glasso" ,r-glasso) ("r-gtools" ,r-gtools) ("r-hmisc" ,r-hmisc) ("r-huge" ,r-huge) ("r-igraph" ,r-igraph) ("r-jpeg" ,r-jpeg) ("r-lavaan" ,r-lavaan) ("r-matrix" ,r-matrix) ("r-pbapply" ,r-pbapply) ("r-plyr" ,r-plyr) ("r-png" ,r-png) ("r-psych" ,r-psych) ("r-rcpp" ,r-rcpp) ("r-reshape2" ,r-reshape2) ("r-tidygraph" ,r-tidygraph))) (home-page "http://sachaepskamp.com/qgraph/") (synopsis "Weighted network visualization and analysis") (description "This package implements tools for weighted network visualization and analysis, as well as Gaussian graphical model computation. It contains graph plotting methods, and tools for psychometric data visualization and graphical model estimation. See Epskamp et al. (2012) @url{doi:10.18637/jss.v048.i04}.") (license license:gpl2))) (define-public r-semplot (package (name "r-semplot") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "semPlot" version)) (sha256 (base32 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr")))) (properties `((upstream-name . "semPlot"))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) ("r-corpcor" ,r-corpcor) ("r-igraph" ,r-igraph) ("r-lavaan" ,r-lavaan) ("r-lisreltor" ,r-lisreltor) ("r-openmx" ,r-openmx) ("r-plyr" ,r-plyr) ("r-qgraph" ,r-qgraph) ("r-regsem" ,r-regsem) ("r-rockchalk" ,r-rockchalk) ("r-sem" ,r-sem) ("r-xml" ,r-xml))) (home-page "https://github.com/SachaEpskamp/semPlot") (synopsis "Unified visualizations of structural equation models") (description "Structural equation modeling (SEM) has a long history of representing models graphically as path diagrams. The semPlot package for R fills the gap between advanced, but time-consuming, graphical software and the limited graphics produced automatically by SEM software. In addition, semPlot offers more functionality than drawing path diagrams: it can act as a common ground for importing SEM results into R. Any result usable as input to semPlot can also be represented in any of the three popular SEM frame-works, as well as translated to input syntax for the R packages @code{sem} and @code{lavaan}.") (license license:gpl2))) (define-public r-cdm (package (name "r-cdm") (version "7.5-15") (source (origin (method url-fetch) (uri (cran-uri "CDM" version)) (sha256 (base32 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l")))) (properties `((upstream-name . "CDM"))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm) ("r-polycor" ,r-polycor) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo))) (home-page "https://github.com/alexanderrobitzsch/CDM") (synopsis "Cognitive diagnosis modeling") (description "This package provides functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. It enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the structured latent class model (SLCA), and regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on estimation and the package structure. For tutorials on how to use the CDM package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as well as Ravand and Robitzsch (2015).") (license license:gpl2+))) (define-public r-tam (package (name "r-tam") (version "3.5-19") (source (origin (method url-fetch) (uri (cran-uri "TAM" version)) (sha256 (base32 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7")))) (properties `((upstream-name . "TAM"))) (build-system r-build-system) (propagated-inputs `(("r-cdm" ,r-cdm) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo))) (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/") (synopsis "Test analysis modules") (description "This package includes tools for marginal maximum likelihood estimation and joint maximum likelihood estimation for unidimensional and multidimensional item response models. The package functionality covers the Rasch model, 2PL model, 3PL model, generalized partial credit model, multi-faceted Rasch model, nominal item response model, structured latent class model, mixture distribution IRT models, and located latent class models. Latent regression models and plausible value imputation are also supported.") (license license:gpl2+))) (define-public r-erm (package (name "r-erm") (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "eRm" version)) (sha256 (base32 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9")))) (properties `((upstream-name . "eRm"))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-psych" ,r-psych))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/package=eRm") (synopsis "Extended Rasch modeling") (description "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear rating scale models} (LRSM), @dfn{partial credit models} (PCM), and @dfn{linear partial credit models} (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, ICC and other plots, automated stepwise item elimination, and a simulation module for various binary data matrices.") (license license:gpl3))) (define-public r-irtoys (package (name "r-irtoys") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "irtoys" version)) (sha256 (base32 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-iheatmapr (package (name "r-iheatmapr") (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "iheatmapr" version)) (sha256 (base32 "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h")))) (properties `((upstream-name . "iheatmapr"))) (build-system r-build-system) (propagated-inputs `(("r-fastcluster" ,r-fastcluster) ("r-ggdendro" ,r-ggdendro) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://docs.ropensci.org/iheatmapr") (synopsis "Interactive, Complex Heatmaps") (description "iheatmapr is an R package for building complex, interactive heatmaps using modular building blocks. \"Complex\" heatmaps are heatmaps in which subplots along the rows or columns of the main heatmap add more information about each row or column. 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(define-public r-dygraphs (package (name "r-dygraphs") (version "1.1.1.6") (source (origin (method url-fetch) (uri (cran-uri "dygraphs" version)) (sha256 (base32 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3")))) (properties `((upstream-name . 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It provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.") (license license:expat))) (define-public r-shinystan (package (name "r-shinystan") (version "2.5.0") (source (origin (method url-fetch) (uri (cran-uri "shinystan" version)) (sha256 (base32 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5")))) (properties `((upstream-name . 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"loo"))) (build-system r-build-system) (inputs `(("pandoc" ,pandoc) ("pandoc-citeproc" ,pandoc-citeproc))) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-matrixstats" ,r-matrixstats))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://mc-stan.org/loo/") (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models") (description "This package provides an implementation of efficient approximate @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}. The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new procedure for regularizing importance weights. As a byproduct of the calculations, we also obtain approximate standard errors for estimated predictive errors and for the comparison of predictive errors between models. The package also provides methods for using stacking and other model weighting techniques to average Bayesian predictive distributions.") (license license:gpl3+))) (define-public r-rstan (package (name "r-rstan") (version "2.21.2") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'set-timezone ;; This package is picky about timezones. (lambda* (#:key inputs #:allow-other-keys) (setenv "TZ" "UTC+1") (setenv "TZDIR" (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")) #t))))) (native-inputs `(("tzdata" ,tzdata-for-tests) ("pandoc" ,pandoc) ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-bh" ,r-bh) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-inline" ,r-inline) ("r-loo" ,r-loo) ("r-pkgbuild" ,r-pkgbuild) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-rcppparallel" ,r-rcppparallel) ("r-stanheaders" ,r-stanheaders) ("r-v8" ,r-v8) ("r-withr" ,r-withr))) (home-page "https://discourse.mc-stan.org/") (synopsis "R interface to Stan") (description "User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the StanHeaders package. 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(license license:gpl3+))) (define-public r-kendall (package (name "r-kendall") (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "Kendall" version)) (sha256 (base32 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn")))) (properties `((upstream-name . "Kendall"))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/Kendall/") (synopsis "Kendall rank correlation and Mann-Kendall trend test") (description "This package computes the Kendall rank correlation and Mann-Kendall trend test.") (license license:gpl2+))) (define-public r-zyp (package (name "r-zyp") (version "0.10-1.1") (source (origin (method url-fetch) (uri (cran-uri "zyp" version)) (sha256 (base32 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9")))) (properties `((upstream-name . "zyp"))) (build-system r-build-system) (propagated-inputs `(("r-kendall" ,r-kendall))) (home-page "https://cran.r-project.org/web/packages/zyp/") (synopsis "Zhang + Yue-Pilon Trends Package") (description "This package contains an efficient implementation of Sen's slope method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in climate data.") (license license:lgpl2.1))) (define-public r-rlinsolve (package (name "r-rlinsolve") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "Rlinsolve" version)) (sha256 (base32 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-zvcv (package (name "r-zvcv") (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "ZVCV" version)) (sha256 (base32 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r")))) (properties `((upstream-name . "ZVCV"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-bh" ,r-bh) ("r-dplyr" ,r-dplyr) ("r-glmnet" ,r-glmnet) ("r-magrittr" ,r-magrittr) ("r-mvtnorm" ,r-mvtnorm) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rlinsolve" ,r-rlinsolve))) (home-page "https://cran.r-project.org/web/packages/ZVCV/") (synopsis "Zero-Variance Control Variates") (description "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method to reduce the variance of Monte Carlo estimators of expectations using the derivatives of the log target. Once the derivatives are available, the only additional computational effort is in solving a linear regression problem. This method has been extended to higher dimensions using regularisation. This package can be used to easily perform ZV-CV or regularised ZV-CV when a set of samples, derivatives and function evaluations are available. Additional functions for applying ZV-CV to two estimators for the normalising constant of the posterior distribution in Bayesian statistics are also supplied.") (license license:gpl2+))) (define-public r-ztype (package (name "r-ztype") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "ztype" version)) (sha256 (base32 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx")))) (properties `((upstream-name . "ztype"))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-rvest" ,r-rvest) ("r-stringr" ,r-stringr))) (home-page "https://cran.r-project.org/web/packages/ztype/") (synopsis "Run a Ztype game loaded with R functions") (description "How fast can you type R functions on your keyboard? Find out by running a @code{zty.pe} game: export R functions as instructions to type to destroy opponents' vessels.") (license license:gpl3))) (define-public r-zseq (package (name "r-zseq") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "Zseq" version)) (sha256 (base32 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi")))) (properties `((upstream-name . "Zseq"))) (build-system r-build-system) (propagated-inputs `(("r-gmp" ,r-gmp))) (home-page "https://cran.r-project.org/web/packages/Zseq/") (synopsis "Integer sequence generator") (description "This package generates well-known integer sequences. The @code{gmp} package is adopted for computing with arbitrarily large numbers. Every function has a hyperlink to its corresponding item in the @dfn{On-Line Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (license license:gpl3+))) (define-public r-isoband (package (name "r-isoband") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) (propagated-inputs `(("r-testthat" ,r-testthat))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/wilkelab/isoband") (synopsis "Generate isolines and isobands from regularly spaced elevation grids") (description "This package provides a fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.") (license license:expat))) (define-public r-ppcor (package (name "r-ppcor") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "ppcor" version)) (sha256 (base32 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a")))) (properties `((upstream-name . "ppcor"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (home-page "https://cran.r-project.org/web/packages/ppcor/") (synopsis "Partial and semi-partial correlation") (description "This package provides users not only with a function to readily calculate the higher-order partial and semi-partial correlations but also with statistics and p-values of the correlation coefficients.") (license license:gpl2))) (define-public r-hrbrthemes (package (name "r-hrbrthemes") (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "hrbrthemes" version)) (sha256 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc")))) (properties `((upstream-name . "hrbrthemes"))) (build-system r-build-system) (propagated-inputs `(("r-extrafont" ,r-extrafont) ("r-gdtools" ,r-gdtools) ("r-ggplot2" ,r-ggplot2) ("r-htmltools" ,r-htmltools) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) ("r-rmarkdown" ,r-rmarkdown) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hrbrmstr/hrbrthemes/") (synopsis "Additional themes, theme components and utilities for @code{ggplot2}") (description "This package provides a compilation of extra @code{ggplot2} themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography.") (license license:expat))) (define-public r-crochet (package (name "r-crochet") (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "crochet" version)) (sha256 (base32 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/agrueneberg/crochet") (synopsis "Implementation Helper for Matrix-Like Types") (description "Functions to help implement the extraction / subsetting / indexing function @code{[} and replacement function @code{[<-} of custom matrix-like types (based on S3, S4, etc.), modeled as closely to the base matrix class as possible (with tests to prove it).") (license license:expat))) (define-public r-boa (package (name "r-boa") (version "1.1.8-2") (source (origin (method url-fetch) (uri (cran-uri "boa" version)) (sha256 (base32 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp")))) (properties `((upstream-name . "boa"))) (build-system r-build-system) (home-page "http://www.jstatsoft.org/v21/i11") (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC") (description "This package provides a menu-driven program and library of functions for carrying out convergence diagnostics and statistical and graphical analysis of @dfn{Markov chain Monte Carlo} (MCMC) sampling output.") (license license:gpl2+))) (define-public r-httpcode (package (name "r-httpcode") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "httpcode" version)) (sha256 (base32 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr")))) (build-system r-build-system) (home-page "https://github.com/sckott/httpcode") (synopsis "HTTP status code helper") (description "@code{httpcode} provides functionality for finding and explaining the meaning of @code{HTTP} status codes. Functions are included for searching for codes by full or partial number, by message, and to get appropriate dog and cat images for many status codes.") (license license:expat))) (define-public r-latex2exp (package (name "r-latex2exp") (version "0.4.0"distributions, using the parametrizations of Nolan.") (license license:gpl2+))) (define-public r-gsl (package (name "r-gsl") (version "2.1-8") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 "159d782nz7fqhgcj3fa79hlmkdrqnkd0ypgzcl71kgas92zhjdpk")))) (build-system r-build-system) (inputs (list gsl)) (home-page "https://cran.r-project.org/web/packages/gsl") (synopsis "Wrapper for the GNU Scientific Library") (description "This package provides an R wrapper for the special functions and quasi random number generators of the GNU Scientific Library.") (license license:gpl2+))) (define-public r-adgoftest (package (name "r-adgoftest") (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ADGofTest" version)) (sha256 (base32 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) (properties `((upstream-name . "ADGofTest"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ADGofTest") (synopsis "Anderson-Darling GoF test") (description "This package provides an implementation of the Anderson-Darling GoF test with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the Anderson-Darling Distribution\".") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-adimpro (package (name "r-adimpro") (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "adimpro" version)) (sha256 (base32 "1p34q78w1ib5xjvxg4c1bal680a55l5dqhiry367x9nzwq8a352c")))) (properties `((upstream-name . "adimpro") (updater-extra-propagated-inputs . ("imagemagick")))) (build-system r-build-system) (propagated-inputs (list r-awsmethods imagemagick)) (native-inputs (list gfortran)) (home-page "https://www.wias-berlin.de/software/imaging/") (synopsis "Adaptive smoothing of digital images") (description "This package implements tools for manipulation of digital images and the Propagation Separation approach by Polzehl and Spokoiny (2006) <DOI:10.1007/s00440-005-0464-1> for smoothing digital images, see Polzehl and Tabelow (2007) <DOI:10.18637/jss.v019.i01>.") (license license:gpl2+))) (define-public r-admisc (package (name "r-admisc") (version "0.35") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 (base32 "0gzdb9dm34qfkjqgfrd3wm96dzhcps4xayyrhp80mzgh14zmnjyg")))) (properties `((upstream-name . "admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") (synopsis "Adrian Dusa's miscellaneous") (description "This package contains miscellaneous functions used to interpret and translate, factorize and negate Sum of Products expressions, for both binary and multi-value crisp sets, and to extract information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly flexible recoding routine and a more flexible alternative to the base function @code{with()}.") (license license:gpl3+))) (define-public r-oro-nifti (package (name "r-oro-nifti") (version "0.11.4") (source (origin (method url-fetch) (uri (cran-uri "oro.nifti" version)) (sha256 (base32 "01mn90qxb7i15zr83xrl2cn4akayfzpm83r5x71zczz3qb9gbr7g")))) (properties `((upstream-name . "oro.nifti"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bitops r-rnifti)) (home-page "https://rigorousanalytics.blogspot.com") (synopsis "Vizualization of medical imaging data") (description "This package provides functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle.") (license license:bsd-3))) (define-public r-mritc (package (name "r-mritc") (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "mritc" version)) (sha256 (base32 "1bpnm2qzq67dgjxsa4wxn51f4a4cxal5r6abgs3m7p5a9a16jmjp")))) (properties `((upstream-name . "mritc"))) (build-system r-build-system) (propagated-inputs (list r-lattice r-misc3d r-oro-nifti)) (home-page "https://cran.r-project.org/package=mritc") (synopsis "MRI tissue classification") (description "This package provides various methods for MRI tissue classification.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-sodium (package (name "r-sodium") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "sodium" version)) (sha256 (base32 "0cbj7mgchi42ri6h1fc24asj7lkcn9n3l0zbabrx89s9zi4im0gx")))) (properties `((upstream-name . "sodium"))) (build-system r-build-system) (inputs (list libsodium)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/sodium") (synopsis "R bindings to the libsodium crypto library") (description "This package provides bindings to libsodium: a library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.") (license license:expat))) (define-public r-softimpute (package (name "r-softimpute") (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "softImpute" version)) (sha256 (base32 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a")))) (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran r-knitr)) (home-page "https://cran.r-project.org/web/packages/softImpute") (synopsis "Matrix completion via iterative soft-thresholded SVD") (description "This package provides iterative methods for matrix completion that use nuclear-norm regularization. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank @dfn{single value decompositions} (SVDs) on large sparse centered matrices (i.e. principal components).") (license license:gpl2))) (define-public r-som (package (name "r-som") (version "0.3-5.1") (source (origin (method url-fetch) (uri (cran-uri "som" version)) (sha256 (base32 "1fbza1jxvwrkf5x3inkj36vshhkn7mz0ajqlxalbfmk6ngjw1x56")))) (properties `((upstream-name . "som"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=som") (synopsis "Self-organizing map") (description "This package implements a self-organizing map which has application in gene clustering. It provides functions like: @itemize @item filtering data by certain floor, ceiling, max/min ratio, and max - min difference; @item normalization of the data; @item get the average distortion measure; @item train a self-organizing map; @item summarize a som object; @item yeast cell cycle. @end itemize") (license license:gpl3+))) (define-public r-fftwtools (package (name "r-fftwtools") (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "fftwtools" version)) (sha256 (base32 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i")))) (build-system r-build-system) (inputs (list fftw)) (native-inputs (list pkg-config)) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description "This package provides a wrapper for several FFTW functions. It provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using the FFTW3 library. The package includes the functions @code{fftw()} and @code{mvfftw()} which are designed to mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. The FFT functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.") (license license:gpl2+))) (define-public r-tiff (package (name "r-tiff") (version "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 "0p41irri0nxg9mm06g8jp5zqssv80g5zg0iifrr7ancjkxqww46z")))) (build-system r-build-system) (inputs (list libtiff libjpeg-turbo zlib)) (native-inputs (list pkg-config)) (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description "This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.") ;; Either of these two license versions. (license (list license:gpl2 license:gpl3)))) (define-public r-nlp (package (name "r-nlp") (version "0.3-0") (source (origin (method url-fetch) (uri (cran-uri "NLP" version)) (sha256 (base32 "1v5kszwj56hdyd07ya9p0caxrd4ckpa1x6d0y6d1xrsi074638n0")))) (properties `((upstream-name . "NLP"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/NLP/") (synopsis "Natural language processing infrastructure") (description "This package provides basic classes and methods for Natural Language Processing.") (license license:gpl3))) (define-public r-tm (package (name "r-tm") (version "0.7-14") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 "103n9m9vh1s1fn2wlab5qm4i1dx4wq0ffl7v69mwa6mvdklfw7ks")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs (list r-bh r-nlp r-rcpp r-slam r-xml2)) (home-page "https://tm.r-forge.r-project.org/") (synopsis "Text mining package") (description "This package provides a framework for text mining applications within R.") (license license:gpl3))) (define-public r-waffle (package (name "r-waffle") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "waffle" version)) (sha256 (base32 "17z05mlnp2k9dywr0bbqz633sq1xs8q9879bl2na1in39qxq0l76")))) (properties `((upstream-name . "waffle"))) (build-system r-build-system) (propagated-inputs (list r-curl r-dt r-extrafont r-ggplot2 r-gridextra r-gtable r-htmlwidgets r-plyr r-rcolorbrewer r-rlang r-stringr)) (home-page "https://github.com/hrbrmstr/waffle/tree/cran") (synopsis "Creating waffle chart visualizations in R") (description "This package creates square pie charts also known as waffle charts. These can be used to communicate parts of a whole for categorical quantities. To emulate the percentage view of a pie chart, a 10x10 grid should be used. In this way each square is representing 1% of the total. Waffle provides tools to create charts as well as stitch them together. Isotype pictograms can be made by using glyphs.") (license license:gpl2+))) (define-public r-waveslim (package (name "r-waveslim") (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "waveslim" version)) (sha256 (base32 "0xd7006skrsvkwj4pkxqbfsbs58rfcpfcfk1lf0gsd2y0wisi60y")))) (build-system r-build-system) (propagated-inputs (list r-multitaper)) (home-page "http://waveslim.blogspot.com") (synopsis "Basic wavelet routines for signal processing") (description "This package provides basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).") (license license:bsd-3))) (define-public r-word2vec (package (name "r-word2vec") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "word2vec" version)) (sha256 (base32 "14ba0cj430d02bd6fay3nl4ldwqyj77iwjm4gzgdc0f6sx597iiq")))) (properties `((upstream-name . "word2vec"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppprogress)) (home-page "https://github.com/bnosac/word2vec") (synopsis "Distributed representations of words") (description "Learn vector representations of words by continuous bag of words and skip-gram implementations of the word2vec algorithm. The techniques are detailed in the paper \"Distributed Representations of Words and Phrases and their Compositionality\" by Mikolov et al. (2013), available at <arXiv:1310.4546>.") (license license:asl2.0))) (define-public r-wordcloud (package (name "r-wordcloud") (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "wordcloud" version)) (sha256 (base32 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-rcpp ;; The "tm" package is only "suggested" according to CRAN, but the ;; wordcloud package cannot be loaded without it. r-tm)) (home-page "https://cran.r-project.org/web/packages/wordcloud") (synopsis "Word clouds") (description "This package provides functionality to create pretty word clouds, visualize differences and similarity between documents, and avoid over-plotting in scatter plots with text.") (license license:lgpl2.1))) (define-public r-colorramps (package (name "r-colorramps") (version "2.3.4") (source (origin (method url-fetch) (uri (cran-uri "colorRamps" version)) (sha256 (base32 "1y4gn6v8wmwq3wcfgdnx1ah2qa53gayvbfa62kp286ga4c8k3prw")))) (properties `((upstream-name . "colorRamps"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/colorRamps") (synopsis "Build color tables") (description "This package provides features to build gradient color maps.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-tidytree (package (name "r-tidytree") (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 (base32 "14i2v6ryqw4cd74n8kz4qwwx730wzx4f0rssg5vgm0vjfsx0kafv")))) (build-system r-build-system) (propagated-inputs (list r-ape r-cli r-dplyr r-lazyeval r-magrittr r-pillar r-rlang r-tibble r-tidyr r-tidyselect r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/GuangchuangYu/tidytree") (synopsis "Tidy tool for phylogenetic tree data manipulation") (description "Phylogenetic trees generally contain multiple components including nodes, edges, branches and associated data. This package provides an approach to convert tree objects to tidy data frames. It also provides tidy interfaces to manipulate tree data.") (license license:artistic2.0))) (define-public r-rvcheck (package (name "r-rvcheck") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a")))) (build-system r-build-system) (propagated-inputs (list r-biocmanager r-yulab-utils)) (home-page "https://cran.r-project.org/web/packages/rvcheck") (synopsis "R package version check") (description "This package provides tools to check the latest release version of R and R packages (on CRAN, Bioconductor or Github).") (license license:artistic2.0))) (define-public r-doc2vec (package (name "r-doc2vec") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "doc2vec" version)) (sha256 (base32 "0249hm0103kxxsi4gks4h20wf6p00gbrk9jf8c148mbja1l56f6v")))) (properties `((upstream-name . "doc2vec"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/bnosac/doc2vec") (synopsis "Distributed representations of sentences, documents and topics") (description "Learn vector representations of sentences, paragraphs or documents by using the Paragraph Vector algorithms, namely the distributed bag of words (PV-DBOW) and the distributed memory (PV-DM) model. Top2vec finds clusters in text documents by combining techniques to embed documents and words and density-based clustering. It does this by embedding documents in the semantic space as defined by the doc2vec algorithm. Next it maps these document embeddings to a lower-dimensional space using the Uniform Manifold Approximation and Projection (UMAP) clustering algorithm and finds dense areas in that space using a Hierarchical Density-Based Clustering technique (HDBSCAN). These dense areas are the topic clusters which can be represented by the corresponding topic vector which is an aggregate of the document embeddings of the documents which are part of that topic cluster. In the same semantic space similar words can be found which are representative of the topic.") (license license:expat))) (define-public r-docopt (package (name "r-docopt") (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "docopt" version)) (sha256 (base32 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz")))) (build-system r-build-system) (home-page "https://github.com/docopt/docopt.R") (synopsis "Command-line interface specification language") (description "This package enables you to define a command-line interface by just giving it a description in the specific format.") (license license:expat))) (define-public r-sparsesvd (package (name "r-sparsesvd") (version "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "sparsesvd" version)) (sha256 (base32 "0dnqjqypjwac8aqdqsqdgcd70lyrfv6idz8q2kzjiv1sxrlwqh5v")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") (synopsis "Sparse truncated singular value decomposition") (description "This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported.") ;; SVDLIBC is released under BSD-2. The R interface is released under ;; BSD-3. (license (list license:bsd-3 license:bsd-2)))) (define-public r-speedglm (package (name "r-speedglm") (version "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "speedglm" version)) (sha256 (base32 "0jxvh9gbhip1hj7hzjs5fj8iw6ibvl6hc0llcg2j9wqgq5vkcrpq")))) (build-system r-build-system) (propagated-inputs (list r-biglm r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/speedglm") (synopsis "Fit linear and generalized linear models to large data sets") (description "This package provides tools for fitting linear models and generalized linear models to large data sets by updating algorithms.") ;; Any version of the GPL (license license:gpl2+))) (define-public r-densityclust (package (name "r-densityclust") (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "densityClust" version)) (sha256 (base32 "0iiq2zal792741z1a23h7cy9jp4hsc7513dxain132526f1yrzsl")))) (properties `((upstream-name . "densityClust"))) (build-system r-build-system) (propagated-inputs (list r-cpp11 r-fnn r-ggplot2 r-ggrepel r-gridextra r-rcolorbrewer r-rtsne)) (home-page "https://cran.r-project.org/web/packages/densityClust") (synopsis "Clustering by fast search and find of density peaks") (description "This package provides an improved implementation (based on k-nearest neighbors) of the density peak clustering algorithm, originally described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle large datasets (> 100,000 samples) very efficiently.") (license license:gpl2+))) (define-public r-combinat (package (name "r-combinat") (version "0.0-8") (source (origin (method url-fetch) (uri (cran-uri "combinat" version)) (sha256 (base32 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/combinat") (synopsis "Combinatorics utilities") (description "This package provides assorted routines for combinatorics.") (license license:gpl2))) (define-public r-qlcmatrix (package (name "r-qlcmatrix") (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "qlcMatrix" version)) (sha256 (base32 "0d38jb653787s05g8syc9wgaljaifmkviijwz5rzcd881glgs8sv")))) (properties `((upstream-name . "qlcMatrix"))) (build-system r-build-system) (propagated-inputs (list r-docopt r-matrix r-slam r-sparsesvd)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/qlcMatrix") (synopsis "Sparse matrix functions for quantitative language comparison") (description "This package provides an extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for the special data format used for @dfn{quantitative language comparison} (QLC).") (license license:gpl3))) (define-public r-qmri (package (name "r-qmri") (version "1.2.7.6") (source (origin (method url-fetch) (uri (cran-uri "qMRI" version)) (sha256 (base32 "0mbxgg80p159vkz05hbzvvip7h5y5rpvjrjnq1vivz855dk0053g")))) (properties `((upstream-name . "qMRI"))) (build-system r-build-system) (propagated-inputs (list r-adimpro r-aws r-awsmethods r-oro-nifti r-stringr)) (native-inputs (list gfortran r-knitr)) (home-page "http://www.wias-berlin.de/research/ats/imaging/") (synopsis "Methods for quantitative magnetic resonance imaging (qMRI)") (description "This package provides implementation of methods for estimation of quantitative maps from @dfn{Multi-Parameter Mapping} (MPM) acquisitions including adaptive smoothing methods in the framework of the ESTATICS model. The smoothing method is described in Mohammadi et al. (2017). <doi:10.20347/WIAS.PREPRINT.2432>. Usage of the package is also described in Polzehl and Tabelow (2019), Magnetic Resonance Brain Imaging, Chapter 6, Springer, Use R! Series. <doi:10.1007/978-3-030-29184-6_6>.") (license license:gpl2+))) (define-public r-ddrtree (package (name "r-ddrtree") (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "DDRTree" version)) (sha256 (base32 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) (properties `((upstream-name . "DDRTree"))) (build-system r-build-system) (propagated-inputs (list r-bh r-irlba r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/DDRTree") (synopsis "Learning principal graphs with DDRTree") (description "This package provides an implementation of the framework of @dfn{reversed graph embedding} (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of the data simultaneously. DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the ordering as well as the intrinsic structure of single cell genomics data. In general, it could be used to reconstruct the temporal progression as well as the bifurcation structure of any data type.") (license license:asl2.0))) (define-public r-corpcor (package (name "r-corpcor") (version "1.6.10") (source (origin (method url-fetch) (uri (cran-uri "corpcor" version)) (sha256 (base32 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i")))) (build-system r-build-system) (home-page "https://strimmerlab.org/software/corpcor/") (synopsis "Efficient estimation of covariance and (partial) correlation") (description "This package implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.") (license license:gpl3+))) (define-public r-rspectra (package (name "r-rspectra") (version "0.16-2") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 "0zma49ah0sycjdx95m8mac21daa7p3gp9cg1mffygzhrjpblkwd2")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/yixuan/RSpectra") (synopsis "Solvers for large-scale Eigenvalue and SVD problems") (description "This package provides an R interface to the Spectra library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than @code{eigen()} if k << n.") ;; MPL 2 or later. (license license:mpl2.0))) (define-public r-vbsr (package (name "r-vbsr") (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "vbsr" version)) (sha256 (base32 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/vbsr") (synopsis "Variational Bayes spike regression regularized linear models") (description "This package provides an efficient algorithm for solving ultra-sparse regularized regression models using a variational Bayes algorithm with a spike prior. The algorithm is solved on a path, with coordinate updates, and is capable of generating very sparse models. Very general model diagnostics for controlling type-1 errors are also provided.") (license license:gpl2))) (define-public r-flare (package (name "r-flare") (version "1.7.0.1") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-lattice r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/flare") (synopsis "Family of Lasso regression implementations") (description "This package provides implementations of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear models.") (license license:gpl2))) (define-public r-lassopv (package (name "r-lassopv") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "lassopv" version)) (sha256 (base32 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) (build-system r-build-system) (propagated-inputs (list r-lars)) (home-page "https://github.com/lingfeiwang/lassopv") (synopsis "Non-parametric p-value estimation for predictors in Lasso") (description "This package enables you to estimate the p-values for predictors x against target variable y in Lasso regression, using the regularization strength when each predictor enters the active set of regularization path for the first time as the statistic.") (license license:gpl3))) (define-public r-splitstackshape (package (name "r-splitstackshape") (version "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "splitstackshape" version)) (sha256 (base32 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) (home-page "https://github.com/mrdwab/splitstackshape") (synopsis "Stack and reshape datasets after splitting concatenated values") (description "Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The @code{concat.split} (cSplit) family of functions provided by this package splits such data into separate cells. This package also includes functions to stack groups of columns and to reshape wide data, even when the data are \"unbalanced\"---something which @code{reshape} (from base R) does not handle, and which @code{melt} and @code{dcast} from @code{reshape2} do not easily handle.") (license license:gpl3))) (define-public r-tfmpvalue (package (name "r-tfmpvalue") (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "TFMPvalue" version)) (sha256 (base32 "1rsxqvq1nkyhwmhm7mf7rd02rvh7xinnhqbqic6q9vicbvkmdnxr")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/ge11232002/TFMPvalue") (synopsis "P-value computation for position weight matrices") (description "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match scores. TFMPvalue provides the accurate calculation of a p-value with a score threshold for position weight matrices, or the score with a given p-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) (define-public r-rnaturalearth (package (name "r-rnaturalearth") (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "rnaturalearth" version)) (sha256 (base32 "1vfkn4bf77mr2n7dhmnl55ma4cvwy2nazhizmdqd98w2ydl13z3p")))) (properties `((upstream-name . "rnaturalearth"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-sf r-terra)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=rnaturalearth") (synopsis "World map data from Natural Earth") (description "This package facilitates mapping by making natural earth map data from @url{https://www.naturalearthdata.com/} more easily available to R users.") (license license:expat))) (define-public r-rnaturalearthdata (package (name "r-rnaturalearthdata") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rnaturalearthdata" version)) (sha256 (base32 "0k8yzgpbf8d2jxxy9vzqfa3z3w4h3i9kp4rc811f4pspxbqzmzp1")))) (properties `((upstream-name . "rnaturalearthdata"))) (build-system r-build-system) (home-page "https://github.com/ropenscilabs/rnaturalearthdata") (synopsis "World vector map data from Natural Earth") (description "This package provides vector map data from @url{https://www.naturalearthdata.com/}. Access functions are provided in the accompanying package @code{rnaturalearth}.") (license license:cc0))) (define-public r-rncl (package (name "r-rncl") (version "0.8.7") (source (origin (method url-fetch) (uri (cran-uri "rncl" version)) (sha256 (base32 "0flrqz7pansy11ds23qv06bcmh6vxqljq0517v6292ibbx7nx1qx")))) (build-system r-build-system) (propagated-inputs (list r-progress r-rcpp)) (home-page "https://github.com/fmichonneau/rncl") (synopsis "Interface to the Nexus class library") (description "This package provides an interface to the Nexus class library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s @code{phylo4(d)}. This functionality is demonstrated with @code{read_newick_phylo()} and @code{read_nexus_phylo()}.") (license license:bsd-2))) (define-public r-phylobase (package (name "r-phylobase") (version "0.8.12") (source (origin (method url-fetch) (uri (cran-uri "phylobase" version)) (sha256 (base32 "084gfzq51acmvzbsfpkqv3kgghdbncnwr008f95yf5b2vihcm0cv")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-rcpp r-rncl r-rnexml)) (native-inputs (list r-knitr)) (home-page "https://github.com/fmichonneau/phylobase") (synopsis "Base package for phylogenetic structures and comparative data") (description "This package provides a base @code{S4} class for comparative methods, incorporating one or more trees and trait data.") (license license:gpl2+))) (define-public r-phylotools (package (name "r-phylotools") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "phylotools" version)) (sha256 (base32 "1dhk1ncp5zi4zl1xfnjz64v983dm7bq7iimfjin80j0bdcpps44w")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-rnexml (package (name "r-rnexml") (version "2.4.11") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 "0ipxdhfzccpqmnfrqdy8bizm80k2chhdlzg3p0dl05p8n35i6s94")))) (build-system r-build-system) (propagated-inputs (list r-ape r-dplyr r-httr r-plyr r-reshape2 r-rlang r-stringi r-stringr r-tidyr r-uuid r-xml r-xml2)) (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/RNeXML/") (synopsis "Semantically rich I/O for the NeXML Format") (description "This package provides access to phyloinformatic data in NeXML format. The package should add new functionality to R such as the possibility to manipulate NeXML objects in more various and refined way and compatibility with @code{ape} objects.") (license license:bsd-3))) (define-public r-rnifti (package (name "r-rnifti") (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 "1s0q1vs6hzg1xadk43rxqxi55swkl7pgsnw45im5vgsz1wxgg375")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/jonclayden/RNifti") (synopsis "Fast R and C++ access to NIfTI images") (description "This package provides very fast read and write access to images stored in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. It also provides a C/C++ API that can be used by other packages.") (license license:gpl2))) (define-public r-shades (package (name "r-shades") (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "shades" version)) (sha256 (base32 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/shades") (synopsis "Simple color manipulation") (description "This package provides functions for easily manipulating colors, creating color scales and calculating color distances.") (license license:bsd-3))) (define-public r-ore (package (name "r-ore") (version "1.7.4.1") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 (base32 "01ayvjyjbarmi7l2jwp7bp4m0k42zy8bvf9rbwynfwmm8mv6vx0j")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") (description "This package provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.") (license license:bsd-3))) (define-public r-reportr (package (name "r-reportr") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "reportr" version)) (sha256 (base32 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) (build-system r-build-system) (propagated-inputs (list r-ore)) (home-page "https://github.com/jonclayden/reportr") (synopsis "General message and error reporting system") (description "This package provides a system for reporting messages, which offers certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current \"output level\".") (license license:gpl2))) (define-public r-tractor-base (package (name "r-tractor-base") (version "3.4.2") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 "12mp5x6c7c82a4z7p39cb478kwwf6lkrgbis6ak00yibsd3n6na3")))) (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs (list r-ore r-reportr r-rnifti r-shades)) (home-page "https://www.tractor-mri.org.uk") (synopsis "Read, manipulate and visualize magnetic resonance images") (description "This package provides functions for working with magnetic resonance images. It supports reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualization; flexible image manipulation; metadata and sparse image handling.") (license license:gpl2))) (define-public r-gridpattern (package (name "r-gridpattern") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "gridpattern" version)) (sha256 (base32 "1fa787m4ns3s7xnai1kqplz32nhy4pa1v6w7kzyjv9qlyfhvrw92")))) (properties `((upstream-name . "gridpattern"))) (build-system r-build-system) (propagated-inputs (list r-glue r-memoise r-png r-rlang r-sf)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://trevorldavis.com/R/gridpattern/") (synopsis "Grid pattern grobs") (description "This package provides grid grobs that fill in a user-defined area with various patterns. It includes enhanced versions of the geometric and image-based patterns originally contained in the ggpattern package as well as original @code{pch}, @code{polygon_tiling}, @code{regular_polygon}, @code{rose}, @code{text}, @code{wave}, and @code{weave} patterns plus support for custom user-defined patterns.") (license license:expat))) (define-public r-gridsvg (package (name "r-gridsvg") (version "1.7-5") (source (origin (method url-fetch) (uri (cran-uri "gridSVG" version)) (sha256 (base32 "1p8qnx9q96bni39x44l40rgcdi9r440zbipdfvkbs2paysx6mkr5")))) (properties `((upstream-name . "gridSVG"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-xml)) (home-page "https://cran.r-project.org/package=gridSVG") (synopsis "Export grid gaphics as SVG") (description "This package provides functions to export graphics drawn with package grid to SVG format. Extra functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.") ;; Any version of the GPL. (license (list license:gpl2 license:gpl3)))) (define-public r-grimport (package (name "r-grimport") (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 "196h7i4y1gzkwlybml9iz78p5xsx7y22nk5pmzibryn5amdbdy05")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs (list ghostscript)) (propagated-inputs (list r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport") (synopsis "Convert, import, and draw PostScript pictures") (description "This package provides functions for converting, importing, and drawing PostScript pictures in R plots.") (license license:gpl2+))) (define-public r-grimport2 (package (name "r-grimport2") (version "0.3-3") (source (origin (method url-fetch) (uri (cran-uri "grImport2" version)) (sha256 (base32 "11glz1yi76235x3di9r7nny0nfcisk12acc4xsm4m2d9ingjh4pn")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-kohonen (package (name "r-kohonen") (version "3.0.12") (source (origin (method url-fetch) (uri (cran-uri "kohonen" version)) (sha256 (base32 "188cxw2fvpfr3dyi8g52igcyc8d5jffyn6rhc84dja52da8lp520")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/kohonen") (synopsis "Supervised and unsupervised self-organising maps") (description "This package provides functions to train @dfn{self-organising maps} (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.") 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It was designed as a R companion to the book \"Introduction to Multivariate Statistical Analysis in Chemometrics\" written by K. Varmuza and P. Filzmoser (2009).") (license license:gpl3+))) (define-public r-chemometricswithr (package (name "r-chemometricswithr") (version "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "ChemometricsWithR" version)) (sha256 (base32 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) (properties `((upstream-name . "ChemometricsWithR"))) (build-system r-build-system) (propagated-inputs (list r-devtools r-kohonen r-mass r-pls)) (home-page "https://github.com/rwehrens/CWR") (synopsis "Chemometrics with R") (description "This package provides functions and scripts used in the book \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences\" by Ron Wehrens, Springer (2011).") 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(license license:gpl3+))) (define-public r-dotcall64 (package (name "r-dotcall64") (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 "06y9y9m5prjvqlprqpanbamgr6jkw27wj7nnha5ayyn08zbxgf11")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") (synopsis "Enhanced foreign function interface supporting long vectors") (description "This package provides @code{.C64()}, an enhanced version of @code{.C()} and @code{.Fortran()} from the R foreign function interface. @code{.C64()} supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.") (license license:gpl2+))) (define-public r-spam (package (name "r-spam") (version "2.10-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 (base32 "0ydc513jg7phzdqg8jp7210ayrrmxq91jafqzx8z1v0172i8d73i")))) (build-system r-build-system) (propagated-inputs (list r-dotcall64 r-rcpp)) (native-inputs (list gfortran r-knitr r-r-rsp)) (home-page "https://www.math.uzh.ch/pages/spam/") (synopsis "Sparse matrix algebra") (description "This package provides a set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: @enumerate @item it only supports (essentially) one sparse matrix format; @item it is based on transparent and simple structure(s); @item it is tailored for MCMC calculations within G(M)RF; @item and it is fast and scalable (with the extension package @code{spam64}). @end enumerate\n") ;; Either of these licenses (license (list license:bsd-3 license:lgpl2.0)))) (define-public r-fields (package (name "r-fields") (version "16.2") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 (base32 "1r5kld45dgigbaavcx3c88ci0jd66zxan3fh2wypwvj7sl69a41r")))) (build-system r-build-system) (propagated-inputs (list r-maps r-spam r-viridislite)) (native-inputs (list gfortran)) (home-page "https://www.image.ucar.edu/fields") (synopsis "Tools for spatial data") (description "This is a package for curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets.") (license license:gpl2+))) (define-public r-spatialextremes (package (name "r-spatialextremes") (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "SpatialExtremes" version)) (sha256 (base32 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3")))) (properties `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) (propagated-inputs (list r-fields r-maps)) (home-page "https://spatialextremes.r-forge.r-project.org/") (synopsis "Modelling spatial extremes") (description "This package provides tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction.") (license license:gpl2+))) (define-public r-drc (package (name "r-drc") (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "drc" version)) (sha256 (base32 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) (build-system r-build-system) (propagated-inputs (list r-car r-gtools r-mass r-multcomp r-plotrix r-scales)) (home-page "https://cran.r-project.org/web/packages/drc") (synopsis "Analysis of dose-response curves") (description "This package provides a suite of flexible and versatile model fitting and after-fitting functions for the analysis of dose-response data.") (license license:gpl2+))) (define-public r-rmeta (package (name "r-rmeta") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "rmeta" version)) (sha256 (base32 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rmeta") (synopsis "Tools for meta-analysis") (description "This package provides functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. It draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.") (license license:gpl2))) (define-public r-bootstrap (package (name "r-bootstrap") (version "2019.6") (source (origin (method url-fetch) (uri (cran-uri "bootstrap" version)) (sha256 (base32 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/bootstrap") (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") (description "This package provides software and data for the book \"An Introduction to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. This package is primarily provided for projects already based on it, and for support of the book. New projects should preferentially use the recommended package \"boot\".") (license license:bsd-3))) (define-public r-survivalroc (package (name "r-survivalroc") (version "1.0.3.1") (source (origin (method url-fetch) (uri (cran-uri "survivalROC" version)) (sha256 (base32 "0p6irjs8a9xxgxwax0y9fzapcib237if3iy8g6lzv793mzmsyx41")))) (properties `((upstream-name . "survivalROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/survivalROC") (synopsis "Time-dependent ROC curve estimation from censored survival data") (description "Compute time-dependent ROC curve from censored survival data using Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") (license license:gpl2+))) (define-public r-locfdr (package (name "r-locfdr") (version "1.1-8") (source (origin (method url-fetch) (uri (cran-uri "locfdr" version)) (sha256 (base32 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/locfdr/") (synopsis "Computes local false discovery rates") (description "This package can be used to compute local false discovery rates.") (license license:gpl2))) (define-public r-logging (package (name "r-logging") (version "0.10-108") (source (origin (method url-fetch) (uri (cran-uri "logging" version)) (sha256 (base32 "13gd40ygx586vs6xcp6clg69a92aj8zxlk1rn3xzkx8klfjimjc5")))) (properties `((upstream-name . "logging"))) (build-system r-build-system) (home-page "https://github.com/WLOGSolutions/r-logging") (synopsis "R logging implementation of log4j") (description "This package implements the R version of the @code{log4j} package. It offers hierarchic loggers, multiple handlers per logger, level based filtering, space handling in messages and custom formatting.") (license license:gpl3))) (define-public r-logistf (package (name "r-logistf") (version "1.26.0") (source (origin (method url-fetch) (uri (cran-uri "logistf" version)) (sha256 (base32 "02qrh07c13khlpz3z3f6qq827h37j91i88n7jn3c8ky6r1lfa5pr")))) (properties `((upstream-name . "logistf"))) (build-system r-build-system) (propagated-inputs (list r-formula-tools r-matrix r-mgcv r-mice)) (home-page "https://cemsiis.meduniwien.ac.at/en/kb/science-research\ /software/statistical-software/firth-correction/") (synopsis "Firth's bias-reduced logistic regression") (description "Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal solution to the problem of separation in logistic regression, see Heinze and Schemper (2002) <doi:10.1002/sim.1047>. If needed, the bias reduction can be turned off such that ordinary maximum likelihood logistic regression is obtained. Two new modifications of Firth's method, FLIC and FLAC, lead to unbiased predictions and are now available in the package as well, see Puhr et al (2017) <doi:10.1002/sim.7273>.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-longdat (package (name "r-longdat") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "LongDat" version)) (sha256 (base32 "1rzkb7byd32jqvhf75zyvy0dlkq79aicz8j0x7lk821qiq4dfv6l")))) (properties `((upstream-name . "LongDat"))) (build-system r-build-system) (propagated-inputs (list r-bestnormalize r-car r-dplyr r-effsize r-emmeans r-ggplot2 r-glmmtmb r-lme4 r-magrittr r-mass r-patchwork r-reshape2 r-rlang r-rstatix r-stringr r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/CCY-dev/LongDat") (synopsis "Tool for covariate-sensitive longitudinal analysis on omics data") (description "This tool takes longitudinal dataset as input and analyzes if there is significant change of the features over time (a proxy for treatments), while detects and controls for covariates simultaneously. LongDat is able to take in several data types as input, including count, proportion, binary, ordinal and continuous data. The output table contains p values, effect sizes and covariates of each feature, making the downstream analysis easy.") (license license:gpl2))) (define-public r-longitudinal (package (name "r-longitudinal") (version "1.1.13") (source (origin (method url-fetch) (uri (cran-uri "longitudinal" version)) (sha256 (base32 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p")))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) (home-page "https://strimmerlab.org/software/longitudinal/") (synopsis "Analysis of multiple time course data") (description "This package contains general data structures and functions for longitudinal data with multiple variables, repeated measurements, and irregularly spaced time points. It also implements a shrinkage estimator of dynamical correlation and dynamical covariance.") (license license:gpl3+))) (define-public r-genenet (package (name "r-genenet") (version "1.2.16") (source (origin (method url-fetch) (uri (cran-uri "GeneNet" version)) (sha256 (base32 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1")))) (properties `((upstream-name . "GeneNet"))) (build-system r-build-system) (propagated-inputs (list r-corpcor r-fdrtool r-longitudinal)) (home-page "https://strimmerlab.org/software/genenet/") (synopsis "Modeling and infic' 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-absfiltergsea (package (name "r-absfiltergsea") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "AbsFilterGSEA" version)) (sha256 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) (properties `((upstream-name . "AbsFilterGSEA"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-deseq" ,r-deseq) ("r-limma" ,r-limma) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo))) (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") (synopsis "Improved false positive control of gene-permuting with absolute filtering") (description "This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.") (license license:gpl2))) (define-public r-calculus (package (name "r-calculus") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 "0hs7hzjl6xjza20v9zx9a1piywxa6w3h2rskr52d1dcbc0vwhinp")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/guidotti/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)))