diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 2964 |
1 files changed, 2850 insertions, 114 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 423bb5b54f..975884e881 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> @@ -10,6 +11,8 @@ ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com> +;;; Copyright © 2018 Leo Famulari <leo@famulari.name> +;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,20 +33,29 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system r) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages 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 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) #:use-module (gnu packages image) + #:use-module (gnu packages javascript) + #:use-module (gnu packages lisp) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -55,14 +67,14 @@ (define-public r-clipr (package (name "r-clipr") - (version "0.4.1") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 - "061x84ildc7g1p91yw5iyj8lpqdf4hqv36as85lw8c6qv9ywbsqv")))) + "1grx0lyww1cxmdvsr44wmbhz9i6zmiwxbchb97gxrfi9gy5kyc7x")))) (build-system r-build-system) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") @@ -71,6 +83,82 @@ the system clipboards.") (license license:gpl3))) +(define-public r-sys + (package + (name "r-sys") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sys" version)) + (sha256 + (base32 + "10ml2492bdllh6cz2zl192ip0fdgjkkgayggd3ghswsj5gjv5hrh")))) + (build-system r-build-system) + (home-page "https://github.com/jeroen/sys") + (synopsis "Powerful and reliable tools for running system commands in R") + (description + "This package provides drop-in replacements for the base @code{system2()} +function with fine control and consistent behavior across platforms. It +supports clean interruption, timeout, background tasks, and streaming STDIN / +STDOUT / STDERR over binary or text connections. The package also provides +functions for evaluating expressions inside a temporary fork. Such +evaluations have no side effects on the main R process, and support reliable +interrupts and timeouts. This provides the basis for a sandboxing +mechanism.") + (license license:expat))) + +(define-public r-askpass + (package + (name "r-askpass") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "askpass" version)) + (sha256 + (base32 + "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) + (build-system r-build-system) + (propagated-inputs `(("r-sys" ,r-sys))) + (home-page "https://github.com/jeroen/askpass") + (synopsis "Safe password entry for R") + (description + "This package provides cross-platform utilities for prompting the user +for credentials or a passphrase, for example to authenticate with a server or +read a protected key.") + (license license:expat))) + +(define-public r-vegan + (package + (name "r-vegan") + (version "2.5-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "vegan" version)) + (sha256 + (base32 + "023xznh0iy0496icpchadmp7a3rk3nj9s48fvwlvp3dssw58yp3c")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-knitr" ,r-knitr) ; needed for vignettes + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-permute" ,r-permute))) + (home-page "https://cran.r-project.org/web/packages/vegan") + (synopsis "Functions for community ecology") + (description + "The vegan package provides tools for descriptive community ecology. It +has most basic functions of diversity analysis, community ordination and +dissimilarity analysis. Most of its multivariate tools can be used for other +data types as well.") + (license license:gpl2+))) + (define-public r-tidyverse (package (name "r-tidyverse") @@ -202,18 +290,17 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "3.0.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1rxbxy6kn7dj90z9hpppr9cnpvnxzknba2dwrdp0lrk5dh462qz3")))) + "15l1qfa3aigba2ghgr2gwcjjy7anagrwg8khsd36fymwkmqj5g69")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-r6" ,r-r6) + `(("r-r6" ,r-r6) ("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") @@ -226,17 +313,18 @@ that.") (define-public r-readxl (package (name "r-readxl") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 - "05ii8knrg4jji6h7bv6bfpn279b6x52yrskdx5rv7b0hcpy22gdn")))) + "1mwm389skl4ahcwsmhvx31pjkrn6y9igpnhsczwg6yza886q7j19")))) (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") @@ -276,17 +364,656 @@ the embedded @code{RapidXML} C++ library.") into a pipeline of data manipulation and visualisation.") (license license:gpl3))) +(define-public r-httpuv + (package + (name "r-httpuv") + (version "1.4.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "httpuv" version)) + (sha256 + (base32 + "0mqd40jckdpkjw1jjd860cdwkb03l6dkh931maijfdaqr1w9hwvn")))) + (build-system r-build-system) + (native-inputs + `(("r-rcpp" ,r-rcpp) + ("pkg-config" ,pkg-config))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-later" ,r-later) + ("r-promises" ,r-promises))) + (home-page "https://github.com/rstudio/httpuv") + (synopsis "HTTP and WebSocket server library for R") + (description + "The httpuv package provides low-level socket and protocol support for +handling HTTP and WebSocket requests directly from within R. It is primarily +intended as a building block for other packages, rather than making it +particularly easy to create complete web applications using httpuv alone.") + ;; This package includes third-party code that was originally released + ;; under various non-copyleft licenses. Full licensing information can be + ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE + (license license:gpl3+))) + +(define-public r-jsonlite + (package + (name "r-jsonlite") + (version "1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "jsonlite" version)) + (sha256 + (base32 + "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8")))) + (build-system r-build-system) + (home-page "http://arxiv.org/abs/1403.2805") + (synopsis "Robust, high performance JSON parser and generator for R") + (description + "The jsonlite package provides a fast JSON parser and generator optimized +for statistical data and the web. It offers flexible, robust, high +performance tools for working with JSON in R and is particularly powerful for +building pipelines and interacting with a web API. In addition to converting +JSON data from/to R objects, jsonlite contains functions to stream, validate, +and prettify JSON data. The unit tests included with the package verify that +all edge cases are encoded and decoded consistently for use with dynamic data +in systems and applications.") + (license license:expat))) + +(define-public r-servr + (package + (name "r-servr") + (version "0.11") + (source (origin + (method url-fetch) + (uri (cran-uri "servr" version)) + (sha256 + (base32 + "0yj3p1risf269n25dd56lqv82dsxv6a0aq4bcc1ddn9wv7h2xdfi")))) + (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 "0.3.6") + (source (origin + (method url-fetch) + (uri (cran-uri "htmltools" version)) + (sha256 + (base32 + "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/rstudio/htmltools/pull/68 + ;; The resource files are in the store and have mode 444. After + ;; copying the files R fails to remove them again because it doesn't + ;; have write access to them. + (add-after 'unpack 'copy-files-without-mode + (lambda _ + (substitute* "R/html_dependency.R" + (("file.copy\\(from, to, " prefix) + (string-append prefix + "copy.mode = FALSE, "))) + #t))))) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-rcpp" ,r-rcpp))) + (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 "1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "htmlwidgets" version)) + (sha256 + (base32 + "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/ramnathv/htmlwidgets") + (synopsis "HTML Widgets for R") + (description + "HTML widgets is a framework for creating HTML widgets that render in +various contexts including the R console, R Markdown documents, and Shiny web +applications.") + (license license:expat))) + +(define-public r-htmltable + (package + (name "r-htmltable") + (version "1.13.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "htmlTable" version)) + (sha256 + (base32 + "1l44b33xgj2698k6nz17r8fl0ink14ryzng803apm9d6bnv357v8")))) + (properties `((upstream-name . "htmlTable"))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-rstudioapi" ,r-rstudioapi) + ("r-stringr" ,r-stringr))) + (home-page "http://gforge.se/packages/") + (synopsis "Advanced tables for Markdown/HTML") + (description + "This package provides functions to build tables with advanced layout +elements such as row spanners, column spanners, table spanners, zebra +striping, and more. While allowing advanced layout, the underlying +CSS-structure is simple in order to maximize compatibility with word +processors such as LibreOffice. The package also contains a few text +formatting functions that help outputting text compatible with HTML or +LaTeX.") + (license license:gpl3+))) + +(define-public r-curl + (package + (name "r-curl") + (version "3.3") + (source (origin + (method url-fetch) + (uri (cran-uri "curl" version)) + (sha256 + (base32 + "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; The environment variable CURL_CA_BUNDLE is only respected when + ;; running Windows, so we disable the platform checks. + ;; This can be removed once the libcurl has been patched. + (add-after 'unpack 'allow-CURL_CA_BUNDLE + (lambda _ + (substitute* "R/onload.R" + (("if \\(!grepl\\(\"mingw\".*") + "if (FALSE)\n")) + (substitute* "src/handle.c" + (("#ifdef _WIN32") "#if 1")) + #t))))) + (inputs + `(("libcurl" ,curl) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/jeroenooms/curl") + (synopsis "HTTP client for R") + (description + "The @code{curl()} and @code{curl_download()} functions provide highly +configurable drop-in replacements for base @code{url()} and +@code{download.file()} with better performance, support for encryption, gzip +compression, authentication, and other @code{libcurl} goodies. The core of +the package implements a framework for performing fully customized requests +where data can be processed either in memory, on disk, or streaming via the +callback or connection interfaces.") + (license license:expat))) + +(define-public r-hwriter + (package + (name "r-hwriter") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "hwriter" version)) + (sha256 + (base32 + "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/hwriter") + (synopsis "Output R objects in HTML format") + (description + "This package provides easy-to-use and versatile functions to output R +objects in HTML format.") + (license license:lgpl2.1+))) + +(define-public r-rjson + (package + (name "r-rjson") + (version "0.2.20") + (source + (origin + (method url-fetch) + (uri (cran-uri "rjson" version)) + (sha256 + (base32 + "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rjson") + (synopsis "JSON library for R") + (description + "This package provides functions to convert R objects into JSON objects +and vice-versa.") + (license license:gpl2+))) + +(define-public r-shiny + (package + (name "r-shiny") + (version "1.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rstudio/shiny.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "041q2gzvzs13syfhbirmkik96asdji8dxnnbs63j7v1ks97hrvvz")))) + (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") + ("showdown/src/showdown.js" . + "showdown/compressed/showdown.js") + ("datepicker/js/bootstrap-datepicker.js" . + "datepicker/js/bootstrap-datepicker.min.js") + ("ionrangeslider/js/ion.rangeSlider.js" . + "ionrangeslider/js/ion.rangeSlider.min.js") + ("bootstrap/js/bootstrap.js" . + "bootstrap/js/bootstrap.min.js") + ("shiny.js" . + "shiny.min.js") + ("jquery.js" . + "jquery.min.js"))))) + #t))))) + (propagated-inputs + `(("r-crayon" ,r-crayon) + ("r-httpuv" ,r-httpuv) + ("r-mime" ,r-mime) + ("r-jsonlite" ,r-jsonlite) + ("r-xtable" ,r-xtable) + ("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-r6" ,r-r6) + ("r-sourcetools" ,r-sourcetools))) + (inputs + `(("js-datatables" ,js-datatables) + ("js-html5shiv" ,js-html5shiv) + ("js-json2" ,js-json2) + ("js-respond" ,js-respond) + ("js-selectize" ,js-selectize) + ("js-strftime" ,js-strftime) + ("js-highlight" ,js-highlight) + ("js-es5-shim" ,js-es5-shim))) + (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))) + +(define-public r-shinydashboard + (package + (name "r-shinydashboard") + (version "0.7.1") + (source (origin + (method url-fetch) + (uri (cran-uri "shinydashboard" version)) + (sha256 + (base32 + "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) + (build-system r-build-system) + ;; The directory inst/AdminLTE/ contains a minified JavaScript file. + ;; Regenerate it from the included sources. + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'generate-minified-javascript + (lambda _ + (with-directory-excursion "inst/AdminLTE" + (delete-file "app.min.js") + (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js"))) + (call-with-output-file "app.min.js" + (lambda (port) + (dump-port minified port)))))))))) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-promises" ,r-promises) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("uglify-js" ,uglify-js))) + (home-page "http://rstudio.github.io/shinydashboard/") + (synopsis "Create dashboards with shiny") + (description "This package provides an extension to the Shiny web +application framework for R, making it easy to create attractive dashboards.") + ;; This package includes software that was released under the Expat + ;; license, but the whole package is released under GPL version 2 or + ;; later. + (license license:gpl2+))) + +(define-public r-shinyfiles + (package + (name "r-shinyfiles") + (version "0.7.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyFiles" version)) + (sha256 + (base32 + "0dlcjrw96x72grg6j915070x8x98l7629pn86gf148iknflm7gd5")))) + (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-crosstalk + (package + (name "r-crosstalk") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "crosstalk" version)) + (sha256 + (base32 + "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-lazyeval" ,r-lazyeval) + ("r-r6" ,r-r6) + ("r-shiny" ,r-shiny))) + (home-page "https://rstudio.github.io/crosstalk/") + (synopsis "Inter-widget interactivity for HTML widgets") + (description + "This package provides building blocks for allowing HTML widgets to +communicate with each other, with Shiny or without (i.e. static @code{.html} +files). It currently supports linked brushing and filtering.") + (license license:expat))) + +(define-public r-rook + (package + (name "r-rook") + (version "1.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rook" version)) + (sha256 + (base32 + "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) + (properties `((upstream-name . "Rook"))) + (build-system r-build-system) + (propagated-inputs `(("r-brew" ,r-brew))) + (home-page "https://cran.r-project.org/web/packages/Rook") + (synopsis "Web server interface for R") + (description + "This package contains the Rook specification and convenience software +for building and running Rook applications. A Rook application is an R +reference class object that implements a @code{call} method or an R closure +that takes exactly one argument, an environment, and returns a list with three +named elements: the @code{status}, the @code{headers}, and the @code{body}.") + (license license:gpl2))) + +(define-public r-miniui + (package + (name "r-miniui") + (version "0.1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "miniUI" version)) + (sha256 + (base32 + "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) + (properties `((upstream-name . "miniUI"))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-shiny" ,r-shiny))) + (home-page "https://cran.r-project.org/web/packages/miniUI/") + (synopsis "Shiny UI widgets for small screens") + (description + "This package provides UI widget and layout functions for writing Shiny apps that +work well on small screens.") + (license license:gpl3))) + +(define-public r-feather + (package + (name "r-feather") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "feather" version)) + (sha256 + (base32 + "138vnlwhkwayyim4rbx6rnf91kzhfij6v2f91ppx2174ky5611h6")))) + (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 ('mapproj' and +'mapdata').") + (license license:gpl2))) + +(define-public r-mapproj + (package + (name "r-mapproj") + (version "1.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "mapproj" version)) + (sha256 + (base32 + "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2")))) + (build-system r-build-system) + (propagated-inputs `(("r-maps" ,r-maps))) + (home-page "https://cran.r-project.org/web/packages/mapproj") + (synopsis "Map projection in R") + (description "This package converts latitude/longitude into projected +coordinates.") + (license (list license:gpl2 ; The R interface + (license:non-copyleft ; The C code + "https://www.gnu.org/licenses/license-list.en.html#lucent102" + "Lucent Public License Version 1.02"))))) + +(define-public r-rgooglemaps + (package + (name "r-rgooglemaps") + (version "1.4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "RgoogleMaps" version)) + (sha256 + (base32 + "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4")))) + (properties `((upstream-name . "RgoogleMaps"))) + (build-system r-build-system) + (propagated-inputs `(("r-png" ,r-png))) + (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") + (synopsis "Use Google Maps in R") + (description "This package serves two purposes: +@enumerate +@item Provide a comfortable R interface to query the Google server for static + maps, and +@item Use the map as a background image to overlay plots within R. This + requires proper coordinate scaling. +@end enumerate\n") + (license license:gpl2+))) + +(define-public r-geosphere + (package + (name "r-geosphere") + (version "1.5-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "geosphere" version)) + (sha256 + (base32 + "186qdm5niq7v3d4w4rngx71znsgi44hnam7698bsx9ar5mg5b6wx")))) + (build-system r-build-system) + (propagated-inputs `(("r-sp" ,r-sp))) + (home-page "https://cran.r-project.org/web/packages/geosphere") + (synopsis "Spherical trigonometry") + (description "This package computes spherical trigonometry for geographic +applications. That is, compute distances and related measures for angular +(longitude/latitude) locations.") + (license license:gpl3+))) + +(define-public r-ggmap + (package + (name "r-ggmap") + (version "2.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggmap" version)) + (sha256 + (base32 + "144x6ycb2c3fvy5c68ww53m6gzi6kfvas7cpbn071z08n4xgb72f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-geosphere" ,r-geosphere) + ("r-ggplot2" ,r-ggplot2) + ("r-jpeg" ,r-jpeg) + ("r-mapproj" ,r-mapproj) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-proto" ,r-proto) + ("r-reshape2" ,r-reshape2) + ("r-rgooglemaps" ,r-rgooglemaps) + ("r-rjson" ,r-rjson) + ("r-scales" ,r-scales))) + (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 "1.1.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "0pp8xjf5lzqg1wr8cwxj4njx99vxwlflwjrd7jvyzwlfpwh7n1qa")))) + "12qh8nba1dxlsmcihrx126wmjyj8n511k17vqj10lfgvpwq2sydy")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -381,13 +1108,13 @@ XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (define-public r-colorspace (package (name "r-colorspace") - (version "1.3-2") + (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 - (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx")))) + (base32 "0mpmvz2sycjp4c9y3v3qin7mdjy812hwi7cyjnblcw6xb1ckq06f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") @@ -497,13 +1224,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1zxylcb0nr4qb5v6j199mc2pfgf2bpf00jrw47jajmv59qb0fwmx")))) + (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498")))) (build-system r-build-system) (home-page "http://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -723,14 +1450,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.4") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "1l28maiqi549z191srncxgabx5fnvf0lld7smzwfd3vr5cx8nqww")))) + "0qhn9jzw7gd0jp9rmqrlbmy5ql6hjsa68pkp0acfz1h215dl8ah9")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -753,14 +1480,14 @@ multi-dimensional data.") (define-public r-powerlaw (package (name "r-powerlaw") - (version "0.70.1") + (version "0.70.2") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 - "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m")))) + "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs @@ -1090,17 +1817,20 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-7") + (version "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "1b62gs7w1xqadqd7ir41jnxlcf14gcqfxd0915kn9ckdlsdrh0sw")))) + "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments - `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\""))) + `(#: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 @@ -1357,14 +2087,14 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.0-11") + (version "1.0-14") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "12hckg3y5j3zh9q1gwxkc27q813p2r42iqp7wdfiq6nj55jrh6w6")))) + "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -1521,14 +2251,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.3") + (version "1.6.4") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "0cayjspry3r2lcbvl77v5v52b2zarri3b8xsf87pw5a3jn9anxcf")))) + "0627cjlg55kzbzcy82w6wykmw2i57qhgfcabn2zy3ydfdswyxij1")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -1603,7 +2333,9 @@ the Kaplan-Meier and Aalen-Johansen methods.") "0ssy2qriiy6zdawriqcbl67qiq68ipml3frq7aqlq70r2fqyyw48")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) - (propagated-inputs `(("r-drr" ,r-drr))) + (propagated-inputs + `(("r-drr" ,r-drr) + ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description @@ -1656,6 +2388,61 @@ 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 "0.10.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "RMySQL" version)) + (sha256 + (base32 + "1gh4b730g2v78jg5iln8fkz808ri2vhnhnw43wzkkjpy53jh48sp")))) + (properties `((upstream-name . "RMySQL"))) + (build-system r-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("mariadb" ,mariadb) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-dbi" ,r-dbi))) + (home-page "https://github.com/r-dbi/RMySQL") + (synopsis "Database interface and MySQL driver for R") + (description + "This package provides a DBI interface to MySQL / MariaDB. The RMySQL +package contains an old implementation based on legacy code from S-PLUS which +is being phased out. A modern MySQL client based on Rcpp is available from +the RMariaDB package.") + (license license:gpl2))) + +(define-public r-rpostgresql + (package + (name "r-rpostgresql") + (version "0.6-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "RPostgreSQL" version)) + (sha256 + (base32 + "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) + (properties `((upstream-name . "RPostgreSQL"))) + (build-system r-build-system) + (inputs + `(("postgresql" ,postgresql))) + (propagated-inputs + `(("r-dbi" ,r-dbi))) + (home-page "https://github.com/tomoakin/RPostgreSQL") + (synopsis "R interface to the PostgreSQL database system") + (description + "This package provides a Database Interface (DBI) compliant driver for R +to access PostgreSQL database systems.") + ;; The whole package is released under GPL version 2. It includes code + ;; under the PostgreSQL license. + (license license:gpl2))) + (define-public r-geometry (package (name "r-geometry") @@ -1689,14 +2476,14 @@ Delaunay triangulation and convex hull computation.") (define-public r-ddalpha (package (name "r-ddalpha") - (version "1.3.4") + (version "1.3.8") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 - "16cn0bhbaz9l9k4y79sv2d4f7pvs7dyka273y89igs5jvr99kfj1")))) + "0gi0hl14ghgf65zxsvgzh9z6xx1nyi49cpx192lmwrwqn3dy7ba0")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -1796,14 +2583,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "1.8.10") + (version "1.8.12") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0n3frgzsfmnan6cp3yyq5h6c28v5pd7q5a42pp6byaa7n7d1v478")))) + "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -1827,21 +2614,42 @@ displays of path diagrams, factor analysis and structural equation models are created using basic graphics.") (license license:gpl2+))) +(define-public r-generics + (package + (name "r-generics") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "generics" version)) + (sha256 + (base32 + "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/generics") + (synopsis "Common S3 generics not provided by base R methods") + (description + "In order to reduce potential package dependencies and conflicts, +generics provides a number of commonly used S3 generics that are not provided +by base R methods related to model fitting.") + (license license:gpl2))) + (define-public r-broom (package (name "r-broom") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1r3831vq0fd5sh5841xr844sghg88z7ws91hg4jgnzbbkxfjp4ag")))) + "0bmf38yvwalqf5j5yrr48nsk5k3n75s0gwcw621hp5lgrgvnp7ns")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) ("r-nlme" ,r-nlme) ("r-purrr" ,r-purrr) ("r-reshape2" ,r-reshape2) @@ -1889,7 +2697,8 @@ provides a one-row summary of model-level statistics.") ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyselect" ,r-tidyselect) - ("r-timedate" ,r-timedate))) + ("r-timedate" ,r-timedate) + ("r-withr" ,r-withr))) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description @@ -2049,14 +2858,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.") (define-public r-jomo (package (name "r-jomo") - (version "2.6-5") + (version "2.6-6") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "109q5m69clrvvialxdxznd0wdb54ajhx84nj8slx8bf909a427mj")))) + "1048qb12cx7fs156jcqzwkfmsjadkgnrqd0krznyxpn873zr9lq2")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) @@ -2097,14 +2906,14 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.3-6") + (version "0.3-7") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "1pkqv4qazih3byws5z6629pp232n8ra56lip7502727b0b4bsndw")))) + "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) @@ -2282,16 +3091,18 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "16wkb26kv6qr34hv5zgqmgq6zzgysg9i78pvy2c097lr60v087v0")))) + "1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn")))) (build-system r-build-system) - (propagated-inputs `(("r-sm" ,r-sm))) + (propagated-inputs + `(("r-sm" ,r-sm) + ("r-zoo" ,r-zoo))) (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") (synopsis "Violin plot") (description @@ -2379,14 +3190,14 @@ where possible.") (define-public r-laeken (package (name "r-laeken") - (version "0.4.6") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 - "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6")))) + "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -2622,21 +3433,18 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.2.0") + (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 - "1pzx4ap4xa07gf9zkd6hacdsnb9sp3kb60a7v7ljl0ywrcpn1fn4")))) + "1skjyi767avc3safajlj3ikk9lf11zzyjybdcmx8m9y59rf319ql")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-crayon" ,r-crayon) - ("r-ps" ,r-ps) - ("r-r6" ,r-r6) - ("r-testthat" ,r-testthat))) + `(("r-ps" ,r-ps) + ("r-r6" ,r-r6))) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description @@ -2693,14 +3501,14 @@ available.") (define-public r-gclus (package (name "r-gclus") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "gclus" version)) (sha256 (base32 - "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn")))) + "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/gclus/") @@ -2812,14 +3620,14 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1q6arybmfqxhp5zqj1fri5pb8v7ywcv7bmgf81rrmgl892p4bn5f")))) + "1xnbb9sr5wn9dmp6m7cr4z7i6pmjvyabnfcx6x7i7mvdjmgvaf5k")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -2857,14 +3665,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.9") + (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "08w5hyq3ysh631d5whgcfv1bb007cdc0bjhb83vwmhazs6rgvyjy")))) + "02bz8zaka5j51zin976n5nmk19a0390d0gwgj4zrbh48hl313rqm")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -2926,14 +3734,14 @@ supports arbitrary vertex/edge/graph attributes.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.1.4") + (version "4.2.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "14dydm4c4dzc4v6ldxpn04q551nczzfablwibrd8lzgja8x9ksic")))) + "0q942g6kqmqxfss1cxb3yg8y5r1k1h5cyy99s1cfisrn6hqc6xhi")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) @@ -3126,14 +3934,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-45") + (version "0.10-46") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "14s1glh5zzdvdl05a2z7ymhgf962svxf8xircghg5sc649lb33n0")))) + "08kjw0bfj5gfcrxpblwqxwna8a5g9gnr7ya61qb02r263pyhm50j")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog) @@ -3270,14 +4078,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "1.4-1") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "10jl5l3xnigiq95829ssq69xbim97k851187dghc30awszcx4clh")))) + "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -3560,14 +4368,14 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "1fbk5i6w6cpam8s3acf4bgdp8hajn4digjjix3i6i4q3p2rvn6zx")))) + "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs @@ -3829,14 +4637,14 @@ multivariate plot methods.") (define-public r-fnn (package (name "r-fnn") - (version "1.1.2.1") + (version "1.1.2.2") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 - "1n61jrcmakqif8f827x4qnlhm2jqpj5fgjj65c4p0kdd8lzw8pqp")))) + "09k3k0h9ikbwq6225l7gd0nhimbji722680cr66c8n7zpvxn06mm")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") @@ -3947,14 +4755,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.6-1") + (version "1.6-2") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "0glfqgxr87900kigmkby2ff7qrjvd6aq595q85y056i5ckjcp615")))) + "0vnss6akk3564kbci3h5rq8ylpckz77cgmflly3gn6fki66f7g96")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -4087,14 +4895,14 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.10") + (version "0.5.16") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "158xg3vj0glk3fslwi6fywwmfym2b6kn3fdmjligdfy5lf68khix")))) + "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -4819,14 +5627,14 @@ to help insert or delete content at a specific location in the document.") (define-public r-abn (package (name "r-abn") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "00k0razgdb5y5f62622fm7rxkcxrxg470nyyb02dvpfp60254kvs")))) + "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) @@ -4947,14 +5755,14 @@ parse and convert strings into cases like snake or camel among others.") (define-public r-prediction (package (name "r-prediction") - (version "0.3.6") + (version "0.3.6.1") (source (origin (method url-fetch) (uri (cran-uri "prediction" version)) (sha256 (base32 - "19d7312f5lkqfglfvlgssnvyw7gl161s0xradcry44r1i6qp05j1")))) + "1znxpacd79fjkf84w3493p1vmafanqfxsspwpwpkmda323bsxj0n")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table))) @@ -4971,14 +5779,14 @@ other add-on packages.") (define-public r-sjlabelled (package (name "r-sjlabelled") - (version "1.0.14") + (version "1.0.16") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 - "0ayfzhm9bwjfaarq5z0gvn9kapjwj3532azgin97nr5fnjdhvgaw")))) + "1zi1ncna16zl9hcy7mzara4kjxqkgwcw9ncp388ss353wwc9y2nc")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -4988,9 +5796,7 @@ other add-on packages.") ("r-prediction" ,r-prediction) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) - ("r-snakecase" ,r-snakecase) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + ("r-snakecase" ,r-snakecase))) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description @@ -5004,14 +5810,14 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.7.6") + (version "2.7.7") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im")))) + "0xm9pmq17maivmjsygwx3bdjd71hf829qbx735hyxa69z9dhp24q")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -5117,14 +5923,14 @@ documents.") (define-public r-writexl (package (name "r-writexl") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 - "0r2v12dc4zqmr1agp6vbw0fc48i278018684x84psjjqfmnv14cf")))) + "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/ropensci/writexl") @@ -5214,14 +6020,14 @@ support for default values, positional argument support, etc.") (define-public r-findpython (package (name "r-findpython") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 - "1y08jk2ffmkf9zpwiz2xymjhfwqvls9vzsnq62v278ghw9d571jl")))) + "1zfcdcp4d48d2pzf5n59kqrfk2z9nnyzkx5j00gfmgfkadnv93x5")))) (build-system r-build-system) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") @@ -5234,21 +6040,21 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "1.1.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "0fzrbj87b274vf96azdnsjxk2nf45d5wy58vzmlah4b4h7q4j524")))) + "1qrp7hc8sm6ryw0zws76al865ansig1xbx8ljxz4wabh60msrz3i")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs `(("r-findpython" ,r-findpython) ("r-getopt" ,r-getopt) ("r-jsonlite" ,r-jsonlite) - ("r-proto" ,r-proto))) + ("r-r6" ,r-r6))) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description @@ -5339,14 +6145,14 @@ Group (Non-)Overlap considerations.") (define-public r-refgenome (package (name "r-refgenome") - (version "1.7.3") + (version "1.7.3.1") (source (origin (method url-fetch) (uri (cran-uri "refGenome" version)) (sha256 (base32 - "15p0ra2p1pwhy5ixbhsz1g79c5sc2aap4i4c8kil0m2syg9y45sn")))) + "1s4lxv5pqk6d0f0a9iclgv88yl346fwvzgraxh0gwpbym1yhh787")))) (properties `((upstream-name . "refGenome"))) (build-system r-build-system) (propagated-inputs @@ -5495,13 +6301,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-43") + (version "0.1-44") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "0hy4qzngcgafxxr6ld7n9a9wy979ji998gpcc32vidwyab66dj5h")))) + (base32 "11n956kid70931z0qyiql3v7nac1cfkamq44kzf9wl670pf8b033")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") @@ -5735,13 +6541,13 @@ and coverage methods to tune the choice of threshold.") (define-public r-ggformula (package (name "r-ggformula") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "ggformula" version)) (sha256 - (base32 "1pmpdfjfbrc6kcpq70cr1kbj2qy711hw940g2aiis6l443z706kh")))) + (base32 "01ngx8qh9lhmagng6abx2ky54zi3iyj5bpxlnw59slagwv7l6icx")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -5780,6 +6586,29 @@ while providing the intuitive capabilities of @code{r-ggplot2}.") used to teach mathematics, statistics, computation and modeling.") (license license:gpl2+))) +(define-public r-raster + (package + (name "r-raster") + (version "2.8-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "raster" version)) + (sha256 + (base32 + "14pcfznxm5kdwd908axkr9v1l0hzxlrwd8kwrz0liqnfh9cx5rsa")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-sp" ,r-sp))) + (home-page "http://www.rspatial.org/") + (synopsis "Geographic data analysis and modeling") + (description + "The package implements basic and high-level functions for reading, +writing, manipulating, analyzing and modeling of gridded spatial data. +Processing of very large files is supported.") + (license license:gpl3+))) + (define-public r-mosaic (package (name "r-mosaic") @@ -6444,13 +7273,13 @@ series.") (define-public r-acceptancesampling (package (name "r-acceptancesampling") - (version "1.0-5") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 - (base32 "18krmmyn8pn11aqd81kbvka68lnd36mnpdh7p3pz9r4m4vjj007x")))) + (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9")))) (properties `((upstream-name . "AcceptanceSampling"))) (build-system r-build-system) @@ -6542,14 +7371,14 @@ cross-sectional, time series, clustered, panel, and longitudinal data.") (define-public r-th-data (package (name "r-th-data") - (version "1.0-9") + (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 - "03xfvww0krw0fn76qmmvrj7dx4shin57qafwhkrggfg25hbqlcfq")))) + "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs @@ -6593,14 +7422,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.3.0") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0kdyy4qp332c4yyvp1cnh48h6ks6ffir5rjcv0py0vm3m8c3hh61")))) + "0mg6y007hfmr601cq4jgxl5ncwbx79kkh7xs2i504m0rinxj8bf5")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -6725,14 +7554,14 @@ detection, parallelism through BLAS and parallel user templates.") (define-public r-sjstats (package (name "r-sjstats") - (version "0.17.2") + (version "0.17.3") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 - "0c7g35vn7r9rylhp0gj1yfslg7jybwrhpqpp7vdcd90xfccih24r")))) + "02na2pzxp88yp52h7vs959fgydiddmns39m9x4i0vz8fp016bdf8")))) (build-system r-build-system) (propagated-inputs `(("r-bayesplot" ,r-bayesplot) @@ -6771,14 +7600,14 @@ models.") (define-public r-glmmtmb (package (name "r-glmmtmb") - (version "0.2.2.0") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 - "1clpkjlmsjmn3m1z5jqv8cgw6bvpqsy4nx6k947r0jya017ny5y5")))) + "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs @@ -6788,7 +7617,7 @@ models.") ("r-rcppeigen" ,r-rcppeigen) ("r-tmb" ,r-tmb))) (native-inputs - `(("r-knitr" ,r-knitr))) + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description @@ -6803,14 +7632,14 @@ differentiation.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "070c3fxmzajq2fy816s5pfqdyjlnzkabj97z7fcsva4h5rnqi9d6")))) + "152xyadj5m171z7dlzzy40y1fp2l9v46525dlw2al3qr0b7zpm61")))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon) @@ -6842,14 +7671,14 @@ results using @code{ggplot2}.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.6.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 - "13qvw2s3r96qfi8kfsn76m050ccnmckl31a9qv94xws8da99v2fk")))) + "0x9pbchmz4qf4c9bi52dhhgv1phfj03q1hnxic8vndl6xwib63cy")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs @@ -7305,14 +8134,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "3.13.1") + (version "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "1z8bj9zbc8h7w1xki9sc2p2rq6lv8gbcmiy9819z54d7lx1i9cnj")))) + "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -7712,18 +8541,17 @@ Scientific.") (define-public r-activity (package (name "r-activity") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 - "1lqajgxfps2h6amz1791vp3f52rs9ghmanq1nqfxqd2jmk3idkrx")))) + "11w2bz6p9xbzdh6773dmbbh6rws0h5dj18p8m0ivzizgq932vdzs")))) (build-system r-build-system) (propagated-inputs `(("r-circular" ,r-circular) - ("r-overlap" ,r-overlap) ("r-pbapply" ,r-pbapply))) (home-page "https://cran.r-project.org/web/packages/activity/") (synopsis "Animal activity statistics") @@ -7775,3 +8603,1911 @@ for evolution along a phylogenetic tree.") Japan, 2007) with Japanese demographic data and some demographic analysis related functions.") (license license:gpl2+))) + +(define-public r-stabledist + (package + (name "r-stabledist") + (version "0.7-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "stabledist" version)) + (sha256 + (base32 + "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86")))) + (build-system r-build-system) + (home-page "http://www.rmetrics.org") + (synopsis "Stable distribution functions") + (description + "This package provides density, probability and quantile functions, and +random number generation for (skew) stable distributions, using the +parametrizations of Nolan.") + (license license:gpl2+))) + +(define-public r-gsl + (package + (name "r-gsl") + (version "1.9-10.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "gsl" version)) + (sha256 + (base32 + "00isw2iha5af4s7rr8svqka9mkl9l26l8h2rnk4r7fkhh7fc97sg")))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (home-page "https://cran.r-project.org/web/packages/gsl") + (synopsis "Wrapper for the GNU Scientific Library") + (description + "This package provides an R wrapper for the special functions and quasi +random number generators of the GNU Scientific Library.") + (license license:gpl2+))) + +(define-public r-adgoftest + (package + (name "r-adgoftest") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ADGofTest" version)) + (sha256 + (base32 + "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) + (properties `((upstream-name . "ADGofTest"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ADGofTest") + (synopsis "Anderson-Darling GoF test") + (description + "This package provides an implementation of the Anderson-Darling GoF test +with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the +Anderson-Darling Distribution\".") + ;; Any version of the GPL. + (license license:gpl3+))) + +(define-public r-softimpute + (package + (name "r-softimpute") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "softImpute" version)) + (sha256 + (base32 + "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq")))) + (properties `((upstream-name . "softImpute"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/softImpute") + (synopsis "Matrix completion via iterative soft-thresholded SVD") + (description + "This package provides iterative methods for matrix completion that use +nuclear-norm regularization. The package includes procedures for centering +and scaling rows, columns or both, and for computing low-rank @dfn{single +value decompositions} (SVDs) on large sparse centered matrices (i.e. principal +components).") + (license license:gpl2))) + +(define-public r-fftwtools + (package + (name "r-fftwtools") + (version "0.9-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fftwtools" version)) + (sha256 + (base32 + "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6")))) + (build-system r-build-system) + (inputs `(("fftw" ,fftw))) + (home-page "https://github.com/krahim/fftwtools") + (synopsis "Wrapper for FFTW3") + (description + "This package provides a wrapper for several FFTW functions. It provides +access to the two-dimensional FFT, the multivariate FFT, and the +one-dimensional real to complex FFT using the FFTW3 library. The package +includes the functions @code{fftw()} and @code{mvfftw()} which are designed to +mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. +The FFT functions have a parameter that allows them to not return the +redundant complex conjugate when the input is real data.") + (license license:gpl2+))) + +(define-public r-tiff + (package + (name "r-tiff") + (version "0.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "tiff" version)) + (sha256 + (base32 + "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) + (build-system r-build-system) + (inputs + `(("libtiff" ,libtiff) + ("libjpeg" ,libjpeg) + ("zlib" ,zlib))) + (home-page "http://www.rforge.net/tiff/") + (synopsis "Read and write TIFF images") + (description + "This package provides an easy and simple way to read, write and display +bitmap images stored in the TIFF format. It can read and write both files and +in-memory raw vectors.") + ;; Either of these two license versions. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-waveslim + (package + (name "r-waveslim") + (version "1.7.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "waveslim" version)) + (sha256 + (base32 + "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://waveslim.blogspot.com") + (synopsis "Basic wavelet routines for signal processing") + (description + "This package provides basic wavelet routines for time series (1D), +image (2D) and array (3D) analysis. The code provided here is based on +wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk +and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from +Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet +pairs (Selesnick 2001, 2002).") + (license license:bsd-3))) + +(define-public r-wordcloud + (package + (name "r-wordcloud") + (version "2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "wordcloud" version)) + (sha256 + (base32 + "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/wordcloud") + (synopsis "Word clouds") + (description + "This package provides functionality to create pretty word clouds, +visualize differences and similarity between documents, and avoid +over-plotting in scatter plots with text.") + (license license:lgpl2.1))) + +(define-public r-colorramps + (package + (name "r-colorramps") + (version "2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "colorRamps" version)) + (sha256 + (base32 + "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z")))) + (properties `((upstream-name . "colorRamps"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/colorRamps") + (synopsis "Build color tables") + (description "This package provides features to build gradient color +maps.") + ;; Any version of the GPL + (license license:gpl3+))) + +(define-public r-tidytree + (package + (name "r-tidytree") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tidytree" version)) + (sha256 + (base32 + "1sx69wvlp7k761cmglrzq2jxkm2iq27x6bhhdcisj62wryj96wb2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-lazyeval" ,r-lazyeval) + ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/GuangchuangYu/tidytree") + (synopsis "Tidy tool for phylogenetic tree data manipulation") + (description + "Phylogenetic trees generally contain multiple components including nodes, +edges, branches and associated data. This package provides an approach to +convert tree objects to tidy data frames. It also provides tidy interfaces to +manipulate tree data.") + (license license:artistic2.0))) + +(define-public r-rvcheck + (package + (name "r-rvcheck") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rvcheck" version)) + (sha256 + (base32 + "1i2g6gyiqyd1pn6y0h6vmlcmg1qb5pv7rym8mkw8jnyc3in9hn8b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rlang" ,r-rlang))) + (home-page "https://cran.r-project.org/web/packages/rvcheck") + (synopsis "R package version check") + (description + "This package provides tools to check the latest release version of R and +R packages (on CRAN, Bioconductor or Github).") + (license license:artistic2.0))) + +(define-public r-docopt + (package + (name "r-docopt") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "docopt" version)) + (sha256 + (base32 + "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068")))) + (build-system r-build-system) + (home-page "https://github.com/docopt/docopt.R") + (synopsis "Command-line interface specification language") + (description + "This package enables you to define a command-line interface by just +giving it a description in the specific format.") + (license license:expat))) + +(define-public r-sparsesvd + (package + (name "r-sparsesvd") + (version "0.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "sparsesvd" version)) + (sha256 + (base32 + "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam")))) + (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-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 "0.13-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "RSpectra" version)) + (sha256 + (base32 + "1sw80chwyyjzf5px278l6xmp94yhwrlj5xh8d3wlw3dnvdkycca7")))) + (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") + (source + (origin + (method url-fetch) + (uri (cran-uri "flare" version)) + (sha256 + (base32 + "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1")))) + (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 packages 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 "1.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "splitstackshape" version)) + (sha256 + (base32 + "03w6h64ga4zqilffdway4l38l5cbman4yrspkzhbigds12aqz25r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://github.com/mrdwab/splitstackshape") + (synopsis "Stack and reshape datasets after splitting concatenated values") + (description + "Online data collection tools like Google Forms often export +multiple-response questions with data concatenated in cells. The +@code{concat.split} (cSplit) family of functions provided by this package +splits such data into separate cells. This package also includes functions to +stack groups of columns and to reshape wide data, even when the data are +\"unbalanced\"---something which @code{reshape} (from base R) does not handle, +and which @code{melt} and @code{dcast} from @code{reshape2} do not easily +handle.") + (license license:gpl3))) + +(define-public r-tfmpvalue + (package + (name "r-tfmpvalue") + (version "0.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "TFMPvalue" version)) + (sha256 + (base32 + "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) + (properties `((upstream-name . "TFMPvalue"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/ge11232002/TFMPvalue") + (synopsis "P-value computation for position weight matrices") + (description + "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) +identification from sequence/alignments, we are interested in the significance +of certain match scores. TFMPvalue provides the accurate calculation of a +p-value with a score threshold for position weight matrices, or the score with +a given p-value. It is an interface to code originally made available by +Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. +Touzet and Varre (2007).") + (license license:gpl2))) + +(define-public r-rnifti + (package + (name "r-rnifti") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RNifti" version)) + (sha256 + (base32 + "07sfzps4yg5zdhbxh6i4rbjvbjvvf2d8i9jcf64ywbmi557sw1zv")))) + (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 "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "shades" version)) + (sha256 + (base32 + "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv")))) + (build-system r-build-system) + (home-page "https://github.com/jonclayden/shades") + (synopsis "Simple color manipulation") + (description + "This package provides functions for easily manipulating colors, +creating color scales and calculating color distances.") + (license license:bsd-3))) + +(define-public r-ore + (package + (name "r-ore") + (version "1.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ore" version)) + (sha256 + (base32 + "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m")))) + (build-system r-build-system) + (home-page "https://github.com/jonclayden/ore") + (synopsis "R interface to the Onigmo regular expression library") + (description + "This package provides an alternative to R's built-in functionality for +handling regular expressions, based on the Onigmo library. It offers +first-class compiled regex objects, partial matching and function-based +substitutions, amongst other features.") + (license license:bsd-3))) + +(define-public r-reportr + (package + (name "r-reportr") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "reportr" version)) + (sha256 + (base32 + "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) + (build-system r-build-system) + (propagated-inputs `(("r-ore" ,r-ore))) + (home-page "https://github.com/jonclayden/reportr") + (synopsis "General message and error reporting system") + (description + "This package provides a system for reporting messages, which offers +certain useful features over the standard R system, such as the incorporation +of output consolidation, message filtering, assertions, expression +substitution, automatic generation of stack traces for debugging, and +conditional reporting based on the current \"output level\".") + (license license:gpl2))) + +(define-public r-tractor-base + (package + (name "r-tractor-base") + (version "3.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tractor.base" version)) + (sha256 + (base32 + "0i62dwra0yh565ryz75byfgqv22bqwz7138zs48w46yj2h8q9hyj")))) + (properties `((upstream-name . "tractor.base"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ore" ,r-ore) + ("r-reportr" ,r-reportr) + ("r-rnifti" ,r-rnifti) + ("r-shades" ,r-shades))) + (home-page "http://www.tractor-mri.org.uk") + (synopsis "Read, manipulate and visualize magnetic resonance images") + (description + "This package provides functions for working with magnetic resonance +images. It supports reading and writing of popular file formats (DICOM, +Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive +visualization; flexible image manipulation; metadata and sparse image +handling.") + (license license:gpl2))) + +(define-public r-grimport + (package + (name "r-grimport") + (version "0.9-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "grImport" version)) + (sha256 + (base32 + "19d05ygpiv47lfzhfih35pdfll0axbrgd6p86l59mmg2d0j0s8bd")))) + (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-kohonen + (package + (name "r-kohonen") + (version "3.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "kohonen" version)) + (sha256 + (base32 + "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/kohonen") + (synopsis "Supervised and unsupervised self-organising maps") + (description + "This package provides functions to train @dfn{self-organising +maps} (SOMs). Also interrogation of the maps and prediction using trained +maps are supported. The name of the package refers to Teuvo Kohonen, the +inventor of the SOM.") + (license license:gpl2+))) + +(define-public r-nnls + (package + (name "r-nnls") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "nnls" version)) + (sha256 + (base32 + "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/nnls") + (synopsis "Lawson-Hanson algorithm for non-negative least squares") + (description + "This package provides an R interface to the Lawson-Hanson implementation +of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows +the combination of non-negative and non-positive constraints.") + (license license:gpl2+))) + +(define-public r-iso + (package + (name "r-iso") + (version "0.0-17") + (source + (origin + (method url-fetch) + (uri (cran-uri "Iso" version)) + (sha256 + (base32 + "0lljc99sdzdqj6d56qbsggibr6pkdwkh821bj70ianikyvmdc1y0")))) + (properties `((upstream-name . "Iso"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://www.stat.auckland.ac.nz/~rolf/") + (synopsis "Functions to perform isotonic regression") + (description + "This package provides support for linear order and unimodal +order (univariate) isotonic regression and bivariate isotonic regression with +linear order on both variables.") + (license license:gpl2+))) + +(define-public r-chemometricswithr + (package + (name "r-chemometricswithr") + (version "0.1.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "ChemometricsWithR" version)) + (sha256 + (base32 + "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) + (properties + `((upstream-name . "ChemometricsWithR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-devtools" ,r-devtools) + ("r-kohonen" ,r-kohonen) + ("r-mass" ,r-mass) + ("r-pls" ,r-pls))) + (home-page "https://github.com/rwehrens/CWR") + (synopsis "Chemometrics with R") + (description + "This package provides functions and scripts used in the book +\"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and +Life Sciences\" by Ron Wehrens, Springer (2011).") + (license license:gpl2+))) + +(define-public r-als + (package + (name "r-als") + (version "0.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ALS" version)) + (sha256 + (base32 + "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) + (properties `((upstream-name . "ALS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-iso" ,r-iso) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/ALS") + (synopsis "Multivariate curve resolution alternating least squares") + (description + "Alternating least squares is often used to resolve components +contributing to data with a bilinear structure; the basic technique may be +extended to alternating constrained least squares. This package provides an +implementation of @dfn{multivariate curve resolution alternating least +squares} (MCR-ALS). + +Commonly applied constraints include unimodality, non-negativity, and +normalization of components. Several data matrices may be decomposed +simultaneously by assuming that one of the two matrices in the bilinear +decomposition is shared between datasets.") + (license license:gpl2+))) + +(define-public r-strucchange + (package + (name "r-strucchange") + (version "1.5-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "strucchange" version)) + (sha256 + (base32 + "0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl")))) + (build-system r-build-system) + (propagated-inputs + `(("r-sandwich" ,r-sandwich) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/strucchange") + (synopsis "Testing, monitoring, and dating structural changes") + (description + "This package provides tools for testing, monitoring and dating +structural changes in (linear) regression models. It features tests/methods +from the generalized fluctuation test framework as well as from the F +test (Chow test) framework. This includes methods to fit, plot and test +fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F +statistics, respectively. It is possible to monitor incoming data online +using fluctuation processes. Finally, the breakpoints in regression models +with structural changes can be estimated together with confidence intervals. +Emphasis is always given to methods for visualizing the data.") + ;; Either of these two GPL versions + (license (list license:gpl2 license:gpl3)))) + +(define-public r-pixmap + (package + (name "r-pixmap") + (version "0.4-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "pixmap" version)) + (sha256 + (base32 + "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/pixmap") + (synopsis "Tools for bitmap images") + (description + "This package provides functions for importing, exporting, plotting and +other manipulations of bitmapped images.") + (license license:gpl2))) + +(define-public r-rapidjsonr + (package + (name "r-rapidjsonr") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rapidjsonr" version)) + (sha256 + (base32 + "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rapidjsonr") + (synopsis "JSON parser") + (description + "This package provides JSON parsing capability through the Rapidjson +library.") + (license license:expat))) + +(define-public r-ontologyindex + (package + (name "r-ontologyindex") + (version "2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ontologyIndex" version)) + (sha256 + (base32 + "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) + (properties `((upstream-name . "ontologyIndex"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ontologyIndex") + (synopsis "Functions for processing ontologies in R") + (description + "This package provides functions for reading ontologies into R as lists +and manipulating sets of ontological terms.") + (license license:gpl2+))) + +(define-public r-bigrquery + (package + (name "r-bigrquery") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "bigrquery" version)) + (sha256 + (base32 + "0z7wsqxla1pg2454l35kkfaz2s9hppwvpz1pds286ddldbbmyzis")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("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-tibble" ,r-tibble))) + (home-page "https://github.com/rstats-db/bigrquery") + (synopsis "R interface to Google's BigQuery API") + (description + "This package provides an R interface to Google's BigQuery database.") + (license license:gpl3))) + +(define-public r-gmp + (package + (name "r-gmp") + (version "0.5-13.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "gmp" version)) + (sha256 + (base32 + "1xd6jjra4niqv1kps91y348lwgvy73p2faxaia4gfzdnrpw7wsxf")))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-CC + (lambda _ (setenv "CC" "gcc") #t))))) + (inputs `(("gmp" ,gmp))) + (home-page "https://cran.r-project.org/web/packages/gmp") + (synopsis "Multiple precision arithmetic") + (description + "This package supports multiple precision arithmetic (big integers and +rationals, prime number tests, matrix computation), \"arithmetic without +limitations\" using the GNU Multiple Precision library.") + ;; Any version of the GPL. + (license license:gpl3+))) + +(define-public r-rmpfr + (package + (name "r-rmpfr") + (version "0.7-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rmpfr" version)) + (sha256 + (base32 + "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc")))) + (properties `((upstream-name . "Rmpfr"))) + (build-system r-build-system) + (inputs + `(("mpfr" ,mpfr))) + (propagated-inputs + `(("r-gmp" ,r-gmp))) + (home-page "http://rmpfr.r-forge.r-project.org/") + (synopsis "R bindings to the MPFR library") + (description + "This package supports arithmetic (via S4 classes and methods) for +arbitrary precision floating point numbers, including transcendental +functions. To this end, the package interfaces with the @dfn{Multiple +Precision Floating-Point Reliable} (MPFR) library.") + (license license:gpl2+))) + +(define-public r-assertive-base + (package + (name "r-assertive-base") + (version "0.0-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.base" version)) + (sha256 + (base32 + "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh")))) + (properties + `((upstream-name . "assertive.base"))) + (build-system r-build-system) + (home-page "https://bitbucket.org/richierocks/assertive.base") + (synopsis "Core of the assertive package") + (description + "This package provides a minimal set of predicates and assertions used by +the assertive package. This is mainly for use by other package developers who +want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-properties + (package + (name "r-assertive-properties") + (version "0.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.properties" version)) + (sha256 + (base32 + "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw")))) + (properties + `((upstream-name . "assertive.properties"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.properties") + (synopsis "Assertions to check properties of variables") + (description + "This package provides a set of predicates and assertions for checking +the properties of variables, such as length, names and attributes. This is +mainly for use by other package developers who want to include run-time +testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-numbers + (package + (name "r-assertive-numbers") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.numbers" version)) + (sha256 + (base32 + "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds")))) + (properties + `((upstream-name . "assertive.numbers"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.numbers") + (synopsis "Assertions to check properties of numbers") + (description + "This package provides a set of predicates and assertions for checking +the properties of numbers. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-sets + (package + (name "r-assertive-sets") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.sets" version)) + (sha256 + (base32 + "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7")))) + (properties + `((upstream-name . "assertive.sets"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.sets") + (synopsis "Assertions to check properties of sets") + (description + "This package provides a set of predicates and assertions for checking +the properties of sets. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-matrices + (package + (name "r-assertive-matrices") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.matrices" version)) + (sha256 + (base32 + "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil")))) + (properties + `((upstream-name . "assertive.matrices"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.matrices") + (synopsis "Assertions to check properties of matrices") + (description + "This package provides a set of predicates and assertions for checking +the properties of matrices. This is mainly for use by other package +developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) + +(define-public r-assertive-models + (package + (name "r-assertive-models") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.models" version)) + (sha256 + (base32 + "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr")))) + (properties + `((upstream-name . "assertive.models"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.models") + (synopsis "Assertions to check properties of models") + (description + "This package provides a set of predicates and assertions for checking +the properties of models. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-reflection + (package + (name "r-assertive-reflection") + (version "0.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.reflection" version)) + (sha256 + (base32 + "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj")))) + (properties + `((upstream-name . "assertive.reflection"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.reflection") + (synopsis "Assertions for checking the state of R") + (description + "This package provides a set of predicates and assertions for checking +the state and capabilities of R, the operating system it is running on, and +the IDE being used. This is mainly for use by other package developers who +want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-types + (package + (name "r-assertive-types") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.types" version)) + (sha256 + (base32 + "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb")))) + (properties + `((upstream-name . "assertive.types"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-properties" ,r-assertive-properties) + ("r-codetools" ,r-codetools))) + (home-page "https://bitbucket.org/richierocks/assertive.types") + (synopsis "Assertions to check types of variables") + (description + "This package provides a set of predicates and assertions for checking +the types of variables. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-files + (package + (name "r-assertive-files") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.files" version)) + (sha256 + (base32 + "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy")))) + (properties + `((upstream-name . "assertive.files"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-numbers" ,r-assertive-numbers))) + (home-page "https://bitbucket.org/richierocks/assertive.files") + (synopsis "Assertions to check properties of files") + (description + "This package provides a set of predicates and assertions for checking +the properties of files and connections. This is mainly for use by other +package developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) + +(define-public r-assertive-code + (package + (name "r-assertive-code") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.code" version)) + (sha256 + (base32 + "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) + (properties + `((upstream-name . "assertive.code"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-properties" ,r-assertive-properties) + ("r-assertive-types" ,r-assertive-types))) + (home-page "https://bitbucket.org/richierocks/assertive.code") + (synopsis "Assertions to check properties of code") + (description + "This package provides a set of predicates and assertions for checking +the properties of code. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-datetimes + (package + (name "r-assertive-datetimes") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.datetimes" version)) + (sha256 + (base32 + "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78")))) + (properties + `((upstream-name . "assertive.datetimes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-types" ,r-assertive-types))) + (home-page "https://bitbucket.org/richierocks/assertive.datetimes") + (synopsis "Assertions to check properties of dates and times") + (description + "This package provides a set of predicates and assertions for checking +the properties of dates and times. This is mainly for use by other package +developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) + +(define-public r-assertive-strings + (package + (name "r-assertive-strings") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.strings" version)) + (sha256 + (base32 + "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm")))) + (properties + `((upstream-name . "assertive.strings"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-types" ,r-assertive-types) + ("r-stringi" ,r-stringi))) + (home-page "https://bitbucket.org/richierocks/assertive.strings") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of strings. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-data-us + (package + (name "r-assertive-data-us") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data.us" version)) + (sha256 + (base32 + "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq")))) + (properties + `((upstream-name . "assertive.data.us"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data.us") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of US-specific complex data types. This is mainly for use by +other package developers who want to include run-time testing features in +their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-data-uk + (package + (name "r-assertive-data-uk") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data.uk" version)) + (sha256 + (base32 + "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b")))) + (properties + `((upstream-name . "assertive.data.uk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data.uk") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of UK-specific complex data types. This is mainly for use by +other package developers who want to include run-time testing features in +their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-data + (package + (name "r-assertive-data") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data" version)) + (sha256 + (base32 + "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s")))) + (properties + `((upstream-name . "assertive.data"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data") + (synopsis "Assertions to check properties of data") + (description + "This package provides a set of predicates and assertions for checking +the properties of (country independent) complex data types. This is mainly +for use by other package developers who want to include run-time testing +features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive + (package + (name "r-assertive") + (version "0.3-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive" version)) + (sha256 + (base32 + "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-code" ,r-assertive-code) + ("r-assertive-data" ,r-assertive-data) + ("r-assertive-data-uk" ,r-assertive-data-uk) + ("r-assertive-data-us" ,r-assertive-data-us) + ("r-assertive-datetimes" ,r-assertive-datetimes) + ("r-assertive-files" ,r-assertive-files) + ("r-assertive-matrices" ,r-assertive-matrices) + ("r-assertive-models" ,r-assertive-models) + ("r-assertive-numbers" ,r-assertive-numbers) + ("r-assertive-properties" ,r-assertive-properties) + ("r-assertive-reflection" ,r-assertive-reflection) + ("r-assertive-sets" ,r-assertive-sets) + ("r-assertive-strings" ,r-assertive-strings) + ("r-assertive-types" ,r-assertive-types) + ("r-knitr" ,r-knitr))) + (home-page "https://bitbucket.org/richierocks/assertive") + (synopsis "Readable check functions to ensure code integrity") + (description + "This package provides lots of predicates (@code{is_*} functions) to +check the state of your variables, and assertions (@code{assert_*} functions) +to throw errors if they aren't in the right form.") + (license license:gpl3+))) + +(define-public r-dotcall64 + (package + (name "r-dotcall64") + (version "1.0-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "dotCall64" version)) + (sha256 + (base32 + "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) + (properties `((upstream-name . "dotCall64"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") + (synopsis "Enhanced foreign function interface supporting long vectors") + (description + "This package provides @code{.C64()}, an enhanced version of @code{.C()} +and @code{.Fortran()} from the R foreign function interface. @code{.C64()} +supports long vectors, arguments of type 64-bit integer, and provides a +mechanism to avoid unnecessary copies of read-only and write-only arguments. +This makes it a convenient and fast interface to C/C++ and Fortran code.") + (license license:gpl2+))) + +(define-public r-spam + (package + (name "r-spam") + (version "2.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spam" version)) + (sha256 + (base32 + "04bfwwna013hrbl4k6w1cdiz5bkc83jlasivriyn5l9gkj2qskr2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dotcall64" ,r-dotcall64))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://www.math.uzh.ch/pages/spam/") + (synopsis "Sparse matrix algebra") + (description + "This package provides a set of functions for sparse matrix algebra. +Differences with other sparse matrix packages are: + +@enumerate +@item it only supports (essentially) one sparse matrix format; +@item it is based on transparent and simple structure(s); +@item it is tailored for MCMC calculations within G(M)RF; +@item and it is fast and scalable (with the extension package @code{spam64}). +@end enumerate\n") + ;; Either of these licenses + (license (list license:bsd-3 license:lgpl2.0)))) + +(define-public r-fields + (package + (name "r-fields") + (version "9.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "fields" version)) + (sha256 + (base32 + "1v7z48a8jmdcil28rj8c3455k6rssr5v9qi6dyhhpbb193bj8121")))) + (build-system r-build-system) + (propagated-inputs + `(("r-maps" ,r-maps) + ("r-spam" ,r-spam))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://www.image.ucar.edu/fields") + (synopsis "Tools for spatial data") + (description + "This is a package for curve, surface and function fitting with an +emphasis on splines, spatial data and spatial statistics. The major methods +include cubic, and thin plate splines, Kriging, and compactly supported +covariance functions for large data sets.") + (license license:gpl2+))) + +(define-public r-spatialextremes + (package + (name "r-spatialextremes") + (version "2.0-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "SpatialExtremes" version)) + (sha256 + (base32 + "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050")))) + (properties + `((upstream-name . "SpatialExtremes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fields" ,r-fields) + ("r-maps" ,r-maps))) + (home-page "http://spatialextremes.r-forge.r-project.org/") + (synopsis "Modelling spatial extremes") + (description + "This package provides tools for the statistical modelling of spatial +extremes using max-stable processes, copula or Bayesian hierarchical models. +More precisely, this package allows (conditional) simulations from various +parametric max-stable models, analysis of the extremal spatial dependence, the +fitting of such processes using composite likelihoods or least square (simple +max-stable processes only), model checking and selection and prediction.") + (license license:gpl2+))) + +(define-public r-drc + (package + (name "r-drc") + (version "3.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "drc" version)) + (sha256 + (base32 + "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-gtools" ,r-gtools) + ("r-mass" ,r-mass) + ("r-multcomp" ,r-multcomp) + ("r-plotrix" ,r-plotrix) + ("r-scales" ,r-scales))) + (home-page "https://cran.r-project.org/web/packages/drc") + (synopsis "Analysis of dose-response curves") + (description + "This package provides a suite of flexible and versatile model fitting +and after-fitting functions for the analysis of dose-response data.") + (license license:gpl2+))) + +(define-public r-rmeta + (package + (name "r-rmeta") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rmeta" version)) + (sha256 + (base32 + "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rmeta") + (synopsis "Tools for meta-analysis") + (description + "This package provides functions for simple fixed and random effects +meta-analysis for two-sample comparisons and cumulative meta-analyses. It +draws standard summary plots, funnel plots, and computes summaries and tests +for association and heterogeneity.") + (license license:gpl2))) + +(define-public r-bootstrap + (package + (name "r-bootstrap") + (version "2017.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bootstrap" version)) + (sha256 + (base32 + "08lmsy7k8wsgv89yc904c6fidcymr1ma2ry4fl0p69p21v4iiwa4")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/bootstrap") + (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") + (description + "This package provides software and data for the book \"An Introduction +to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. +This package is primarily provided for projects already based on it, and for +support of the book. New projects should preferentially use the recommended +package \"boot\".") + (license license:bsd-3))) + +(define-public r-survivalroc + (package + (name "r-survivalroc") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "survivalROC" version)) + (sha256 + (base32 + "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) + (properties `((upstream-name . "survivalROC"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/survivalROC") + (synopsis "Time-dependent ROC curve estimation from censored survival data") + (description + "Compute time-dependent ROC curve from censored survival data using +Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, +Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") + (license license:gpl2+))) + +(define-public r-longitudinal + (package + (name "r-longitudinal") + (version "1.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "longitudinal" version)) + (sha256 + (base32 + "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l")))) + (build-system r-build-system) + (propagated-inputs `(("r-corpcor" ,r-corpcor))) + (home-page "http://strimmerlab.org/software/longitudinal/") + (synopsis "Analysis of multiple time course data") + (description + "This package contains general data structures and functions for +longitudinal data with multiple variables, repeated measurements, and +irregularly spaced time points. It also implements a shrinkage estimator of +dynamical correlation and dynamical covariance.") + (license license:gpl3+))) + +(define-public r-genenet + (package + (name "r-genenet") + (version "1.2.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "GeneNet" version)) + (sha256 + (base32 + "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p")))) + (properties `((upstream-name . "GeneNet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corpcor" ,r-corpcor) + ("r-fdrtool" ,r-fdrtool) + ("r-longitudinal" ,r-longitudinal))) + (home-page "http://strimmerlab.org/software/genenet/") + (synopsis "Modeling and inferring gene networks") + (description + "This package analyzes gene expression (time series) data with focus on +the inference of gene networks. In particular, GeneNet implements the methods +of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) +for learning large-scale gene association networks (including assignment of +putative directions).") + (license license:gpl3+))) + +(define-public r-rbamtools + (package + (name "r-rbamtools") + (version "2.16.11.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rbamtools" version)) + (sha256 + (base32 + "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj")))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-refgenome" ,r-refgenome))) + (home-page "https://cran.r-project.org/web/packages/rbamtools") + (synopsis "Read and write BAM (binary alignment) files") + (description + "This package provides an R interface to functions of the SAMtools +library.") + (license license:artistic2.0))) + +(define-public r-protviz + (package + (name "r-protviz") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "protViz" version)) + (sha256 + (base32 + "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1")))) + (properties `((upstream-name . "protViz"))) + (build-system r-build-system) + (inputs + `(("perl" ,perl) + ("python-2" ,python-2))) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/protViz/protViz/") + (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") + (description + "This package helps with quality checks, visualizations and analysis of +mass spectrometry data, coming from proteomics experiments. The package is +developed, tested and used at the Functional Genomics Center Zurich, where it +is used mainly for prototyping, teaching, and having fun with proteomics data. +But it can also be used to do data analysis for small scale data sets.") + (license license:gpl3))) + +(define-public r-cmprsk + (package + (name "r-cmprsk") + (version "2.2-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "cmprsk" version)) + (sha256 + (base32 + "1imr3wpnj4g57n2x4ryahl4lk8lvq9y2r7319zv3k82mznha8bcm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-survival" ,r-survival))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/cmprsk") + (synopsis "Subdistribution analysis of competing risks") + (description + "This package provides tool for estimation, testing and regression +modeling of subdistribution functions in competing risks, as described in +Gray (1988), A class of K-sample tests for comparing the cumulative incidence +of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), +A proportional hazards model for the subdistribution of a competing risk, +JASA, 94:496-509.") + (license license:gpl2+))) + +(define-public r-etm + (package + (name "r-etm") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "etm" version)) + (sha256 + (base32 + "0ws103b3pmli0z4xbyfxkly2wnnnxnnwc0r66qjjqjrlvm7pffl1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-lattice" ,r-lattice) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/etm") + (synopsis "Empirical transition matrix") + (description + "The @dfn{empirical transition matrix} (etm) package permits to estimate +the matrix of transition probabilities for any time-inhomogeneous multistate +model with finite state space using the Aalen-Johansen estimator.") + (license license:expat))) + +(define-public r-epi + (package + (name "r-epi") + (version "2.32") + (source + (origin + (method url-fetch) + (uri (cran-uri "Epi" version)) + (sha256 + (base32 + "14n24xlm7pwdc54w2hlpjhfal1zpzm87rv3rjfckiz47d3w7dwqm")))) + (properties `((upstream-name . "Epi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cmprsk" ,r-cmprsk) + ("r-data-table" ,r-data-table) + ("r-etm" ,r-etm) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-numderiv" ,r-numderiv) + ("r-plyr" ,r-plyr) + ("r-survival" ,r-survival) + ("r-zoo" ,r-zoo))) + (home-page "http://BendixCarstensen.com/Epi/") + (synopsis "Statistical analysis in epidemiology") + (description + "This package provides functions for demographic and epidemiological +analysis in the Lexis diagram, i.e. register and cohort follow-up data, in +particular representation, manipulation and simulation of multistate data - +the Lexis suite of functions, which includes interfaces to the @code{mstate}, +@code{etm} and @code{cmprsk} packages. It also contains functions for +Age-Period-Cohort and Lee-Carter modeling and a function for interval censored +data and some useful functions for tabulation and plotting, as well as a +number of epidemiological data sets.") + (license license:gpl2))) + +(define-public r-ppls + (package + (name "r-ppls") + (version "1.6-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ppls" version)) + (sha256 + (base32 + "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ppls") + (synopsis "Penalized partial least squares") + (description + "This package contains linear and nonlinear regression methods based on +partial least squares and penalization techniques. Model parameters are +selected via cross-validation, and confidence intervals ans tests for the +regression coefficients can be conducted via jackknifing.") + (license license:gpl2+))) + +(define-public r-huge + (package + (name "r-huge") + (version "1.2.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "huge" version)) + (sha256 + (base32 + "134d951x42vy9dcmf155fbvik2934nh6qm2w5jlx3x2c6cf7faq4")))) + (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/huge") + (synopsis "High-dimensional undirected graph estimation") + (description + "This package provides a general framework for high-dimensional +undirected graph estimation. It integrates data preprocessing, neighborhood +screening, graph estimation, and model selection techniques into a pipeline.") + (license license:gpl2))) + +(define-public r-parcor + (package + (name "r-parcor") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "parcor" version)) + (sha256 + (base32 + "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-epi" ,r-epi) + ("r-genenet" ,r-genenet) + ("r-glmnet" ,r-glmnet) + ("r-mass" ,r-mass) + ("r-ppls" ,r-ppls))) + (home-page "https://cran.r-project.org/web/packages/parcor") + (synopsis "Regularized estimation of partial correlation matrices") + (description + "This package estimates the matrix of partial correlations based on +different regularized regression methods: lasso, adaptive lasso, PLS, and +Ridge Regression. In addition, the package provides model selection for +lasso, adaptive lasso and Ridge regression based on cross-validation.") + (license license:gpl2+))) + +(define-public r-mcmc + (package + (name "r-mcmc") + (version "0.9-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "mcmc" version)) + (sha256 + (base32 + "1i3rahph8pbhi5dsyjnkazqklg4lhh3azlyvx4kvabx50q0awxn6")))) + (build-system r-build-system) + (home-page "http://www.stat.umn.edu/geyer/mcmc/") + (synopsis "Markov chain Monte Carlo") + (description + "This package simulates continuous distributions of random vectors using +@dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R +function that evaluates the log unnormalized density. Algorithms are random +walk Metropolis algorithm (function @code{metrop}), simulated +tempering (function @code{temper}), and morphometric random walk +Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity +by change of variable.") + (license license:expat))) |