;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
+;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
+;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (guix build-system r)
+ #:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
#:use-module (gnu packages javascript)
+ #:use-module (gnu packages libevent)
#:use-module (gnu packages lisp-xyz)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
+ #:use-module (gnu packages xml)
#:use-module (gnu packages xorg))
(define-public r-rticles
(define-public r-ggpmisc
(package
(name "r-ggpmisc")
- (version "0.3.5")
+ (version "0.3.6")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpmisc" version))
(sha256
(base32
- "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
+ "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
+ ("r-glue" ,r-glue)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-lubridate" ,r-lubridate)
objects.")
(license license:gpl3)))
+(define-public r-mboost
+ (package
+ (name "r-mboost")
+ (version "2.9-3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "mboost" version))
+ (sha256
+ (base32
+ "1qp5c43kc0939sss5w3hhn794lbi69wgfsa31sq4c8vzh35pjqmf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)
+ ("r-matrix" ,r-matrix)
+ ("r-nnls" ,r-nnls)
+ ("r-partykit" ,r-partykit)
+ ("r-quadprog" ,r-quadprog)
+ ("r-stabs" ,r-stabs)
+ ("r-survival" ,r-survival)))
+ (home-page "https://github.com/boost-R/mboost")
+ (synopsis "Model-based boosting")
+ (description
+ "This package provides a functional gradient descent algorithm (boosting)
+for optimizing general risk functions utilizing component-wise (penalised)
+least squares estimates or regression trees as base-learners for fitting
+generalized linear, additive and interaction models to potentially
+high-dimensional data.")
+ (license license:gpl2)))
+
(define-public r-sys
(package
(name "r-sys")
(define-public r-callr
(package
(name "r-callr")
- (version "3.4.3")
+ (version "3.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
- "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
+ "1hgc4mfwv83104fh93v8g2srpwzjayq7krgzi9r0apq784r61642"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
(uri (cran-uri "httpuv" version))
(sha256
(base32
- "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))))
+ "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))
+ ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
+ ;; only contains fixes for building on Solaris.
+ (patches (search-patches "r-httpuv-1.5.4-unvendor-libuv.patch"))
+ (modules '((guix build utils)
+ (ice-9 ftw)
+ (srfi srfi-1)))
+ (snippet
+ `(begin
+ (delete-file-recursively "src/libuv")
+ ;; Cannot unbundle http-parser, because it contains local
+ ;; modifications.
+ #t))))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unbundle-libuv
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* (find-files "src" "\\.cpp$|\\.h$")
+ (("\"libuv/include/uv\\.h\"")
+ "<uv.h>"))
+ ;; Fix https://github.com/rstudio/httpuv/issues/282
+ (substitute* "src/http.cpp"
+ (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
+ "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
+ #t)))))
+ (inputs
+ `(("libuv" ,libuv)))
(propagated-inputs
`(("r-bh" ,r-bh)
("r-later" ,r-later)
(define-public r-jsonlite
(package
(name "r-jsonlite")
- (version "1.7.0")
+ (version "1.7.1")
(source (origin
(method url-fetch)
(uri (cran-uri "jsonlite" version))
(sha256
(base32
- "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
+ "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
initiative to bring PASSTEC 2000 functionalities to R.")
(license license:gpl2+)))
+(define-public r-partykit
+ (package
+ (name "r-partykit")
+ (version "1.2-9")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "partykit" version))
+ (sha256
+ (base32
+ "18nc6vvj1cy8ly2hqixg544sbg8vbpzwsr1cdlzrqfykd0pzgkvf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-formula" ,r-formula)
+ ("r-inum" ,r-inum)
+ ("r-libcoin" ,r-libcoin)
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-rpart" ,r-rpart)
+ ("r-survival" ,r-survival)))
+ (home-page "http://partykit.R-Forge.R-project.org/partykit")
+ (synopsis "Toolkit for recursive partytioning")
+ (description
+ "This package provides a toolkit with infrastructure for representing,
+summarizing, and visualizing tree-structured regression and classification
+models.")
+ (license license:gpl2+)))
+
(define-public r-plogr
(package
(name "r-plogr")
bindings that call a C++ function.")
(license license:expat)))
+(define-public r-bisquerna
+ (package
+ (name "r-bisquerna")
+ (version "1.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "BisqueRNA" version))
+ (sha256
+ (base32
+ "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
+ (properties `((upstream-name . "BisqueRNA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-limsolve" ,r-limsolve)))
+ (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
+ (synopsis "Decomposition of bulk expression with single-cell sequencing")
+ (description "This package provides tools to accurately estimate cell type
+abundances from heterogeneous bulk expression. A reference-based method
+utilizes single-cell information to generate a signature matrix and
+transformation of bulk expression for accurate regression based estimates.
+A marker-based method utilizes known cell-specific marker genes to measure
+relative abundances across samples.")
+ (license license:gpl3)))
+
(define-public r-auc
(package
(name "r-auc")
(define-public r-ffbase
(package
(name "r-ffbase")
- (version "0.12.8")
+ (version "0.13.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ffbase" version))
(sha256
(base32
- "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
+ "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bit" ,r-bit)
print, summary, etc.")
(license license:gpl2+)))
+(define-public r-laplacesdemon
+ (package
+ (name "r-laplacesdemon")
+ (version "16.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "LaplacesDemon" version))
+ (sha256
+ (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
+ (properties `((upstream-name . "LaplacesDemon")))
+ (build-system r-build-system)
+ (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
+ (synopsis "Complete environment for Bayesian inference")
+ (description
+ "This package provides a complete environment for Bayesian inference using
+a variety of different samplers.")
+ (license license:expat)))
+
(define-public r-rmtstat
(package
(name "r-rmtstat")
(define-public r-squarem
(package
(name "r-squarem")
- (version "2020.3")
+ (version "2020.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "SQUAREM" version))
(sha256
(base32
- "17l05i87vwvcsk79fbg52zrx04zdlwiiyl3ga8qafs7mqx0j976q"))))
+ "1r2yxfiqbpwy5ccg94r7f6sz7lh5aq0xjpf632s42wgmml1dvlzb"))))
(properties `((upstream-name . "SQUAREM")))
(build-system r-build-system)
(home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
with the package @code{optim}.")
(license license:gpl2+)))
+(define-public r-useful
+ (package
+ (name "r-useful")
+ (version "1.2.6")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "useful" version))
+ (sha256
+ (base32
+ "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
+ (properties `((upstream-name . "useful")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-plyr" ,r-plyr)
+ ("r-purrr" ,r-purrr)
+ ("r-scales" ,r-scales)))
+ (home-page "https://github.com/jaredlander/useful")
+ (synopsis "Collection of handy, useful functions")
+ (description "This package provides a set of little functions that have been
+found useful to do little odds and ends such as plotting the results of K-means
+clustering, substituting special text characters, viewing parts of a
+@code{data.frame}, constructing formulas from text and building design and
+response matrices.")
+ (license license:bsd-3)))
+
(define-public r-ordinal
(package
(name "r-ordinal")
(define-public r-vctrs
(package
(name "r-vctrs")
- (version "0.3.2")
+ (version "0.3.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "vctrs" version))
(sha256
(base32
- "05s8v3ms4jaim44c7m4y0dnv8mysj9b26cdfyrfgcjpllayrjib2"))))
+ "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
supports arbitrary vertex/edge/graph attributes.")
(license license:gpl2+)))
+(define-public r-stabs
+ (package
+ (name "r-stabs")
+ (version "0.6-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "stabs" version))
+ (sha256
+ (base32
+ "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/hofnerb/stabs")
+ (synopsis "Stability selection with error control")
+ (description
+ "This package provides resampling procedures to assess the stability of
+selected variables with additional finite sample error control for
+high-dimensional variable selection procedures such as Lasso or boosting.
+Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
+complementary pairs stability selection with improved error bounds
+(Shah & Samworth, 2013) are implemented. The package can be combined with
+arbitrary user specified variable selection approaches.")
+ (license license:gpl2)))
+
(define-public r-statnet-common
(package
(name "r-statnet-common")
(define-public r-ttr
(package
(name "r-ttr")
- (version "0.24.0")
+ (version "0.24.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "TTR" version))
(sha256
(base32
- "0dcmfr98bxhdhszsdr1yjhvy4kplnfm88fh8sdzrkjank1qsxia2"))))
+ "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
(properties `((upstream-name . "TTR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-trend
(package
(name "r-trend")
- (version "1.1.2")
+ (version "1.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "trend" version))
(sha256
(base32
- "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
+ "0bj40acr1sc7vfxdcsdja3g28xsmrclmgb3n94p89gfjcgp8nv1d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-extradistr" ,r-extradistr)))
(define-public r-heatmaply
(package
(name "r-heatmaply")
- (version "1.1.0")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "heatmaply" version))
(sha256
(base32
- "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
+ "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
(define-public r-zip
(package
(name "r-zip")
- (version "2.1.0")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "zip" version))
(sha256
(base32
- "1dfsagb7bx35x4zx6f5xk2sk057fbyhskkpw3w72b805cjw920da"))))
+ "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
(build-system r-build-system)
(home-page "https://github.com/gaborcsardi/zip")
(synopsis "Cross-platform Zip compression")
(define-public r-maptools
(package
(name "r-maptools")
- (version "1.0-1")
+ (version "1.0-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "maptools" version))
(sha256
(base32
- "0fs1y3cbymcq4f76wd27h5a7ihdmxii3ca8x29x32xgxhmasni4l"))))
+ "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
(define-public r-renv
(package
(name "r-renv")
- (version "0.11.0")
+ (version "0.12.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "renv" version))
(sha256
(base32
- "0dd63jr240pg95a6p058s5kcclfmscihdy89v212msihmwvylwh3"))))
+ "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5"))))
(properties `((upstream-name . "renv")))
(build-system r-build-system)
(native-inputs
(define-public r-officer
(package
(name "r-officer")
- (version "0.3.12")
+ (version "0.3.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "officer" version))
(sha256
(base32
- "1wk9h6bz77s5j6lgksmlrmi1vyaa35c766gq6hgb1dp0dz0x342x"))))
+ "15v5dishdsrw95nj6f7x23llzla3sgbvw35ibdk8ld3miwzxb2kr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magrittr" ,r-magrittr)
(define-public r-insight
(package
(name "r-insight")
- (version "0.9.0")
+ (version "0.9.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
- "1ajc8c5mi3ma5411lmlqp2ihkk5n0h8a1c0r3j07wk33p31c1qvl"))))
+ "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
(define-public r-writexl
(package
(name "r-writexl")
- (version "1.3")
+ (version "1.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "writexl" version))
(sha256
(base32
- "0lah0r2pd996s0vdbi614j3h52dbxmifha6f19v53p2b7fr32wjd"))))
+ "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
(home-page "https://github.com/ropensci/writexl")
(define-public r-deriv
(package
(name "r-deriv")
- (version "4.0")
+ (version "4.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Deriv" version))
(sha256
(base32
- "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
+ "16rq65x1xhxvqwn4p427divay3b9fgam2lxccxb8529adnrxmw6p"))))
(properties `((upstream-name . "Deriv")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/Deriv")
(define-public r-rnifti
(package
(name "r-rnifti")
- (version "1.1.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "RNifti" version))
(sha256
(base32
- "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
+ "1a5s75iwwngzmi7y69j7xkcrrfvjyjrfalv9ldpgwii4cwkbyf10"))))
(properties `((upstream-name . "RNifti")))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
(define-public r-haplo-stats
(package
(name "r-haplo-stats")
- (version "1.8.2")
+ (version "1.8.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "haplo.stats" version))
(sha256
(base32
- "13gc980jk1pas7mz9b4nmwqd64qhh2c0xhq1z06z67jgv7k8n7dc"))))
+ "1f5cyyyavkf4l6kksp87s8d92vjrnhxmpz6j737pa527pn3gghf9"))))
(properties `((upstream-name . "haplo.stats")))
(build-system r-build-system)
(propagated-inputs
(define-public r-xmlparsedata
(package
(name "r-xmlparsedata")
- (version "1.0.3")
+ (version "1.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "xmlparsedata" version))
(sha256
(base32
- "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
+ "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
(properties `((upstream-name . "xmlparsedata")))
(build-system r-build-system)
(home-page "https://github.com/r-lib/xmlparsedata#readme")
(define-public r-ingredients
(package
(name "r-ingredients")
- (version "1.3.1")
+ (version "2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ingredients" version))
(sha256
(base32
- "0l0dqrm9am6wk8jcf8cdhc6xnrna9cqr5wz6lsnczq2gf6ybhjg1"))))
+ "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
(properties `((upstream-name . "ingredients")))
(build-system r-build-system)
(propagated-inputs
(define-public r-xgboost
(package
(name "r-xgboost")
- (version "1.1.1.1")
+ (version "1.2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "xgboost" version))
(sha256
(base32
- "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
+ "16hpvv2hwdzcyg90z7c1g5d2hj011qk8mivy4l2nqd2g7rkjwis4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
(define-public r-kableextra
(package
(name "r-kableextra")
- (version "1.1.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "kableExtra" version))
(sha256
(base32
- "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
+ "0n25y7zwpspvkd62rd6x8c22dg2ys27smlpdz5brqs5ddv7x9dis"))))
(properties `((upstream-name . "kableExtra")))
(build-system r-build-system)
(propagated-inputs
("r-htmltools" ,r-htmltools)
("r-knitr" ,r-knitr)
("r-magrittr" ,r-magrittr)
- ("r-readr" ,r-readr)
("r-rmarkdown" ,r-rmarkdown)
("r-rstudioapi" ,r-rstudioapi)
("r-rvest" ,r-rvest)
("r-viridislite" ,r-viridislite)
("r-webshot" ,r-webshot)
("r-xml2" ,r-xml2)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://haozhu233.github.io/kableExtra/")
(synopsis "Construct complex tables with pipe syntax")
(description
(define-public r-systemfonts
(package
(name "r-systemfonts")
- (version "0.2.3")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "systemfonts" version))
(sha256
(base32
- "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
+ "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax"))))
(properties `((upstream-name . "systemfonts")))
(build-system r-build-system)
+ (propagated-inputs
+ `(("r-cpp11" ,r-cpp11)))
(inputs
`(("fontconfig" ,fontconfig)
("zlib" ,zlib)))
(define-public r-openmx
(package
(name "r-openmx")
- (version "2.17.4")
+ (version "2.18.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "OpenMx" version))
(sha256
(base32
- "07y4w7xdb63p5kkrj6sdx1kabbsgbbj7nw9hc690jy84r15aryal"))))
+ "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
(properties `((upstream-name . "OpenMx")))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
("r-digest" ,r-digest)
+ ("r-lifecycle" ,r-lifecycle)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-rcpp" ,r-rcpp)
(define-public r-bdgraph
(package
(name "r-bdgraph")
- (version "2.62")
+ (version "2.63")
(source
(origin
(method url-fetch)
(uri (cran-uri "BDgraph" version))
(sha256
(base32
- "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
+ "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
(properties `((upstream-name . "BDgraph")))
(build-system r-build-system)
(propagated-inputs
counting and recursive k-means partitioning.")
(license license:gpl3)))
+(define-public r-hardhat
+ (package
+ (name "r-hardhat")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "hardhat" version))
+ (sha256
+ (base32
+ "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
+ (properties `((upstream-name . "hardhat")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-glue" ,r-glue)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)
+ ("r-vctrs" ,r-vctrs)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/tidymodels/hardhat")
+ (synopsis "Construct modeling packages")
+ (description
+ "Building modeling packages is hard. A large amount of effort generally
+goes into providing an implementation for a new method that is efficient,
+fast, and correct, but often less emphasis is put on the user interface. A
+good interface requires specialized knowledge about S3 methods and formulas,
+which the average package developer might not have. The goal of
+@code{hardhat} is to reduce the burden around building new modeling packages
+by providing functionality for preprocessing, predicting, and validating
+input.")
+ (license license:expat)))
+
(define-public r-shapforxgboost
(package
(name "r-shapforxgboost")
(define-public r-conquer
(package
(name "r-conquer")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "conquer" version))
(sha256
(base32
- "1c7id7wgspma5bdcirrhw7f9fp709zxpj31klivasdbvd4jgi4vb"))))
+ "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
(properties `((upstream-name . "conquer")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rfast
(package
(name "r-rfast")
- (version "1.9.9")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rfast" version))
(sha256
(base32
- "18m8xhg24kygwhq7avdp1hibilicb5wppi2wdmc36fkqljc274y0"))))
+ "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy"))))
(properties `((upstream-name . "Rfast")))
(build-system r-build-system)
(propagated-inputs
addition, objects which include the k-d tree search structure can be returned
to speed up repeated queries of the same set of target points.")
(license license:bsd-3)))
+
+(define-public r-muhaz
+ (package
+ (name "r-muhaz")
+ (version "1.2.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "muhaz" version))
+ (sha256
+ (base32
+ "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
+ (properties `((upstream-name . "muhaz")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-survival" ,r-survival)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/muhaz/")
+ (synopsis "Hazard function estimation in survival analysis")
+ (description
+ "This package produces a smooth estimate of the hazard function for
+censored data.")
+ ;; Any version of the GPL.
+ (license license:gpl3+)))
+
+(define-public r-flexsurv
+ (package
+ (name "r-flexsurv")
+ (version "1.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "flexsurv" version))
+ (sha256
+ (base32
+ "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
+ (properties `((upstream-name . "flexsurv")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-desolve" ,r-desolve)
+ ("r-mstate" ,r-mstate)
+ ("r-muhaz" ,r-muhaz)
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-quadprog" ,r-quadprog)
+ ("r-rcpp" ,r-rcpp)
+ ("r-survival" ,r-survival)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/chjackson/flexsurv-dev")
+ (synopsis "Flexible parametric survival and multi-state models")
+ (description
+ "This package provides flexible parametric models for time-to-event data,
+including the Royston-Parmar spline model, generalized gamma and generalized F
+distributions. Any user-defined parametric distribution can be fitted, given
+at least an R function defining the probability density or hazard. There are
+also tools for fitting and predicting from fully parametric multi-state
+models.")
+ (license license:gpl2+)))
+
+(define-public r-transphylo
+ (package
+ (name "r-transphylo")
+ (version "1.4.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "TransPhylo" version))
+ (sha256
+ (base32
+ "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
+ (properties `((upstream-name . "TransPhylo")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
+ (synopsis "Inference of transmission tree from a dated phylogeny")
+ (description
+ "This is a package to infer transmission trees from a dated phylogeny.
+It includes methods to simulate and analyze outbreaks. The methodology is
+described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
+and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
+ (license license:gpl2+)))
+
+(define-public r-km-ci
+ (package
+ (name "r-km-ci")
+ (version "0.5-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "km.ci" version))
+ (sha256
+ (base32
+ "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
+ (properties `((upstream-name . "km.ci")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-survival" ,r-survival)))
+ (home-page "https://cran.r-project.org/web/packages/km.ci/")
+ (synopsis "Confidence intervals for the Kaplan-Meier estimator")
+ (description
+ "This package computes various @dfn{confidence intervals} (CI) for the
+Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
+variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
+Nair and Hall and Wellner.")
+ (license license:gpl2+)))
+
+(define-public r-kmsurv
+ (package
+ (name "r-kmsurv")
+ (version "0.1-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "KMsurv" version))
+ (sha256
+ (base32
+ "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
+ (properties `((upstream-name . "KMsurv")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/KMsurv/")
+ (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
+ (description
+ "This package provides data sets and functions for Klein and Moeschberger
+(1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
+Springer.")
+ (license license:gpl3+)))
+
+(define-public r-survmisc
+ (package
+ (name "r-survmisc")
+ (version "0.5.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "survMisc" version))
+ (sha256
+ (base32
+ "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
+ (properties `((upstream-name . "survMisc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-km-ci" ,r-km-ci)
+ ("r-kmsurv" ,r-kmsurv)
+ ("r-knitr" ,r-knitr)
+ ("r-survival" ,r-survival)
+ ("r-xtable" ,r-xtable)
+ ("r-zoo" ,r-zoo)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://cran.r-project.org/web/packages/survMisc/")
+ (synopsis "Miscellaneous functions for survival data")
+ (description
+ "This package provides a collection of functions to help in the analysis
+of right-censored survival data. These extend the methods available in
+the @code{survival} package.")
+ (license license:gpl2)))
+
+(define-public r-exactranktests
+ (package
+ (name "r-exactranktests")
+ (version "0.8-31")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "exactRankTests" version))
+ (sha256
+ (base32
+ "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
+ (properties
+ `((upstream-name . "exactRankTests")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
+ (synopsis "Exact distributions for rank and permutation tests")
+ (description
+ "This package computes exact conditional p-values and quantiles using an
+implementation of the Shift-Algorithm by Streitberg & Roehmel.")
+ (license license:gpl2+)))
+
+(define-public r-maxstat
+ (package
+ (name "r-maxstat")
+ (version "0.7-25")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "maxstat" version))
+ (sha256
+ (base32
+ "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
+ (properties `((upstream-name . "maxstat")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-exactranktests" ,r-exactranktests)
+ ("r-mvtnorm" ,r-mvtnorm)))
+ (home-page "https://cran.r-project.org/web/packages/maxstat/")
+ (synopsis "Maximally selected rank statistics")
+ (description
+ "This package provides maximally selected rank statistics with several
+p-value approximations.")
+ (license license:gpl2+)))
+
+(define-public r-survminer
+ (package
+ (name "r-survminer")
+ (version "0.4.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "survminer" version))
+ (sha256
+ (base32
+ "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
+ (properties `((upstream-name . "survminer")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-broom" ,r-broom)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggpubr" ,r-ggpubr)
+ ("r-gridextra" ,r-gridextra)
+ ("r-magrittr" ,r-magrittr)
+ ("r-maxstat" ,r-maxstat)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-scales" ,r-scales)
+ ("r-survival" ,r-survival)
+ ("r-survmisc" ,r-survmisc)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://rpkgs.datanovia.com/survminer/index.html")
+ (synopsis "Drawing survival curves using ggplot2")
+ (description
+ "This package contains the function @code{ggsurvplot()} for easily
+drawing beautiful and 'ready-to-publish' survival curves with the 'number at
+risk' table and 'censoring count plot'. Other functions are also available to
+plot adjusted curves for Cox model and to visually examine Cox model
+assumptions.")
+ (license license:gpl2)))
+
+(define-public r-forge
+ (package
+ (name "r-forge")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "forge" version))
+ (sha256
+ (base32
+ "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
+ (properties `((upstream-name . "forge")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-magrittr" ,r-magrittr)
+ ("r-rlang" ,r-rlang)))
+ (home-page "https://cran.r-project.org/web/packages/forge/")
+ (synopsis "Cast values into shape")
+ (description
+ "This package provides helper functions with a consistent interface to
+coerce and verify the types and shapes of values for input checking.")
+ (license license:asl2.0)))
+
+(define-public r-config
+ (package
+ (name "r-config")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "config" version))
+ (sha256
+ (base32
+ "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs"))))
+ (properties `((upstream-name . "config")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/rstudio/config")
+ (synopsis "Manage environment specific configuration values")
+ (description
+ "This package lets you manage configuration values across multiple
+environments (e.g. development, test, production). It reads values using a
+function that determines the current environment and returns the appropriate
+value.")
+ (license license:gpl3)))
+
+(define-public r-adaptivesparsity
+ (package
+ (name "r-adaptivesparsity")
+ (version "1.6")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "AdaptiveSparsity" version))
+ (sha256
+ (base32
+ "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
+ (properties
+ `((upstream-name . "AdaptiveSparsity")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'link-against-armadillo
+ (lambda _
+ (substitute* "src/Makevars"
+ (("PKG_LIBS=" prefix)
+ (string-append prefix "-larmadillo")))
+ #t)))))
+ (propagated-inputs
+ `(("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (inputs
+ `(("armadillo" ,armadillo)))
+ (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
+ (synopsis "Adaptive sparsity models")
+ (description
+ "This package implements the Figueiredo machine learning algorithm for
+adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
+geometric models.")
+ (license license:lgpl3+)))
+
+(define-public r-diffusionmap
+ (package
+ (name "r-diffusionmap")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diffusionMap" version))
+ (sha256
+ (base32
+ "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
+ (properties `((upstream-name . "diffusionMap")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-scatterplot3d" ,r-scatterplot3d)))
+ (home-page "https://www.r-project.org")
+ (synopsis "Diffusion map")
+ (description "This package implements the diffusion map method of data
+parametrization, including creation and visualization of diffusion maps,
+clustering with diffusion K-means and regression using the adaptive regression
+model.")
+ (license license:gpl2)))
+
+(define-public r-igraph
+ (package
+ (name "r-igraph")
+ (version "1.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "igraph" version))
+ (sha256
+ (base32
+ "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs
+ `(("gmp" ,gmp)
+ ("glpk" ,glpk)
+ ("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-pkgconfig" ,r-pkgconfig)))
+ (home-page "https://igraph.org")
+ (synopsis "Network analysis and visualization")
+ (description
+ "This package provides routines for simple graphs and network analysis.
+It can handle large graphs very well and provides functions for generating
+random and regular graphs, graph visualization, centrality methods and much
+more.")
+ (license license:gpl2+)))
+
+(define-public r-workflows
+ (package
+ (name "r-workflows")
+ (version "0.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "workflows" version))
+ (sha256
+ (base32
+ "1d5njd1xdl8kghlbar4acgl9hxq83p6k7yks592cvakmcz7f853m"))))
+ (properties `((upstream-name . "workflows")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cli" ,r-cli)
+ ("r-ellipsis" ,r-ellipsis)
+ ("r-generics" ,r-generics)
+ ("r-glue" ,r-glue)
+ ("r-hardhat" ,r-hardhat)
+ ("r-parsnip" ,r-parsnip)
+ ("r-rlang" ,r-rlang)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/tidymodels/workflows")
+ (synopsis "Modeling workflows")
+ (description
+ "A workflow is an object that can bundle together your pre-processing,
+modeling, and post-processing requests. For example, if you have a
+@code{recipe} and @code{parsnip} model, these can be combined into a
+workflow. The advantages are:
+
+@enumerate
+@item You don’t have to keep track of separate objects in your workspace.
+@item The recipe prepping and model fitting can be executed using a single
+ call to @code{fit()}.
+@item If you have custom tuning parameter settings, these can be defined using
+ a simpler interface when combined with @code{tune}.
+@item In the future, workflows will be able to add post-processing operations,
+ such as modifying the probability cutoff for two-class models.
+@end enumerate
+")
+ (license license:expat)))
+
+(define-public r-gpfit
+ (package
+ (name "r-gpfit")
+ (version "1.0-8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "GPfit" version))
+ (sha256
+ (base32
+ "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
+ (properties `((upstream-name . "GPfit")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)
+ ("r-lhs" ,r-lhs)))
+ (home-page "https://cran.r-project.org/web/packages/GPfit/")
+ (synopsis "Gaussian Processes modeling")
+ (description
+ "This package provides a computationally stable approach of fitting a
+@dfn{Gaussian Process} (GP) model to a deterministic simulator.")
+ (license license:gpl2)))
+
+(define-public r-yardstick
+ (package
+ (name "r-yardstick")
+ (version "0.0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "yardstick" version))
+ (sha256
+ (base32
+ "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
+ (properties `((upstream-name . "yardstick")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
+ ("r-proc" ,r-proc)
+ ("r-rlang" ,r-rlang)
+ ("r-tidyselect" ,r-tidyselect)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/tidymodels/yardstick")
+ (synopsis "Tidy characterizations of model performance")
+ (description
+ "This package provides tidy tools for quantifying how well a model fits
+to a data set such as confusion matrices, class probability curve summaries,
+and regression metrics (e.g., RMSE).")
+ (license license:gpl2)))
+
+(define-public r-rsample
+ (package
+ (name "r-rsample")
+ (version "0.0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rsample" version))
+ (sha256
+ (base32
+ "0s6hgq0rcv3ianyidq3n9z34y5ww51gaggqkwmwns9yyxmwfjcm8"))))
+ (properties `((upstream-name . "rsample")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-furrr" ,r-furrr)
+ ("r-generics" ,r-generics)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-tidyselect" ,r-tidyselect)
+ ("r-vctrs" ,r-vctrs)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://rsample.tidymodels.org")
+ (synopsis "General resampling infrastructure")
+ (description
+ "This package provides classes and functions to create and summarize
+different types of resampling objects (e.g. bootstrap, cross-validation).")
+ (license license:gpl2)))
+
+(define-public r-dicedesign
+ (package
+ (name "r-dicedesign")
+ (version "1.8-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "DiceDesign" version))
+ (sha256
+ (base32
+ "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
+ (properties `((upstream-name . "DiceDesign")))
+ (build-system r-build-system)
+ (home-page "http://dice.emse.fr/")
+ (synopsis "Designs of computer experiments")
+ (description
+ "This package provides tools to create some specific @code{Space-Filling
+Design} (SFD) and to test their quality.")
+ (license license:gpl3)))
+
+(define-public r-dials
+ (package
+ (name "r-dials")
+ (version "0.0.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "dials" version))
+ (sha256
+ (base32
+ "0jxmlcy20y57chflx91fqz6c4pbdckzr7jirq4s72vp723avrr4p"))))
+ (properties `((upstream-name . "dials")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dicedesign" ,r-dicedesign)
+ ("r-dplyr" ,r-dplyr)
+ ("r-glue" ,r-glue)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-scales" ,r-scales)
+ ("r-tibble" ,r-tibble)
+ ("r-vctrs" ,r-vctrs)
+ ("r-withr" ,r-withr)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://dials.tidymodels.org/")
+ (synopsis "Tools for creating tuning parameter values")
+ (description
+ "Many models contain tuning parameters (i.e. parameters that cannot be
+directly estimated from the data). These tools can be used to define objects
+for creating, simulating, or validating values for such parameters.")
+ (license license:gpl2)))
+
+(define-public r-tune
+ (package
+ (name "r-tune")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tune" version))
+ (sha256
+ (base32
+ "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
+ (properties `((upstream-name . "tune")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cli" ,r-cli)
+ ("r-crayon" ,r-crayon)
+ ("r-dials" ,r-dials)
+ ("r-dplyr" ,r-dplyr)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-glue" ,r-glue)
+ ("r-gpfit" ,r-gpfit)
+ ("r-hardhat" ,r-hardhat)
+ ("r-lifecycle" ,r-lifecycle)
+ ("r-parsnip" ,r-parsnip)
+ ("r-purrr" ,r-purrr)
+ ("r-recipes" ,r-recipes)
+ ("r-rlang" ,r-rlang)
+ ("r-rsample" ,r-rsample)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-vctrs" ,r-vctrs)
+ ("r-workflows" ,r-workflows)
+ ("r-yardstick" ,r-yardstick)))
+ (home-page "https://github.com/tidymodels/tune")
+ (synopsis "Tidy tuning tools")
+ (description
+ "The ability to tune models is important. @code{tune} contains functions
+and classes to be used in conjunction with other @code{tidymodels} packages
+for finding reasonable values of hyper-parameters in models, pre-processing
+methods, and post-processing steps.")
+ (license license:expat)))
+
+(define-public r-tidyposterior
+ (package
+ (name "r-tidyposterior")
+ (version "0.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tidyposterior" version))
+ (sha256
+ (base32
+ "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
+ (properties `((upstream-name . "tidyposterior")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-lifecycle" ,r-lifecycle)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-rsample" ,r-rsample)
+ ("r-rstanarm" ,r-rstanarm)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-vctrs" ,r-vctrs)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://tidyposterior.tidymodels.org")
+ (synopsis "Bayesian analysis to compare models using resampling statistics")
+ (description
+ "This package can be used to conduct post hoc analyses of resampling
+results generated by models. For example, if two models are evaluated with
+the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
+are 10 paired statistics. These can be used to make comparisons between
+models without involving a test set.")
+ (license license:gpl2)))
+
+(define-public r-tidypredict
+ (package
+ (name "r-tidypredict")
+ (version "0.4.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tidypredict" version))
+ (sha256
+ (base32
+ "1fx1nr8fry3nwy2391g26zkqakdf8f3j7zyrihbc0qhscvbdskiy"))))
+ (properties `((upstream-name . "tidypredict")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
+ ("r-knitr" ,r-knitr)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://tidypredict.tidymodels.org")
+ (synopsis "Run predictions inside the database")
+ (description
+ "This package parses a fitted R model object, and returns a formula in
+Tidy Eval code that calculates the predictions. It works with several
+database backends because it leverages @code{dplyr} and @code{dbplyr} for the
+final SQL translation of the algorithm. It currently supports @code{lm()},
+@code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
+@code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
+ (license license:gpl3)))
+
+(define-public r-janeaustenr
+ (package
+ (name "r-janeaustenr")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "janeaustenr" version))
+ (sha256
+ (base32
+ "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
+ (properties `((upstream-name . "janeaustenr")))
+ (build-system r-build-system)
+ (home-page "https://github.com/juliasilge/janeaustenr")
+ (synopsis "Jane Austen's complete novels")
+ (description
+ "This package provides the full texts for Jane Austen's six completed
+novels, ready for text analysis. These novels are \"Sense and Sensibility\",
+\"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
+and \"Persuasion\".")
+ (license license:expat)))
+
+(define-public r-tokenizers
+ (package
+ (name "r-tokenizers")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tokenizers" version))
+ (sha256
+ (base32
+ "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
+ (properties `((upstream-name . "tokenizers")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)
+ ("r-snowballc" ,r-snowballc)
+ ("r-stringi" ,r-stringi)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://lincolnmullen.com/software/tokenizers/")
+ (synopsis "Fast, consistent tokenization of natural language text")
+ (description
+ "This is a package for converting natural language text into tokens.
+It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
+sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
+Treebank, regular expressions, as well as functions for counting characters,
+words, and sentences, and a function for splitting longer texts into separate
+documents, each with the same number of words. The tokenizers have a
+consistent interface, and the package is built on the @code{stringi} and
+@code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
+ (license license:expat)))
+
+(define-public r-hunspell
+ (package
+ (name "r-hunspell")
+ (version "3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "hunspell" version))
+ (sha256
+ (base32
+ "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1"))))
+ (properties `((upstream-name . "hunspell")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-digest" ,r-digest)
+ ("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/ropensci/hunspell#readme")
+ (synopsis "High-performance stemmer, tokenizer, and spell checker")
+ (description
+ "This package provides a low-level spell checker and morphological
+analyzer based on the famous @code{hunspell} library. The package can analyze
+or check individual words as well as parse text, LaTeX, HTML or XML documents.
+For a more user-friendly interface use the @code{spelling} package which
+builds on this package to automate checking of files, documentation and
+vignettes in all common formats.")
+ ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
+ ;; MPL; in addition to these licenses the rest of the R wrapper is also
+ ;; available under the Expat license.
+ (license (list license:gpl2
+ license:lgpl2.1
+ license:mpl1.1
+ license:expat))))
+
+(define-public r-tidytext
+ (package
+ (name "r-tidytext")
+ (version "0.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tidytext" version))
+ (sha256
+ (base32
+ "0kwbpffdnqrb6hgrrmrfnx890imbzvp5bs6sj1k72if28qijarm5"))))
+ (properties `((upstream-name . "tidytext")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
+ ("r-hunspell" ,r-hunspell)
+ ("r-janeaustenr" ,r-janeaustenr)
+ ("r-matrix" ,r-matrix)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-tokenizers" ,r-tokenizers)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/juliasilge/tidytext")
+ (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
+ (description
+ "This is a package for text mining for word processing and sentiment
+analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
+ (license license:expat)))
+
+(define-public r-parsnip
+ (package
+ (name "r-parsnip")
+ (version "0.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "parsnip" version))
+ (sha256
+ (base32
+ "12121qj1800i7g3km5kqzlb7hms55crmp6il575c2i475h5qx8d3"))))
+ (properties `((upstream-name . "parsnip")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
+ ("r-globals" ,r-globals)
+ ("r-glue" ,r-glue)
+ ("r-magrittr" ,r-magrittr)
+ ("r-prettyunits" ,r-prettyunits)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-vctrs" ,r-vctrs)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://parsnip.tidymodels.org")
+ (synopsis "Common API to modeling and analysis functions")
+ (description
+ "This package provides a common interface to allow users to specify a
+model without having to remember the different argument names across different
+functions or computational engines (e.g. R, Spark, Stan, etc).")
+ (license license:gpl2)))
+
+(define-public r-infer
+ (package
+ (name "r-infer")
+ (version "0.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "infer" version))
+ (sha256
+ (base32
+ "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
+ (properties `((upstream-name . "infer")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-glue" ,r-glue)
+ ("r-magrittr" ,r-magrittr)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/tidymodels/infer")
+ (synopsis "Tidy statistical inference")
+ (description
+ "The objective of this package is to perform inference using an
+expressive statistical grammar that coheres with the Tidy design framework.")
+ (license license:cc0)))
+
+(define-public r-modeldata
+ (package
+ (name "r-modeldata")
+ (version "0.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "modeldata" version))
+ (sha256
+ (base32
+ "13q6hhbwqbwnjvg8bz6iwwfx96p1saqq3r34cjrbnpgzmr1nn11l"))))
+ (properties `((upstream-name . "modeldata")))
+ (build-system r-build-system)
+ (home-page "https://modeldata.tidymodels.org")
+ (synopsis "Data sets useful for modeling packages")
+ (description
+ "This package provides data sets used for demonstrating or testing
+model-related packages.")
+ (license license:expat)))
+
+(define-public r-tidymodels
+ (package
+ (name "r-tidymodels")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tidymodels" version))
+ (sha256
+ (base32
+ "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
+ (properties `((upstream-name . "tidymodels")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-broom" ,r-broom)
+ ("r-cli" ,r-cli)
+ ("r-crayon" ,r-crayon)
+ ("r-dials" ,r-dials)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-infer" ,r-infer)
+ ("r-magrittr" ,r-magrittr)
+ ("r-modeldata" ,r-modeldata)
+ ("r-parsnip" ,r-parsnip)
+ ("r-purrr" ,r-purrr)
+ ("r-recipes" ,r-recipes)
+ ("r-rlang" ,r-rlang)
+ ("r-rsample" ,r-rsample)
+ ("r-rstudioapi" ,r-rstudioapi)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-tune" ,r-tune)
+ ("r-workflows" ,r-workflows)
+ ("r-yardstick" ,r-yardstick)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("pandoc" ,pandoc)
+ ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
+ (home-page "https://github.com/tidymodels/tidymodels")
+ (synopsis "Tidy collection for modeling and statistical analysis")
+ (description
+ "The tidy modeling \"verse\" is a collection of packages for modeling and
+statistical analysis that share the underlying design philosophy, grammar, and
+data structures of the tidyverse.")
+ (license license:gpl3)))
+
+(define-public r-mlecens
+ (package
+ (name "r-mlecens")
+ (version "0.1-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "MLEcens" version))
+ (sha256
+ (base32
+ "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
+ (properties `((upstream-name . "MLEcens")))
+ (build-system r-build-system)
+ (home-page "http://stat.ethz.ch/~maathuis/")
+ (synopsis "Computation of the MLE for bivariate (interval) censored data")
+ (description
+ "This package contains functions to compute the nonparametric
+@dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
+@code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
+To be more precise, we consider the situation where we observe a set of
+rectangles that are known to contain the unobservable realizations of (X,Y).
+We compute the MLE based on such a set of rectangles. The methods can also be
+used for univariate censored data (see data set @code{cosmesis}), and for
+censored data with competing risks (see data set @code{menopause}). The
+package also provides functions to visualize the observed data and the MLE.")
+ (license license:gpl2+)))
+
+(define-public r-perm
+ (package
+ (name "r-perm")
+ (version "1.0-0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "perm" version))
+ (sha256
+ (base32
+ "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
+ (properties `((upstream-name . "perm")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/perm/")
+ (synopsis "Exact or asymptotic permutation tests")
+ (description
+ "This package provides several methods for performing permutation tests.
+It has three main functions, to perform linear permutation tests. These tests
+are tests where the test statistic is the sum of the product of a
+covariate (usually group indicator) and the scores.")
+ ;; Any version of the GPL
+ (license license:gpl2+)))
+
+(define-public r-qtl
+ (package
+ (name "r-qtl")
+ (version "1.46-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "qtl" version))
+ (sha256
+ (base32
+ "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
+ (build-system r-build-system)
+ (home-page "https://rqtl.org/")
+ (synopsis "R package for analyzing QTL experiments in genetics")
+ (description "R/qtl is an extension library for the R statistics system.
+It is used to analyze experimental crosses for identifying genes contributing
+to variation in quantitative traits (so-called quantitative trait loci, QTLs).
+
+Using a hidden Markov model, R/qtl estimates genetic maps, to identify
+genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
+genome scans.")
+ (license license:gpl3)))
+
+(define-public r-qtl2
+ (package
+ (name "r-qtl2")
+ (version "0.22-11")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "qtl2" version))
+ (sha256
+ (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://kbroman.org/qtl2/")
+ (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
+ (description
+ "This package provides a set of tools to perform @dfn{Quantitative Trait
+Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
+@code{R/qtl} package to better handle high-dimensional data and complex cross
+designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
+ (license license:gpl3)))
+
+(define-public r-seqminer
+ (package
+ (name "r-seqminer")
+ (version "8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "seqminer" version))
+ (sha256
+ (base32
+ "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://seqminer.genomic.codes")
+ (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
+ (description
+ "This package provides tools to integrate nucleotide sequencing
+data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
+ ;; Any version of the GPL is acceptable
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-maldiquant
+ (package
+ (name "r-maldiquant")
+ (version "1.19.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "MALDIquant" version))
+ (sha256
+ (base32
+ "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
+ (properties `((upstream-name . "MALDIquant")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/MALDIquant")
+ (synopsis "Quantitative analysis of mass spectrometry data")
+ (description
+ "This package provides a complete analysis pipeline for matrix-assisted
+laser desorption/ionization-time-of-flight (MALDI-TOF) and other
+two-dimensional mass spectrometry data. In addition to commonly used plotting
+and processing methods it includes distinctive features, namely baseline
+subtraction methods such as morphological filters (TopHat) or the
+statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
+alignment using warping functions, handling of replicated measurements as well
+as allowing spectra with different resolutions.")
+ (license license:gpl3+)))
+
+(define-public r-seurat
+ (package
+ (name "r-seurat")
+ (version "3.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "Seurat" version))
+ (sha256
+ (base32
+ "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
+ (properties `((upstream-name . "Seurat")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-cluster" ,r-cluster)
+ ("r-cowplot" ,r-cowplot)
+ ("r-fitdistrplus" ,r-fitdistrplus)
+ ("r-future" ,r-future)
+ ("r-future-apply" ,r-future-apply)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-ggridges" ,r-ggridges)
+ ("r-httr" ,r-httr)
+ ("r-ica" ,r-ica)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-leiden" ,r-leiden)
+ ("r-lmtest" ,r-lmtest)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-miniui" ,r-miniui)
+ ("r-patchwork" ,r-patchwork)
+ ("r-pbapply" ,r-pbapply)
+ ("r-plotly" ,r-plotly)
+ ("r-png" ,r-png)
+ ("r-rann" ,r-rann)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppannoy" ,r-rcppannoy)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rcppprogress" ,r-rcppprogress)
+ ("r-reticulate" ,r-reticulate)
+ ("r-rlang" ,r-rlang)
+ ("r-rocr" ,r-rocr)
+ ("r-rsvd" ,r-rsvd)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scales" ,r-scales)
+ ("r-sctransform" ,r-sctransform)
+ ("r-shiny" ,r-shiny)
+ ("r-spatstat" ,r-spatstat)
+ ("r-tibble" ,r-tibble)
+ ("r-uwot" ,r-uwot)))
+ (home-page "http://www.satijalab.org/seurat")
+ (synopsis "Seurat is an R toolkit for single cell genomics")
+ (description
+ "This package is an R package designed for QC, analysis, and
+exploration of single cell RNA-seq data. It easily enables widely-used
+analytical techniques, including the identification of highly variable genes,
+dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
+algorithms; density clustering, hierarchical clustering, k-means, and the
+discovery of differentially expressed genes and markers.")
+ (license license:gpl3)))
+
+(define-public r-phangorn
+ (package
+ (name "r-phangorn")
+ (version "2.5.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "phangorn" version))
+ (sha256
+ (base32
+ "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-fastmatch" ,r-fastmatch)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-quadprog" ,r-quadprog)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/KlausVigo/phangorn")
+ (synopsis "Phylogenetic analysis in R")
+ (description
+ "Phangorn is a package for phylogenetic analysis in R. It supports
+estimation of phylogenetic trees and networks using Maximum Likelihood,
+Maximum Parsimony, distance methods and Hadamard conjugation.")
+ (license license:gpl2+)))
+
+(define-public r-diversitree
+ (package
+ (name "r-diversitree")
+ (version "0.9-13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diversitree" version))
+ (sha256
+ (base32
+ "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-desolve" ,r-desolve)
+ ("r-rcpp" ,r-rcpp)
+ ("r-subplex" ,r-subplex)))
+ (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+ (synopsis "Comparative 'phylogenetic' analyses of diversification")
+ (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+ (license license:gpl2+)))
+
+(define-public r-absfiltergsea
+ (package
+ (name "r-absfiltergsea")
+ (version "1.5.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "AbsFilterGSEA" version))
+ (sha256
+ (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+ (properties `((upstream-name . "AbsFilterGSEA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-deseq" ,r-deseq)
+ ("r-limma" ,r-limma)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+ (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+ (description
+ "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+ Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+ (license license:gpl2)))
HCoop / jackhill / guix / guix.git / blobdiff