;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
+;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
;;; 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>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages networking)
+ #:use-module (gnu packages node)
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages pulseaudio) ;libsndfile
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages statistics)
#:use-module (gnu packages web)
#:use-module (gnu packages xorg))
+(define-public r-rticles
+ (package
+ (name "r-rticles")
+ (version "0.14")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rticles" version))
+ (sha256
+ (base32
+ "1377fib4asazhhki4aajvld0wa35vd3zjvyl3lf2hjm2qk3vyak7"))))
+ (properties `((upstream-name . "rticles")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-tinytex" ,r-tinytex)
+ ("r-xfun" ,r-xfun)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://github.com/rstudio/rticles")
+ (synopsis "Article formats for R Markdown")
+ (description
+ "This package provides a suite of custom R Markdown formats and templates
+for authoring journal articles and conference submissions.")
+ (license license:gpl3)))
+
(define-public r-bezier
(package
(name "r-bezier")
degree elevation and curve fitting.")
(license license:gpl2+)))
+(define-public r-v8
+ (package
+ (name "r-v8")
+ (version "3.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "V8" version))
+ (sha256
+ (base32
+ "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
+ (properties `((upstream-name . "V8")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'find-v8
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "configure"
+ (("^PKG_LIBS=.*")
+ (string-append "PKG_LIBS="
+ (assoc-ref inputs "node")
+ "/lib/libnode.so.64\n")))
+ (setenv "INCLUDE_DIR"
+ (string-append
+ (assoc-ref inputs "node")
+ "/include/node"))
+ (setenv "LIB_DIR"
+ (string-append
+ (assoc-ref inputs "node") "/lib"))
+ #t)))))
+ (inputs
+ `(("node" ,libnode)))
+ (propagated-inputs
+ `(("r-curl" ,r-curl)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://jeroen.cran.dev/V8")
+ (synopsis "Embedded JavaScript and WebAssembly engine for R")
+ (description
+ "This package provides an R interface to V8: Google's JavaScript and
+WebAssembly engine.")
+ (license license:expat)))
+
+(define-public r-dot
+ (package
+ (name "r-dot")
+ (version "0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "DOT" version))
+ (sha256
+ (base32
+ "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
+ (properties `((upstream-name . "DOT")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-v8" ,r-v8)))
+ (home-page "http://haghish.com/dot")
+ (synopsis "Render and Export DOT Graphs in R")
+ (description
+ "This package provides tools to render DOT diagram markup language in R
+and also provides the possibility to export the graphs in PostScript and
+SVG (Scalable Vector Graphics) formats. In addition, it supports literate
+programming packages such as @code{knitr} and @code{rmarkdown}.")
+ (license license:expat)))
+
(define-public r-clipr
(package
(name "r-clipr")
the system clipboards.")
(license license:gpl3)))
+(define-public r-zoo
+ (package
+ (name "r-zoo")
+ (version "1.8-8")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "zoo" version))
+ (sha256
+ (base32
+ "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)))
+ (home-page "http://zoo.R-Forge.R-project.org/")
+ (synopsis "S3 infrastructure for regular and irregular time series")
+ (description "This package contains an S3 class with methods for totally
+ordered indexed observations. It is particularly aimed at irregular time
+series of numeric vectors/matrices and factors.")
+ (license license:gpl2+)))
+
(define-public r-ggpmisc
(package
(name "r-ggpmisc")
respecting the grammar of its graphics paradigm.")
(license license:gpl2+)))
+(define-public r-gprofiler
+ (package
+ (name "r-gprofiler")
+ (version "0.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gProfileR" version))
+ (sha256
+ (base32
+ "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
+ (properties `((upstream-name . "gProfileR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-plyr" ,r-plyr)
+ ("r-rcurl" ,r-rcurl)))
+ (home-page "https://cran.r-project.org/web/packages/gProfileR/")
+ (synopsis "Interface to the g:Profiler toolkit")
+ (description
+ "This package provides tools for functional enrichment analysis,
+gene identifier conversion and mapping homologous genes across related
+organisms via the @code{g:Profiler} toolkit.")
+ (license license:gpl2+)))
+
+(define-public r-gprofiler2
+ (package
+ (name "r-gprofiler2")
+ (version "0.1.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gprofiler2" version))
+ (sha256
+ (base32
+ "112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb"))))
+ (properties `((upstream-name . "gprofiler2")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-crosstalk" ,r-crosstalk)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-plotly" ,r-plotly)
+ ("r-rcurl" ,r-rcurl)
+ ("r-tidyr" ,r-tidyr)
+ ("r-viridislite" ,r-viridislite)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
+ (synopsis "Interface to the g:Profiler toolset")
+ (description
+ "This package provides a toolset for functional enrichment analysis and
+visualization, gene/protein/SNP identifier conversion and mapping orthologous
+genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
+The main tools are:
+
+@enumerate
+@item @code{g:GOSt}, functional enrichment analysis and visualization of gene
+ lists;
+@item @code{g:Convert}, gene/protein/transcript identifier conversion across
+ various namespaces;
+@item @code{g:Orth}, orthology search across species;
+@item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
+ genes and variant effects.
+@end enumerate
+
+This package is an R interface corresponding to the 2019 update of
+@code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
+higher.")
+ (license license:gpl2+)))
+
(define-public r-oenb
(package
(name "r-oenb")
(define-public r-jsonlite
(package
(name "r-jsonlite")
- (version "1.6.1")
+ (version "1.7.0")
(source (origin
(method url-fetch)
(uri (cran-uri "jsonlite" version))
(sha256
(base32
- "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
+ "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
(build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://arxiv.org/abs/1403.2805")
(synopsis "Robust, high performance JSON parser and generator for R")
(description
(define-public r-htmltools
(package
(name "r-htmltools")
- (version "0.4.0")
+ (version "0.5.0")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
- "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
+ "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-digest" ,r-digest)
- ("r-rcpp" ,r-rcpp)
+ `(("r-base64enc" ,r-base64enc)
+ ("r-digest" ,r-digest)
("r-rlang" ,r-rlang)))
(home-page "https://cran.r-project.org/web/packages/htmltools")
(synopsis "R tools for HTML")
(define-public r-htmltable
(package
(name "r-htmltable")
- (version "1.13.3")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "htmlTable" version))
(sha256
- (base32
- "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
+ (base32 "0ma52kajzxfg9w811d6ldhghzn9xhyr8bh7k5v265k82bzx7rac6"))))
(properties `((upstream-name . "htmlTable")))
(build-system r-build-system)
(propagated-inputs
("r-magrittr" ,r-magrittr)
("r-rstudioapi" ,r-rstudioapi)
("r-stringr" ,r-stringr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "http://gforge.se/packages/")
(synopsis "Advanced tables for Markdown/HTML")
(description
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/rstudio/shiny.git")
+ (url "https://github.com/rstudio/shiny")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fbreitwieser/sankeyD3.git")
+ (url "https://github.com/fbreitwieser/sankeyD3")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(define-public r-rcpp
(package
(name "r-rcpp")
- (version "1.0.4.6")
+ (version "1.0.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
- (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
+ (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq"))))
(build-system r-build-system)
(home-page "http://www.rcpp.org")
(synopsis "Seamless R and C++ integration")
(define-public r-calibrate
(package
(name "r-calibrate")
- (version "1.7.5")
+ (version "1.7.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "calibrate" version))
(sha256
- (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
+ (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)))
(define-public r-circlize
(package
(name "r-circlize")
- (version "0.4.9")
+ (version "0.4.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "circlize" version))
(sha256
(base32
- "14944vn0n5d095mpjyag4fz8vy04m6wxb6mmyygi8q813akikm3h"))))
+ "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-colorspace" ,r-colorspace)
(define-public r-getoptlong
(package
(name "r-getoptlong")
- (version "1.0.0")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "GetoptLong" version))
(sha256
(base32
- "1fswgy5j4xaipqs7nk7nzrl66vrchhxrk0w7hcsbyij3sxgn3z9j"))))
+ "1p89v2qzqfxyrmqzkv245716n9i4bllnq77a6gw811mgdhxbd51l"))))
(properties `((upstream-name . "GetoptLong")))
(build-system r-build-system)
(inputs
`(("r-bit" ,r-bit)
("r-fastmatch" ,r-fastmatch)
("r-ff" ,r-ff)))
- (home-page "http://github.com/edwindj/ffbase")
+ (home-page "https://github.com/edwindj/ffbase")
(synopsis "Basic statistical functions for package 'ff'")
(description
"This package extends the out of memory vectors of @code{ff} with
(define-public r-gower
(package
(name "r-gower")
- (version "0.2.1")
+ (version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "gower" version))
(sha256
(base32
- "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
+ "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
(build-system r-build-system)
(home-page "https://github.com/markvanderloo/gower")
(synopsis "Gower's distance")
(define-public r-broom
(package
(name "r-broom")
- (version "0.5.6")
+ (version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "broom" version))
(sha256
(base32
- "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
+ "0bq8w1ckrladzck2g0mgiyjdrzi06kbqalk5q3pfvj1607fdv3d5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
("r-dplyr" ,r-dplyr)
+ ("r-ellipsis" ,r-ellipsis)
("r-generics" ,r-generics)
- ("r-nlme" ,r-nlme)
+ ("r-glue" ,r-glue)
("r-purrr" ,r-purrr)
- ("r-reshape2" ,r-reshape2)
+ ("r-rlang" ,r-rlang)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)))
(define-public r-recipes
(package
(name "r-recipes")
- (version "0.1.12")
+ (version "0.1.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "recipes" version))
(sha256
(base32
- "0hbnrqgzazg401nk5fhljif7wnspicki179qf215r34y9wm8g3xj"))))
+ "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-glue" ,r-glue)
("r-gower" ,r-gower)
("r-ipred" ,r-ipred)
+ ("r-lifecycle" ,r-lifecycle)
("r-lubridate" ,r-lubridate)
("r-magrittr" ,r-magrittr)
("r-matrix" ,r-matrix)
("r-scales" ,r-scales)))
(native-inputs
`(("r-knitr" ,r-knitr))) ; for vignettes
- (home-page "http://github.com/slowkow/ggrepel")
+ (home-page "https://github.com/slowkow/ggrepel")
(synopsis "Repulsive text and label geometries for ggplot2")
(description
"This package provides text and label geometries for ggplot2 that help to
(define-public r-mice
(package
(name "r-mice")
- (version "3.9.0")
+ (version "3.10.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mice" version))
(sha256
(base32
- "1wycbc2iqp68gfzvqx1gsn5n1k1h4bg79dy8m5msqf226hy83ncn"))))
+ "0w81shmd2crpdlh66pnm27v4n06aayganq6kkalirln4c0ci2nyi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
("r-lattice" ,r-lattice)
("r-rcpp" ,r-rcpp)
("r-tidyr" ,r-tidyr)))
(define-public r-vioplot
(package
(name "r-vioplot")
- (version "0.3.4")
+ (version "0.3.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "vioplot" version))
(sha256
(base32
- "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
+ "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-sm" ,r-sm)
("r-zoo" ,r-zoo)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
(synopsis "Violin plot")
(description
(define-public r-processx
(package
(name "r-processx")
- (version "3.4.2")
+ (version "3.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "processx" version))
(sha256
- (base32
- "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
+ (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ps" ,r-ps)
(define-public r-xfun
(package
(name "r-xfun")
- (version "0.14")
+ (version "0.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
- (base32 "183f6d7lr116f90j37a8hfr6ni1x9xkqj79s8lnky1jwr6zj3ha9"))))
+ (base32 "1fdipwrl45bznb17da4169ria5jax0f2649yj5accw6qr6wsc8bj"))))
(build-system r-build-system)
;; knitr itself depends on xfun
#;
(define-public r-pillar
(package
(name "r-pillar")
- (version "1.4.4")
+ (version "1.4.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
- "0viymfp1rkr7ig3m1b016r75hk8qbr9cqsjc6c20ks9pm5svmsp1"))))
+ "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
("r-crayon" ,r-crayon)
+ ("r-ellipsis" ,r-ellipsis)
("r-fansi" ,r-fansi)
+ ("r-lifecycle" ,r-lifecycle)
("r-rlang" ,r-rlang)
("r-utf8" ,r-utf8)
("r-vctrs" ,r-vctrs)))
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.23")
+ (version "0.24")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "084jd1m2i3zyxxlls7skq3jxv3b5cgps3yk60q1yzyy9sxslab7m"))))
+ "0mc9i7r45s5kagcfig508dbyf6jir6q4ghq9cxqvnpxp6ymh4qpr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
(define-public r-cubature
(package
(name "r-cubature")
- (version "2.0.4")
+ (version "2.0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "cubature" version))
(sha256
(base32
- "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
+ "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/bnaras/cubature")
(synopsis "Adaptive multivariate integration over hypercubes")
(description
(define-public r-radiant-data
(package
(name "r-radiant-data")
- (version "1.3.4")
+ (version "1.3.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "radiant.data" version))
(sha256
(base32
- "19sjjb49inrfl7jzq4zpwhdslni0zrp30bl58pisin29ka3ylpzs"))
+ "19gbc7k1hsi6hg6ka8i70wlw8j9fs9wkpn36761lzbcyam6vgqn0"))
(modules '((guix build utils)))
(snippet
'(begin
(define-public r-renv
(package
(name "r-renv")
- (version "0.10.0")
+ (version "0.11.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "renv" version))
(sha256
(base32
- "0yy24kq60dh9n68my132xhhkbnbs7q91z55b1yd6ymr7rxj32mif"))))
+ "0dd63jr240pg95a6p058s5kcclfmscihdy89v212msihmwvylwh3"))))
(properties `((upstream-name . "renv")))
(build-system r-build-system)
(native-inputs
(define-public r-rstatix
(package
(name "r-rstatix")
- (version "0.5.0")
+ (version "0.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "rstatix" version))
(sha256
(base32
- "0ikbjmr58ah39rlwyiix50kl3yk9j7jngsvl6hh973392qdvmch6"))))
+ "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
(properties `((upstream-name . "rstatix")))
(build-system r-build-system)
(propagated-inputs
("r-car" ,r-car)
("r-corrplot" ,r-corrplot)
("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
("r-magrittr" ,r-magrittr)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
(define-public r-ggpubr
(package
(name "r-ggpubr")
- (version "0.3.0")
+ (version "0.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggpubr" version))
(sha256
(base32
- "1dly74cnn8iq7vsgmcz0czszdsmg5cgzm4w3s0v30k4psmmzqbxq"))))
+ "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cowplot" ,r-cowplot)
(define-public r-rdpack
(package
(name "r-rdpack")
- (version "0.11-1")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rdpack" version))
(sha256
(base32
- "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
+ "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw"))))
(properties `((upstream-name . "Rdpack")))
(build-system r-build-system)
(propagated-inputs
(define-public r-officer
(package
(name "r-officer")
- (version "0.3.11")
+ (version "0.3.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "officer" version))
(sha256
(base32
- "0nwasra2kb5wplcim7n57kynwhyg4vsk3fz42mbpm0hig1lzl9pp"))))
+ "1wk9h6bz77s5j6lgksmlrmi1vyaa35c766gq6hgb1dp0dz0x342x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magrittr" ,r-magrittr)
to help insert or delete content at a specific location in the document.")
(license license:gpl3)))
+(define-public r-profilemodel
+ (package
+ (name "r-profilemodel")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "profileModel" version))
+ (sha256
+ (base32
+ "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
+ (properties `((upstream-name . "profileModel")))
+ (build-system r-build-system)
+ (home-page "https://github.com/ikosmidis/profileModel")
+ (synopsis "Profiling inference functions for various model classes")
+ (description
+ "This package provides tools that can be used to calculate, evaluate,
+plot and use for inference the profiles of *arbitrary* inference functions for
+arbitrary @code{glm}-like fitted models with linear predictors. More information
+on the methods that are implemented can be found in Kosmidis (2008)
+@url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
+ (license license:gpl2+)))
+
+(define-public r-brglm
+ (package
+ (name "r-brglm")
+ (version "0.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "brglm" version))
+ (sha256
+ (base32
+ "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
+ (properties `((upstream-name . "brglm")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-profilemodel" ,r-profilemodel)))
+ (home-page "https://github.com/ikosmidis/brglm")
+ (synopsis "Bias reduction in binomial-response generalized linear models")
+ (description
+ "Fit generalized linear models with binomial responses using either an
+adjusted-score approach to bias reduction or maximum penalized likelihood
+where penalization is by Jeffreys invariant prior. These procedures return
+estimates with improved frequentist properties (bias, mean squared error) that
+are always finite even in cases where the maximum likelihood estimates are
+infinite (data separation). Fitting takes place by fitting generalized linear
+models on iteratively updated pseudo-data. The interface is essentially the
+same as @code{glm}. More flexibility is provided by the fact that custom
+pseudo-data representations can be specified and used for model fitting.
+Functions are provided for the construction of confidence intervals for the
+reduced-bias estimates.")
+ (license license:gpl2+)))
+
+(define-public r-entropy
+ (package
+ (name "r-entropy")
+ (version "1.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "entropy" version))
+ (sha256
+ (base32
+ "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
+ (properties `((upstream-name . "entropy")))
+ (build-system r-build-system)
+ (home-page "https://www.strimmerlab.org/software/entropy/")
+ (synopsis "Estimation of entropy, mutual information and related quantities")
+ (description
+ "This package implements various estimators of entropy, such as the
+shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
+Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
+estimator. It also offers an R interface to the NSB estimator. Furthermore,
+it provides functions for estimating Kullback-Leibler divergence, chi-squared,
+mutual information, and chi-squared statistic of independence. In addition
+there are functions for discretizing continuous random variables.")
+ (license license:gpl3+)))
+
(define-public r-abn
(package
(name "r-abn")
- (version "2.2")
+ (version "2.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "abn" version))
(sha256
(base32
- "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
+ "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc"))))
(build-system r-build-system)
(inputs
`(("gsl" ,gsl)))
(propagated-inputs
- `(("r-lme4" ,r-lme4)
+ `(("r-boot" ,r-boot)
+ ("r-brglm" ,r-brglm)
+ ("r-entropy" ,r-entropy)
+ ("r-lme4" ,r-lme4)
("r-mass" ,r-mass)
+ ("r-moments" ,r-moments)
("r-nnet" ,r-nnet)
("r-rcpp" ,r-rcpp)
("r-rcpparmadillo" ,r-rcpparmadillo)
(define-public r-sjlabelled
(package
(name "r-sjlabelled")
- (version "1.1.5")
+ (version "1.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjlabelled" version))
(sha256
(base32
- "0grskmd7wrw31lkf85z6xz0bv246m6grvqkijvqi4q8zkl6p5vb3"))))
+ "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-insight" ,r-insight)))
(define-public r-flextable
(package
(name "r-flextable")
- (version "0.5.9")
+ (version "0.5.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "flextable" version))
(sha256
(base32
- "1rkz0nhwjy1l8sb0kmna5v492n2ydnk7gydswnmf88r8vfyjczhw"))))
+ "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
("r-officer" ,r-officer)
("r-rlang" ,r-rlang)
("r-rmarkdown" ,r-rmarkdown)
+ ("r-uuid" ,r-uuid)
("r-xml2" ,r-xml2)))
(home-page "https://davidgohel.github.io/flextable")
(synopsis "Functions for tabular reporting")
(define-public r-doby
(package
(name "r-doby")
- (version "4.6.5")
+ (version "4.6.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "doBy" version))
(sha256
(base32
- "1ckazh701b4ilg8bj17ji903538jmb49d997gm49ah5j5jc1x0g7"))))
+ "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
(properties `((upstream-name . "doBy")))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-deriv" ,r-deriv)
("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
("r-magrittr" ,r-magrittr)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
- ("r-plyr" ,r-plyr)
("r-pbkrtest" ,r-pbkrtest)
("r-tibble" ,r-tibble)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
(synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
(description
(define-public r-mosaicdata
(package
(name "r-mosaicdata")
- (version "0.17.0")
+ (version "0.18.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaicData" version))
(sha256
- (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
+ (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
(properties `((upstream-name . "mosaicData")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/mosaicData/")
(define-public r-raster
(package
(name "r-raster")
- (version "3.1-5")
+ (version "3.3-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "raster" version))
(sha256
(base32
- "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
+ "144mva2dx7ffkq7z0fixr4z76ci1s4lizlyv5r7v07fd4nzg5hby"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
(define-public r-magick
(package
(name "r-magick")
- (version "2.3")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "magick" version))
(sha256
(base32
- "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
+ "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
(build-system r-build-system)
(inputs
`(("imagemagick" ,imagemagick)
("r-magrittr" ,r-magrittr)
("r-rcpp" ,r-rcpp)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
(home-page "https://github.com/ropensci/magick")
(synopsis "Advanced graphics and image-processing in R")
(description
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.4.6")
+ (version "1.4.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "0mxk7ghlv4r6sna4897q1la2xgyn1dw3r9srhm9x4h5l4701avfa"))))
+ "0h884qn4cip03w0h5psrz5y9zkm2wppklrhdz2chm2xk13zqnq5k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
(define-public r-bayesplot
(package
(name "r-bayesplot")
- (version "1.7.1")
+ (version "1.7.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayesplot" version))
(sha256
(base32
- "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
+ "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
(build-system r-build-system)
(inputs
`(("pandoc" ,ghc-pandoc)
("pandoc-citeproc" ,ghc-pandoc-citeproc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-ggplot2" ,r-ggplot2)
(define-public r-glmmtmb
(package
(name "r-glmmtmb")
- (version "1.0.1")
+ (version "1.0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "glmmTMB" version))
(sha256
(base32
- "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm"))))
+ "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
(properties `((upstream-name . "glmmTMB")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bayestestr
(package
(name "r-bayestestr")
- (version "0.6.0")
+ (version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
- "0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1"))))
+ "1nrycyzznzrlwnfwk1w3ixdq0bj82nri9kb2qiaiw8wwzwrsl1hd"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-performance
(package
(name "r-performance")
- (version "0.4.6")
+ (version "0.4.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "08i9ngvga06abs2k50gvkh6iwl4r77bkmmchsqjibsy09wdvd8xj"))))
+ "0gw165wm2a0vjsvyll8z9k6qd156z3jf4priy1r745v63x4mnb5k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
(define-public r-ggeffects
(package
(name "r-ggeffects")
- (version "0.14.3")
+ (version "0.15.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
- "06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd"))))
+ "1bqvbhw5la3cj3v0gwava117ff24b1p450azln402gsxgfl3vw7r"))))
(build-system r-build-system)
(propagated-inputs
`(("r-insight" ,r-insight)
(define-public r-effectsize
(package
(name "r-effectsize")
- (version "0.3.0")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "effectsize" version))
(sha256
(base32
- "0kijp4wamkidaxysc11dd4vhvnm4wnbi87871wcbwn27k5b6i5dg"))))
+ "1n5b5434sd8f1v95bfjwg92v879rkaj8zpm6ldnrg0kgfb0gy6q4"))))
(properties `((upstream-name . "effectsize")))
(build-system r-build-system)
(propagated-inputs
(define-public r-sjplot
(package
(name "r-sjplot")
- (version "2.8.3")
+ (version "2.8.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjPlot" version))
(sha256
- (base32 "0ip1rkjlhyf3axlc8qqss1qq1f0xrda890c1jmcbhm98wwjw264f"))))
+ (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
(properties `((upstream-name . "sjPlot")))
(build-system r-build-system)
(propagated-inputs
(define-public r-fs
(package
(name "r-fs")
- (version "1.4.1")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "fs" version))
(sha256
(base32
- "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
+ "09rpazjba9jy448j6rq989fw3wv3xhng7fn8p8gr22gyx0n0y1zr"))))
(build-system r-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
(define-public r-rcppgsl
(package
(name "r-rcppgsl")
- (version "0.3.7")
+ (version "0.3.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppGSL" version))
(sha256
- (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
+ (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
(properties `((upstream-name . "RcppGSL")))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
("gsl" ,gsl)))
- (native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
(home-page "https://cran.r-project.org/web/packages/RcppGSL/")
(synopsis "Rcpp integration for GSL vectors and matrices")
(description
(define-public r-rcppparallel
(package
(name "r-rcppparallel")
- (version "5.0.1")
+ (version "5.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppParallel" version))
(sha256
(base32
- "029yyjnixggqmddazwxh1wqid1h7xpwpi4sgixyhbb4kmvqlwfkd"))))
+ "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
(properties `((upstream-name . "RcppParallel")))
(build-system r-build-system)
(home-page "https://rcppcore.github.io/RcppParallel/")
(define-public r-docopt
(package
(name "r-docopt")
- (version "0.6.1")
+ (version "0.7.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "docopt" version))
(sha256
(base32
- "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
+ "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
(build-system r-build-system)
(home-page "https://github.com/docopt/docopt.R")
(synopsis "Command-line interface specification language")
(define-public r-iso
(package
(name "r-iso")
- (version "0.0-18")
+ (version "0.0-18.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Iso" version))
(sha256
(base32
- "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
+ "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
(properties `((upstream-name . "Iso")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(define-public r-bigrquery
(package
(name "r-bigrquery")
- (version "1.3.0")
+ (version "1.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bigrquery" version))
(sha256
(base32
- "0j8asipnb4fg4kk3apy37ywqq78ncmqh9wq015xpww2zb9shnbvf"))))
+ "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
(define-public r-gmp
(package
(name "r-gmp")
- (version "0.5-13.6")
+ (version "0.6-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gmp" version))
(sha256
(base32
- "0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
+ "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
(build-system r-build-system)
(arguments
'(#:phases
(define-public r-genenet
(package
(name "r-genenet")
- (version "1.2.14")
+ (version "1.2.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "GeneNet" version))
(sha256
(base32
- "0cdhrj15rz0w0pyw3r8mikrzsdh95y5i1c0pa3cn0c2bjnjx3x3n"))))
+ "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
(properties `((upstream-name . "GeneNet")))
(build-system r-build-system)
(propagated-inputs
(define-public r-cmprsk
(package
(name "r-cmprsk")
- (version "2.2-9")
+ (version "2.2-10")
(source
(origin
(method url-fetch)
(uri (cran-uri "cmprsk" version))
(sha256
- (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
+ (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)))
(define-public r-future
(package
(name "r-future")
- (version "1.17.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "future" version))
(sha256
(base32
- "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
+ "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
(define-public r-future-apply
(package
(name "r-future-apply")
- (version "1.5.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "future.apply" version))
(sha256
(base32
- "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
+ "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
(properties `((upstream-name . "future.apply")))
(build-system r-build-system)
(propagated-inputs
(define-public r-blockmodeling
(package
(name "r-blockmodeling")
- (version "0.3.6")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "blockmodeling" version))
(sha256
(base32
- "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
+ "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
(define-public r-gamlss-dist
(package
(name "r-gamlss-dist")
- (version "5.1-6")
+ (version "5.1-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "gamlss.dist" version))
(sha256
- (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
+ (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
(properties `((upstream-name . "gamlss.dist")))
(build-system r-build-system)
(propagated-inputs `(("r-mass" ,r-mass)))
(define-public r-lavaan
(package
(name "r-lavaan")
- (version "0.6-5")
+ (version "0.6-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "lavaan" version))
(sha256
(base32
- "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
+ "0sfv58r2kxinax62bx6j3kkfx07qm16ddwf5qz392q33h9zs009h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
(define-public r-nonnest2
(package
(name "r-nonnest2")
- (version "0.5-3")
+ (version "0.5-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "nonnest2" version))
(sha256
(base32
- "1mnv4pa583ir9s03h952hk40lwdywr3g88g76sk1zsa54rcmn82c"))))
+ "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-compquadform" ,r-compquadform)
("r-tibble" ,r-tibble)))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "http://github.com/rnabioco/valr")
+ (home-page "https://github.com/rnabioco/valr")
(synopsis "Genome interval arithmetic in R")
(description
"This package enables you to read and manipulate genome intervals and
(define-public r-picante
(package
(name "r-picante")
- (version "1.8.1")
+ (version "1.8.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "picante" version))
(sha256
(base32
- "1b16zm8zjjsl181b8krkdcrbcw347kf772c4w7y5332qmfi7jhz0"))))
+ "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ape" ,r-ape)
(define-public r-lemon
(package
(name "r-lemon")
- (version "0.4.4")
+ (version "0.4.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "lemon" version))
(sha256
(base32
- "0m9hqwi709j9iwsxn8jh63741jiyr7ppwgqaw2zkv285p3m5wvd5"))))
+ "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-plyr" ,r-plyr)
("r-rlang" ,r-rlang)
("r-scales" ,r-scales)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/stefanedwards/lemon")
(synopsis "Freshen up your ggplot2 plots")
(description
(define-public r-units
(package
(name "r-units")
- (version "0.6-6")
+ (version "0.6-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "units" version))
(sha256
(base32
- "11x6xz1fbml28xmrhgn4sii9vfyj3gyfc1dfxahdg9cszdmcgdnh"))))
+ "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
(build-system r-build-system)
(inputs
`(("udunits" ,udunits)))
(define-public r-spdata
(package
(name "r-spdata")
- (version "0.3.5")
+ (version "0.3.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "spData" version))
(sha256
(base32
- "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
+ "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
(properties `((upstream-name . "spData")))
(build-system r-build-system)
(propagated-inputs
(define-public r-sf
(package
(name "r-sf")
- (version "0.9-3")
+ (version "0.9-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
- "0qh9jxj88rhkwcd95g0l57cdrz5qqjw1b9yysz1hp9cp99485hcx"))))
+ "1xgmnz01pxvpg2ins1h65mlcrafqihlljcjlag8spq9ii7d5i7mx"))))
(build-system r-build-system)
(inputs
`(("gdal" ,gdal)
(define-public r-spdep
(package
(name "r-spdep")
- (version "1.1-3")
+ (version "1.1-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "spdep" version))
(sha256
(base32
- "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
+ "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
("r-sf" ,r-sf)
("r-sp" ,r-sp)
("r-spdata" ,r-spdata)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/r-spatial/spdep/")
(synopsis "Spatial dependence: weighting schemes, statistics and models")
(description
(define-public r-polspline
(package
(name "r-polspline")
- (version "1.1.18")
+ (version "1.1.19")
(source
(origin
(method url-fetch)
(uri (cran-uri "polspline" version))
(sha256
- (base32 "00h1xg89wncfj2nk68zv7vphfcc68s7k0l5s9511bzxz8khhw9fz"))))
+ (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/polspline/")
(define-public r-rms
(package
(name "r-rms")
- (version "5.1-4")
+ (version "6.0-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "rms" version))
(sha256
- (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
+ (base32 "0m88m63d19qz03x8v56h4rrblln3d2943spi1v4wxxnbcdk22np9"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-ggplot2" ,r-ggplot2)
+ `(("r-cluster" ,r-cluster)
+ ("r-digest" ,r-digest)
+ ("r-ggplot2" ,r-ggplot2)
("r-hmisc" ,r-hmisc)
("r-htmltable" ,r-htmltable)
("r-htmltools" ,r-htmltools)
("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
("r-multcomp" ,r-multcomp)
("r-nlme" ,r-nlme)
("r-polspline" ,r-polspline)
(define-public r-ldheatmap
(package
(name "r-ldheatmap")
- (version "0.99-7")
+ (version "0.99-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "LDheatmap" version))
(sha256
(base32
- "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
+ "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
(properties `((upstream-name . "LDheatmap")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bookdown
(package
(name "r-bookdown")
- (version "0.18")
+ (version "0.20")
(source (origin
(method url-fetch)
(uri (cran-uri "bookdown" version))
(sha256
(base32
- "1my6g16phx21v5cvfqcnjibh3zcv02xkix347aafd6a7r3hnxpq5"))))
+ "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
(define-public r-rjava
(package
(name "r-rjava")
- (version "0.9-12")
+ (version "0.9-13")
(source
(origin
(method url-fetch)
(uri (cran-uri "rJava" version))
(sha256
(base32
- "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
+ "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
(properties `((upstream-name . "rJava")))
(build-system r-build-system)
(arguments
(define-public r-msigdbr
(package
(name "r-msigdbr")
- (version "7.0.1")
+ (version "7.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "msigdbr" version))
(sha256
(base32
- "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
+ "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-magrittr" ,r-magrittr)
("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/igordot/msigdbr")
(synopsis "MSigDB gene sets for multiple organisms")
(description
(define-public r-ggforce
(package
(name "r-ggforce")
- (version "0.3.1")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggforce" version))
(sha256
(base32
- "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
+ "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
(define-public r-europepmc
(package
(name "r-europepmc")
- (version "0.3")
+ (version "0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "europepmc" version))
(sha256
(base32
- "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
+ "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-plyr" ,r-plyr)
("r-progress" ,r-progress)
("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
("r-urltools" ,r-urltools)
("r-xml2" ,r-xml2)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/ropensci/europepmc/")
(synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
(description
(define-public r-ggraph
(package
(name "r-ggraph")
- (version "2.0.2")
+ (version "2.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggraph" version))
(sha256
(base32
- "1ckq82hg52vr2wydkqv2wrppgjyvddd6bwqzrngqlm7j71xapjl0"))))
+ "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
function for computing a matrix of correlation p-values.")
(license license:gpl2)))
+;; This package includes minified JavaScript files. When upgrading please
+;; check that there are no new minified JavaScript files.
(define-public r-flexdashboard
(package
(name "r-flexdashboard")
- (version "0.5.1.1")
+ (version "0.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "flexdashboard" version))
(sha256
(base32
- "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
- (build-system r-build-system)
- (arguments
- `(#:modules ((guix build utils)
+ "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete bundled minified JavaScript files
+ (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
+ (delete-file "inst/www/sly/sly.min.js")
+ (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
+ (delete-file "inst/www/prism/prism.js")
+ #t))))
+ (build-system r-build-system)
+ (arguments
+ `(#:modules ((guix build utils)
(guix build r-build-system)
(srfi srfi-1)
(srfi srfi-26)
(for-each (lambda (source target)
(format #t "Processing ~a --> ~a~%"
source target)
- (delete-file target)
(let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
(call-with-output-file target
(lambda (port)
(define-public r-ingredients
(package
(name "r-ingredients")
- (version "1.2.0")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ingredients" version))
(sha256
(base32
- "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
+ "1mp1rgi3nnr8mjddpbyi24zvqcbihz0d8np2j13cbjc089n6jci8"))))
(properties `((upstream-name . "ingredients")))
(build-system r-build-system)
(propagated-inputs
classification and regression models.")
(license license:gpl3)))
+(define-public r-dae
+ (package
+ (name "r-dae")
+ (version "3.1-27")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "dae" version))
+ (sha256
+ (base32
+ "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-plyr" ,r-plyr)))
+ (native-inputs
+ `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
+ (home-page "http://chris.brien.name")
+ (synopsis "Functions useful in the design and ANOVA of experiments")
+ (description
+ "This package provides functions useful in the design and ANOVA of
+experiments. The content falls into the following groupings:
+
+@enumerate
+@item data,
+@item factor manipulation functions,
+@item design functions,
+@item ANOVA functions,
+@item matrix functions,
+@item projector and canonical efficiency functions, and
+@item miscellaneous functions.
+@end enumerate
+
+There is a vignette called @code{DesignNotes} describing how to use the design
+functions for randomizing and assessing designs. The ANOVA functions
+facilitate the extraction of information when the @code{Error} function has
+been used in the call to @code{aov}.")
+ (license license:gpl2)))
+
(define-public r-dalex
(package
(name "r-dalex")
- (version "1.2.1")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "DALEX" version))
(sha256
(base32
- "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
+ "1azbnykaddsfp2qmxmhpjz76zg78msxv6n2jqkq4gwbgqa5vdfd2"))))
(properties `((upstream-name . "DALEX")))
(build-system r-build-system)
(propagated-inputs
(define-public r-xgboost
(package
(name "r-xgboost")
- (version "1.0.0.2")
+ (version "1.1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "xgboost" version))
(sha256
(base32
- "1ld2w51c5fy3bl0kvjn1iplffc4lmin9s9zz5xx7xsm44d6j6kzd"))))
+ "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
(define-public r-umap
(package
(name "r-umap")
- (version "0.2.5.0")
+ (version "0.2.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "umap" version))
(sha256
(base32
- "0qp8zbh6fn8kn6q2h2lyjgmq3pr6gqwsd8ymqx25px13zjhxch9d"))))
+ "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
(build-system r-build-system)
(propagated-inputs
`(("r-openssl" ,r-openssl)
(define-public r-rhpcblasctl
(package
(name "r-rhpcblasctl")
- (version "0.20-17")
+ (version "0.20-137")
(source
(origin
(method url-fetch)
(uri (cran-uri "RhpcBLASctl" version))
(sha256
(base32
- "0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
+ "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
(properties `((upstream-name . "RhpcBLASctl")))
(build-system r-build-system)
(home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
(define-public r-patchwork
(package
(name "r-patchwork")
- (version "1.0.0")
+ (version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "patchwork" version))
(sha256
(base32
- "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb"))))
+ "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/MacoskoLab/liger.git")
+ (url "https://github.com/MacoskoLab/liger")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(define-public r-systemfonts
(package
(name "r-systemfonts")
- (version "0.2.1")
+ (version "0.2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "systemfonts" version))
(sha256
(base32
- "0dna00xai0pw76b4830yy4r5j1hq7f7kla67v0iz39cjm4rq4ygq"))))
+ "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
(properties `((upstream-name . "systemfonts")))
(build-system r-build-system)
(inputs
(define-public r-parameters
(package
(name "r-parameters")
- (version "0.6.1")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
- "0mylxkf1y6mk4kf6c57x102sf4c800pfasjcfbf1hnsh6ya0m6dy"))))
+ "1cmb2hc6f4qdx9aj586zhllckzs6s5sznbqrywvgmhp6a2saaqax"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rgdal
(package
(name "r-rgdal")
- (version "1.4-8")
+ (version "1.5-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgdal" version))
(sha256
- (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
+ (base32 "0jvb5ykp539mi0hqs05w4w8wz45blc4nvkhs70aqmzyx27hadfiq"))))
(properties `((upstream-name . "rgdal")))
(build-system r-build-system)
(inputs
(propagated-inputs
`(("r-sp" ,r-sp)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
(home-page "http://rgdal.r-forge.r-project.org")
(synopsis "Bindings for the Geospatial Data Abstraction Library")
(description
(define-public r-abcrlda
(package
(name "r-abcrlda")
- (version "1.0.2")
+ (version "1.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "abcrlda" version))
(sha256
(base32
- "0zjdrbg3zx0znqnh0dvmifs9c12b8vjhbaf3nbwab9xh25nsmg75"))))
+ "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
(properties `((upstream-name . "abcrlda")))
(build-system r-build-system)
(home-page "https://ieeexplore.ieee.org/document/8720003/")
(define-public r-showtextdb
(package
(name "r-showtextdb")
- (version "2.0")
+ (version "3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "showtextdb" version))
(sha256
(base32
- "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
+ "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
(properties `((upstream-name . "showtextdb")))
(build-system r-build-system)
(propagated-inputs
(define-public r-showtext
(package
(name "r-showtext")
- (version "0.8")
+ (version "0.8-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "showtext" version))
(sha256
(base32
- "15v90s061iz9i655xin7kqb6ahnski55pgz3329wcz60bnbjb82x"))))
+ "1n1cd9f4zrv45k5953akclqh1jh7fy122dqkgmbfi5h122v6p2h0"))))
(properties `((upstream-name . "showtext")))
(build-system r-build-system)
(inputs
(define-public r-mda
(package
(name "r-mda")
- (version "0.5")
+ (version "0.5-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "mda" version))
(sha256
(base32
- "01pjrz9xv1rx78ndy0x9dc32ws8brcvwyb500m1f0dqd42375vmx"))))
+ "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
(properties `((upstream-name . "mda")))
(build-system r-build-system)
(propagated-inputs `(("r-class" ,r-class)))
(define-public r-elasticnet
(package
(name "r-elasticnet")
- (version "1.1.1")
+ (version "1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "elasticnet" version))
(sha256
(base32
- "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
+ "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
(properties `((upstream-name . "elasticnet")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gamlss
(package
(name "r-gamlss")
- (version "5.1-6")
+ (version "5.1-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "gamlss" version))
(sha256
(base32
- "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
+ "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
(properties `((upstream-name . "gamlss")))
(build-system r-build-system)
(propagated-inputs
(define-public r-seewave
(package
(name "r-seewave")
- (version "2.1.5")
+ (version "2.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "seewave" version))
(sha256
(base32
- "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
+ "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
(properties `((upstream-name . "seewave")))
(build-system r-build-system)
+ (inputs
+ `(("libsndfile" ,libsndfile)))
(propagated-inputs
`(("r-tuner" ,r-tuner)))
(home-page "http://rug.mnhn.fr/seewave")
(define-public r-gdina
(package
(name "r-gdina")
- (version "2.7.9")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "GDINA" version))
(sha256
(base32
- "13pmj069r04h38hg61ibyn1ab15zdy9m0qv60vi25ahgsmg6ccvx"))))
+ "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
(properties `((upstream-name . "GDINA")))
(build-system r-build-system)
(propagated-inputs
(define-public r-actuar
(package
(name "r-actuar")
- (version "2.3-3")
+ (version "3.0-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "actuar" version))
(sha256
(base32
- "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
+ "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
(properties `((upstream-name . "actuar")))
(build-system r-build-system)
(propagated-inputs `(("r-expint" ,r-expint)))
(define-public r-rsvg
(package
(name "r-rsvg")
- (version "2.0")
+ (version "2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rsvg" version))
(sha256
(base32
- "0r066lvyfvhsjjpiad259f1m3qk5w7hxhbyjzhlryzf3fy0hvh29"))))
+ "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
(properties `((upstream-name . "rsvg")))
(build-system r-build-system)
(inputs
`(("librsvg" ,librsvg)
("zlib" ,zlib)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
(home-page "https://github.com/jeroen/rsvg#readme")
(synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
(description
(define-public r-emplik
(package
(name "r-emplik")
- (version "1.0-4.3")
+ (version "1.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "emplik" version))
(sha256
(base32
- "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c"))))
+ "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
(properties `((upstream-name . "emplik")))
(build-system r-build-system)
(propagated-inputs
(define-public r-quanteda
(package
(name "r-quanteda")
- (version "2.0.1")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "quanteda" version))
(sha256
(base32
- "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
+ "0qxvm75g6r0d1clj8b19gjqwkfrqypapf4zysb8nyfbmn33h8xc7"))))
(properties `((upstream-name . "quanteda")))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
+ ("r-digest" ,r-digest)
("r-extrafont" ,r-extrafont)
("r-fastmatch" ,r-fastmatch)
("r-ggplot2" ,r-ggplot2)
(define-public r-sem
(package
(name "r-sem")
- (version "3.1-9")
+ (version "3.1-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "sem" version))
(sha256
(base32
- "1f9c6g6pfx66gd2pappcsqh484ah6a0x4z47hpd46rah0817hcsa"))))
+ "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
(properties `((upstream-name . "sem")))
(build-system r-build-system)
(propagated-inputs
(define-public r-semtools
(package
(name "r-semtools")
- (version "0.5-2")
+ (version "0.5-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "semTools" version))
(sha256
(base32
- "1zj841pszfsikzp82cmh463qyc4xhdrqjqcnhc2r8mcflv12irv6"))))
+ "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
(properties `((upstream-name . "semTools")))
(build-system r-build-system)
(propagated-inputs
(define-public r-stanheaders
(package
(name "r-stanheaders")
- (version "2.19.2")
+ (version "2.21.0-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "StanHeaders" version))
(sha256
(base32
- "0cmk0fzczx7dcywcw1dhm6gfq84qlsx77qrsk4z3bf3dhr4bznam"))))
+ "1zyph2x47x9a5baj5d79a1lzj7gajirisajvkrcngrjvw8bq7810"))))
(properties `((upstream-name . "StanHeaders")))
(build-system r-build-system)
(inputs `(("pandoc" ,ghc-pandoc)))
+ (propagated-inputs
+ `(("r-rcppeigen" ,r-rcppeigen)
+ ("r-rcppparallel" ,r-rcppparallel)))
(native-inputs
`(("gfortran" ,gfortran)
("r-knitr" ,r-knitr))) ; for vignettes
(define-public r-openmx
(package
(name "r-openmx")
- (version "2.17.3")
+ (version "2.17.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "OpenMx" version))
(sha256
(base32
- "1s2pcg281ag3qz2wz8yi826f2d3kj3qg916js7zz0nsrljcyv5bc"))))
+ "07y4w7xdb63p5kkrj6sdx1kabbsgbbj7nw9hc690jy84r15aryal"))))
(properties `((upstream-name . "OpenMx")))
(build-system r-build-system)
(propagated-inputs
(define-public r-iheatmapr
(package
(name "r-iheatmapr")
- (version "0.4.12")
+ (version "0.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "iheatmapr" version))
(sha256
(base32
- "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
+ "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h"))))
(properties `((upstream-name . "iheatmapr")))
(build-system r-build-system)
(propagated-inputs
("r-jsonlite" ,r-jsonlite)
("r-knitr" ,r-knitr)
("r-magrittr" ,r-magrittr)
- ("r-plyr" ,r-plyr)
("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-s4vectors" ,r-s4vectors)
("r-scales" ,r-scales)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://docs.ropensci.org/iheatmapr")
(synopsis "Interactive, Complex Heatmaps")
(description
(define-public r-rstantools
(package
(name "r-rstantools")
- (version "2.0.0")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rstantools" version))
(sha256
(base32
- "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
+ "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
(properties `((upstream-name . "rstantools")))
(build-system r-build-system)
(inputs `(("pandoc" ,ghc-pandoc)))
(propagated-inputs
`(("r-desc" ,r-desc)
- ("r-rcpp" ,r-rcpp)))
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppparallel" ,r-rcppparallel)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://mc-stan.org/rstantools/")
(synopsis "Tools for developing R packages interfacing with Stan")
(description
(define-public r-loo
(package
(name "r-loo")
- (version "2.2.0")
+ (version "2.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "loo" version))
(sha256
- (base32
- "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
+ (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
(properties `((upstream-name . "loo")))
(build-system r-build-system)
(inputs
(propagated-inputs
`(("r-checkmate" ,r-checkmate)
("r-matrixstats" ,r-matrixstats)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://mc-stan.org/loo/")
(synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
(description
(define-public r-rstan
(package
(name "r-rstan")
- (version "2.19.3")
+ (version "2.21.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rstan" version))
(sha256
(base32
- "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
+ "0fxxh2jmrgfp98195qkqli1r9ni457vnjdvqm5l91j6aagkbk8zz"))))
(properties `((upstream-name . "rstan")))
(build-system r-build-system)
(arguments
#t)))))
(native-inputs
`(("tzdata" ,tzdata-for-tests)
- ("pandoc" ,ghc-pandoc)))
+ ("pandoc" ,ghc-pandoc)
+ ("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-bh" ,r-bh)
("r-ggplot2" ,r-ggplot2)
("r-pkgbuild" ,r-pkgbuild)
("r-rcpp" ,r-rcpp)
("r-rcppeigen" ,r-rcppeigen)
- ("r-stanheaders" ,r-stanheaders)))
+ ("r-rcppparallel" ,r-rcppparallel)
+ ("r-stanheaders" ,r-stanheaders)
+ ("r-v8" ,r-v8)))
(home-page "https://discourse.mc-stan.org/")
(synopsis "R interface to Stan")
(description
climate data.")
(license license:lgpl2.1)))
+(define-public r-rlinsolve
+ (package
+ (name "r-rlinsolve")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Rlinsolve" version))
+ (sha256
+ (base32
+ "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
+ (properties `((upstream-name . "Rlinsolve")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-rdpack" ,r-rdpack)))
+ (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
+ (synopsis "Iterative solvers for (sparse) linear system of equations")
+ (description
+ "Solving a system of linear equations is one of the most fundamental
+computational problems for many fields of mathematical studies, such as
+regression problems from statistics or numerical partial differential
+equations. This package provides basic stationary iterative solvers such as
+Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
+Nonstationary, also known as Krylov subspace methods are also provided.
+Sparse matrix computation is also supported in that solving large and sparse
+linear systems can be manageable using the @code{Matrix} package along with
+@code{RcppArmadillo}.")
+ (license license:gpl3+)))
+
(define-public r-zvcv
(package
(name "r-zvcv")
- (version "1.0.0")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ZVCV" version))
(sha256
(base32
- "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8"))))
+ "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
(properties `((upstream-name . "ZVCV")))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)
+ ("r-bh" ,r-bh)
+ ("r-dplyr" ,r-dplyr)
("r-glmnet" ,r-glmnet)
+ ("r-magrittr" ,r-magrittr)
("r-mvtnorm" ,r-mvtnorm)
- ("r-partitions" ,r-partitions)
("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-rlinsolve" ,r-rlinsolve)))
(home-page "https://cran.r-project.org/web/packages/ZVCV/")
(synopsis "Zero-Variance Control Variates")
(description
(define-public r-isoband
(package
(name "r-isoband")
- (version "0.2.1")
+ (version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "isoband" version))
(sha256
(base32
- "1ndlnv4g9pbd02y50sx4ffg2ccwqbi7fm2v1lh22wdd8pq33d20q"))))
+ "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
(properties `((upstream-name . "isoband")))
(build-system r-build-system)
(propagated-inputs
- `(("r-rcpp" ,r-rcpp)
- ("r-testthat" ,r-testthat)))
+ `(("r-testthat" ,r-testthat)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/wilkelab/isoband")
(define-public r-crochet
(package
(name "r-crochet")
- (version "2.2.0")
+ (version "2.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "crochet" version))
(sha256
(base32
- "1cbv79nyycxk6f8ldcsnn2pvgxqlnrj0qs19nhafnq2clxy863k6"))))
+ "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
(build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/agrueneberg/crochet")
(synopsis "Implementation Helper for Matrix-Like Types")
(description
(define-public r-brms
(package
(name "r-brms")
- (version "2.12.0")
+ (version "2.13.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "brms" version))
(sha256
(base32
- "1699lwkklfhjz7fddawlig552g2zvrc34mqwrzqjgl35r9fm08gs"))))
+ "13gnc517yssvi2mnih5bln06hcbn4y80gd9h3szacs6n3mwpig5f"))))
(properties `((upstream-name . "brms")))
(build-system r-build-system)
(propagated-inputs
and prediction with Aalen-Johansen or simulation in competing risks and
multi-state models.")
(license license:gpl2+)))
+
+(define-public r-scatterpie
+ (package
+ (name "r-scatterpie")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "scatterpie" version))
+ (sha256
+ (base32
+ "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
+ (properties `((upstream-name . "scatterpie")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggforce" ,r-ggforce)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-rlang" ,r-rlang)
+ ("r-rvcheck" ,r-rvcheck)
+ ("r-tidyr" ,r-tidyr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://cran.r-project.org/web/packages/scatterpie/")
+ (synopsis "Scatter pie plot")
+ (description
+ "This package creates scatterpie plots, especially useful for plotting
+pies on a map.")
+ (license license:artistic2.0)))
+
+(define-public r-boruta
+ (package
+ (name "r-boruta")
+ (version "7.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Boruta" version))
+ (sha256
+ (base32
+ "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
+ (properties `((upstream-name . "Boruta")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-ranger" ,r-ranger)))
+ (home-page "https://gitlab.com/mbq/Boruta/")
+ (synopsis "Wrapper algorithm for all relevant feature selection")
+ (description
+ "This package provides an all relevant feature selection wrapper
+algorithm. It finds relevant features by comparing original attributes'
+importance with importance achievable at random, estimated using their
+permuted copies (shadows).")
+ (license license:gpl2+)))
+
+(define-public r-directlabels
+ (package
+ (name "r-directlabels")
+ (version "2020.6.17")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "directlabels" version))
+ (sha256
+ (base32
+ "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-quadprog" ,r-quadprog)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "http://directlabels.r-forge.r-project.org/")
+ (synopsis "Direct labels for multicolor plots")
+ (description
+ "This package provides an extensible framework for automatically placing
+direct labels onto multicolor plots. Label positions are described using
+positioning methods that can be re-used across several different plots. There
+are heuristics for examining @code{trellis} and @code{ggplot} objects and
+inferring an appropriate positioning method.")
+ (license license:gpl3)))
+
+(define-public r-lsd
+ (package
+ (name "r-lsd")
+ (version "4.1-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "LSD" version))
+ (sha256
+ (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
+ (properties `((upstream-name . "LSD")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/LSD/")
+ (synopsis "Lots of superior depictions tool creates colorful plots")
+ (description
+ "This package creates lots of colorful plots in a multitude of variations.
+Try a demo of the LSD by running @code{demotour()}.")
+ ;; Either version
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-fourcseq
+ (package
+ (name "r-fourcseq")
+ (version "1.21.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FourCSeq" version))
+ (sha256
+ (base32 "0lhcjw2hmmdafq52c5fvpm1crnzynbslamzh7r6ygifmzaz2pa8x"))))
+ (properties `((upstream-name . "FourCSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq2" ,r-deseq2)
+ ("r-fda" ,r-fda)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gtools" ,r-gtools)
+ ("r-lsd" ,r-lsd)
+ ("r-matrix" ,r-matrix)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
+ (synopsis "Analysis of multiplexed 4C sequencing data")
+ (description
+ "This package is an R package dedicated to the analysis of (multiplexed)
+4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
+interactions between DNA elements and identify differential interactions
+between conditions. The statistical analysis in R starts with individual bam
+files for each sample as inputs. To obtain these files, the package contains
+a Python script to demultiplex libraries and trim off primer sequences. With
+a standard alignment software the required bam files can be then be
+generated.")
+ (license license:gpl3+)))
+
+(define-public r-phylogram
+ (package
+ (name "r-phylogram")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "phylogram" version))
+ (sha256
+ (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
+ (properties `((upstream-name . "phylogram")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-ape" ,r-ape)))
+ (home-page "https://github.com/ropensci/phylogram/")
+ (synopsis "Dendrograms for evolutionary analysis")
+ (description
+ "The @code{r-phylogram} package is a tool for for developing phylogenetic
+trees as deeply-nested lists known as \"dendrogram\" objects. It provides
+functions for conversion between \"dendrogram\" and \"phylo\" class objects,
+as well as several tools for command-line tree manipulation and import/export
+via Newick parenthetic text. This improves accessibility to the comprehensive
+range of object-specific analytical and tree-visualization functions found
+across a wide array of bioinformatic R packages.")
+ (license license:gpl3)))
+
+(define-public r-kmer
+ (package
+ (name "r-kmer")
+ (version "1.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "kmer" version))
+ (sha256
+ (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
+ (properties `((upstream-name . "kmer")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-openssl" ,r-openssl)
+ ("r-phylogram" ,r-phylogram)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/shaunpwilkinson/kmer/")
+ (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
+ (description
+ "@code{r-kmer} is an R package for rapidly computing distance matrices
+and clustering large sequence datasets using fast alignment-free k-mer
+counting and recursive k-means partitioning.")
+ (license license:gpl3)))
+
+(define-public r-shapforxgboost
+ (package
+ (name "r-shapforxgboost")
+ (version "0.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "SHAPforxgboost" version))
+ (sha256
+ (base32
+ "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
+ (properties
+ `((upstream-name . "SHAPforxgboost")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bbmisc" ,r-bbmisc)
+ ("r-data-table" ,r-data-table)
+ ("r-ggextra" ,r-ggextra)
+ ("r-ggforce" ,r-ggforce)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggpubr" ,r-ggpubr)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-xgboost" ,r-xgboost)))
+ (home-page "https://github.com/liuyanguu/SHAPforxgboost")
+ (synopsis "SHAP Plots for XGBoost")
+ (description
+ "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
+using @dfn{SHAP} (Shapley additive explanation) visualization plots for
+@code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
+and force plot. It relies on the @code{XGBoost} package to produce SHAP
+values.")
+ (license license:expat)))
+
+(define-public r-rismed
+ (package
+ (name "r-rismed")
+ (version "2.1.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "RISmed" version))
+ (sha256
+ (base32
+ "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l"))))
+ (properties `((upstream-name . "RISmed")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/RISmed")
+ (synopsis "Download content from NCBI databases")
+ (description
+ "This package provides a set of tools to extract bibliographic
+content from the National Center for Biotechnology Information (NCBI)
+databases, including PubMed. The name RISmed is a portmanteau of
+RIS (for Research Information Systems, a common tag format for
+bibliographic data) and PubMed.")
+ (license license:gpl2+)))
+
+(define-public r-semver
+ (package
+ (name "r-semver")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "semver" version))
+ (sha256
+ (base32
+ "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
+ (properties `((upstream-name . "semver")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-rcpp" ,r-rcpp)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/johndharrison/semver")
+ (synopsis "Parser for Semantic Versioning 2.0.0")
+ (description
+ "This package provides tools and functions for parsing, rendering and
+operating on semantic version strings. Semantic versioning is a simple set of
+rules and requirements that dictate how version numbers are assigned and
+incremented as outlined at @url{http://semver.org}.")
+ (license license:expat)))
+
+(define-public r-binman
+ (package
+ (name "r-binman")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "binman" version))
+ (sha256
+ (base32
+ "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"))))
+ (properties `((upstream-name . "binman")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-httr" ,r-httr)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rappdirs" ,r-rappdirs)
+ ("r-semver" ,r-semver)
+ ("r-xml2" ,r-xml2)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/ropensci/binman")
+ (synopsis "Binary download manager")
+ (description
+ "This package provides tools and functions for managing the download of
+binary files. Binary repositories are defined in the YAML format. Defining
+new pre-download, download and post-download templates allow additional
+repositories to be added.")
+ (license license:expat)))
+
+(define-public r-wdman
+ (package
+ (name "r-wdman")
+ (version "0.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "wdman" version))
+ (sha256
+ (base32
+ "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
+ (properties `((upstream-name . "wdman")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-binman" ,r-binman)
+ ("r-processx" ,r-processx)
+ ("r-semver" ,r-semver)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://docs.ropensci.org/wdman/")
+ (synopsis "Webdriver/Selenium binary manager")
+ (description
+ "There are a number of binary files associated with the
+Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
+@url{https://sites.google.com/a/chromium.org/chromedriver/},
+@url{https://github.com/mozilla/geckodriver},
+@url{http://phantomjs.org/download.html}, and
+@url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
+more information). This package provides functions to download these binaries
+and to manage processes involving them.")
+ (license license:expat)))
+
+(define-public r-rselenium
+ (package
+ (name "r-rselenium")
+ (version "1.7.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "RSelenium" version))
+ (sha256
+ (base32
+ "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
+ (properties `((upstream-name . "RSelenium")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-binman" ,r-binman)
+ ("r-catools" ,r-catools)
+ ("r-httr" ,r-httr)
+ ("r-openssl" ,r-openssl)
+ ("r-wdman" ,r-wdman)
+ ("r-xml" ,r-xml)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://docs.ropensci.org/RSelenium/")
+ (synopsis "R bindings for Selenium WebDriver")
+ (description
+ "This package provides a set of R bindings for the Selenium 2.0
+WebDriver (see @url{https://selenium.dev/documentation/en/} for more
+information) using the @code{JsonWireProtocol} (see
+@url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
+information). Selenium 2.0 WebDriver allows driving a web browser natively as
+a user would either locally or on a remote machine using the Selenium server
+it marks a leap forward in terms of web browser automation. Selenium
+automates web browsers (commonly referred to as browsers). Using RSelenium
+you can automate browsers locally or remotely.")
+ (license license:agpl3+)))
+
+(define-public r-conquer
+ (package
+ (name "r-conquer")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "conquer" version))
+ (sha256
+ (base32
+ "1c7id7wgspma5bdcirrhw7f9fp709zxpj31klivasdbvd4jgi4vb"))))
+ (properties `((upstream-name . "conquer")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (home-page "https://github.com/XiaoouPan/conquer")
+ (synopsis "Convolution-type smoothed quantile regression")
+ (description
+ "This package provides fast and accurate convolution-type smoothed
+quantile regression, implemented using Barzilai-Borwein gradient descent with
+a Huber regression warm start. Confidence intervals for regression
+coefficients are constructed using multiplier bootstrap.")
+ (license license:gpl3)))
+
+(define-public r-fastshap
+ (package
+ (name "r-fastshap")
+ (version "0.0.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fastshap" version))
+ (sha256
+ (base32
+ "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
+ (properties `((upstream-name . "fastshap")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abind" ,r-abind)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-tibble" ,r-tibble)))
+ (home-page "https://github.com/bgreenwell/fastshap")
+ (synopsis "Fast approximate Shapley values")
+ (description
+ "This package computes fast (relative to other implementations)
+approximate Shapley values for any supervised learning model. Shapley values
+help to explain the predictions from any black box model using ideas from game
+theory; see @url{Strumbel and Kononenko (2014),
+doi.org/10.1007/s10115-013-0679-x} for details.")
+ (license license:gpl2+)))
+
+(define-public r-metrics
+ (package
+ (name "r-metrics")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Metrics" version))
+ (sha256
+ (base32
+ "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
+ (properties `((upstream-name . "Metrics")))
+ (build-system r-build-system)
+ (home-page "https://github.com/mfrasco/Metrics")
+ (synopsis "Evaluation metrics for machine learning")
+ (description
+ "This package provides an implementation of evaluation metrics in R that
+are commonly used in supervised machine learning. It implements metrics for
+regression, time series, binary classification, classification, and
+information retrieval problems. It has zero dependencies and a consistent,
+simple interface for all functions.")
+ (license license:bsd-3)))
+
+(define-public r-iml
+ (package
+ (name "r-iml")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "iml" version))
+ (sha256
+ (base32
+ "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
+ (properties `((upstream-name . "iml")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-checkmate" ,r-checkmate)
+ ("r-data-table" ,r-data-table)
+ ("r-formula" ,r-formula)
+ ("r-future" ,r-future)
+ ("r-future-apply" ,r-future-apply)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-metrics" ,r-metrics)
+ ("r-prediction" ,r-prediction)
+ ("r-r6" ,r-r6)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/christophM/iml")
+ (synopsis "Interpretable machine learning")
+ (description
+ "This package provides interpretability methods to analyze the behavior
+and predictions of any machine learning model. Implemented methods are:
+
+@itemize
+@item Feature importance described by Fisher et al. (2018),
+@item accumulated local effects plots described by Apley (2018),
+@item partial dependence plots described by Friedman (2001),
+@item individual conditional expectation ('ice') plots described by Goldstein
+ et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
+@item local models (variant of 'lime') described by Ribeiro et. al (2016),
+@item the Shapley Value described by Strumbelj et. al (2014)
+ @url{https://doi.org/10.1007/s10115-013-0679-x},
+@item feature interactions described by Friedman et. al
+ @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
+@end itemize
+")
+ (license license:expat)))
HCoop / jackhill / guix / guix.git / blobdiff