diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1003 |
1 files changed, 796 insertions, 207 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5ede11a4e3..2c202e8508 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17,11 +17,14 @@ ;;; 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> +;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -45,6 +48,7 @@ #: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) @@ -67,6 +71,7 @@ #: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) @@ -86,6 +91,32 @@ #:use-module (gnu packages web) #:use-module (gnu packages xorg)) +(define-public r-rticles + (package + (name "r-rticles") + (version "0.15") + (source + (origin + (method url-fetch) + (uri (cran-uri "rticles" version)) + (sha256 + (base32 + "0svh2bcqnlqdxdpw5afz1b980i2q13k8cxpq6flfqbi3dlwf3h8l")))) + (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") @@ -277,14 +308,14 @@ organisms via the @code{g:Profiler} toolkit.") (define-public r-gprofiler2 (package (name "r-gprofiler2") - (version "0.1.9") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "gprofiler2" version)) (sha256 (base32 - "112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb")))) + "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg")))) (properties `((upstream-name . "gprofiler2"))) (build-system r-build-system) (propagated-inputs @@ -492,14 +523,14 @@ objects.") (define-public r-sys (package (name "r-sys") - (version "3.3") + (version "3.4") (source (origin (method url-fetch) (uri (cran-uri "sys" version)) (sha256 (base32 - "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6")))) + "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p")))) (build-system r-build-system) (home-page "https://github.com/jeroen/sys") (synopsis "Powerful and reliable tools for running system commands in R") @@ -616,19 +647,21 @@ single step.") (define-public r-rvest (package (name "r-rvest") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 - (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf")))) + (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) ("r-magrittr" ,r-magrittr) ("r-selectr" ,r-selectr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/rvest") (synopsis "Simple web scraping for R") (description @@ -800,8 +833,35 @@ into a pipeline of data manipulation and visualisation.") (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) @@ -849,13 +909,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.17") + (version "0.18") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "0lxkjr7mwdk96cdpx66j92nn4w2vkgn2j2bbg7kd4238jsk9srs7")))) + "0xfbf1a1w34hbsx4jrdr4rqf22v7gf1p37ngknglv1dyxih7ipja")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) @@ -1754,14 +1814,14 @@ component analysis (with robust methods, and parallelized functions).") (define-public r-ape (package (name "r-ape") - (version "5.4") + (version "5.4-1") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "0f74x9vx9sxpns2hlq4w2x80cd2gw42isfgncvs9pqbjf4hiyqnr")))) + "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -1830,14 +1890,14 @@ colors are provided.") (define-public r-glue (package (name "r-glue") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 - "1j1va4vi3g9sl0cyjdwxvh5lvh10x8k9qvnsr9zyxddcbk9qgdpq")))) + "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz")))) (build-system r-build-system) ;; knitr depends on glue, so we can't add knitr here to build the ;; vignettes. @@ -1896,13 +1956,13 @@ error stream.") (define-public r-pls (package (name "r-pls") - (version "2.7-2") + (version "2.7-3") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 - (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7")))) + (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg")))) (build-system r-build-system) (home-page "https://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") @@ -1930,13 +1990,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.3.3") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1x10zgvq75gnkmzqhbqn6jyvp9h1y4qxgnbdds0bwmc8ad8md903")))) + (base32 "1cxfhnff22fbsr9vynhql0rhhrqfxvkb6kv11h2m740r9scwcs44")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -1948,13 +2008,13 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.0.8") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 - (base32 "188r2ba7y5j80mnfqdf210af40yd28jjgx7rbya4iwcfx7rzqjdi")))) + (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -2234,19 +2294,21 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.13.4") + (version "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4")))) + "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/dendextend") (synopsis "Extending 'dendrogram' functionality in R") (description @@ -2311,14 +2373,14 @@ any subsequent lookup as it keeps the hash table in memory.") (define-public r-ff (package (name "r-ff") - (version "2.2-14.2") + (version "4.0.2") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 - "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q")))) + "1qbfmhk4v76q145yalqaiaffklvkfs615b5m0imxyjyjcvx1nbn0")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) (home-page "http://ff.r-forge.r-project.org/") @@ -2334,14 +2396,14 @@ in main memory.") (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) @@ -2577,14 +2639,14 @@ quantile mixture from L-moments and trimmed L-moments.") (define-public r-distillery (package (name "r-distillery") - (version "1.0-7") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 - "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249")))) + "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh")))) (build-system r-build-system) (home-page "https://ral.ucar.edu/staff/ericg/") (synopsis "Functions for confidence intervals and object information") @@ -2981,14 +3043,14 @@ contexts.") (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") @@ -3358,14 +3420,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "1.9.12.31") + (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5")))) + "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -3563,13 +3625,13 @@ color labels, layout, etc.") (define-public r-stringdist (package (name "r-stringdist") - (version "0.9.5.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 - (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi")))) + (base32 "0nb3iwpl4f3xxirns1frwvarpyrl4i5f74h8r6h80cg0a4mpdgcb")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") @@ -3637,14 +3699,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.") (define-public r-jomo (package (name "r-jomo") - (version "2.7-1") + (version "2.7-2") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "0cdy9m4ylarkk9d0v1s61k2d877l4bbxly8a4jwhfy43fdvskz1w")))) + "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) @@ -3710,14 +3772,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.10.0") + (version "3.11.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0w81shmd2crpdlh66pnm27v4n06aayganq6kkalirln4c0ci2nyi")))) + "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -3789,14 +3851,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.6.3") + (version "1.6.6") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f")))) + "1qn1bbzfk4w3mqrzisshw5xx7x249sgmj6qdi39lkqb58a4mf4kh")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs @@ -4359,13 +4421,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.15") + (version "0.16") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "1fdipwrl45bznb17da4169ria5jax0f2649yj5accw6qr6wsc8bj")))) + (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -4422,14 +4484,14 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.3.1") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "025si8gqwsj79lna3s0hdzxmymjyzbjq3ddan7n6chah6n3kbrhp")))) + "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -4509,14 +4571,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.24") + (version "0.25") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0mc9i7r45s5kagcfig508dbyf6jir6q4ghq9cxqvnpxp6ymh4qpr")))) + "0zbhzxxjlkdj9byxyab477p7cnws5y87nyg989lkzarxdc7dglza")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -4655,14 +4717,14 @@ of these tests are also included.") (define-public r-ttr (package (name "r-ttr") - (version "0.23-6") + (version "0.24.2") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg")))) + "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs @@ -4979,14 +5041,14 @@ interface.") (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))) @@ -5010,14 +5072,14 @@ sample Robust Rank-Order Distributional Test.") (define-public r-expm (package (name "r-expm") - (version "0.999-4") + (version "0.999-5") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 - "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q")))) + "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,gfortran))) @@ -5152,14 +5214,14 @@ functions to enforce symmetric scales or add tags to facetted plots.") (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) @@ -5345,14 +5407,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.3.9") + (version "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "19gbc7k1hsi6hg6ka8i70wlw8j9fs9wkpn36761lzbcyam6vgqn0")) + "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c")) (modules '((guix build utils))) (snippet '(begin @@ -5811,14 +5873,14 @@ misclassification probabilities of different models.") (define-public r-zip (package (name "r-zip") - (version "2.0.4") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 - "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb")))) + "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") @@ -5893,14 +5955,14 @@ simple method for converting between file types.") (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) @@ -6042,14 +6104,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (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 @@ -6492,14 +6554,14 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i")))) + "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50")))) (build-system r-build-system) (inputs `(("hdf5" ,hdf5) @@ -6637,14 +6699,14 @@ references and Rd files.") (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) @@ -6904,14 +6966,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.8.5") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0ggczjd112kclknyxxqvjkzwzazfhjwglchafzamk4zb08ww7y7k")))) + "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7071,14 +7133,14 @@ documents.") (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") @@ -7260,14 +7322,14 @@ Group (Non-)Overlap considerations.") (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") @@ -7765,14 +7827,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.3-7") + (version "3.3-13") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "144mva2dx7ffkq7z0fixr4z76ci1s4lizlyv5r7v07fd4nzg5hby")))) + "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -7993,31 +8055,22 @@ distributed on a compute cluster.") (define-public r-abjutils (package (name "r-abjutils") - (version "0.2.3") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "abjutils" version)) (sha256 - (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv")))) + (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd")))) (build-system r-build-system) (propagated-inputs - `(("r-devtools" ,r-devtools) - ("r-dplyr" ,r-dplyr) - ("r-furrr" ,r-furrr) - ("r-future" ,r-future) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) + `(("r-dplyr" ,r-dplyr) ("r-magrittr" ,r-magrittr) - ("r-progress" ,r-progress) ("r-purrr" ,r-purrr) - ("r-readr" ,r-readr) ("r-rlang" ,r-rlang) ("r-rstudioapi" ,r-rstudioapi) - ("r-scales" ,r-scales) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/abjur/abjutils/") (synopsis "Collection of tools for jurimetrical analysis") @@ -8109,14 +8162,14 @@ hemoglobin to reticulocytes (OFF-score), as well as example data.") (define-public r-parmigene (package (name "r-parmigene") - (version "1.0.2") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "parmigene" version)) (sha256 (base32 - "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d")))) + "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/parmigene/") (synopsis "Mutual information estimation for gene network reconstruction") @@ -8777,14 +8830,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.4.8") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0h884qn4cip03w0h5psrz5y9zkm2wppklrhdz2chm2xk13zqnq5k")))) + "09nap4aazpbsswqzk0d4kjngwd8sib222s31yd08sd1sqw432c6k")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -8828,14 +8881,13 @@ Cohen (1988).") (define-public r-libcoin (package (name "r-libcoin") - (version "1.0-5") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 - (base32 - "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a")))) + (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) (home-page "https://cran.r-project.org/web/packages/libcoin") @@ -8885,8 +8937,8 @@ correlation, censored, ordered and multivariate problems.") "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl")))) (build-system r-build-system) (inputs - `(("pandoc" ,ghc-pandoc) - ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + `(("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc))) (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs @@ -8911,14 +8963,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.7.16") + (version "1.7.18") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44")))) + "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs @@ -9014,14 +9066,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.7.0") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "1nrycyzznzrlwnfwk1w3ixdq0bj82nri9kb2qiaiw8wwzwrsl1hd")))) + "1c82bpxg2ha93rna4sy9pdp422dnk6b378dcg8x04clfg0y0lsi2")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs @@ -9041,14 +9093,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.4.7") + (version "0.4.8") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0gw165wm2a0vjsvyll8z9k6qd156z3jf4priy1r745v63x4mnb5k")))) + "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -9068,14 +9120,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.15.0") + (version "0.15.1") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "1bqvbhw5la3cj3v0gwava117ff24b1p450azln402gsxgfl3vw7r")))) + "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -9098,14 +9150,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "1n5b5434sd8f1v95bfjwg92v879rkaj8zpm6ldnrg0kgfb0gy6q4")))) + "0h9f260gb8707pcssf8dq7dakpq1ggkxr5kpbrbl8sn8h3qbvws9")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -9214,18 +9266,17 @@ back to file after modifications.") (define-public r-fs (package (name "r-fs") - (version "1.4.2") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 - "09rpazjba9jy448j6rq989fw3wv3xhng7fn8p8gr22gyx0n0y1zr")))) + "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn")))) (build-system r-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + `(("r-knitr" ,r-knitr))) (home-page "https://fs.r-lib.org") (synopsis "Cross-platform file system operations based on libuv") (description @@ -9318,15 +9369,17 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.1.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf")))) + "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") (description @@ -9866,7 +9919,7 @@ Bioconductor packages.") ("libpng" ,libpng) ("glu" ,glu) ("libx11" ,libx11) - ("ghc-pandoc" ,ghc-pandoc) + ("pandoc" ,pandoc) ("zlib" ,zlib))) (propagated-inputs `(("r-crosstalk" ,r-crosstalk) @@ -9989,18 +10042,19 @@ features (e.g. local modes).") (define-public r-arm (package (name "r-arm") - (version "1.11-1") + (version "1.11-2") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 - "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv")))) + "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-coda" ,r-coda) + ("r-hmisc" ,r-hmisc) ("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) @@ -10755,14 +10809,14 @@ Touzet and Varre (2007).") (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))) @@ -11397,14 +11451,14 @@ who want to include run-time testing features in their own packages.") (define-public r-assertive-reflection (package (name "r-assertive-reflection") - (version "0.0-4") + (version "0.0-5") (source (origin (method url-fetch) (uri (cran-uri "assertive.reflection" version)) (sha256 (base32 - "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj")))) + "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2")))) (properties `((upstream-name . "assertive.reflection"))) (build-system r-build-system) @@ -11500,14 +11554,14 @@ who want to include run-time testing features in their own packages.") (define-public r-assertive-datetimes (package (name "r-assertive-datetimes") - (version "0.0-2") + (version "0.0-3") (source (origin (method url-fetch) (uri (cran-uri "assertive.datetimes" version)) (sha256 (base32 - "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78")))) + "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1")))) (properties `((upstream-name . "assertive.datetimes"))) (build-system r-build-system) @@ -11630,14 +11684,14 @@ features in their own packages.") (define-public r-assertive (package (name "r-assertive") - (version "0.3-5") + (version "0.3-6") (source (origin (method url-fetch) (uri (cran-uri "assertive" version)) (sha256 (base32 - "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3")))) + "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4")))) (build-system r-build-system) (propagated-inputs `(("r-assertive-base" ,r-assertive-base) @@ -11656,6 +11710,8 @@ features in their own packages.") ("r-assertive-strings" ,r-assertive-strings) ("r-assertive-types" ,r-assertive-types) ("r-knitr" ,r-knitr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bitbucket.org/richierocks/assertive") (synopsis "Readable check functions to ensure code integrity") (description @@ -12011,14 +12067,14 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.40") + (version "2.41") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5")))) + "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs @@ -12538,19 +12594,22 @@ users of rARPACK are advised to switch to the RSpectra package.") (define-public r-compositions (package (name "r-compositions") - (version "1.40-5") + (version "2.0-0") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 - "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7")))) + "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr")))) (build-system r-build-system) (propagated-inputs `(("r-bayesm" ,r-bayesm) + ("r-mass" ,r-mass) ("r-robustbase" ,r-robustbase) ("r-tensora" ,r-tensora))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://www.stat.boogaart.de/compositions") (synopsis "Compositional data analysis") (description @@ -12861,14 +12920,14 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-6") + (version "0.6-7") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "0sfv58r2kxinax62bx6j3kkfx07qm16ddwf5qz392q33h9zs009h")))) + "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -13087,14 +13146,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "1.1") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94")))) + "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -13671,14 +13730,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.1-25") + (version "0.1-28") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph")))) + "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") @@ -13695,14 +13754,14 @@ tessellation.") (define-public r-sf (package (name "r-sf") - (version "0.9-4") + (version "0.9-5") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "1xgmnz01pxvpg2ins1h65mlcrafqihlljcjlag8spq9ii7d5i7mx")))) + "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -13934,13 +13993,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.0-0") + (version "6.0-1") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "0m88m63d19qz03x8v56h4rrblln3d2943spi1v4wxxnbcdk22np9")))) + (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -13977,21 +14036,61 @@ generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.") (license license:gpl2+))) +(define-public r-arsenal + (package + (name "r-arsenal") + (version "3.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "arsenal" version)) + (sha256 + (base32 + "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0")))) + (properties `((upstream-name . "arsenal"))) + (build-system r-build-system) + (propagated-inputs `(("r-knitr" ,r-knitr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/mayoverse/arsenal") + (synopsis "Functions for large-scale statistical summaries") + (description + "This package provides an arsenal of R functions for large-scale +statistical summaries, which are streamlined to work within the latest +reporting tools in R and RStudio and which use formulas and versatile +summary statistics for summary tables and models. The primary functions +include + +@enumerate +@item @code{tableby}, a Table-1-like summary of multiple variable types by the + levels of one or more categorical variables; +@item @code{paired}, a Table-1-like summary of multiple variable types paired + across two time points; +@item @code{modelsum}, which performs simple model fits on one or more + endpoints for many variables (univariate or adjusted for covariates); +@item @code{freqlist}, a powerful frequency table across many categorical + variables; +@item @code{comparedf}, a function for comparing @code{data.frames}; and +@item @code{write2}, a function to output tables to a document. +@end enumerate +") + (license license:gpl2+))) + (define-public r-haplo-stats (package (name "r-haplo-stats") - (version "1.7.9") + (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 - "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx")))) + "1f5cyyyavkf4l6kksp87s8d92vjrnhxmpz6j737pa527pn3gghf9")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs - `(("r-rms" ,r-rms))) + `(("r-arsenal" ,r-arsenal) + ("r-rms" ,r-rms))) (native-inputs `(("r-r-rsp" ,r-r-rsp))) ; for vignettes (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") @@ -14028,14 +14127,14 @@ lines. It includes maximum likelihood and Bayesian tools.") (define-public r-ibdreg (package (name "r-ibdreg") - (version "0.2.5") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "ibdreg" version)) (sha256 (base32 - "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g")))) + "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq")))) (build-system r-build-system) (home-page "https://www.mayo.edu/research/labs/\ statistical-genetics-genetic-epidemiology/software") @@ -14186,7 +14285,7 @@ SELECT or UPDATE queries to an end-point.") ("r-rmarkdown" ,r-rmarkdown) ("r-tinytex" ,r-tinytex) ("r-xfun" ,r-xfun) - ("pandoc" ,ghc-pandoc))) + ("pandoc" ,pandoc))) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for @@ -14279,19 +14378,22 @@ and a QP solver.") (define-public r-hierfstat (package (name "r-hierfstat") - (version "0.04-22") + (version "0.5-7") (source (origin (method url-fetch) (uri (cran-uri "hierfstat" version)) (sha256 (base32 - "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx")))) + "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-adegenet" ,r-adegenet) + ("r-gaston" ,r-gaston) ("r-gtools" ,r-gtools))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/hierfstat/") (synopsis "Estimation and tests of hierarchical F-statistics") (description @@ -14985,19 +15087,20 @@ graphics using Vega.") (define-public r-gbm (package (name "r-gbm") - (version "2.1.5") + (version "2.1.8") (source (origin (method url-fetch) (uri (cran-uri "gbm" version)) (sha256 (base32 - "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6")))) + "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx")))) (build-system r-build-system) (propagated-inputs - `(("r-gridextra" ,r-gridextra) - ("r-lattice" ,r-lattice) + `(("r-lattice" ,r-lattice) ("r-survival" ,r-survival))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/gbm-developers/gbm") (synopsis "Generalized boosted regression models") (description @@ -15410,14 +15513,14 @@ regular expressions from human readable expressions") (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") @@ -15731,14 +15834,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-ingredients (package (name "r-ingredients") - (version "1.3.0") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 - "1mp1rgi3nnr8mjddpbyi24zvqcbihz0d8np2j13cbjc089n6jci8")))) + "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs @@ -15771,14 +15874,14 @@ feature effects. Key functions are: (define-public r-ibreakdown (package (name "r-ibreakdown") - (version "1.2.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "iBreakDown" version)) (sha256 (base32 - "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk")))) + "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108")))) (properties `((upstream-name . "iBreakDown"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) @@ -15794,17 +15897,56 @@ contributions in a concise graphical way. This package works for classification and regression models.") (license license:gpl3))) +(define-public r-dae + (package + (name "r-dae") + (version "3.1-27") + (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 "1.3.0") + (version "1.3.1.1") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1azbnykaddsfp2qmxmhpjz76zg78msxv6n2jqkq4gwbgqa5vdfd2")))) + "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -15968,14 +16110,14 @@ the current document.") (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) @@ -16058,14 +16200,14 @@ LargeVis method of Tang et al. (2016) is also provided.") (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 @@ -16074,7 +16216,6 @@ LargeVis method of Tang et al. (2016) is also provided.") ("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) @@ -16083,6 +16224,8 @@ LargeVis method of Tang et al. (2016) is also provided.") ("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 @@ -16388,16 +16531,18 @@ both R code and compiled C/C++/FORTRAN code.") (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))) @@ -16534,14 +16679,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.8.0") + (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "1cmb2hc6f4qdx9aj586zhllckzs6s5sznbqrywvgmhp6a2saaqax")))) + "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -16563,13 +16708,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-12") + (version "1.5-16") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "0jvb5ykp539mi0hqs05w4w8wz45blc4nvkhs70aqmzyx27hadfiq")))) + (base32 "0rwlsafqxgqflfid4ciaa9qz3f75fgw8hilhaqj558gdxg8bzigp")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -17229,14 +17374,14 @@ package.") (define-public r-showtext (package (name "r-showtext") - (version "0.8-1") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "showtext" version)) (sha256 (base32 - "1n1cd9f4zrv45k5953akclqh1jh7fy122dqkgmbfi5h122v6p2h0")))) + "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid")))) (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs @@ -17950,7 +18095,7 @@ the align-and-count method.") (native-inputs `(("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) - ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + ("pandoc-citeproc" ,pandoc-citeproc))) (home-page "https://github.com/andreyshabalin/filematrix") (synopsis "File-backed matrix class with convenient read and write access") (description @@ -18700,14 +18845,14 @@ actigraphy-measured activity counts data.") (define-public r-fda (package (name "r-fda") - (version "5.1.4") + (version "5.1.5.1") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x")))) + "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs @@ -19443,14 +19588,14 @@ statistical shape analysis and archetypal analysis.") (define-public r-adamethods (package (name "r-adamethods") - (version "1.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "adamethods" version)) (sha256 (base32 - "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh")))) + "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj")))) (properties `((upstream-name . "adamethods"))) (build-system r-build-system) (propagated-inputs @@ -19651,14 +19796,14 @@ problems (food web problems, linear programming problems).") (define-public r-shinycssloaders (package (name "r-shinycssloaders") - (version "0.3") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "shinycssloaders" version)) (sha256 (base32 - "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d")))) + "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl")))) (properties `((upstream-name . "shinycssloaders"))) (build-system r-build-system) @@ -20179,14 +20324,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "0qxvm75g6r0d1clj8b19gjqwkfrqypapf4zysb8nyfbmn33h8xc7")))) + "1wlrd7g2b459pnkqhihxhn74f37py1c9pxrdzp5xzp4mnbdxcsj8")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs @@ -20492,17 +20637,17 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.21.0-5") + (version "2.21.0-6") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "1zyph2x47x9a5baj5d79a1lzj7gajirisajvkrcngrjvw8bq7810")))) + "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) - (inputs `(("pandoc" ,ghc-pandoc))) + (inputs `(("pandoc" ,pandoc))) (propagated-inputs `(("r-rcppeigen" ,r-rcppeigen) ("r-rcppparallel" ,r-rcppparallel))) @@ -20563,19 +20708,20 @@ Complete access to optimized C functions is made available with (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) @@ -20675,14 +20821,14 @@ output in R.") (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 @@ -21156,7 +21302,7 @@ using the @code{rstan} and @code{rstanarm} packages).") "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9")))) (properties `((upstream-name . "rstantools"))) (build-system r-build-system) - (inputs `(("pandoc" ,ghc-pandoc))) + (inputs `(("pandoc" ,pandoc))) (propagated-inputs `(("r-desc" ,r-desc) ("r-rcpp" ,r-rcpp) @@ -21186,8 +21332,8 @@ recommendations for developers.") (properties `((upstream-name . "loo"))) (build-system r-build-system) (inputs - `(("pandoc" ,ghc-pandoc) - ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + `(("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc))) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-matrixstats" ,r-matrixstats))) @@ -21210,14 +21356,14 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.21.1") + (version "2.21.2") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "0fxxh2jmrgfp98195qkqli1r9ni457vnjdvqm5l91j6aagkbk8zz")))) + "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments @@ -21233,7 +21379,7 @@ techniques to average Bayesian predictive distributions.") #t))))) (native-inputs `(("tzdata" ,tzdata-for-tests) - ("pandoc" ,ghc-pandoc) + ("pandoc" ,pandoc) ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-bh" ,r-bh) @@ -21246,7 +21392,8 @@ techniques to average Bayesian predictive distributions.") ("r-rcppeigen" ,r-rcppeigen) ("r-rcppparallel" ,r-rcppparallel) ("r-stanheaders" ,r-stanheaders) - ("r-v8" ,r-v8))) + ("r-v8" ,r-v8) + ("r-withr" ,r-withr))) (home-page "https://discourse.mc-stan.org/") (synopsis "R interface to Stan") (description @@ -21264,19 +21411,19 @@ need to derive the partial derivatives.") (define-public r-rstanarm (package (name "r-rstanarm") - (version "2.19.3") + (version "2.21.1") (source (origin (method url-fetch) (uri (cran-uri "rstanarm" version)) (sha256 (base32 - "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s")))) + "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8")))) (properties `((upstream-name . "rstanarm"))) (build-system r-build-system) (inputs - `(("pandoc" ,ghc-pandoc) - ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + `(("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc))) (propagated-inputs `(("r-bayesplot" ,r-bayesplot) ("r-bh" ,r-bh) @@ -21293,6 +21440,8 @@ need to derive the partial derivatives.") ("r-shinystan" ,r-shinystan) ("r-stanheaders" ,r-stanheaders) ("r-survival" ,r-survival))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://mc-stan.org/rstanarm/") (synopsis "Bayesian applied regression modeling via Stan") (description @@ -21769,7 +21918,7 @@ subpopulation type designs.") (build-system r-build-system) (inputs `(("jupyter" ,python-nbconvert) - ("pandoc" ,ghc-pandoc))) + ("pandoc" ,pandoc))) (home-page "https://cran.r-project.org/web/packages/nbconvertR/") (synopsis "Vignette engine wrapping Jupyter notebooks") (description @@ -21864,14 +22013,14 @@ is also implemented here.") (define-public r-aws (package (name "r-aws") - (version "2.4-2") + (version "2.4-3") (source (origin (method url-fetch) (uri (cran-uri "aws" version)) (sha256 (base32 - "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq")))) + "0ccm8ffjf8bylhfr64j9wzi49hzigz4bs172pvkb0bi4d5vdr0l5")))) (properties `((upstream-name . "aws"))) (build-system r-build-system) @@ -22028,19 +22177,20 @@ infinite-precision rational arithmetic.") (define-public r-rxnat (package (name "r-rxnat") - (version "1.0.8") + (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "Rxnat" version)) (sha256 (base32 - "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg")))) + "06w99b5lvpycykzlga6grw33zkajwbb04s89s37wy9zxy42vc4cb")))) (properties `((upstream-name . "Rxnat"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) + `(("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) ("r-rcurl" ,r-rcurl))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -22092,14 +22242,14 @@ included in this package as well.") (define-public r-brms (package (name "r-brms") - (version "2.13.3") + (version "2.13.5") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "13gnc517yssvi2mnih5bln06hcbn4y80gd9h3szacs6n3mwpig5f")))) + "0a2m5wr134sxflmiq5jzvanzn81fv7xndy9gyvrq3bay9vakic69")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -22267,13 +22417,13 @@ Try a demo of the LSD by running @code{demotour()}.") (define-public r-fourcseq (package (name "r-fourcseq") - (version "1.21.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "FourCSeq" version)) (sha256 - (base32 "0lhcjw2hmmdafq52c5fvpm1crnzynbslamzh7r6ygifmzaz2pa8x")))) + (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b")))) (properties `((upstream-name . "FourCSeq"))) (build-system r-build-system) (propagated-inputs @@ -22541,14 +22691,14 @@ you can automate browsers locally or remotely.") (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 @@ -22564,3 +22714,442 @@ 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))) + +(define-public r-goftest + (package + (name "r-goftest") + (version "1.2-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "goftest" version)) + (sha256 + (base32 + "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4")))) + (properties `((upstream-name . "goftest"))) + (build-system r-build-system) + (home-page "https://github.com/baddstats/goftest") + (synopsis "Classical Goodness-of-Fit tests for univariate distributions") + (description + "This package provides Cramer-Von Mises and Anderson-Darling tests of +goodness-of-fit for continuous univariate distributions, using efficient +algorithms.") + (license license:gpl2+))) + +(define-public r-tensor + (package + (name "r-tensor") + (version "1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "tensor" version)) + (sha256 + (base32 + "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1")))) + (properties `((upstream-name . "tensor"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/tensor/") + (synopsis "Tensor product of arrays") + (description + "The tensor product of two arrays is notionally an outer product of the +arrays collapsed in specific extents by summing along the appropriate +diagonals. This package allows you to compute the tensor product of arrays.") + (license license:gpl2+))) + +(define-public r-spatstat-utils + (package + (name "r-spatstat-utils") + (version "1.17-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.utils" version)) + (sha256 + (base32 + "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r")))) + (properties + `((upstream-name . "spatstat.utils"))) + (build-system r-build-system) + (home-page "http://www.spatstat.org") + (synopsis "Utility functions for spatstat") + (description + "This package contains utility functions for the @code{spatstat} package +which may also be useful for other purposes.") + (license license:gpl2+))) + +(define-public r-spatstat-data + (package + (name "r-spatstat-data") + (version "1.4-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.data" version)) + (sha256 + (base32 + "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9")))) + (properties `((upstream-name . "spatstat.data"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-spatstat-utils" ,r-spatstat-utils))) + (home-page "http://www.spatstat.org") + (synopsis "Datasets for spatstat") + (description + "This package contains all the datasets for the @code{spatstat} +package.") + (license license:gpl2+))) + +(define-public r-spatstat + (package + (name "r-spatstat") + (version "1.64-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat" version)) + (sha256 + (base32 + "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya")))) + (properties `((upstream-name . "spatstat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-deldir" ,r-deldir) + ("r-goftest" ,r-goftest) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-nlme" ,r-nlme) + ("r-polyclip" ,r-polyclip) + ("r-rpart" ,r-rpart) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-utils" ,r-spatstat-utils) + ("r-tensor" ,r-tensor))) + (home-page "http://www.spatstat.org") + (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") + (description + "This package provides a comprehensive toolbox for analysing Spatial +Point Patterns. It is focused mainly on two-dimensional point patterns, +including multitype/marked points, in any spatial region. It also supports +three-dimensional point patterns, space-time point patterns in any number of +dimensions, point patterns on a linear network, and patterns of other +geometrical objects. It supports spatial covariate data such as pixel images +and contains over 2000 functions for plotting spatial data, exploratory data +analysis, model-fitting, simulation, spatial sampling, model diagnostics, and +formal inference.") + (license license:gpl2+))) + +(define-public r-gaston + (package + (name "r-gaston") + (version "1.5.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "gaston" version)) + (sha256 + (base32 + "1bx6iqfjb9lf3vn0z7v8wjv9m7issvqsnymm4qsgl3622s6qz6rg")))) + (properties `((upstream-name . "gaston"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppparallel" ,r-rcppparallel))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/gaston/") + (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models") + (description + "This is a package for the manipulation of genetic data (SNPs). +Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix, +@dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms +for linear mixed models (AIREML).") + (license license:gpl3))) + +(define-public r-cpp11 + (package + (name "r-cpp11") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "cpp11" version)) + (sha256 + (base32 + "1113y61lj4cg1d2yjavdx9zih5rzb4pnxmj5v3sr4bhzlxz2scda")))) + (properties `((upstream-name . "cpp11"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/r-lib/cpp11") + (synopsis "C++11 Interface for R's C Interface") + (description + "This package provides a header only, C++11 interface to R's C interface. +Compared to other approaches @code{cpp11} strives to be safe against long +jumps from the C API as well as C++ exceptions, conform to normal R function +semantics and supports interaction with @code{ALTREP} vectors.") + (license license:expat))) + +(define-public r-rcppziggurat + (package + (name "r-rcppziggurat") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppZiggurat" version)) + (sha256 + (base32 + "0zmr3nvm5j0fpwxk3x9kxpwqbr66ldfvd10zy8xlgjbslz9myvfv")))) + (properties `((upstream-name . "RcppZiggurat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppgsl" ,r-rcppgsl))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/") + (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations") + (description + "The Ziggurat generator for normally distributed random numbers, +originally proposed by Marsaglia and Tsang (2000, +@url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few +times starting with Leong et al (2005, +@url{https://doi.org/10.18637/jss.v012.i07}). This package provides an +aggregation for comparing different implementations in order to provide a +'faster but good enough' alternative for use with R and C++ code.") + (license license:gpl2+))) + +(define-public r-rfast + (package + (name "r-rfast") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rfast" version)) + (sha256 + (base32 + "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy")))) + (properties `((upstream-name . "Rfast"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rcppziggurat" ,r-rcppziggurat))) + (home-page "https://github.com/RfastOfficial/Rfast") + (synopsis "Collection of efficient and fast R functions") + (description + "This package provides a collection of fast (utility) functions for data +analysis. Column- and row- wise means, medians, variances, minimums, +maximums, many t, F and G-square tests, many regressions (normal, logistic, +Poisson), are some of the many fast functions.") + (license license:gpl2+))) + +(define-public r-clusterr + (package + (name "r-clusterr") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ClusterR" version)) + (sha256 + (base32 + "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm")))) + (properties `((upstream-name . "ClusterR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gmp" ,r-gmp) + ("r-gtools" ,r-gtools) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/mlampros/ClusterR") + (synopsis "Clustering") + (description + "This package provides Gaussian mixture models, k-means, +mini-batch-kmeans, k-medoids and affinity propagation clustering with the +option to plot, validate, predict (new data) and estimate the optimal number +of clusters. The package takes advantage of @code{RcppArmadillo} to speed up +the computationally intensive parts of the functions. For more information, +see + +@enumerate +@item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia + Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, + @url{https://doi.org/10.18637/jss.v001.i04}; +@item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital + Library, @url{https://doi.org/10.1145/1772690.1772862}; +@item \"Armadillo: a template-based C++ library + for linear algebra\" by Sanderson et al (2016), The Journal of Open Source + Software, @url{https://doi.org/10.21105/joss.00026}; +@item \"Clustering by Passing Messages Between Data Points\" by Brendan + J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, + pp. 972-976, @url{https://doi.org/10.1126/science.1136800}. +@end enumerate +") + (license license:gpl3))) + +(define-public r-spectrum + (package + (name "r-spectrum") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Spectrum" version)) + (sha256 + (base32 + "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw")))) + (properties `((upstream-name . "Spectrum"))) + (build-system r-build-system) + (propagated-inputs + `(("r-clusterr" ,r-clusterr) + ("r-diptest" ,r-diptest) + ("r-ggplot2" ,r-ggplot2) + ("r-rfast" ,r-rfast))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/Spectrum/") + (synopsis "Fast adaptive spectral clustering for single and multi-view data") + (description + "This package provides a self-tuning spectral clustering method for +single or multi-view data. Spectrum uses a new type of adaptive density aware +kernel that strengthens connections in the graph based on common nearest +neighbours. It uses a tensor product graph data integration and diffusion +procedure to integrate different data sources and reduce noise. Spectrum uses +either the eigengap or multimodality gap heuristics to determine the number of +clusters. The method is sufficiently flexible so that a wide range of +Gaussian and non-Gaussian structures can be clustered with automatic selection +of K.") + (license license:agpl3+))) + +(define-public r-nabor + (package + (name "r-nabor") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "nabor" version)) + (sha256 + (base32 + "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7")))) + (properties `((upstream-name . "nabor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://cran.r-project.org/web/packages/nabor/") + (synopsis "Wrapper for K nearest neighbour library for low dimensions") + (description + "This package provides an R wrapper for libnabo, an exact or approximate +k nearest neighbour library which is optimised for low dimensional +spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is +designed as a drop-in replacement for the RANN function @code{nn2}. In +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))) |