diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1703 |
1 files changed, 1585 insertions, 118 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f32d45d2a4..a39c0e64cb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> +;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> @@ -18,12 +19,16 @@ ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de> +;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com> ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com> ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net> ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es> +;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org> +;;; Copyright © 2020 Vinicius Monego <monego@posteo.net> +;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -47,6 +52,7 @@ #: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) @@ -69,6 +75,7 @@ #: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) @@ -86,19 +93,20 @@ #:use-module (gnu packages tcl) #:use-module (gnu packages tls) #:use-module (gnu packages web) + #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) (define-public r-rticles (package (name "r-rticles") - (version "0.14") + (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "1377fib4asazhhki4aajvld0wa35vd3zjvyl3lf2hjm2qk3vyak7")))) + "0svh2bcqnlqdxdpw5afz1b980i2q13k8cxpq6flfqbi3dlwf3h8l")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs @@ -245,17 +253,18 @@ series of numeric vectors/matrices and factors.") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin")))) + "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) + ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-lubridate" ,r-lubridate) @@ -305,14 +314,14 @@ 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 @@ -517,6 +526,35 @@ functions are simplified but can be faster or have other advantages.") objects.") (license license:gpl3))) +(define-public r-mboost + (package + (name "r-mboost") + (version "2.9-3") + (source (origin + (method url-fetch) + (uri (cran-uri "mboost" version)) + (sha256 + (base32 + "1qp5c43kc0939sss5w3hhn794lbi69wgfsa31sq4c8vzh35pjqmf")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-matrix" ,r-matrix) + ("r-nnls" ,r-nnls) + ("r-partykit" ,r-partykit) + ("r-quadprog" ,r-quadprog) + ("r-stabs" ,r-stabs) + ("r-survival" ,r-survival))) + (home-page "https://github.com/boost-R/mboost") + (synopsis "Model-based boosting") + (description + "This package provides a functional gradient descent algorithm (boosting) +for optimizing general risk functions utilizing component-wise (penalised) +least squares estimates or regression trees as base-learners for fitting +generalized linear, additive and interaction models to potentially +high-dimensional data.") + (license license:gpl2))) + (define-public r-sys (package (name "r-sys") @@ -746,14 +784,14 @@ same time tries to group instances from the same class together.") (define-public r-callr (package (name "r-callr") - (version "3.4.3") + (version "3.4.4") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1")))) + "1hgc4mfwv83104fh93v8g2srpwzjayq7krgzi9r0apq784r61642")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -830,8 +868,35 @@ 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) @@ -853,13 +918,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.7.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq")))) + "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -1860,14 +1925,14 @@ 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. @@ -1903,6 +1968,32 @@ of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER initiative to bring PASSTEC 2000 functionalities to R.") (license license:gpl2+))) +(define-public r-partykit + (package + (name "r-partykit") + (version "1.2-9") + (source (origin + (method url-fetch) + (uri (cran-uri "partykit" version)) + (sha256 + (base32 + "18nc6vvj1cy8ly2hqixg544sbg8vbpzwsr1cdlzrqfykd0pzgkvf")))) + (build-system r-build-system) + (propagated-inputs + `(("r-formula" ,r-formula) + ("r-inum" ,r-inum) + ("r-libcoin" ,r-libcoin) + ("r-mvtnorm" ,r-mvtnorm) + ("r-rpart" ,r-rpart) + ("r-survival" ,r-survival))) + (home-page "http://partykit.R-Forge.R-project.org/partykit") + (synopsis "Toolkit for recursive partytioning") + (description + "This package provides a toolkit with infrastructure for representing, +summarizing, and visualizing tree-structured regression and classification +models.") + (license license:gpl2+))) + (define-public r-plogr (package (name "r-plogr") @@ -2098,6 +2189,31 @@ where the bound function accepts additional arguments.") bindings that call a C++ function.") (license license:expat))) +(define-public r-bisquerna + (package + (name "r-bisquerna") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "BisqueRNA" version)) + (sha256 + (base32 + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) + (properties `((upstream-name . "BisqueRNA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limsolve" ,r-limsolve))) + (home-page "https://www.biorxiv.org/content/10.1101/669911v1") + (synopsis "Decomposition of bulk expression with single-cell sequencing") + (description "This package provides tools to accurately estimate cell type +abundances from heterogeneous bulk expression. A reference-based method +utilizes single-cell information to generate a signature matrix and +transformation of bulk expression for accurate regression based estimates. +A marker-based method utilizes known cell-specific marker genes to measure +relative abundances across samples.") + (license license:gpl3))) + (define-public r-auc (package (name "r-auc") @@ -2145,14 +2261,14 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.") (define-public r-shape (package (name "r-shape") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 - "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl")))) + "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/shape") (synopsis "Functions for plotting graphical shapes") @@ -2264,19 +2380,21 @@ 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 @@ -2364,14 +2482,14 @@ 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) @@ -2530,6 +2648,25 @@ selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.") (license license:gpl2+))) +(define-public r-laplacesdemon + (package + (name "r-laplacesdemon") + (version "16.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "LaplacesDemon" version)) + (sha256 + (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1")))) + (properties `((upstream-name . "LaplacesDemon"))) + (build-system r-build-system) + (home-page "https://github.com/LaplacesDemonR/LaplacesDemon") + (synopsis "Complete environment for Bayesian inference") + (description + "This package provides a complete environment for Bayesian inference using +a variety of different samplers.") + (license license:expat))) + (define-public r-rmtstat (package (name "r-rmtstat") @@ -2652,14 +2789,14 @@ or excesses over a high threshold.") (define-public r-lmtest (package (name "r-lmtest") - (version "0.9-37") + (version "0.9-38") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 - "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx")))) + "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) @@ -2697,13 +2834,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.15") + (version "0.3.16") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z")))) + "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") @@ -3011,14 +3148,14 @@ 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") @@ -3388,14 +3525,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.0.7") + (version "2.0.8") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc")))) + "0ymds7ql2dv994m73h68dnhbsws8bl09p2rqvl6xsq6c6xr0yryg")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -3637,6 +3774,36 @@ algorithm. The interface of @code{ucminf} is designed for easy interchange with the package @code{optim}.") (license license:gpl2+))) +(define-public r-useful + (package + (name "r-useful") + (version "1.2.6") + (source (origin + (method url-fetch) + (uri (cran-uri "useful" version)) + (sha256 + (base32 + "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1")))) + (properties `((upstream-name . "useful"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr) + ("r-purrr" ,r-purrr) + ("r-scales" ,r-scales))) + (home-page "https://github.com/jaredlander/useful") + (synopsis "Collection of handy, useful functions") + (description "This package provides a set of little functions that have been +found useful to do little odds and ends such as plotting the results of K-means +clustering, substituting special text characters, viewing parts of a +@code{data.frame}, constructing formulas from text and building design and +response matrices.") + (license license:bsd-3))) + (define-public r-ordinal (package (name "r-ordinal") @@ -3945,14 +4112,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.12-0") + (version "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz")))) + "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (home-page "https://github.com/joshuaulrich/xts") @@ -4242,13 +4409,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.4.3") + (version "3.4.4") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj")))) + (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) @@ -4389,13 +4556,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.16") + (version "0.17") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg")))) + (base32 "1zd5qi1rrz3b1lpisapa2yscanz39ghaamf28g7aq3z9ai2a2ymj")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -4452,14 +4619,14 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.3.2") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "05s8v3ms4jaim44c7m4y0dnv8mysj9b26cdfyrfgcjpllayrjib2")))) + "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -4583,6 +4750,30 @@ automatically.") supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) +(define-public r-stabs + (package + (name "r-stabs") + (version "0.6-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "stabs" version)) + (sha256 + (base32 + "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9")))) + (build-system r-build-system) + (home-page "https://github.com/hofnerb/stabs") + (synopsis "Stability selection with error control") + (description + "This package provides resampling procedures to assess the stability of +selected variables with additional finite sample error control for +high-dimensional variable selection procedures such as Lasso or boosting. +Both, standard stability selection (Meinshausen & Buhlmann, 2010) and +complementary pairs stability selection with improved error bounds +(Shah & Samworth, 2013) are implemented. The package can be combined with +arbitrary user specified variable selection approaches.") + (license license:gpl2))) + (define-public r-statnet-common (package (name "r-statnet-common") @@ -4685,14 +4876,14 @@ of these tests are also included.") (define-public r-ttr (package (name "r-ttr") - (version "0.24.0") + (version "0.24.2") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "0dcmfr98bxhdhszsdr1yjhvy4kplnfm88fh8sdzrkjank1qsxia2")))) + "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs @@ -4887,20 +5078,21 @@ University Press, 2000.") (define-public r-tsa (package (name "r-tsa") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 - "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q")))) + "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb")))) (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs `(("r-leaps" ,r-leaps) ("r-locfit" ,r-locfit) - ("r-mgcv" ,r-mgcv))) + ("r-mgcv" ,r-mgcv) + ("r-tseries" ,r-tseries))) (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description @@ -4912,14 +5104,14 @@ Cryer and Kung-Sik Chan.") (define-public r-extradistr (package (name "r-extradistr") - (version "1.8.11") + (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 - "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3")))) + "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs @@ -5009,14 +5201,14 @@ 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))) @@ -5182,14 +5374,14 @@ 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) @@ -5841,14 +6033,14 @@ misclassification probabilities of different models.") (define-public r-zip (package (name "r-zip") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 - "1dfsagb7bx35x4zx6f5xk2sk057fbyhskkpw3w72b805cjw920da")))) + "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") @@ -5923,14 +6115,14 @@ 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) @@ -6072,14 +6264,14 @@ 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 @@ -6667,14 +6859,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.12") + (version "0.3.14") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1wk9h6bz77s5j6lgksmlrmi1vyaa35c766gq6hgb1dp0dz0x342x")))) + "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) @@ -6934,14 +7126,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.9.0") + (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1ajc8c5mi3ma5411lmlqp2ihkk5n0h8a1c0r3j07wk33p31c1qvl")))) + "0853kq4j8kic8z2gh5mxfqkwxjs4bdphlajzyvxka7af4r04bfmi")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7068,14 +7260,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.5.10") + (version "0.5.11") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8")))) + "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -7101,14 +7293,14 @@ 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") @@ -7290,14 +7482,14 @@ 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") @@ -7723,18 +7915,17 @@ and coverage methods to tune the choice of threshold.") (define-public r-mosaiccore (package (name "r-mosaiccore") - (version "0.6.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "mosaicCore" version)) (sha256 - (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z")))) + (base32 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj")))) (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) - ("r-lazyeval" ,r-lazyeval) ("r-mass" ,r-mass) ("r-rlang" ,r-rlang) ("r-tidyr" ,r-tidyr))) @@ -7776,13 +7967,13 @@ while providing the intuitive capabilities of @code{r-ggplot2}.") (define-public r-mosaicdata (package (name "r-mosaicdata") - (version "0.18.0") + (version "0.20.1") (source (origin (method url-fetch) (uri (cran-uri "mosaicData" version)) (sha256 - (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz")))) + (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji")))) (properties `((upstream-name . "mosaicData"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mosaicData/") @@ -9061,14 +9252,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.4.8") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l")))) + "01csmn52d6rhlmcj7gi6ckc6v6a8pymnrpx9l729h13igxsnaf28")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -9088,14 +9279,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47")))) + "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -9780,14 +9971,14 @@ This package provides an R interface.") (define-public r-rcpphnsw (package (name "r-rcpphnsw") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppHNSW" version)) (sha256 (base32 - "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv")))) + "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -9934,14 +10125,14 @@ to colexicographical order.") (define-public r-misc3d (package (name "r-misc3d") - (version "0.8-4") + (version "0.9-0") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 - "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) + "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/misc3d/") (synopsis "Miscellaneous 3D Plots") @@ -10777,14 +10968,14 @@ Touzet and Varre (2007).") (define-public r-rnifti (package (name "r-rnifti") - (version "1.1.0") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn")))) + "0h837jdspy071ckij8szqd8149bm113jpqwbclg87is4brsm5jzg")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -11744,13 +11935,13 @@ Differences with other sparse matrix packages are: (define-public r-fields (package (name "r-fields") - (version "10.3") + (version "11.4") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 - (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9")))) + (base32 "0x8hbl0rn7gnhn7w45wd757g9in27884qr6vy30xrk150qaq941y")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,r-maps) @@ -12009,14 +12200,14 @@ JASA, 94:496-509.") (define-public r-etm (package (name "r-etm") - (version "1.1") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "etm" version)) (sha256 (base32 - "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd")))) + "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) @@ -12664,20 +12855,22 @@ transformation, respectively.") (define-public r-shinyjs (package (name "r-shinyjs") - (version "1.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjs" version)) (sha256 (base32 - "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9")))) + "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://deanattali.com/shinyjs") (synopsis "Improve the user experience of your Shiny apps") (description @@ -13698,14 +13891,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.1-28") + (version "0.1-29") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5")))) + "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") @@ -13722,14 +13915,14 @@ tessellation.") (define-public r-sf (package (name "r-sf") - (version "0.9-5") + (version "0.9-6") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf")))) + "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -14046,14 +14239,14 @@ include (define-public r-haplo-stats (package (name "r-haplo-stats") - (version "1.8.2") + (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 - "13gc980jk1pas7mz9b4nmwqd64qhh2c0xhq1z06z67jgv7k8n7dc")))) + "1f5cyyyavkf4l6kksp87s8d92vjrnhxmpz6j737pa527pn3gghf9")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs @@ -15481,14 +15674,14 @@ 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") @@ -15802,14 +15995,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-ingredients (package (name "r-ingredients") - (version "1.3.1") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 - "0l0dqrm9am6wk8jcf8cdhc6xnrna9cqr5wz6lsnczq2gf6ybhjg1")))) + "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs @@ -15907,14 +16100,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "1.3.1.1") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs")))) + "1yn61cbqvyycn617pzhd7kgd34xsnmqvj3s10inn2ywycybk7byi")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -16078,14 +16271,14 @@ 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) @@ -16168,14 +16361,14 @@ 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 @@ -16184,7 +16377,6 @@ 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) @@ -16193,6 +16385,8 @@ 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 @@ -16498,16 +16692,18 @@ both R code and compiled C/C++/FORTRAN code.") (define-public r-systemfonts (package (name "r-systemfonts") - (version "0.2.3") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 - "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb")))) + "0ldxgcayyisp2gcbv4xw9zpb48bp4czi8016kq5nqdqhv1qb3sz0")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) + (propagated-inputs + `(("r-cpp11" ,r-cpp11))) (inputs `(("fontconfig" ,fontconfig) ("zlib" ,zlib))) @@ -16644,14 +16840,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.8.2") + (version "0.8.5") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh")))) + "1vax5p1znq2ddbks2i614hbrnn2x6x71942xx49p813qk8dh284l")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -17962,14 +18158,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.1-7") + (version "5.2-0") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8")))) + "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs @@ -20111,14 +20307,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.12") + (version "8.13") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b")))) + "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -20673,19 +20869,20 @@ 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) @@ -20785,14 +20982,14 @@ 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 @@ -22284,14 +22481,14 @@ multi-state models.") (define-public r-scatterpie (package (name "r-scatterpie") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "scatterpie" version)) (sha256 (base32 - "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb")))) + "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1")))) (properties `((upstream-name . "scatterpie"))) (build-system r-build-system) (propagated-inputs @@ -22471,6 +22668,39 @@ and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning.") (license license:gpl3))) +(define-public r-hardhat + (package + (name "r-hardhat") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "hardhat" version)) + (sha256 + (base32 + "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs")))) + (properties `((upstream-name . "hardhat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-glue" ,r-glue) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tidymodels/hardhat") + (synopsis "Construct modeling packages") + (description + "Building modeling packages is hard. A large amount of effort generally +goes into providing an implementation for a new method that is efficient, +fast, and correct, but often less emphasis is put on the user interface. A +good interface requires specialized knowledge about S3 methods and formulas, +which the average package developer might not have. The goal of +@code{hardhat} is to reduce the burden around building new modeling packages +by providing functionality for preprocessing, predicting, and validating +input.") + (license license:expat))) + (define-public r-shapforxgboost (package (name "r-shapforxgboost") @@ -22655,14 +22885,14 @@ 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 @@ -22988,14 +23218,14 @@ aggregation for comparing different implementations in order to provide a (define-public r-rfast (package (name "r-rfast") - (version "1.9.9") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 - "18m8xhg24kygwhq7avdp1hibilicb5wppi2wdmc36fkqljc274y0")))) + "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs @@ -23117,3 +23347,1240 @@ 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))) + +(define-public r-muhaz + (package + (name "r-muhaz") + (version "1.2.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "muhaz" version)) + (sha256 + (base32 + "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk")))) + (properties `((upstream-name . "muhaz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-survival" ,r-survival))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/muhaz/") + (synopsis "Hazard function estimation in survival analysis") + (description + "This package produces a smooth estimate of the hazard function for +censored data.") + ;; Any version of the GPL. + (license license:gpl3+))) + +(define-public r-flexsurv + (package + (name "r-flexsurv") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "flexsurv" version)) + (sha256 + (base32 + "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr")))) + (properties `((upstream-name . "flexsurv"))) + (build-system r-build-system) + (propagated-inputs + `(("r-desolve" ,r-desolve) + ("r-mstate" ,r-mstate) + ("r-muhaz" ,r-muhaz) + ("r-mvtnorm" ,r-mvtnorm) + ("r-quadprog" ,r-quadprog) + ("r-rcpp" ,r-rcpp) + ("r-survival" ,r-survival) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/chjackson/flexsurv-dev") + (synopsis "Flexible parametric survival and multi-state models") + (description + "This package provides flexible parametric models for time-to-event data, +including the Royston-Parmar spline model, generalized gamma and generalized F +distributions. Any user-defined parametric distribution can be fitted, given +at least an R function defining the probability density or hazard. There are +also tools for fitting and predicting from fully parametric multi-state +models.") + (license license:gpl2+))) + +(define-public r-transphylo + (package + (name "r-transphylo") + (version "1.4.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "TransPhylo" version)) + (sha256 + (base32 + "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9")))) + (properties `((upstream-name . "TransPhylo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/TransPhylo/") + (synopsis "Inference of transmission tree from a dated phylogeny") + (description + "This is a package to infer transmission trees from a dated phylogeny. +It includes methods to simulate and analyze outbreaks. The methodology is +described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)} +and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.") + (license license:gpl2+))) + +(define-public r-km-ci + (package + (name "r-km-ci") + (version "0.5-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "km.ci" version)) + (sha256 + (base32 + "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v")))) + (properties `((upstream-name . "km.ci"))) + (build-system r-build-system) + (propagated-inputs + `(("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/km.ci/") + (synopsis "Confidence intervals for the Kaplan-Meier estimator") + (description + "This package computes various @dfn{confidence intervals} (CI) for the +Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods +variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by +Nair and Hall and Wellner.") + (license license:gpl2+))) + +(define-public r-kmsurv + (package + (name "r-kmsurv") + (version "0.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "KMsurv" version)) + (sha256 + (base32 + "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm")))) + (properties `((upstream-name . "KMsurv"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/KMsurv/") + (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis") + (description + "This package provides data sets and functions for Klein and Moeschberger +(1997), \"Survival Analysis, Techniques for Censored and Truncated Data\", +Springer.") + (license license:gpl3+))) + +(define-public r-survmisc + (package + (name "r-survmisc") + (version "0.5.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "survMisc" version)) + (sha256 + (base32 + "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm")))) + (properties `((upstream-name . "survMisc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-km-ci" ,r-km-ci) + ("r-kmsurv" ,r-kmsurv) + ("r-knitr" ,r-knitr) + ("r-survival" ,r-survival) + ("r-xtable" ,r-xtable) + ("r-zoo" ,r-zoo))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/survMisc/") + (synopsis "Miscellaneous functions for survival data") + (description + "This package provides a collection of functions to help in the analysis +of right-censored survival data. These extend the methods available in +the @code{survival} package.") + (license license:gpl2))) + +(define-public r-exactranktests + (package + (name "r-exactranktests") + (version "0.8-31") + (source + (origin + (method url-fetch) + (uri (cran-uri "exactRankTests" version)) + (sha256 + (base32 + "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw")))) + (properties + `((upstream-name . "exactRankTests"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/exactRankTests/") + (synopsis "Exact distributions for rank and permutation tests") + (description + "This package computes exact conditional p-values and quantiles using an +implementation of the Shift-Algorithm by Streitberg & Roehmel.") + (license license:gpl2+))) + +(define-public r-maxstat + (package + (name "r-maxstat") + (version "0.7-25") + (source + (origin + (method url-fetch) + (uri (cran-uri "maxstat" version)) + (sha256 + (base32 + "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg")))) + (properties `((upstream-name . "maxstat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-exactranktests" ,r-exactranktests) + ("r-mvtnorm" ,r-mvtnorm))) + (home-page "https://cran.r-project.org/web/packages/maxstat/") + (synopsis "Maximally selected rank statistics") + (description + "This package provides maximally selected rank statistics with several +p-value approximations.") + (license license:gpl2+))) + +(define-public r-survminer + (package + (name "r-survminer") + (version "0.4.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "survminer" version)) + (sha256 + (base32 + "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff")))) + (properties `((upstream-name . "survminer"))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpubr" ,r-ggpubr) + ("r-gridextra" ,r-gridextra) + ("r-magrittr" ,r-magrittr) + ("r-maxstat" ,r-maxstat) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-survival" ,r-survival) + ("r-survmisc" ,r-survmisc) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://rpkgs.datanovia.com/survminer/index.html") + (synopsis "Drawing survival curves using ggplot2") + (description + "This package contains the function @code{ggsurvplot()} for easily +drawing beautiful and 'ready-to-publish' survival curves with the 'number at +risk' table and 'censoring count plot'. Other functions are also available to +plot adjusted curves for Cox model and to visually examine Cox model +assumptions.") + (license license:gpl2))) + +(define-public r-forge + (package + (name "r-forge") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "forge" version)) + (sha256 + (base32 + "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa")))) + (properties `((upstream-name . "forge"))) + (build-system r-build-system) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang))) + (home-page "https://cran.r-project.org/web/packages/forge/") + (synopsis "Cast values into shape") + (description + "This package provides helper functions with a consistent interface to +coerce and verify the types and shapes of values for input checking.") + (license license:asl2.0))) + +(define-public r-config + (package + (name "r-config") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "config" version)) + (sha256 + (base32 + "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs")))) + (properties `((upstream-name . "config"))) + (build-system r-build-system) + (propagated-inputs + `(("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/rstudio/config") + (synopsis "Manage environment specific configuration values") + (description + "This package lets you manage configuration values across multiple +environments (e.g. development, test, production). It reads values using a +function that determines the current environment and returns the appropriate +value.") + (license license:gpl3))) + +(define-public r-adaptivesparsity + (package + (name "r-adaptivesparsity") + (version "1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "AdaptiveSparsity" version)) + (sha256 + (base32 + "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91")))) + (properties + `((upstream-name . "AdaptiveSparsity"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'link-against-armadillo + (lambda _ + (substitute* "src/Makevars" + (("PKG_LIBS=" prefix) + (string-append prefix "-larmadillo"))) + #t))))) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (inputs + `(("armadillo" ,armadillo))) + (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity") + (synopsis "Adaptive sparsity models") + (description + "This package implements the Figueiredo machine learning algorithm for +adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian +geometric models.") + (license license:lgpl3+))) + +(define-public r-diffusionmap + (package + (name "r-diffusionmap") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "diffusionMap" version)) + (sha256 + (base32 + "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j")))) + (properties `((upstream-name . "diffusionMap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-scatterplot3d" ,r-scatterplot3d))) + (home-page "https://www.r-project.org") + (synopsis "Diffusion map") + (description "This package implements the diffusion map method of data +parametrization, including creation and visualization of diffusion maps, +clustering with diffusion K-means and regression using the adaptive regression +model.") + (license license:gpl2))) + +(define-public r-igraph + (package + (name "r-igraph") + (version "1.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "igraph" version)) + (sha256 + (base32 + "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (inputs + `(("gmp" ,gmp) + ("glpk" ,glpk) + ("libxml2" ,libxml2) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-pkgconfig" ,r-pkgconfig))) + (home-page "https://igraph.org") + (synopsis "Network analysis and visualization") + (description + "This package provides routines for simple graphs and network analysis. +It can handle large graphs very well and provides functions for generating +random and regular graphs, graph visualization, centrality methods and much +more.") + (license license:gpl2+))) + +(define-public r-workflows + (package + (name "r-workflows") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "workflows" version)) + (sha256 + (base32 + "1d5njd1xdl8kghlbar4acgl9hxq83p6k7yks592cvakmcz7f853m")))) + (properties `((upstream-name . "workflows"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-ellipsis" ,r-ellipsis) + ("r-generics" ,r-generics) + ("r-glue" ,r-glue) + ("r-hardhat" ,r-hardhat) + ("r-parsnip" ,r-parsnip) + ("r-rlang" ,r-rlang))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tidymodels/workflows") + (synopsis "Modeling workflows") + (description + "A workflow is an object that can bundle together your pre-processing, +modeling, and post-processing requests. For example, if you have a +@code{recipe} and @code{parsnip} model, these can be combined into a +workflow. The advantages are: + +@enumerate +@item You don’t have to keep track of separate objects in your workspace. +@item The recipe prepping and model fitting can be executed using a single + call to @code{fit()}. +@item If you have custom tuning parameter settings, these can be defined using + a simpler interface when combined with @code{tune}. +@item In the future, workflows will be able to add post-processing operations, + such as modifying the probability cutoff for two-class models. +@end enumerate +") + (license license:expat))) + +(define-public r-gpfit + (package + (name "r-gpfit") + (version "1.0-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "GPfit" version)) + (sha256 + (base32 + "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby")))) + (properties `((upstream-name . "GPfit"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-lhs" ,r-lhs))) + (home-page "https://cran.r-project.org/web/packages/GPfit/") + (synopsis "Gaussian Processes modeling") + (description + "This package provides a computationally stable approach of fitting a +@dfn{Gaussian Process} (GP) model to a deterministic simulator.") + (license license:gpl2))) + +(define-public r-yardstick + (package + (name "r-yardstick") + (version "0.0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "yardstick" version)) + (sha256 + (base32 + "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq")))) + (properties `((upstream-name . "yardstick"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) + ("r-proc" ,r-proc) + ("r-rlang" ,r-rlang) + ("r-tidyselect" ,r-tidyselect))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tidymodels/yardstick") + (synopsis "Tidy characterizations of model performance") + (description + "This package provides tidy tools for quantifying how well a model fits +to a data set such as confusion matrices, class probability curve summaries, +and regression metrics (e.g., RMSE).") + (license license:gpl2))) + +(define-public r-rsample + (package + (name "r-rsample") + (version "0.0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "rsample" version)) + (sha256 + (base32 + "0s6hgq0rcv3ianyidq3n9z34y5ww51gaggqkwmwns9yyxmwfjcm8")))) + (properties `((upstream-name . "rsample"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-furrr" ,r-furrr) + ("r-generics" ,r-generics) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://rsample.tidymodels.org") + (synopsis "General resampling infrastructure") + (description + "This package provides classes and functions to create and summarize +different types of resampling objects (e.g. bootstrap, cross-validation).") + (license license:gpl2))) + +(define-public r-dicedesign + (package + (name "r-dicedesign") + (version "1.8-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "DiceDesign" version)) + (sha256 + (base32 + "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp")))) + (properties `((upstream-name . "DiceDesign"))) + (build-system r-build-system) + (home-page "http://dice.emse.fr/") + (synopsis "Designs of computer experiments") + (description + "This package provides tools to create some specific @code{Space-Filling +Design} (SFD) and to test their quality.") + (license license:gpl3))) + +(define-public r-dials + (package + (name "r-dials") + (version "0.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "dials" version)) + (sha256 + (base32 + "0jxmlcy20y57chflx91fqz6c4pbdckzr7jirq4s72vp723avrr4p")))) + (properties `((upstream-name . "dials"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dicedesign" ,r-dicedesign) + ("r-dplyr" ,r-dplyr) + ("r-glue" ,r-glue) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-tibble" ,r-tibble) + ("r-vctrs" ,r-vctrs) + ("r-withr" ,r-withr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://dials.tidymodels.org/") + (synopsis "Tools for creating tuning parameter values") + (description + "Many models contain tuning parameters (i.e. parameters that cannot be +directly estimated from the data). These tools can be used to define objects +for creating, simulating, or validating values for such parameters.") + (license license:gpl2))) + +(define-public r-tune + (package + (name "r-tune") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tune" version)) + (sha256 + (base32 + "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1")))) + (properties `((upstream-name . "tune"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-crayon" ,r-crayon) + ("r-dials" ,r-dials) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-glue" ,r-glue) + ("r-gpfit" ,r-gpfit) + ("r-hardhat" ,r-hardhat) + ("r-lifecycle" ,r-lifecycle) + ("r-parsnip" ,r-parsnip) + ("r-purrr" ,r-purrr) + ("r-recipes" ,r-recipes) + ("r-rlang" ,r-rlang) + ("r-rsample" ,r-rsample) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-vctrs" ,r-vctrs) + ("r-workflows" ,r-workflows) + ("r-yardstick" ,r-yardstick))) + (home-page "https://github.com/tidymodels/tune") + (synopsis "Tidy tuning tools") + (description + "The ability to tune models is important. @code{tune} contains functions +and classes to be used in conjunction with other @code{tidymodels} packages +for finding reasonable values of hyper-parameters in models, pre-processing +methods, and post-processing steps.") + (license license:expat))) + +(define-public r-tidyposterior + (package + (name "r-tidyposterior") + (version "0.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "tidyposterior" version)) + (sha256 + (base32 + "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg")))) + (properties `((upstream-name . "tidyposterior"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) + ("r-ggplot2" ,r-ggplot2) + ("r-lifecycle" ,r-lifecycle) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-rsample" ,r-rsample) + ("r-rstanarm" ,r-rstanarm) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://tidyposterior.tidymodels.org") + (synopsis "Bayesian analysis to compare models using resampling statistics") + (description + "This package can be used to conduct post hoc analyses of resampling +results generated by models. For example, if two models are evaluated with +the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there +are 10 paired statistics. These can be used to make comparisons between +models without involving a test set.") + (license license:gpl2))) + +(define-public r-tidypredict + (package + (name "r-tidypredict") + (version "0.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "tidypredict" version)) + (sha256 + (base32 + "1fx1nr8fry3nwy2391g26zkqakdf8f3j7zyrihbc0qhscvbdskiy")))) + (properties `((upstream-name . "tidypredict"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) + ("r-knitr" ,r-knitr) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://tidypredict.tidymodels.org") + (synopsis "Run predictions inside the database") + (description + "This package parses a fitted R model object, and returns a formula in +Tidy Eval code that calculates the predictions. It works with several +database backends because it leverages @code{dplyr} and @code{dbplyr} for the +final SQL translation of the algorithm. It currently supports @code{lm()}, +@code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()}, +@code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.") + (license license:gpl3))) + +(define-public r-janeaustenr + (package + (name "r-janeaustenr") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "janeaustenr" version)) + (sha256 + (base32 + "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr")))) + (properties `((upstream-name . "janeaustenr"))) + (build-system r-build-system) + (home-page "https://github.com/juliasilge/janeaustenr") + (synopsis "Jane Austen's complete novels") + (description + "This package provides the full texts for Jane Austen's six completed +novels, ready for text analysis. These novels are \"Sense and Sensibility\", +\"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\", +and \"Persuasion\".") + (license license:expat))) + +(define-public r-tokenizers + (package + (name "r-tokenizers") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tokenizers" version)) + (sha256 + (base32 + "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98")))) + (properties `((upstream-name . "tokenizers"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-snowballc" ,r-snowballc) + ("r-stringi" ,r-stringi))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://lincolnmullen.com/software/tokenizers/") + (synopsis "Fast, consistent tokenization of natural language text") + (description + "This is a package for converting natural language text into tokens. +It includes tokenizers for shingled n-grams, skip n-grams, words, word stems, +sentences, paragraphs, characters, shingled characters, lines, tweets, Penn +Treebank, regular expressions, as well as functions for counting characters, +words, and sentences, and a function for splitting longer texts into separate +documents, each with the same number of words. The tokenizers have a +consistent interface, and the package is built on the @code{stringi} and +@code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.") + (license license:expat))) + +(define-public r-hunspell + (package + (name "r-hunspell") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "hunspell" version)) + (sha256 + (base32 + "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1")))) + (properties `((upstream-name . "hunspell"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ropensci/hunspell#readme") + (synopsis "High-performance stemmer, tokenizer, and spell checker") + (description + "This package provides a low-level spell checker and morphological +analyzer based on the famous @code{hunspell} library. The package can analyze +or check individual words as well as parse text, LaTeX, HTML or XML documents. +For a more user-friendly interface use the @code{spelling} package which +builds on this package to automate checking of files, documentation and +vignettes in all common formats.") + ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or + ;; MPL; in addition to these licenses the rest of the R wrapper is also + ;; available under the Expat license. + (license (list license:gpl2 + license:lgpl2.1 + license:mpl1.1 + license:expat)))) + +(define-public r-tidytext + (package + (name "r-tidytext") + (version "0.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "tidytext" version)) + (sha256 + (base32 + "0kwbpffdnqrb6hgrrmrfnx890imbzvp5bs6sj1k72if28qijarm5")))) + (properties `((upstream-name . "tidytext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) + ("r-hunspell" ,r-hunspell) + ("r-janeaustenr" ,r-janeaustenr) + ("r-matrix" ,r-matrix) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tokenizers" ,r-tokenizers))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/juliasilge/tidytext") + (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools") + (description + "This is a package for text mining for word processing and sentiment +analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") + (license license:expat))) + +(define-public r-parsnip + (package + (name "r-parsnip") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "parsnip" version)) + (sha256 + (base32 + "12121qj1800i7g3km5kqzlb7hms55crmp6il575c2i475h5qx8d3")))) + (properties `((upstream-name . "parsnip"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) + ("r-globals" ,r-globals) + ("r-glue" ,r-glue) + ("r-magrittr" ,r-magrittr) + ("r-prettyunits" ,r-prettyunits) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://parsnip.tidymodels.org") + (synopsis "Common API to modeling and analysis functions") + (description + "This package provides a common interface to allow users to specify a +model without having to remember the different argument names across different +functions or computational engines (e.g. R, Spark, Stan, etc).") + (license license:gpl2))) + +(define-public r-infer + (package + (name "r-infer") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "infer" version)) + (sha256 + (base32 + "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g")))) + (properties `((upstream-name . "infer"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-glue" ,r-glue) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tidymodels/infer") + (synopsis "Tidy statistical inference") + (description + "The objective of this package is to perform inference using an +expressive statistical grammar that coheres with the Tidy design framework.") + (license license:cc0))) + +(define-public r-modeldata + (package + (name "r-modeldata") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "modeldata" version)) + (sha256 + (base32 + "13q6hhbwqbwnjvg8bz6iwwfx96p1saqq3r34cjrbnpgzmr1nn11l")))) + (properties `((upstream-name . "modeldata"))) + (build-system r-build-system) + (home-page "https://modeldata.tidymodels.org") + (synopsis "Data sets useful for modeling packages") + (description + "This package provides data sets used for demonstrating or testing +model-related packages.") + (license license:expat))) + +(define-public r-tidymodels + (package + (name "r-tidymodels") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tidymodels" version)) + (sha256 + (base32 + "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4")))) + (properties `((upstream-name . "tidymodels"))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-cli" ,r-cli) + ("r-crayon" ,r-crayon) + ("r-dials" ,r-dials) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-infer" ,r-infer) + ("r-magrittr" ,r-magrittr) + ("r-modeldata" ,r-modeldata) + ("r-parsnip" ,r-parsnip) + ("r-purrr" ,r-purrr) + ("r-recipes" ,r-recipes) + ("r-rlang" ,r-rlang) + ("r-rsample" ,r-rsample) + ("r-rstudioapi" ,r-rstudioapi) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-tune" ,r-tune) + ("r-workflows" ,r-workflows) + ("r-yardstick" ,r-yardstick))) + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes + (home-page "https://github.com/tidymodels/tidymodels") + (synopsis "Tidy collection for modeling and statistical analysis") + (description + "The tidy modeling \"verse\" is a collection of packages for modeling and +statistical analysis that share the underlying design philosophy, grammar, and +data structures of the tidyverse.") + (license license:gpl3))) + +(define-public r-mlecens + (package + (name "r-mlecens") + (version "0.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "MLEcens" version)) + (sha256 + (base32 + "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945")))) + (properties `((upstream-name . "MLEcens"))) + (build-system r-build-system) + (home-page "http://stat.ethz.ch/~maathuis/") + (synopsis "Computation of the MLE for bivariate (interval) censored data") + (description + "This package contains functions to compute the nonparametric +@dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of +@code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly. +To be more precise, we consider the situation where we observe a set of +rectangles that are known to contain the unobservable realizations of (X,Y). +We compute the MLE based on such a set of rectangles. The methods can also be +used for univariate censored data (see data set @code{cosmesis}), and for +censored data with competing risks (see data set @code{menopause}). The +package also provides functions to visualize the observed data and the MLE.") + (license license:gpl2+))) + +(define-public r-perm + (package + (name "r-perm") + (version "1.0-0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "perm" version)) + (sha256 + (base32 + "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk")))) + (properties `((upstream-name . "perm"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/perm/") + (synopsis "Exact or asymptotic permutation tests") + (description + "This package provides several methods for performing permutation tests. +It has three main functions, to perform linear permutation tests. These tests +are tests where the test statistic is the sum of the product of a +covariate (usually group indicator) and the scores.") + ;; Any version of the GPL + (license license:gpl2+))) + +(define-public r-qtl + (package + (name "r-qtl") + (version "1.46-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "qtl" version)) + (sha256 + (base32 + "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a")))) + (build-system r-build-system) + (home-page "https://rqtl.org/") + (synopsis "R package for analyzing QTL experiments in genetics") + (description "R/qtl is an extension library for the R statistics system. +It is used to analyze experimental crosses for identifying genes contributing +to variation in quantitative traits (so-called quantitative trait loci, QTLs). + +Using a hidden Markov model, R/qtl estimates genetic maps, to identify +genotyping errors, and to perform single-QTL and two-QTL, two-dimensional +genome scans.") + (license license:gpl3))) + +(define-public r-qtl2 + (package + (name "r-qtl2") + (version "0.22-11") + (source (origin + (method url-fetch) + (uri (cran-uri "qtl2" version)) + (sha256 + (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-jsonlite" ,r-jsonlite) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rsqlite" ,r-rsqlite) + ("r-yaml" ,r-yaml))) + (home-page "https://kbroman.org/qtl2/") + (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") + (description + "This package provides a set of tools to perform @dfn{Quantitative Trait +Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the +@code{R/qtl} package to better handle high-dimensional data and complex cross +designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") + (license license:gpl3))) + +(define-public r-seqminer + (package + (name "r-seqminer") + (version "8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "seqminer" version)) + (sha256 + (base32 + "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (home-page "http://seqminer.genomic.codes") + (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") + (description + "This package provides tools to integrate nucleotide sequencing +data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") + ;; Any version of the GPL is acceptable + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-maldiquant + (package + (name "r-maldiquant") + (version "1.19.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "MALDIquant" version)) + (sha256 + (base32 + "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57")))) + (properties `((upstream-name . "MALDIquant"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/MALDIquant") + (synopsis "Quantitative analysis of mass spectrometry data") + (description + "This package provides a complete analysis pipeline for matrix-assisted +laser desorption/ionization-time-of-flight (MALDI-TOF) and other +two-dimensional mass spectrometry data. In addition to commonly used plotting +and processing methods it includes distinctive features, namely baseline +subtraction methods such as morphological filters (TopHat) or the +statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak +alignment using warping functions, handling of replicated measurements as well +as allowing spectra with different resolutions.") + (license license:gpl3+))) + +(define-public r-seurat + (package + (name "r-seurat") + (version "3.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "Seurat" version)) + (sha256 + (base32 + "0jipc4xpmx56jzc31w6nsl77ah8x8wq7jclg2mxhjql4ixkwmz54")))) + (properties `((upstream-name . "Seurat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-cowplot" ,r-cowplot) + ("r-fitdistrplus" ,r-fitdistrplus) + ("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-ggridges" ,r-ggridges) + ("r-httr" ,r-httr) + ("r-ica" ,r-ica) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-jsonlite" ,r-jsonlite) + ("r-kernsmooth" ,r-kernsmooth) + ("r-leiden" ,r-leiden) + ("r-lmtest" ,r-lmtest) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-miniui" ,r-miniui) + ("r-patchwork" ,r-patchwork) + ("r-pbapply" ,r-pbapply) + ("r-plotly" ,r-plotly) + ("r-png" ,r-png) + ("r-rann" ,r-rann) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppannoy" ,r-rcppannoy) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppprogress" ,r-rcppprogress) + ("r-reticulate" ,r-reticulate) + ("r-rlang" ,r-rlang) + ("r-rocr" ,r-rocr) + ("r-rsvd" ,r-rsvd) + ("r-rtsne" ,r-rtsne) + ("r-scales" ,r-scales) + ("r-sctransform" ,r-sctransform) + ("r-shiny" ,r-shiny) + ("r-spatstat" ,r-spatstat) + ("r-tibble" ,r-tibble) + ("r-uwot" ,r-uwot))) + (home-page "http://www.satijalab.org/seurat") + (synopsis "Seurat is an R toolkit for single cell genomics") + (description + "This package is an R package designed for QC, analysis, and +exploration of single cell RNA-seq data. It easily enables widely-used +analytical techniques, including the identification of highly variable genes, +dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering +algorithms; density clustering, hierarchical clustering, k-means, and the +discovery of differentially expressed genes and markers.") + (license license:gpl3))) + +(define-public r-phangorn + (package + (name "r-phangorn") + (version "2.5.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "phangorn" version)) + (sha256 + (base32 + "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-fastmatch" ,r-fastmatch) + ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-quadprog" ,r-quadprog) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/KlausVigo/phangorn") + (synopsis "Phylogenetic analysis in R") + (description + "Phangorn is a package for phylogenetic analysis in R. It supports +estimation of phylogenetic trees and networks using Maximum Likelihood, +Maximum Parsimony, distance methods and Hadamard conjugation.") + (license license:gpl2+))) + +(define-public r-diversitree + (package + (name "r-diversitree") + (version "0.9-14") + (source + (origin + (method url-fetch) + (uri (cran-uri "diversitree" version)) + (sha256 + (base32 + "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-desolve" ,r-desolve) + ("r-rcpp" ,r-rcpp) + ("r-subplex" ,r-subplex))) + (home-page "https://www.zoology.ubc.ca/prog/diversitree") + (synopsis "Comparative 'phylogenetic' analyses of diversification") + (description "This package contains a number of comparative \"phylogenetic\" +methods, mostly focusing on analysing diversification and character evolution. +Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) +and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and +Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods +include Markov models of discrete and continuous trait evolution and constant +rate speciation and extinction.") + (license license:gpl2+))) + +(define-public r-absfiltergsea + (package + (name "r-absfiltergsea") + (version "1.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AbsFilterGSEA" version)) + (sha256 + (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) + (properties `((upstream-name . "AbsFilterGSEA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-deseq" ,r-deseq) + ("r-limma" ,r-limma) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") + (synopsis "Improved false positive control of gene-permuting with absolute filtering") + (description + "This package provides a function that performs gene-permuting of a gene-set +enrichment analysis (GSEA) calculation with or without the absolute filtering. + Without filtering, users can perform (original) two-tailed or one-tailed +absolute GSEA.") + (license license:gpl2))) |