diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1121 |
1 files changed, 1045 insertions, 76 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index efcc2dccb5..df869794db 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,6 +36,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) + #:use-module (gnu packages haskell) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -164,19 +166,19 @@ package is a port of the Python package @code{cssselect}.") (define-public r-reprex (package (name "r-reprex") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "1l44pxjiz3g0jkk3v6rg5jps3llihfiah0qyv40s0bxvxa6gm8v9")))) + "1ws5gds453xgfili87r35rz1wn2i7jbqissq98csbiddpkgls8sx")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-clipr" ,r-clipr) - ("r-knitr" ,r-knitr) + ("r-fs" ,r-fs) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-whisker" ,r-whisker) @@ -318,14 +320,14 @@ component analysis (with robust methods, and parallelized functions).") (define-public r-ape (package (name "r-ape") - (version "5.1") + (version "5.2") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "0vm2065993wf4hdqarxqykhfz9aaj0rrb98alhkq4qw1d2kdrmdp")))) + "05b4yka5cirdgxd4d7iiaqvr428pk3j6n9q6dvg5j38kdj2h5sr7")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -490,13 +492,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1zm9qkyvy1fvcjvmgw51iqw8x1xzkpy7rx7xnchwfj0xpzal0ljx")))) + (base32 "0ai8igdkysmks1ihbp3h3s552da2hskxqwrvp4cx7vwn91x9f3wd")))) (build-system r-build-system) (home-page "http://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -508,19 +510,21 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.0.0") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 - "10iz8057mixl9j73pq2cbp4ib6dadfsgi3fcsjjm7l3wwb9issd9")))) + "1i1rrax7x7r2bplig5cfc50lx85jc4n9a3qmvbdviaj22wr2lghs")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) + ("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-desc" ,r-desc) + ("r-prettyunits" ,r-prettyunits) ("r-r6" ,r-r6) ("r-rprojroot" ,r-rprojroot) ("r-withr" ,r-withr))) @@ -535,14 +539,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "1rjj229nq9fsl4ki4m75ybsavjgpqqhsr1zjzapwicsrxv6212px")))) + "0mm0avvan528zbrcrxigl5fkd7za01fb0qhlqrqvm3ar0115cqa8")))) (build-system r-build-system) (propagated-inputs `(("r-desc" ,r-desc) @@ -562,13 +566,13 @@ you to rapidly iterate while developing a package.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.18") + (version "0.12.19") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "006kpg2ph109rh1l13lqk26pp4as4fvl5661vrcczjygacgd1v7w")))) + (base32 "10mmiaawv9iwglc6z4y51mdpsfb1sivqmwr6xnfqkllcnpabdbk3")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -788,14 +792,14 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.8.0") + (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "1virn3c232xwcq3d0hhkgjh5gpzl01s39iwii5gxcm9mnsxjzdrh")))) + "1jiani6zwfajky2vafvay2hq158nh99rdrk3j00lycspds9v35fd")))) (build-system r-build-system) (propagated-inputs `(("r-fpc" ,r-fpc) @@ -887,14 +891,14 @@ in main memory.") (define-public r-ffbase (package (name "r-ffbase") - (version "0.12.3") + (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 - "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5")))) + "1h5x6rbb1nrpzf4ywkizn8ij0bz3mlz46byh46ylxhicg1ribi24")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit) @@ -932,14 +936,14 @@ quantities.") (define-public r-reshape (package (name "r-reshape") - (version "0.8.7") + (version "0.8.8") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 - "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig")))) + "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) @@ -1346,17 +1350,18 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.0-9") + (version "1.0-11") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6")))) + "12hckg3y5j3zh9q1gwxkc27q813p2r42iqp7wdfiq6nj55jrh6w6")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) + ("r-npsurv" ,r-npsurv) ("r-survival" ,r-survival))) (home-page "http://riskassessment.r-forge.r-project.org") (synopsis "Fitting a parametric distribution from data") @@ -1624,14 +1629,14 @@ calendar objects.") (define-public r-magic (package (name "r-magic") - (version "1.5-8") + (version "1.5-9") (source (origin (method url-fetch) (uri (cran-uri "magic" version)) (sha256 (base32 - "083cgpp3v03li0h8597b3g21pd9lkbmn9pyssblnhc800mpc52vz")))) + "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind))) @@ -2224,14 +2229,14 @@ acceptance regions, log-ratio plots and Q-Q plots.") (define-public r-sm (package (name "r-sm") - (version "2.2-5.5") + (version "2.2-5.6") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 - "1rw2mxygxsmk8mn4wag1ppjgzk0rlvh6zd8q02qrhjrn9jhi5qj3")))) + "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") @@ -2314,14 +2319,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.11-0") + (version "0.11-1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "1v50yn4bsjzdyk7r90isn6dxmpkapillrhpx3gqsshd180vwzqk9")))) + "17d3g14xkxa1a5z5gd3gk1xjqfkjg1ik3i12q0arina8frql3jhd")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (home-page "https://github.com/joshuaulrich/xts") @@ -2499,14 +2504,14 @@ plotting. a three dimensional point cloud.") (define-public r-ggridges (package (name "r-ggridges") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 - "1znvsbl3px8dddpjgdrygnpz4s685wizi0jnjvx2hrz58i0chjqj")))) + "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -2546,14 +2551,14 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "07as3dr7vwx02p3qgzlmxz1dlrd3x3lysrzp222ip9jcjpydp8wg")))) + "1r2yih4c0bdmbx0qrarlf0m1p5z30sri755zmdazsq2pw76zp07g")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -2701,20 +2706,19 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and (define-public r-webshot (package (name "r-webshot") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 - "07r71zzmggp4jf92x4ws4wg6v1x98vaj01lsar85bnb30n5vx8gh")))) + "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr")))) (build-system r-build-system) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-processx" ,r-processx) - ("r-withr" ,r-withr))) + `(("r-callr" ,r-callr) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description @@ -2761,14 +2765,14 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.3") + (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 - "1r11dd49ngmjgbjdv28a9c1jp8cg1l50x0acbsamzz576p8i2wl9")))) + "0991ywgc2dsraba91kkj37akhfzhzn02cnz7c88hhdis9kag3pwv")))) (build-system r-build-system) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") @@ -2845,14 +2849,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "1bgpr5i5399jf9n6pg2mm4aamisbhppg082ad0wv1j4g0rlxf1gy")))) + "08w5hyq3ysh631d5whgcfv1bb007cdc0bjhb83vwmhazs6rgvyjy")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -2960,14 +2964,14 @@ generation, and 2D/3D network visualization.") (define-public r-ttr (package (name "r-ttr") - (version "0.23-3") + (version "0.23-4") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "07r62ngyzjl4aszdxnr3n6bnbcgcap32yhd430jsilicg8n06di1")))) + "18mzyv6cmxmqyqsfwlx2b2k055887mfgc2jgj8xkn8c6m56n05zb")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs @@ -3168,14 +3172,14 @@ Cryer and Kung-Sik Chan.") (define-public r-extradistr (package (name "r-extradistr") - (version "1.8.9") + (version "1.8.10") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 - "1fg8vjpal33y51iqzglk1yvy46d7js0l0wfbdy698lq8a06hq19p")))) + "00lvqp5bb3iak5myiz4rqm887bkq9sdh7aybmz84mmfni6q01m28")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs @@ -3238,14 +3242,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "1.4") + (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "1hd23b8v2kpqp5gr0va8p2q7j8w9rik6ks7zrr4b8mb2mwrakk74")))) + "10jl5l3xnigiq95829ssq69xbim97k851187dghc30awszcx4clh")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -3294,14 +3298,14 @@ sample Robust Rank-Order Distributional Test.") (define-public r-expm (package (name "r-expm") - (version "0.999-2") + (version "0.999-3") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 - "1mihl67kvv1xv0figp25jkmwfn4iwkcx15cng2348y8gm6zybw9q")))) + "04k4a6g071jkjc0d30ncmf713dj16brcs9m6pj43hnycc1caq6si")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,gfortran))) @@ -3359,14 +3363,14 @@ creation and manipulation of WAVE audio files.") (define-public r-np (package (name "r-np") - (version "0.60-8") + (version "0.60-9") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 - "17h67a510wh83800ri6g02wvznrlhigxni8shyijz1iaxcpk8k4j")))) + "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -3498,14 +3502,14 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "1hqgszbiv99dibhwr21v21ll4s2hjn3ccqdicsm0z3gk77bh8iyb")))) + "1fbk5i6w6cpam8s3acf4bgdp8hajn4digjjix3i6i4q3p2rvn6zx")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs @@ -3521,14 +3525,14 @@ environment within Shiny.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "0.9.5") + (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "0mbxfqn79nphii4hb6kxl2wc0w0ra16y378rp2yw9a9926zdb7mb")) + "1f98ahki0kyb27gl55a859zb0lsvk9gddd9f54y767xfs6h89cgk")) (modules '((guix build utils))) (snippet '(begin @@ -3562,7 +3566,9 @@ environment within Shiny.") ("r-rstudioapi" ,r-rstudioapi) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles) ("r-shinyace" ,r-shinyace) + ("r-summarytools" ,r-summarytools) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-writexl" ,r-writexl))) @@ -4057,14 +4063,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "0.9-3") + (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "0hxbv01im9zk1qrwgigpc510w6x0kzdzip4gx2jzfqmmwr8m17r8")))) + "1753kgyc4kmbb5h6knz5wgvvvj8v77kzm8lz0kwz05m5k3spa24k")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -4085,14 +4091,14 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "0.7.4") + (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "125zc499gj702x2bch95lsfzk2qb4dzv3604x9afym2i3ylrmm64")))) + "0xhwn37makzm85zb6w5acc7svzibxcnz69rks0kxw22vapkxwz1i")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -4234,14 +4240,14 @@ quizzes to create self-paced tutorials for learning about R and R packages.") (define-public r-analytics (package (name "r-analytics") - (version "2.0") + (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "analytics" version)) (sha256 (base32 - "1jkdjqc3fnvvsgi6x9ncf36rxzq0a55cmgkcv92mfmpcramg2lk6")))) + "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) @@ -4254,7 +4260,8 @@ quizzes to create self-paced tutorials for learning about R and R packages.") ("r-robust" ,r-robust) ("r-trend" ,r-trend) ("r-tsa" ,r-tsa) - ("r-urca" ,r-urca))) + ("r-urca" ,r-urca) + ("r-vim" ,r-vim))) (home-page "https://cran.r-project.org/web/packages/analytics/") (synopsis "Collection of data analysis tools") (description @@ -4534,14 +4541,14 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "135qj7bcc3mwn0vg55hiiadf66lx6zaxvkicfmfw9x0zr7ah2r6x")))) + "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes @@ -4576,14 +4583,14 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "1s6p4cj909kc635fh5xpl87bqlcdj3dn3r1wk5g40abimk2b0pva")))) + "0h222q80li8rs3cv4c5lvv3g91ygd51w43ay6fwyk9q9d315vwrj")))) (build-system r-build-system) (inputs `(("hdf5" ,hdf5) @@ -4666,14 +4673,14 @@ functions.") (define-public r-rdpack (package (name "r-rdpack") - (version "0.9-0") + (version "0.10-1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "067w0w6kza0hkzcnx58danl83yfvl9yjacr47mnid2bg856gdd1b")))) + "0bbjnw88h54v40hzim00i8yd3p4rk9i84zfdmgcbnylscwvsf0av")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -4774,14 +4781,14 @@ other add-on packages.") (define-public r-sjlabelled (package (name "r-sjlabelled") - (version "1.0.13") + (version "1.0.14") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 - "0xizj7mrhnbn8kwjgm076si9w68a7lgrx4vj1sbqmv9jx055h8wv")))) + "0ayfzhm9bwjfaarq5z0gvn9kapjwj3532azgin97nr5fnjdhvgaw")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -4807,14 +4814,14 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.7.4") + (version "2.7.5") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "11cy09k1d2y5wwqvafqxr01hzk4x68ji2pqlwj7fnpw27i3ap4q4")))) + "05fjqfr2rfk11065zqkzb9mbqd6mgdkw9jdhq3by425a7f8m2dcg")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -5217,14 +5224,14 @@ containing one or more SNPs that evolved under directional selection.") (define-public r-proc (package (name "r-proc") - (version "1.12.1") + (version "1.13.0") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 - "05ad69a6fxy9k903cw3h4q59ch2jv6qfg9yjdbw3cgiiazcafrlj")))) + "0ain17clympkx09ym7gydylcd93096dxzqx1qzci310yq2l7fknm")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs @@ -5855,13 +5862,13 @@ detection.") (define-public r-abps (package (name "r-abps") - (version "0.2") + (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ABPS" version)) (sha256 - (base32 "1k3f5i34f4w2khkszb4qhwwcpiy7gsfh82vjr6rypwg6rx5rjclq")))) + (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) (properties `((upstream-name . "ABPS"))) (build-system r-build-system) (propagated-inputs `(("r-kernlab" ,r-kernlab))) @@ -6160,6 +6167,52 @@ representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.") (license license:gpl2))) +(define-public r-quic + (package + (name "r-quic") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "QUIC" version)) + (sha256 + (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) + (properties `((upstream-name . "QUIC"))) + (build-system r-build-system) + (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") + (synopsis "Regularized sparse inverse covariance matrix estimation") + (description + "This package implements the regularized Gaussian maximum likelihood +estimation of the inverse of a covariance matrix. It uses Newton's method and +coordinate descent to solve the regularized inverse covariance matrix +estimation problem.") + ;; The project home page states that the release is under GPLv3 or later. + ;; The CRAN page only says GPL-3. + (license license:gpl3+))) + +(define-public r-abundant + (package + (name "r-abundant") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abundant" version)) + (sha256 + (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-quic" ,r-quic))) + (home-page "https://cran.r-project.org/web/packages/abundant/") + (synopsis "Abundant regression and high-dimensional principal fitted components") + (description + "This package provides tools to fit and predict with the high-dimensional +principal fitted components model. This model is described by Cook, Forzani, +and Rothman (2012) @url{doi:10.1214/11-AOS962}.") + ;; The DESCRIPTION file states GPL-2, but since it directly depends on a + ;; GPLv3+ package (QUIC) this likely means GPLv2+. + (license license:gpl2+))) + (define-public r-ac3net (package (name "r-ac3net") @@ -6256,3 +6309,919 @@ a header row or not. The dataset should contain only one independent variable (x) and one dependent variable (y) and can contain a weight for each observation.") (license license:gpl2))) + +(define-public r-aspi + (package + (name "r-aspi") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "aspi" version)) + (sha256 + (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) + (build-system r-build-system) + (home-page + "https://cran.r-project.org/web/packages/aspi/") + (synopsis + "Analysis of symmetry of parasitic infections") + (description + "This package provides tools for the analysis and visualization of bilateral + asymmetry in parasitic infections.") + (license license:gpl3+))) + +(define-public r-sandwich + (package + (name "r-sandwich") + (version "2.5-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "sandwich" version)) + (sha256 + (base32 + "168kq5kk34xbhfsxsanard9zriyp6cw0s09ralzb57kk42pl9hbc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/sandwich/") + (synopsis "Robust Covariance Matrix Estimators") + (description + "This package provides model-robust standard error estimators for +cross-sectional, time series, clustered, panel, and longitudinal data.") + ;; Either version of the license. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-th-data + (package + (name "r-th-data") + (version "1.0-9") + (source + (origin + (method url-fetch) + (uri (cran-uri "TH.data" version)) + (sha256 + (base32 + "03xfvww0krw0fn76qmmvrj7dx4shin57qafwhkrggfg25hbqlcfq")))) + (properties `((upstream-name . "TH.data"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/TH.data/") + (synopsis "Shared data sets") + (description + "This package contains supporting data sets that are used in other +packages maintained by Torsten Hothorn.") + (license license:gpl3))) + +(define-public r-multcomp + (package + (name "r-multcomp") + (version "1.4-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "multcomp" version)) + (sha256 + (base32 + "0fm78g4zjc6ank316qfw977864shmy890znn4fahwc8jjdhpc252")))) + (build-system r-build-system) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-mvtnorm" ,r-mvtnorm) + ("r-sandwich" ,r-sandwich) + ("r-survival" ,r-survival) + ("r-th-data" ,r-th-data))) + (home-page "https://cran.r-project.org/web/packages/multcomp/") + (synopsis "Simultaneous inference in general parametric models") + (description + "Simultaneous tests and confidence intervals for general linear +hypotheses in parametric models, including linear, generalized linear, linear +mixed effects, and survival models. The package includes demos reproducing +analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, +Hothorn, Westfall, 2010, CRC Press).") + (license license:gpl2))) + +(define-public r-emmeans + (package + (name "r-emmeans") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "emmeans" version)) + (sha256 + (base32 + "0kdyy4qp332c4yyvp1cnh48h6ks6ffir5rjcv0py0vm3m8c3hh61")))) + (build-system r-build-system) + (propagated-inputs + `(("r-estimability" ,r-estimability) + ("r-mvtnorm" ,r-mvtnorm) + ("r-plyr" ,r-plyr) + ("r-xtable" ,r-xtable))) + (home-page "https://github.com/rvlenth/emmeans") + (synopsis "Estimated marginal means, aka least-squares means") + (description + "This package provides tools to obtain @dfn{estimated marginal +means} (EMMs) for many linear, generalized linear, and mixed models. It can +be used to compute contrasts or linear functions of EMMs, trends, and +comparisons of slopes.") + ;; Either version of the license. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-pwr + (package + (name "r-pwr") + (version "1.2-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pwr" version)) + (sha256 + (base32 + "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/heliosdrm/pwr") + (synopsis "Basic functions for power analysis") + (description + "This package provides power analysis functions along the lines of +Cohen (1988).") + (license license:gpl3+))) + +(define-public r-coin + (package + (name "r-coin") + (version "1.2-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "coin" version)) + (sha256 + (base32 + "1fq58793bymzig1syjg2lvn6hsxfwkhh00jfrchh3c0y7rfhc66m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-modeltools" ,r-modeltools) + ("r-multcomp" ,r-multcomp) + ("r-mvtnorm" ,r-mvtnorm) + ("r-survival" ,r-survival))) + (home-page "http://coin.r-forge.r-project.org") + (synopsis "Conditional inference procedures in a permutation test framework") + (description + "This package provides conditional inference procedures for the general +independence problem including two-sample, K-sample (non-parametric ANOVA), +correlation, censored, ordered and multivariate problems.") + (license license:gpl2))) + +(define-public r-bayesplot + (package + (name "r-bayesplot") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "bayesplot" version)) + (sha256 + (base32 + "0in9cq2ybpa7njrwqx4l6nc8i01cjswsvzwlyiw465pi74aapr57")))) + (build-system r-build-system) + (inputs + `(("pandoc" ,ghc-pandoc) + ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggridges" ,r-ggridges) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang))) + (home-page "http://mc-stan.org/bayesplot") + (synopsis "Plotting for Bayesian models") + (description + "This package provides plotting functions for posterior analysis, model +checking, and MCMC diagnostics. The package is designed not only to provide +convenient functionality for users, but also a common set of functions that +can be easily used by developers working on a variety of R packages for +Bayesian modeling.") + (license license:gpl3+))) + +(define-public r-tmb + (package + (name "r-tmb") + (version "1.7.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "TMB" version)) + (sha256 + (base32 + "0bpc504nz8xfwr8ack52dj4hpjcykn6zyf8n228z32dw9d5n96dl")))) + (properties `((upstream-name . "TMB"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "http://tmb-project.org") + (synopsis "Template model builder: a general random effect tool") + (description + "With this tool, a user should be able to quickly implement complex +random effect models through simple C++ templates. The package combines +@code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated +matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available +from R) to obtain an efficient implementation of the applied Laplace +approximation with exact derivatives. Key features are: Automatic sparseness +detection, parallelism through BLAS and parallel user templates.") + (license license:gpl2))) + +(define-public r-sjstats + (package + (name "r-sjstats") + (version "0.17.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sjstats" version)) + (sha256 + (base32 + "0s9b0xr8gmcm0kh48jkwk8ns0lqknd8kpys4f7czf0xwzmcx2n1z")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bayesplot" ,r-bayesplot) + ("r-broom" ,r-broom) + ("r-coin" ,r-coin) + ("r-crayon" ,r-crayon) + ("r-dplyr" ,r-dplyr) + ("r-emmeans" ,r-emmeans) + ("r-glmmtmb" ,r-glmmtmb) + ("r-lme4" ,r-lme4) + ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-modelr" ,r-modelr) + ("r-nlme" ,r-nlme) + ("r-purrr" ,r-purrr) + ("r-pwr" ,r-pwr) + ("r-rlang" ,r-rlang) + ("r-sjlabelled" ,r-sjlabelled) + ("r-sjmisc" ,r-sjmisc) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/strengejacke/sjstats") + (synopsis "Functions for common statistical computations") + (description + "This package provides a collection of convenient functions for common +statistical computations, which are not directly provided by R's @code{base} +or @code{stats} packages. This package aims at providing, first, shortcuts +for statistical measures, which otherwise could only be calculated with +additional effort. Second, these shortcut functions are generic, and can be +applied not only to vectors, but also to other objects as well. The focus of +most functions lies on summary statistics or fit measures for regression +models, including generalized linear models, mixed effects models and Bayesian +models.") + (license license:gpl3))) + +(define-public r-glmmtmb + (package + (name "r-glmmtmb") + (version "0.2.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "glmmTMB" version)) + (sha256 + (base32 + "1clpkjlmsjmn3m1z5jqv8cgw6bvpqsy4nx6k947r0jya017ny5y5")))) + (properties `((upstream-name . "glmmTMB"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lme4" ,r-lme4) + ("r-matrix" ,r-matrix) + ("r-nlme" ,r-nlme) + ("r-rcppeigen" ,r-rcppeigen) + ("r-tmb" ,r-tmb))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/glmmTMB") + (synopsis "Generalized linear mixed models") + (description + "Fit linear and generalized linear mixed models with various extensions, +including zero-inflation. The models are fitted using maximum likelihood +estimation via the Template Model Builder. Random effects are assumed to be +Gaussian on the scale of the linear predictor and are integrated out using the +Laplace approximation. Gradients are calculated using automatic +differentiation.") + (license license:agpl3+))) + +(define-public r-ggeffects + (package + (name "r-ggeffects") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggeffects" version)) + (sha256 + (base32 + "00l02g7yssqxmcmbrzk2wsj3i9ywd0xsy0rmbfh57q1qi76a1wq1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-crayon" ,r-crayon) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) + ("r-prediction" ,r-prediction) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-sjlabelled" ,r-sjlabelled) + ("r-sjmisc" ,r-sjmisc) + ("r-sjstats" ,r-sjstats) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/strengejacke/ggeffects") + (synopsis "Create tidy data frames of marginal effects for ggplot") + (description + "This package provides tools to compute marginal effects from statistical +models and return the result as tidy data frames. These data frames are ready +to use with the @code{ggplot2} package. Marginal effects can be calculated +for many different models. Interaction terms, splines and polynomial terms +are also supported. The two main functions are @code{ggpredict()} and +@code{ggeffect()}. There is a generic @code{plot()} method to plot the +results using @code{ggplot2}.") + (license license:gpl3))) + +(define-public r-sjplot + (package + (name "r-sjplot") + (version "2.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sjPlot" version)) + (sha256 + (base32 + "13qvw2s3r96qfi8kfsn76m050ccnmckl31a9qv94xws8da99v2fk")))) + (properties `((upstream-name . "sjPlot"))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-forcats" ,r-forcats) + ("r-ggeffects" ,r-ggeffects) + ("r-ggplot2" ,r-ggplot2) + ("r-glmmtmb" ,r-glmmtmb) + ("r-knitr" ,r-knitr) + ("r-lme4" ,r-lme4) + ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) + ("r-modelr" ,r-modelr) + ("r-nlme" ,r-nlme) + ("r-psych" ,r-psych) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-sjlabelled" ,r-sjlabelled) + ("r-sjmisc" ,r-sjmisc) + ("r-sjstats" ,r-sjstats) + ("r-tidyr" ,r-tidyr))) + (home-page "https://strengejacke.github.io/sjPlot/") + (synopsis "Data visualization for statistics in social science") + (description + "This package represents a collection of plotting and table output +functions for data visualization. Results of various statistical +analyses (that are commonly used in social sciences) can be visualized using +this package, including simple and cross tabulated frequencies, histograms, +box plots, (generalized) linear models, mixed effects models, principal +component analysis and correlation matrices, cluster analyses, scatter plots, +stacked scales, effects plots of regression models (including interaction +terms) and much more. This package supports labelled data.") + (license license:gpl3))) + +(define-public r-ini + (package + (name "r-ini") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ini" version)) + (sha256 + (base32 + "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) + (build-system r-build-system) + (home-page "https://github.com/dvdscripter/ini") + (synopsis "Read and write configuration files") + (description + "This package provides tools to parse simple @code{.ini} configuration +files to an structured list. Users can manipulate this resulting list with +@code{lapply()} functions. This same structured list can be used to write +back to file after modifications.") + (license license:gpl3))) + +(define-public r-gh + (package + (name "r-gh") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gh" version)) + (sha256 + (base32 + "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k")))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-ini" ,r-ini) + ("r-jsonlite" ,r-jsonlite))) + (home-page "https://github.com/r-lib/gh#readme") + (synopsis "Access the GitHub API via R") + (description + "This package provides a minimal R client to access the GitHub API.") + (license license:expat))) + +(define-public r-fs + (package + (name "r-fs") + (version "1.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "fs" version)) + (sha256 + (base32 + "0kqqaqqml8x3r1mdld40iwns0ylj2f52qsdh1vcn39f7w7c2ka8j")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://fs.r-lib.org") + (synopsis "Cross-platform file system operations based on libuv") + (description + "This package provides a cross-platform interface to file system +operations, built on top of the libuv C library.") + (license license:gpl3))) + +(define-public r-clisymbols + (package + (name "r-clisymbols") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "clisymbols" version)) + (sha256 + (base32 + "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86")))) + (build-system r-build-system) + (home-page "https://github.com/gaborcsardi/clisymbols") + (synopsis "Unicode symbols at the R prompt") + (description + "This package provides a small subset of Unicode symbols, that are useful +when building command line applications. They fall back to alternatives on +terminals that do not support Unicode.") + (license license:expat))) + +(define-public r-usethis + (package + (name "r-usethis") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "usethis" version)) + (sha256 + (base32 + "1gadckx3sxz9gxvpkprj9x7zcgg2nz5m4q0vi76ya9li1v03rwwn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-clipr" ,r-clipr) + ("r-clisymbols" ,r-clisymbols) + ("r-crayon" ,r-crayon) + ("r-curl" ,r-curl) + ("r-desc" ,r-desc) + ("r-fs" ,r-fs) + ("r-gh" ,r-gh) + ("r-git2r" ,r-git2r) + ("r-glue" ,r-glue) + ("r-rlang" ,r-rlang) + ("r-rprojroot" ,r-rprojroot) + ("r-rstudioapi" ,r-rstudioapi) + ("r-whisker" ,r-whisker))) + (home-page "https://github.com/r-lib/usethis") + (synopsis "Automate R package and project setup") + (description + "This package helps you to automate R package and project setup tasks +that are otherwise performed manually. This includes setting up unit testing, +test coverage, continuous integration, Git, GitHub integration, licenses, +Rcpp, RStudio projects, and more.") + (license license:gpl3))) + +(define-public r-sessioninfo + (package + (name "r-sessioninfo") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "sessioninfo" version)) + (sha256 + (base32 + "01c0m8yzadpwd825hky6as0f8ka4xyz7zfy0ih2iy7qqw11w6qn5")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-withr" ,r-withr))) + (home-page "https://github.com/r-lib/sessioninfo#readme") + (synopsis "R session information") + (description + "This package provides tools to query and print information about the +current R session. It is similar to @code{utils::sessionInfo()}, but includes +more information about packages, and where they were installed from.") + (license license:gpl2))) + +(define-public r-remotes + (package + (name "r-remotes") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "remotes" version)) + (sha256 + (base32 + "1xkzlciv68jyf4j8hads0i47nxbgsy1kv7258c6zzyq66z0amhss")))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/remotes#readme") + (synopsis "R package installation from remote repositories") + (description + "Download and install R packages stored in GitHub, BitBucket, or plain +subversion or git repositories. This package is a lightweight replacement of +the @code{install_*} functions in the @code{devtools} package. Indeed most of +the code was copied over from @code{devtools}.") + (license license:gpl2+))) + +(define-public r-xopen + (package + (name "r-xopen") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "xopen" version)) + (sha256 + (base32 + "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-processx" ,r-processx))) + (home-page "https://github.com/r-lib/xopen#readme") + (synopsis "Open system files, URLs, anything") + (description + "This package provides a cross-platform solution to open files, +directories or URLs with their associated programs.") + (license license:expat))) + +(define-public r-rcmdcheck + (package + (name "r-rcmdcheck") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rcmdcheck" version)) + (sha256 + (base32 + "13liz9lmx9xgc0f7pjiz3sp8ygvazx2zslbiwz3p9fimfsx1yfsg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-callr" ,r-callr) + ("r-cli" ,r-cli) + ("r-crayon" ,r-crayon) + ("r-desc" ,r-desc) + ("r-digest" ,r-digest) + ("r-pkgbuild" ,r-pkgbuild) + ("r-prettyunits" ,r-prettyunits) + ("r-r6" ,r-r6) + ("r-rprojroot" ,r-rprojroot) + ("r-withr" ,r-withr) + ("r-xopen" ,r-xopen))) + (home-page "https://github.com/r-Lib/rcmdcheck#readme") + (synopsis "Run R CMD check from R and capture results") + (description + "Run @code{R CMD check} from R programmatically, and capture the results +of the individual checks.") + (license license:expat))) + +(define-public r-rapportools + (package + (name "r-rapportools") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rapportools" version)) + (sha256 + (base32 + "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-pander" ,r-pander) + ("r-plyr" ,r-plyr) + ("r-reshape" ,r-reshape))) + (home-page "https://cran.r-project.org/web/packages/rapportools/") + (synopsis "Miscellaneous helper functions with sane defaults for reporting") + (description + "This package provides helper functions that act as wrappers to more +advanced statistical methods with the advantage of having sane defaults for +quick reporting.") + (license license:agpl3+))) + +(define-public r-pander + (package + (name "r-pander") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pander" version)) + (sha256 + (base32 + "0gd7rqkpbraznip8jmri9lqa8ajg1sryyplhd6m633wg91whiipi")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-rcpp" ,r-rcpp))) + (home-page "https://rapporter.github.io/pander") + (synopsis "Render R objects into Pandoc's markdown") + (description + "The main aim of the pander R package is to provide a minimal and easy +tool for rendering R objects into Pandoc's markdown. The package is also +capable of exporting/converting complex Pandoc documents (reports) in various +ways.") + ;; This package is licensed under either the AGPLv3+ or the very rarely + ;; used OSL 3.0. + (license license:agpl3+))) + +(define-public r-summarytools + (package + (name "r-summarytools") + (version "0.8.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "summarytools" version)) + (sha256 + (base32 + "0z836m6ib9bznwcawn6xf8gck05ydxwi3bx4jbrbyqql4kci8zwb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-lubridate" ,r-lubridate) + ("r-matrixstats" ,r-matrixstats) + ("r-pander" ,r-pander) + ("r-pryr" ,r-pryr) + ("r-rapportools" ,r-rapportools) + ("r-rcurl" ,r-rcurl))) + (home-page "https://github.com/dcomtois/summarytools") + (synopsis "Tools to quickly and neatly summarize data") + (description + "This package provides tools for data frame summaries, cross-tabulations, +weight-enabled frequency tables and common univariate statistics in concise +tables available in a variety of formats (plain ASCII, Markdown and HTML). A +good point-of-entry for exploring data, both for experienced and new R +users.") + (license license:gpl2))) + +(define-public r-lsei + (package + (name "r-lsei") + (version "1.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "lsei" version)) + (sha256 + (base32 + "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://www.stat.auckland.ac.nz/~yongwang") + (synopsis "Solve regression problems under equality/inequality constraints") + (description + "It contains functions that solve least squares linear regression +problems under linear equality/inequality constraints. Functions for solving +quadratic programming problems are also available, which transform such +problems into least squares ones first.") + (license license:gpl2+))) + +(define-public r-npsurv + (package + (name "r-npsurv") + (version "0.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "npsurv" version)) + (sha256 + (base32 + "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lsei" ,r-lsei))) + (home-page "https://www.stat.auckland.ac.nz/~yongwang") + (synopsis "Nonparametric survival analysis") + (description + "This package contains functions for non-parametric survival analysis of +exact and interval-censored observations.") + (license license:gpl2+))) + +(define-public r-clusteval + (package + (name "r-clusteval") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "clusteval" version)) + (sha256 + (base32 + "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mvtnorm" ,r-mvtnorm) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/clusteval/") + (synopsis "Evaluation of clustering algorithms") + (description + "This R package provides a suite of tools to evaluate clustering +algorithms, clusterings, and individual clusters.") + (license license:expat))) + +(define-public r-tweedie + (package + (name "r-tweedie") + (version "2.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "tweedie" version)) + (sha256 + (base32 + "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/tweedie/") + (synopsis "Evaluation of Tweedie exponential family models") + (description + "Maximum likelihood computations for Tweedie families, including the +series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and +the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), +and related methods.") + (license license:gpl2+))) + +(define-public r-rcppgsl + (package + (name "r-rcppgsl") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppGSL" version)) + (sha256 + (base32 + "16pdapq31729db53agnb48jkvdm97167n3bigy5zazc3q3isis1m")))) + (properties `((upstream-name . "RcppGSL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("gsl" ,gsl))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://cran.r-project.org/web/packages/RcppGSL/") + (synopsis "Rcpp integration for GSL vectors and matrices") + (description + "The GNU Scientific Library (or GSL) is a collection of numerical +routines for scientific computing. It is particularly useful for C and C++ +programs as it provides a standard C interface to a wide range of mathematical +routines. There are over 1000 functions in total with an extensive test +suite. The RcppGSL package provides an easy-to-use interface between GSL data +structures and R using concepts from Rcpp which is itself a package that eases +the interfaces between R and C++.") + (license license:gpl2+))) + +(define-public r-mvabund + (package + (name "r-mvabund") + (version "3.13.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "mvabund" version)) + (sha256 + (base32 + "1z8bj9zbc8h7w1xki9sc2p2rq6lv8gbcmiy9819z54d7lx1i9cnj")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-rcppgsl" ,r-rcppgsl) + ("r-statmod" ,r-statmod) + ("r-tweedie" ,r-tweedie))) + (home-page "https://cran.r-project.org/web/packages/mvabund/") + (synopsis "Statistical methods for analysing multivariate abundance data") + (description + "This package provides a set of tools for displaying, modeling and +analysing multivariate abundance data in community ecology.") + (license license:lgpl2.1+))) + +(define-public r-afex + (package + (name "r-afex") + (version "0.22-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "afex" version)) + (sha256 + (base32 + "065wbxljl77zqvc2c4gpfpfyc6mbnnrf24q399q9bxmrz3sapj8n")))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-lme4" ,r-lme4) + ("r-lmertest" ,r-lmertest) + ("r-pbkrtest" ,r-pbkrtest) + ("r-reshape2" ,r-reshape2))) + (home-page "https://afex.singmann.science/") + (synopsis "Analysis of factorial experiments") + (description + "This package provides convenience functions for analyzing factorial +experiments using ANOVA or mixed models.") + (license license:gpl2+))) + +(define-public r-lmertest + (package + (name "r-lmertest") + (version "3.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lmerTest" version)) + (sha256 + (base32 + "0pia69sc8bn37mkiprdf91iilziqb865f94k6x6c26i33fg7rq4m")))) + (properties `((upstream-name . "lmerTest"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-numderiv" ,r-numderiv))) + (home-page "https://github.com/runehaubo/lmerTestR") + (synopsis "Tests in linear mixed effects models") + (description + "This package provides p-values in type I, II or III anova and summary +tables for @code{lmer} model fits via Satterthwaite's degrees of freedom +method. A Kenward-Roger method is also available via the @code{pbkrtest} +package. Model selection methods include step, drop1 and anova-like tables +for random effects (ranova). Methods for Least-Square means (LS-means) and +tests of linear contrasts of fixed effects are also available.") + (license license:gpl2+))) + +(define-public r-r2glmm + (package + (name "r-r2glmm") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "r2glmm" version)) + (sha256 + (base32 + "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-afex" ,r-afex) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-lmertest" ,r-lmertest) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-pbkrtest" ,r-pbkrtest))) + (home-page "https://github.com/bcjaeger/r2glmm") + (synopsis "Compute R squared for mixed (multilevel) models") + (description + "This package computes model and semi partial R squared with confidence +limits for the linear and generalized linear mixed model (LMM and GLMM). The +R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM +using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et +al. (2016)).") + (license license:gpl2))) |