diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 3088 |
1 files changed, 2949 insertions, 139 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eb6bf9c38b..f08a204fb8 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. ;;; @@ -31,8 +32,15 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system r) + #:use-module (gnu packages base) #:use-module (gnu packages compression) + #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) + #:use-module (gnu packages gl) + #:use-module (gnu packages gnome) + #:use-module (gnu packages gtk) + #:use-module (gnu packages haskell) + #:use-module (gnu packages image) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -41,7 +49,27 @@ #:use-module (gnu packages python) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) - #:use-module (gnu packages web)) + #:use-module (gnu packages web) + #:use-module (gnu packages xorg)) + +(define-public r-clipr + (package + (name "r-clipr") + (version "0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "clipr" version)) + (sha256 + (base32 + "061x84ildc7g1p91yw5iyj8lpqdf4hqv36as85lw8c6qv9ywbsqv")))) + (build-system r-build-system) + (home-page "https://github.com/mdlincoln/clipr") + (synopsis "Read and write from the system clipboard") + (description + "This package provides simple utility functions to read from and write to +the system clipboards.") + (license license:gpl3))) (define-public r-tidyverse (package @@ -143,20 +171,23 @@ package is a port of the Python package @code{cssselect}.") (define-public r-reprex (package (name "r-reprex") - (version "0.1.2") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "105d9vsmqfilgpw8psfb2wyiz1hvcycvh4cqhb3ab37lm3rcavvs")))) + "1ws5gds453xgfili87r35rz1wn2i7jbqissq98csbiddpkgls8sx")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) - ("r-knitr" ,r-knitr) + ("r-clipr" ,r-clipr) + ("r-fs" ,r-fs) + ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) - ("r-whisker" ,r-whisker))) + ("r-whisker" ,r-whisker) + ("r-withr" ,r-withr))) (home-page "https://github.com/tidyverse/reprex") (synopsis "Prepare reproducible R code examples for sharing") (description @@ -171,17 +202,18 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "2.0.4") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1053qqq632z94pqq2v5dynjpgyv1b1c8zvidmcllw7zn8zha8gqf")))) + "1rxbxy6kn7dj90z9hpppr9cnpvnxzknba2dwrdp0lrk5dh462qz3")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) + `(("r-base64enc" ,r-base64enc) + ("r-r6" ,r-r6) ("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") @@ -293,14 +325,14 @@ 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) @@ -369,14 +401,14 @@ colors are provided.") (define-public r-glue (package (name "r-glue") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 - "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr")))) + "1vhw5497lpfr4m8lcx9bs0fgdp4ax0sycrk6n8yksp33qd25m7kq")))) (build-system r-build-system) (home-page "https://github.com/tidyverse/glue") (synopsis "Interpreted string literals") @@ -430,14 +462,14 @@ error stream.") (define-public r-pls (package (name "r-pls") - (version "2.6-0") + (version "2.7-0") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 (base32 - "15j59p5x0rkdrk7iqzkipsy50rsyjl31w8zxc4w3v1j5gzxhi1rx")))) + "0xaqqgmdvfh7g7v1m4bcwjqzph68b9cq3bn4kjisfsadl54i5p2x")))) (build-system r-build-system) (home-page "http://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") @@ -465,13 +497,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.1.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1zm9qkyvy1fvcjvmgw51iqw8x1xzkpy7rx7xnchwfj0xpzal0ljx")))) + (base32 "1zxylcb0nr4qb5v6j199mc2pfgf2bpf00jrw47jajmv59qb0fwmx")))) (build-system r-build-system) (home-page "http://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -480,17 +512,75 @@ print, summary, plot, update, etc. processes. Most of its code is based on the @code{psutil} Python package.") (license license:bsd-3))) +(define-public r-pkgbuild + (package + (name "r-pkgbuild") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pkgbuild" version)) + (sha256 + (base32 + "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))) + (home-page "https://github.com/r-pkgs/pkgbuild") + (synopsis "Find tools needed to build R packages") + (description + "This package provides functions used to build R packages. It locates +compilers needed to build R packages on various platforms and ensures the PATH +is configured appropriately so R can use them.") + (license license:gpl3))) + +(define-public r-pkgload + (package + (name "r-pkgload") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pkgload" version)) + (sha256 + (base32 + "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii")))) + (build-system r-build-system) + (propagated-inputs + `(("r-desc" ,r-desc) + ("r-pkgbuild" ,r-pkgbuild) + ("r-rlang" ,r-rlang) + ("r-rprojroot" ,r-rprojroot) + ("r-rstudioapi" ,r-rstudioapi) + ("r-withr" ,r-withr))) + (home-page "https://github.com/r-lib/pkgload") + (synopsis "Simulate package installation and attach") + (description + "This package simulates the process of installing a package and then +attaching it. This is a key part of the @code{devtools} package as it allows +you to rapidly iterate while developing a package.") + (license license:gpl3))) + (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.18") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "006kpg2ph109rh1l13lqk26pp4as4fvl5661vrcczjygacgd1v7w")))) + (base32 "1hlbw4k79q9ich4w27b01gsvwrsnrflii8zjlcmgfzm1vpq8ndxp")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") (description @@ -709,14 +799,14 @@ 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) @@ -808,14 +898,14 @@ in main memory.") (define-public r-ffbase (package (name "r-ffbase") - (version "0.12.3") + (version "0.12.7") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 - "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5")))) + "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit) @@ -853,14 +943,14 @@ 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) @@ -1267,17 +1357,18 @@ 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") @@ -1502,14 +1593,14 @@ the Kaplan-Meier and Aalen-Johansen methods.") (define-public r-dimred (package (name "r-dimred") - (version "0.1.0") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 - "0fasca5fsbrxdwv30hch7vb9snb844l7l8p5fjf239dq45xfy37v")))) + "0ssy2qriiy6zdawriqcbl67qiq68ipml3frq7aqlq70r2fqyyw48")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs `(("r-drr" ,r-drr))) @@ -1545,14 +1636,14 @@ 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))) @@ -1678,14 +1769,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-6") + (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq")))) + "01xcg3c121ndfpz9dirqxszknh4yb1p222p7f1wbwwhdrg1i27cw")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -1705,14 +1796,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "1.8.4") + (version "1.8.10") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf")))) + "0n3frgzsfmnan6cp3yyq5h6c28v5pd7q5a42pp6byaa7n7d1v478")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -1739,22 +1830,23 @@ created using basic graphics.") (define-public r-broom (package (name "r-broom") - (version "0.4.5") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1mrrqqw1bmjf2v88ziqwb5y86g29h0a3rsx2jpw0hrzrzb8i5kcb")))) + "1r3831vq0fd5sh5841xr844sghg88z7ws91hg4jgnzbbkxfjp4ag")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) + `(("r-backports" ,r-backports) + ("r-dplyr" ,r-dplyr) ("r-nlme" ,r-nlme) - ("r-plyr" ,r-plyr) - ("r-psych" ,r-psych) + ("r-purrr" ,r-purrr) ("r-reshape2" ,r-reshape2) ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") @@ -1772,14 +1864,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "1vqh3pxs4n1azhnd1lzg91vasya6g323kllhbrw177j7kdxqyimy")))) + "0bwijw4427v2k5z3qci2kyr5dyzql8b3lvf88rwy16p741jckjsn")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -1903,20 +1995,73 @@ can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.") (license license:gpl3+))) +(define-public r-ucminf + (package + (name "r-ucminf") + (version "1.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ucminf" version)) + (sha256 + (base32 + "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/ucminf/") + (synopsis "General-purpose unconstrained non-linear optimization") + (description + "This package provides an implementation of an algorithm for +general-purpose unconstrained non-linear optimization. The algorithm is of +quasi-Newton type with BFGS updating of the inverse Hessian and soft line +search with a trust region type monitoring of the input to the line search +algorithm. The interface of @code{ucminf} is designed for easy interchange +with the package @code{optim}.") + (license license:gpl2+))) + +(define-public r-ordinal + (package + (name "r-ordinal") + (version "2018.8-25") + (source + (origin + (method url-fetch) + (uri (cran-uri "ordinal" version)) + (sha256 + (base32 + "03cv9hcrw8j3lhamzhz8sk2p3ns4cw9z41x49h301k2b3pajv43h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-numderiv" ,r-numderiv) + ("r-ucminf" ,r-ucminf))) + (home-page "https://github.com/runehaubo/ordinal") + (synopsis "Regression models for ordinal data") + (description + "This package provides an implementation of cumulative link (mixed) +models also known as ordered regression models, proportional odds models, +proportional hazards models for grouped survival times and ordered models. +Estimation is via maximum likelihood and mixed models are fitted with the +Laplace approximation and adaptive Gauss-Hermite quadrature.") + (license license:gpl2+))) + (define-public r-jomo (package (name "r-jomo") - (version "2.6-3") + (version "2.6-5") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "14s8q0j5zgl1g1pfxg3a4y1jzvs0wl61ir4992wsj7safskj7zvi")))) + "109q5m69clrvvialxdxznd0wdb54ajhx84nj8slx8bf909a427mj")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-ordinal" ,r-ordinal) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/jomo/") (synopsis "Multilevel Joint Modelling Multiple Imputation") @@ -1932,14 +2077,14 @@ impute compatibly with the substantive model.") (define-public r-pan (package (name "r-pan") - (version "1.4") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 - "1p3nigmhrnlch86g89hn7l0wvkifx3k9n59g0psi95yck43kza76")))) + "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/pan/") @@ -1977,14 +2122,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.1.0") + (version "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0xpn215yfzib4hw09cwilnyg9zbvq460njavfvm84mvgwbm25byi")))) + "1p0ipbqk5aqdi7iikw3qrjyvdi9sdhpnw1h5mwakwvv0yl0pzbyx")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -2092,14 +2237,14 @@ 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/") @@ -2182,17 +2327,16 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.10-2") + (version "0.11-2") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "1i11fczks4lh8rpi6xbm9bm7f3jpcp6xw03kv178g3n3361qhmc1")))) + "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) - (native-inputs `(("gfortran" ,gfortran))) (home-page "https://github.com/joshuaulrich/xts") (synopsis "Extensible time series") (description @@ -2368,14 +2512,14 @@ 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) @@ -2415,14 +2559,14 @@ 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) @@ -2570,20 +2714,19 @@ 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 @@ -2630,14 +2773,14 @@ 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") @@ -2669,18 +2812,19 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.2.3") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1rzhssprqgam1nq3s0f5rzxhxsq02azcghvxf6k8kmsmddf1n7f8")))) + "1q6arybmfqxhp5zqj1fri5pb8v7ywcv7bmgf81rrmgl892p4bn5f")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) + ("r-fansi" ,r-fansi) ("r-rlang" ,r-rlang) ("r-utf8" ,r-utf8))) (home-page "https://github.com/r-lib/pillar") @@ -2713,14 +2857,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.6") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "16y9dldaff2kx1fkm92p7zlph0dcrdmlmavpdgf5y9jbhmc8g83f")))) + "08w5hyq3ysh631d5whgcfv1bb007cdc0bjhb83vwmhazs6rgvyjy")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -2737,17 +2881,18 @@ automatically.") (define-public r-metap (package (name "r-metap") - (version "0.9") + (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 - "03vg0mb6q7j2z0pkxykbak0hcp6dcak7zxs1lw9hswz9kqrq5jhz")))) + "18rzvqfzyk8fn54gjvy2qd21nk9w69j7ihww477ma3f3ab6i982h")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + `(("r-lattice" ,r-lattice) + ("r-rdpack" ,r-rdpack))) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description @@ -2781,14 +2926,14 @@ supports arbitrary vertex/edge/graph attributes.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.1.2") + (version "4.1.4") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "0h3g687214rlycca0fjrpy1lqbqsrginxqhmhl2mb2jinqqxcfgd")))) + "14dydm4c4dzc4v6ldxpn04q551nczzfablwibrd8lzgja8x9ksic")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) @@ -2827,14 +2972,14 @@ 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 @@ -2934,6 +3079,26 @@ Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.") (license license:gpl2))) +(define-public r-aggregation + (package + (name "r-aggregation") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "aggregation" version)) + (sha256 + (base32 + "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/aggregation/") + (synopsis "Methods for p-value aggregation") + (description + "This package contains functionality for performing the following methods +of p-value aggregation: Fisher's method, the Lancaster method (weighted +Fisher's method), and Sidak correction.") + (license license:gpl3))) + (define-public r-quantmod (package (name "r-quantmod") @@ -3010,21 +3175,20 @@ University Press, 2000.") (define-public r-tsa (package (name "r-tsa") - (version "1.01") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 - "0cm97hwxm6vfgy9mc3kgwq6dnmn86p8a4avnfjbai048qnwrn6hx")))) + "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q")))) (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs `(("r-leaps" ,r-leaps) ("r-locfit" ,r-locfit) - ("r-mgcv" ,r-mgcv) - ("r-tseries" ,r-tseries))) + ("r-mgcv" ,r-mgcv))) (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description @@ -3036,14 +3200,14 @@ 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 @@ -3106,14 +3270,14 @@ 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))) @@ -3162,14 +3326,14 @@ 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))) @@ -3227,14 +3391,14 @@ 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) @@ -3277,14 +3441,14 @@ exponentiation.") (define-public r-heatmaply (package (name "r-heatmaply") - (version "0.14.1") + (version "0.15.2") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 - "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc")))) + "0h8s5djzj4mrmaswlcaap6jbwxrkbzc43bbqik3qf8vrqz335w04")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -3316,6 +3480,36 @@ dendrograms.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) +(define-public r-h5 + (package + (name "r-h5") + (version "0.9.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "h5" version)) + (sha256 + (base32 + "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib) + ("hdf5" ,hdf5))) + (native-inputs + `(("which" ,which))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/mannau/h5") + (synopsis "Interface to the HDF5 Library") + (description + "This package provides an S4 interface to the HDF5 library supporting +fast storage and retrieval of R-objects like vectors, matrices and arrays to +binary files in a language independent format. The HDF5 format can therefore +be used as an alternative to R's save/load mechanism. Since h5 is able to +access only subsets of stored data it can also handle data sets which do not +fit into memory.") + (license license:bsd-2))) + (define-public r-cgdsr (package (name "r-cgdsr") @@ -3366,14 +3560,14 @@ 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 @@ -3389,14 +3583,14 @@ 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 @@ -3430,7 +3624,9 @@ 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))) @@ -3633,14 +3829,14 @@ multivariate plot methods.") (define-public r-fnn (package (name "r-fnn") - (version "1.1") + (version "1.1.2.1") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 - "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj")))) + "1n61jrcmakqif8f827x4qnlhm2jqpj5fgjj65c4p0kdd8lzw8pqp")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") @@ -3925,14 +4121,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "0.9-2") + (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "075lmb3b62171cw2dg8fv1vwmvfzg39r1ji7jwb8s5k9dz88ry1v")))) + "1753kgyc4kmbb5h6knz5wgvvvj8v77kzm8lz0kwz05m5k3spa24k")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -3953,14 +4149,14 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "0.7.3") + (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "04j2phymxgkk4hv9pfa5w3s98w5d7fvm11blrdhxmray4n618msw")))) + "0xhwn37makzm85zb6w5acc7svzibxcnz69rks0kxw22vapkxwz1i")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -4047,33 +4243,6 @@ to the cluster management tool @code{sfCluster}, but can also used without it.") (license license:gpl2+))) -(define-public r-codedepends - (package - (name "r-codedepends") - (version "0.5-3") - (source - (origin - (method url-fetch) - (uri (cran-uri "CodeDepends" version)) - (sha256 - (base32 - "03p82s0abca2jimzqvxdzykfzca7c7fhm5xsjxybcksr4gggr5sc")))) - (properties `((upstream-name . "CodeDepends"))) - (build-system r-build-system) - (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-xml" ,r-xml))) - (home-page "http://cran.r-project.org/web/packages/CodeDepends") - (synopsis "Analysis of R code for reproducible research and code comprehension") - (description - "This package provides tools for analyzing R expressions or blocks of -code and determining the dependencies between them. It focuses on R scripts, -but can be used on the bodies of functions. There are many facilities -including the ability to summarize or get a high-level view of code, -determining dependencies between variables, code improvement suggestions.") - ;; Any version of the GPL - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-rappdirs (package (name "r-rappdirs") @@ -4129,14 +4298,14 @@ 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) @@ -4149,7 +4318,8 @@ 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 @@ -4163,14 +4333,14 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.8") + (version "1.10") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0zwb4ikf021nw7axdn7qlr6bq4xkph3anfy314idkspy1iil4nmr")))) + "0bz3lxbisjwn6cv23090zivpy0bxcncr82g5qja13l37i8xnvqsq")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs @@ -4280,14 +4450,14 @@ and adds the annotation to the plot.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.1.7") + (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "110ny8p41kmbz0a5rl0mv9cqpjkx6yr3ybflp1r0fmcvhwv7cr3i")))) + "0rkpcjb1x7lvhj68aam5airbi534jqyiq12x5xk40a25iifhghq6")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -4296,8 +4466,10 @@ and adds the annotation to the plot.") ("r-ggrepel" ,r-ggrepel) ("r-ggsci" ,r-ggsci) ("r-ggsignif" ,r-ggsignif) + ("r-glue" ,r-glue) ("r-gridextra" ,r-gridextra) ("r-magrittr" ,r-magrittr) + ("r-polynom" ,r-polynom) ("r-purrr" ,r-purrr) ("r-scales" ,r-scales) ("r-tidyr" ,r-tidyr))) @@ -4424,6 +4596,27 @@ packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.") (license license:gpl2))) +(define-public r-fansi + (package + (name "r-fansi") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fansi" version)) + (sha256 + (base32 + "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/brodieG/fansi") + (synopsis "ANSI control sequence aware string functions") + (description + "This package provides counterparts to R string manipulation functions +that account for the effects of ANSI text formatting control sequences.") + (license license:gpl2+))) + (define-public r-nbclust (package (name "r-nbclust") @@ -4448,14 +4641,14 @@ 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) @@ -4495,6 +4688,432 @@ patterned after functions in the Python @code{itertools} module, and others patterned after functions in the snow package.") (license license:gpl2))) +(define-public r-polynom + (package + (name "r-polynom") + (version "1.3-9") + (source + (origin + (method url-fetch) + (uri (cran-uri "polynom" version)) + (sha256 + (base32 + "1s4xxv5rvpigawknvq27v9vzvs83phfsj5h8mim2lmf5bj950nnk")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/polynom/") + (synopsis "Functions for univariate polynomial manipulations") + (description + "This package provides a collection of functions to implement a class for +univariate polynomial manipulations.") + (license license:gpl2))) + +(define-public r-gbrd + (package + (name "r-gbrd") + (version "0.4-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "gbRd" version)) + (sha256 + (base32 + "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82")))) + (properties `((upstream-name . "gbRd"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/gbRd/") + (synopsis "Utilities for processing Rd objects and files") + (description + "This package provides utilities for processing Rd objects and files. +Extract argument descriptions and other parts of the help pages of +functions.") + (license license:gpl2+))) + +(define-public r-rjags + (package + (name "r-rjags") + (version "4-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "rjags" version)) + (sha256 + (base32 + "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-coda" ,r-coda))) + (inputs + `(("jags" ,jags))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://mcmc-jags.sourceforge.net") + (synopsis "Bayesian graphical models using MCMC") + (description + "This package provides an R interface to the JAGS MCMC library. JAGS is +Just Another Gibbs Sampler. It is a program for analysis of Bayesian +hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") + (license license:gpl2))) + +(define-public r-rdpack + (package + (name "r-rdpack") + (version "0.10-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rdpack" version)) + (sha256 + (base32 + "0bbjnw88h54v40hzim00i8yd3p4rk9i84zfdmgcbnylscwvsf0av")))) + (properties `((upstream-name . "Rdpack"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bibtex" ,r-bibtex) + ("r-gbrd" ,r-gbrd))) + (home-page "https://github.com/GeoBosh/Rdpack") + (synopsis "Update and manipulate Rd documentation objects") + (description + "This package provides functions for manipulation of R documentation +objects, including functions @code{reprompt()} and @code{ereprompt()} for +updating Rd documentation for functions, methods and classes; it also includes +Rd macros for citations and import of references from bibtex files for use in +Rd files and roxygen2 comments, as well as many functions for manipulation of +references and Rd files.") + (license license:gpl2+))) + +(define-public r-officer + (package + (name "r-officer") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "officer" version)) + (sha256 + (base32 + "14b6ii9h3fi5g8ja929mfhxps9r7x78flqjdy437y9aygkhmiz2i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-magrittr" ,r-magrittr) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-uuid" ,r-uuid) + ("r-xml2" ,r-xml2) + ("r-zip" ,r-zip))) + (home-page "https://davidgohel.github.io/officer") + (synopsis "Manipulation of Word and PowerPoint documents") + (description + "This package provides tools to access and manipulate Word and PowerPoint +documents from R. The package focuses on tabular and graphical reporting from +R; it also provides two functions that let users get document content into +data objects. A set of functions lets add and remove images, tables and +paragraphs of text in new or existing documents. When working with PowerPoint +presentations, slides can be added or removed; shapes inside slides can also +be added or removed. When working with Word documents, a cursor can be used +to help insert or delete content at a specific location in the document.") + (license license:gpl3))) + +(define-public r-abn + (package + (name "r-abn") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "abn" version)) + (sha256 + (base32 + "00k0razgdb5y5f62622fm7rxkcxrxg470nyyb02dvpfp60254kvs")))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-nnet" ,r-nnet) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rjags" ,r-rjags))) + (home-page "http://www.r-bayesian-networks.org") + (synopsis "Modelling multivariate data with additive bayesian networks") + (description + "Bayesian network analysis is a form of probabilistic graphical models +which derives from empirical data a directed acyclic graph, DAG, describing +the dependency structure between random variables. An additive Bayesian +network model consists of a form of a DAG where each node comprises a +@dfn{generalized linear model} (GLM). Additive Bayesian network models are +equivalent to Bayesian multivariate regression using graphical modelling, they +generalises the usual multivariable regression, GLM, to multiple dependent +variables. This package provides routines to help determine optimal Bayesian +network models for a given data set, where these models are used to identify +statistical dependencies in messy, complex data.") + (license license:gpl2+))) + +(define-public r-acd + (package + (name "r-acd") + (version "1.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACD" version)) + (sha256 + (base32 + "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6")))) + (properties `((upstream-name . "ACD"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ACD/") + (synopsis "Categorical data analysis with complete or missing responses") + (description + "This package provides tools for categorical data analysis with complete +or missing responses.") + (license license:gpl2+))) + +(define-public r-acdm + (package + (name "r-acdm") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACDm" version)) + (sha256 + (base32 + "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil")))) + (properties `((upstream-name . "ACDm"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-plyr" ,r-plyr) + ("r-rsolnp" ,r-rsolnp) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/ACDm/") + (synopsis "Tools for Autoregressive Conditional Duration Models") + (description + "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle +and Russell, 1998) models. It creates trade, price or volume durations from +transactions (tic) data, performs diurnal adjustments, fits various ACD models +and tests them.") + (license license:gpl2+))) + +(define-public r-overlap + (package + (name "r-overlap") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "overlap" version)) + (sha256 + (base32 + "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/overlap/") + (synopsis "Estimates of coefficient of overlapping for animal activity patterns") + (description + "This package provides functions to fit kernel density functions to data +on temporal activity patterns of animals; estimate coefficients of overlapping +of densities for two species; and calculate bootstrap estimates of confidence +intervals.") + (license license:gpl3+))) + +(define-public r-snakecase + (package + (name "r-snakecase") + (version "0.9.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "snakecase" version)) + (sha256 + (base32 + "1g6xai53dl24ws0mwhqrkcv583ziaq505cv3z8v5dhjgy98kilyj")))) + (build-system r-build-system) + (propagated-inputs + `(("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/Tazinho/snakecase") + (synopsis "Convert strings into any case") + (description + "This package provides a consistent, flexible and easy to use tool to +parse and convert strings into cases like snake or camel among others.") + (license license:gpl3))) + +(define-public r-prediction + (package + (name "r-prediction") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "prediction" version)) + (sha256 + (base32 + "19d7312f5lkqfglfvlgssnvyw7gl161s0xradcry44r1i6qp05j1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://github.com/leeper/prediction") + (synopsis "Tidy, type-safe prediction methods") + (description + "This package provides the @code{prediction()} function, a type-safe +alternative to @code{predict()} that always returns a data frame. The package +currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"}) +from the @code{stats} package, as well as numerous other model classes from +other add-on packages.") + (license license:expat))) + +(define-public r-sjlabelled + (package + (name "r-sjlabelled") + (version "1.0.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "sjlabelled" version)) + (sha256 + (base32 + "0ayfzhm9bwjfaarq5z0gvn9kapjwj3532azgin97nr5fnjdhvgaw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-haven" ,r-haven) + ("r-magrittr" ,r-magrittr) + ("r-prediction" ,r-prediction) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-snakecase" ,r-snakecase) + ("r-tibble" ,r-tibble) + ("r-tidyselect" ,r-tidyselect))) + (home-page "https://github.com/strengejacke/sjlabelled") + (synopsis "Labelled data utility functions") + (description + "This package provides a collection of functions dealing with labelled +data, like reading and writing data between R and other statistical software +packages. This includes easy ways to get, set or change value and variable +label attributes, to convert labelled vectors into factors or numeric (and +vice versa), or to deal with multiple declared missing values.") + (license license:gpl3))) + +(define-public r-sjmisc + (package + (name "r-sjmisc") + (version "2.7.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "sjmisc" version)) + (sha256 + (base32 + "1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-crayon" ,r-crayon) + ("r-dplyr" ,r-dplyr) + ("r-haven" ,r-haven) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-sjlabelled" ,r-sjlabelled) + ("r-stringdist" ,r-stringdist) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/strengejacke/sjmisc") + (synopsis "Data and variable transformation functions") + (description + "This package is a collection of miscellaneous utility functions, +supporting data transformation tasks like recoding, dichotomizing or grouping +variables, setting and replacing missing values. The data transformation +functions also support labelled data, and all integrate seamlessly into a +tidyverse workflow.") + (license license:gpl3))) + +(define-public r-nortest + (package + (name "r-nortest") + (version "1.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "nortest" version)) + (sha256 + (base32 + "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/nortest/") + (synopsis "Tests for normality") + (description + "This package provides five omnibus tests for testing the composite +hypothesis of normality.") + (license license:gpl2+))) + +(define-public r-moonbook + (package + (name "r-moonbook") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "moonBook" version)) + (sha256 + (base32 + "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6")))) + (properties `((upstream-name . "moonBook"))) + (build-system r-build-system) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-nortest" ,r-nortest) + ("r-purrr" ,r-purrr) + ("r-sjmisc" ,r-sjmisc) + ("r-stringr" ,r-stringr) + ("r-survival" ,r-survival))) + (home-page "https://github.com/cardiomoon/moonBook") + (synopsis "Functions and datasets for the book by Keon-Woong Moon") + (description + "This package provides several analysis-related functions for the book +entitled \"R statistics and graph for medical articles\" (written in Korean), +version 1, by Keon-Woong Moon with Korean demographic data with several plot +functions.") + (license license:gpl2))) + +(define-public r-flextable + (package + (name "r-flextable") + (version "0.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "flextable" version)) + (sha256 + (base32 + "0fa42dvf0wyl91w4v0rywm3xgw9n03cfyl28ficrv8iabz4k4382")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdtools" ,r-gdtools) + ("r-htmltools" ,r-htmltools) + ("r-knitr" ,r-knitr) + ("r-officer" ,r-officer) + ("r-r6" ,r-r6) + ("r-rmarkdown" ,r-rmarkdown) + ("r-stringr" ,r-stringr) + ("r-xml2" ,r-xml2))) + (home-page "https://davidgohel.github.io/flextable") + (synopsis "Functions for tabular reporting") + (description + "This package provides tools to create pretty tables for HTML documents +and other formats. Functions are provided to let users create tables, modify +and format their content. It extends the @code{officer} package and can be +used within R markdown documents when rendering to HTML and to Word +documents.") + (license license:gpl3))) + (define-public r-writexl (package (name "r-writexl") @@ -4688,14 +5307,14 @@ Group (Non-)Overlap considerations.") (define-public r-doby (package (name "r-doby") - (version "4.6-1") + (version "4.6-2") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "1y02awzid23bxz8hx6j8pxd6i7jaq8pdw3k60rag8y6m69incrw5")))) + "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -4792,14 +5411,14 @@ 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 @@ -4944,3 +5563,2194 @@ developers to generate user interfaces easy to maintain.") models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward.") (license license:gpl2+))) + +(define-public r-infotheo + (package + (name "r-infotheo") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "infotheo" version)) + (sha256 + (base32 + "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv")))) + (build-system r-build-system) + (home-page "http://homepage.meyerp.com/software") + (synopsis "Information-theoretic measures") + (description + "This package implements various measures of information theory based on +several entropy estimators.") + (license license:gpl3+))) + +(define-public r-abcoptim + (package + (name "r-abcoptim") + (version "0.15.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABCoptim" version)) + (sha256 + (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) + (properties `((upstream-name . "ABCoptim"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/gvegayon/ABCoptim/") + (synopsis "Optimization of Artificial Bee Colony algorithm") + (description + "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis +Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as +simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) +algorithms, and uses only common control parameters such as colony size and +maximum cycle number. The @code{r-abcoptim} implements the Artificial bee +colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. + This version is a work-in-progress and is written in R code.") + (license license:expat))) + +(define-public r-abcp2 + (package + (name "r-abcp2") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABCp2" version)) + (sha256 + (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) + (properties `((upstream-name . "ABCp2"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ABCp2/") + (synopsis "Approximate Bayesian Computational Model for Estimating P2") + (description + "This package tests the goodness of fit of a distribution of offspring to the Normal, +Poisson, and Gamma distribution and estimates the proportional paternity of the +second male (P2) based on the best fit distribution.") + (license license:gpl2))) + +(define-public r-abcrf + (package + (name "r-abcrf") + (version "1.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcrf" version)) + (sha256 + (base32 "06vy3inikrr9hv36q4djhrgzi9zizdfnhz17wpra8kadmr7qj441")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-ranger" ,r-ranger) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-readr" ,r-readr) + ("r-stringr" ,r-stringr))) + (home-page "https://cran.r-project.org/web/packages/abcrf/") + (synopsis "Approximate bayesian computation via random forests") + (description + "This package performs approximate bayesian computation (ABC) model choice and +parameter inference via random forests. This machine learning tool named random +forests (RF) can conduct selection among the highly complex models covered by +ABC algorithms.") + (license license:gpl2+))) + +(define-public r-abctools + (package + (name "r-abctools") + (version "1.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "abctools" version)) + (sha256 + (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abc" ,r-abc) + ("r-abind" ,r-abind) + ("r-hmisc" ,r-hmisc) + ("r-plyr" ,r-plyr))) + (home-page "https://github.com/dennisprangle/abctools/") + (synopsis "Tools for ABC analyses") + (description + "This @code{r-abctools} package provides tools for approximate Bayesian computation +including summary statistic selection and assessing coverage. This includes +recent dimension reduction algorithms to tune the choice of summary statistics, +and coverage methods to tune the choice of threshold.") + (license license:gpl2+))) + +(define-public r-ggstance + (package + (name "r-ggstance") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggstance" version)) + (sha256 + (base32 "0v7f3xdaaridw6d4jvnsfwxmpjrasvx5vl555wsrn50aah17fkvh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-plyr" ,r-plyr) + ("r-rlang" ,r-rlang) + ("r-withr" ,r-withr))) + (home-page "https://cran.r-project.org/web/packages/ggstance/") + (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") + (description + "This package is a @code{r-ggplot2} extension that provides flipped components: +@enumerate +@item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms; +@item vertical versions of @code{r-ggplot2} positions. +@end enumerate") + (license license:gpl3))) + +(define-public r-mosaiccore + (package + (name "r-mosaiccore") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mosaicCore" version)) + (sha256 + (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z")))) + (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))) + (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") + (synopsis "Common utilities for mosaic family packages") + (description + "Common utilities used in other Mosaic family packages are collected here.") + (license license:gpl2+))) + +(define-public r-ggformula + (package + (name "r-ggformula") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggformula" version)) + (sha256 + (base32 "1pmpdfjfbrc6kcpq70cr1kbj2qy711hw940g2aiis6l443z706kh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-ggstance" ,r-ggstance) + ("r-magrittr" ,r-magrittr) + ("r-mosaiccore" ,r-mosaiccore) + ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/ProjectMOSAIC/ggformula/") + (synopsis "Formula interface for the @code{r-ggplot2}") + (description + "The @code{r-ggformula} introduces a family of graphics functions, gf_point(), +gf_density(), and so on, bring the formula interface to ggplot(). This captures +and extends the excellent simplicity of the lattice-graphics formula interface, +while providing the intuitive capabilities of @code{r-ggplot2}.") + (license license:expat))) + +(define-public r-mosaicdata + (package + (name "r-mosaicdata") + (version "0.17.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mosaicData" version)) + (sha256 + (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9")))) + (properties `((upstream-name . "mosaicData"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/mosaicData/") + (synopsis "Data sets for project Mosaic") + (description + "This package provides data sets from project Mosaic @url{http://mosaic-web.org} +used to teach mathematics, statistics, computation and modeling.") + (license license:gpl2+))) + +(define-public r-mosaic + (package + (name "r-mosaic") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mosaic" version)) + (sha256 + (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-ggdendro" ,r-ggdendro) + ("r-ggformula" ,r-ggformula) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-glue" ,r-glue) + ("r-gridextra" ,r-gridextra) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-lazyeval" ,r-lazyeval) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mosaiccore" ,r-mosaiccore) + ("r-mosaicdata" ,r-mosaicdata) + ("r-readr" ,r-readr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/ProjectMOSAIC/mosaic/") + (synopsis "Mathematics, statistics, and computation teaching utilities") + (description + "This package contain data sets and utilities from +@url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics, +statistics, computation and modeling. Project MOSAIC is a community of +educators working to tie together aspects of quantitative work that students +in science, technology, engineering and mathematics will need in their +professional lives, but which are usually taught in isolation, if at all.") + (license license:gpl2+))) + +(define-public r-abd + (package + (name "r-abd") + (version "0.2-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "abd" version)) + (sha256 + (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-mosaic" ,r-mosaic) + ("r-nlme" ,r-nlme))) + (home-page "https://cran.r-project.org/web/packages/abd/") + (synopsis "Analysis of biological data") + (description + "The @code{r-abd} package contains data sets and sample code for the Analysis of +biological data by Michael Whitlock and Dolph Schluter.") + (license license:gpl2))) + +(define-public r-svgui + (package + (name "r-svgui") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "svGUI" version)) + (sha256 + (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc")))) + (properties `((upstream-name . "svGUI"))) + (build-system r-build-system) + (home-page "https://github.com/SciViews/svGUI/") + (synopsis "Functions for managing GUI clients in R") + (description + "The SciViews @code{svGUI} package eases the management of Graphical User +Interfaces (GUI) in R. It is independent from any particular GUI widgets. It +centralizes info about GUI elements currently used, and it dispatches GUI +calls to the particular toolkits in use in function of the context.") + (license license:gpl2))) + +(define-public r-svdialogs + (package + (name "r-svdialogs") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "svDialogs" version)) + (sha256 + (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97")))) + (properties `((upstream-name . "svDialogs"))) + (build-system r-build-system) + (inputs + `(("yad" ,yad) + ("zenity" ,zenity))) + (propagated-inputs + `(("r-rstudioapi" ,r-rstudioapi) + ("r-svgui" ,r-svgui))) + (home-page "https://github.com/SciViews/svDialogs/") + (synopsis "Portable dialog boxes") + (description + "This package helps to construct standard dialog boxes for your GUI, including +message boxes, input boxes, list, file or directory selection, and others. In +case R cannot display GUI dialog boxes, a simpler command line version of these +interactive elements is also provided as a fallback solution.") + (license license:gpl2))) + +(define-public r-abe + (package + (name "r-abe") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abe" version)) + (sha256 + (base32 + "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/abe/") + (synopsis "Augmented backward elimination") + (description + "This package performs augmented backward elimination and checks the +stability of the obtained model. Augmented backward elimination combines +significance or information based criteria with the change in estimate to +either select the optimal model for prediction purposes or to serve as a tool +to obtain a practically sound, highly interpretable model.") + (license license:gpl2+))) + +(define-public r-abf2 + (package + (name "r-abf2") + (version "0.7-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abf2" version)) + (sha256 + (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/abf2/") + (synopsis "Load gap-free axon @code{r-abf2} files") + (description + "This package loads electrophysiology data from ABF2 files, as created by +Axon Instruments/Molecular Devices software. Only files recorded in gap-free +mode are currently supported.") + (license license:artistic2.0))) + +(define-public r-abhgenotyper + (package + (name "r-abhgenotyper") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABHgenotypeR" version)) + (sha256 + (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l")))) + (properties `((upstream-name . "ABHgenotypeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-reshape2" ,r-reshape2))) + (home-page "https://github.com/StefanReuscher/ABHgenotypeR/") + (synopsis "Visualize and manipulate ABH genotypes") + (description + "The @code{r-abhgenotyper} package provides simple imputation, +error-correction and plotting capacities for genotype data. The package is +supposed to serve as an intermediate but independent analysis tool between the +TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities +not found in either TASSEL or @code{r-qtl} in addition to visualization of +genotypes as \"graphical genotypes\".") + (license license:gpl3))) + +(define-public r-abjutils + (package + (name "r-abjutils") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abjutils" version)) + (sha256 + (base32 "0qrsc4if7aif73qp95lw6b5986c2r0jn7m39123zij8k15vc935b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-devtools" ,r-devtools) + ("r-dplyr" ,r-dplyr) + ("r-glue" ,r-glue) + ("r-httr" ,r-httr) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-progress" ,r-progress) + ("r-purrr" ,r-purrr) + ("r-rstudioapi" ,r-rstudioapi) + ("r-scales" ,r-scales) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/abjur/abjutils/") + (synopsis "Collection of tools for jurimetrical analysis") + (description + "This package implements general purpose tools, such as functions for +sampling and basic manipulation of Brazilian lawsuits identification number. +It also implements functions for text cleaning, such as accentuation +removal.") + (license license:expat))) + +(define-public r-abnormality + (package + (name "r-abnormality") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abnormality" version)) + (sha256 + (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/abnormality/") + (synopsis "Measure a subject's abnormality with respect to a reference population") + (description + "This package contains functions to implement the methodology and +considerations laid out by Marks et al. in the article \"Measuring abnormality +in high dimensional spaces: applications in biomechanical gait analysis\". +Using high-dimensional datasets to measure a subject's overall level of +abnormality as compared to a reference population is often needed in outcomes +research.") + (license license:expat))) + +(define-public r-abodoutlier + (package + (name "r-abodoutlier") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abodOutlier" version)) + (sha256 + (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj")))) + (properties `((upstream-name . "abodOutlier"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster))) + (home-page "https://cran.r-project.org/web/packages/abodOutlier/") + (synopsis "Angle-based outlier detection") + (description + "This package performs angle-based outlier detection on a given data +frame. It offers three methods to process data: +@enumerate +@item full but slow implementation using all the data that has cubic + complexity; +@item a fully randomized method; +@item a method using k-nearest neighbours. +@end enumerate +These algorithms are well suited for high dimensional data outlier +detection.") + (license license:expat))) + +(define-public r-abps + (package + (name "r-abps") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABPS" version)) + (sha256 + (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) + (properties `((upstream-name . "ABPS"))) + (build-system r-build-system) + (propagated-inputs `(("r-kernlab" ,r-kernlab))) + (home-page "https://cran.r-project.org/web/packages/ABPS/") + (synopsis "Abnormal blood profile score to detect blood doping") + (description + "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS). +The ABPS is a part of the Athlete biological passport program of the World +anti-doping agency, which combines several blood parameters into a single +score in order to detect blood doping. The package also contains functions to +calculate other scores used in anti-doping programs, such as the ratio of +hemoglobin to reticulocytes (OFF-score), as well as example data.") + (license license:gpl2+))) + +(define-public r-parmigene + (package + (name "r-parmigene") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "parmigene" version)) + (sha256 + (base32 + "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/parmigene/") + (synopsis "Mutual information estimation for gene network reconstruction") + (description + "This package provides a parallel estimation of the mutual information +based on entropy estimates from k-nearest neighbors distances and algorithms +for the reconstruction of gene regulatory networks.") + (license license:agpl3+))) + +(define-public r-pscl + (package + (name "r-pscl") + (version "1.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pscl" version)) + (sha256 + (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://github.com/atahk/pscl/") + (synopsis "Political science computational laboratory") + (description + "The @code{pscl} is an R package providing classes and methods for: +@enumerate +@item Bayesian analysis of roll call data (item-response models); +@item elementary Bayesian statistics; +@item maximum likelihood estimation of zero-inflated and hurdle models for count +data; +@item utility functions. +@end enumerate") + (license license:gpl2))) + +(define-public r-accelmissing + (package + (name "r-accelmissing") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "accelmissing" version)) + (sha256 + (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mice" ,r-mice) + ("r-pscl" ,r-pscl))) + (home-page "https://cran.r-project.org/web/packages/accelmissing/") + (synopsis "Missing value imputation for accelerometer data") + (description + "This package provides a statistical method to impute the missing values in +accelerometer data. The methodology includes both parametric and +semi-parametric multiple imputations under the zero-inflated Poisson lognormal +model. It also provides multiple functions to preprocess the accelerometer data +previous to the missing data imputation. These include detecting the wearing +and the non-wearing time, selecting valid days and subjects, and creating plots.") + (license license:gpl2+))) + +(define-public r-mhsmm + (package + (name "r-mhsmm") + (version "0.4.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "mhsmm" version)) + (sha256 + (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) + (build-system r-build-system) + (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) + (home-page "https://github.com/jaredo/mhsmm/") + (synopsis "Inference for hidden Markov and semi-Markov models") + (description + "The @code{r-mhsmm} package implements estimation and prediction methods for +hidden Markov and semi-Markov models for multiple observation sequences. Such +techniques are of interest when observed data is thought to be dependent on some +unobserved (or hidden) state. Also, this package is suitable for equidistant +time series data, with multivariate and/or missing data. Allows user defined +emission distributions.") + (license license:gpl2+))) + +(define-public r-nleqslv + (package + (name "r-nleqslv") + (version "3.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "nleqslv" version)) + (sha256 + (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/nleqslv/") + (synopsis "Solve systems of nonlinear equations") + (description + "The @code{r-nleqslv} package solves a system of nonlinear equations using a +Broyden or a Newton method with a choice of global strategies such as line +search and trust region. There are options for using a numerical or user +supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a +singular or ill-conditioned Jacobian.") + (license license:gpl2+))) + +(define-public r-physicalactivity + (package + (name "r-physicalactivity") + (version "0.2-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "PhysicalActivity" version)) + (sha256 + (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln")))) + (properties + `((upstream-name . "PhysicalActivity"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") + (synopsis "Procesing accelerometer data for physical activity measurement") + (description + "This @code{r-physicalactivity} package provides a function @code{wearingMarking} +for classification of monitor wear and nonwear time intervals in accelerometer +data collected to assess physical activity. The package also contains functions +for making plots of accelerometer data and obtaining the summary of various +information including daily monitor wear time and the mean monitor wear time +during valid days. The revised package version 0.2-1 improved the functions +regarding speed, robustness and add better support for time zones and daylight +saving. In addition, several functions were added: +@enumerate +@item the @code{markDelivery} can classify days for ActiGraph delivery by mail; +@item the @code{markPAI} can categorize physical activity intensity level based +on user-defined cut-points of accelerometer counts. +@end enumerate + It also supports importing ActiGraph (AGD) files with @code{readActigraph} and +@code{queryActigraph} functions.") + (license license:gpl3+))) + +(define-public r-acc + (package + (name "r-acc") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "acc" version)) + (sha256 + (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-circlize" ,r-circlize) + ("r-dbi" ,r-dbi) + ("r-ggplot2" ,r-ggplot2) + ("r-iterators" ,r-iterators) + ("r-mhsmm" ,r-mhsmm) + ("r-nleqslv" ,r-nleqslv) + ("r-physicalactivity" ,r-physicalactivity) + ("r-plyr" ,r-plyr) + ("r-r-utils" ,r-r-utils) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rsqlite" ,r-rsqlite) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/acc/") + (synopsis "Exploring accelerometer data") + (description + "This package processes accelerometer data from uni-axial and tri-axial devices +and generates data summaries. Also, includes functions to plot, analyze, and +simulate accelerometer data.") + (license license:gpl2+))) + +(define-public r-rbenchmark + (package + (name "r-rbenchmark") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rbenchmark" version)) + (sha256 + (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rbenchmark/") + (synopsis "Benchmarking routine for R") + (description + "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark, +and is intended to facilitate benchmarking of arbitrary R code. The library +consists of just one function, benchmark, which is a simple wrapper around +system.time. Given a specification of the benchmarking process (counts of +replications, evaluation environment) and an arbitrary number of expressions, +benchmark evaluates each of the expressions in the specified environment, +replicating the evaluation as many times as specified, and returning the results +conveniently wrapped into a data frame.") + (license license:gpl2+))) + +(define-public r-dvmisc + (package + (name "r-dvmisc") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "dvmisc" version)) + (sha256 + (base32 "1dy0yykskwhkql19bhzmbwsgv028afc8jh9yqwbczj6f3vpv31zh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-rbenchmark" ,r-rbenchmark) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/dvmisc/") + (synopsis "Faster computation of common statistics and miscellaneous functions") + (description + "This package implements faster versions of base R functions (e.g. mean, standard +deviation, covariance, weighted mean), mostly written in C++, along with +miscellaneous functions for various purposes (e.g. create the histogram with +fitted probability density function or probability mass function curve, create +the body mass index groups, assess the linearity assumption in logistic +regression).") + (license license:gpl2))) + +(define-public r-accelerometry + (package + (name "r-accelerometry") + (version "3.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "accelerometry" version)) + (sha256 + (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dvmisc" ,r-dvmisc) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/accelerometry/") + (synopsis "Functions for processing accelerometer data") + (description + "This package provides a collection of functions that perform operations on +time-series accelerometer data, such as identify the non-wear time, flag minutes +that are part of an activity bout, and find the maximum 10-minute average count +value. The functions are generally very flexible, allowing for a variety of +algorithms to be implemented.") + (license license:gpl3))) + +(define-public r-absim + (package + (name "r-absim") + (version "0.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "AbSim" version)) + (sha256 + (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) + (properties `((upstream-name . "AbSim"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-powerlaw" ,r-powerlaw))) + (home-page "https://cran.r-project.org/web/packages/AbSim/") + (synopsis "Time resolved simulations of antibody repertoires") + (description + "This package provides simulation methods for the evolution of antibody repertoires. + The heavy and light chain variable region of both human and C57BL/6 mice can +be simulated in a time-dependent fashion. Both single lineages using one set of +V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins +with an initial V-D-J recombination event, starting the first phylogenetic tree. + Upon completion, the main loop of the algorithm begins, with each iteration +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") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Ac3net" version)) + (sha256 + (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) + (properties `((upstream-name . "Ac3net"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://cran.r-project.org/web/packages/Ac3net/") + (synopsis "Inferring directional conservative causal core gene networks") + (description "This package infers directional Conservative causal core +(gene) networks (C3NET). This is a version of the algorithm C3NET with +directional network.") + (license license:gpl3+))) + +(define-public r-aca + (package + (name "r-aca") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACA" version)) + (sha256 + (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) + (properties `((upstream-name . "ACA"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ACA/") + (synopsis "Abrupt change-point or aberration detection in point series") + (description + "This package offers an interactive function for the detection of breakpoints in +series.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-acceptancesampling + (package + (name "r-acceptancesampling") + (version "1.0-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcceptanceSampling" version)) + (sha256 + (base32 "18krmmyn8pn11aqd81kbvka68lnd36mnpdh7p3pz9r4m4vjj007x")))) + (properties + `((upstream-name . "AcceptanceSampling"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") + (synopsis "Creation and evaluation of acceptance sampling plans") + (description + "This @code{r-acceptancesampling} provides functionality for creating and evaluating +acceptance sampling plans. Acceptance sampling is a methodology commonly used +in quality control and improvement. International standards of acceptance +sampling provide sampling plans for specific circumstances. The aim of this +package is to provide an easy-to-use interface to visualize single, double or +multiple sampling plans. In addition, methods have been provided to enable the +user to assess sampling plans against pre-specified levels of performance, as +measured by the probability of acceptance for a given level of quality in the +lot.") + (license license:gpl3+))) + +(define-public r-acclma + (package + (name "r-acclma") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACCLMA" version)) + (sha256 + (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) + (properties `((upstream-name . "ACCLMA"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ACCLMA/") + (synopsis "ACC & LMA graph plotting") + (description + "This package contains a function that imports data from a @acronym{CSV, +Comma-Separated Values} file, or uses manually entered data from the format (x, +y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration +Curve} vs @acronym{LOI, Line of Independence} graph and +@acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main +function is @code{plotLMA} (source file, header) that takes a data set and plots the +appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a +string) was passed, a manual data entry window is opened. The header parameter +indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has +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 "1.7.15") + (source + (origin + (method url-fetch) + (uri (cran-uri "TMB" version)) + (sha256 + (base32 + "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs")))) + (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 "0.17.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "sjstats" version)) + (sha256 + (base32 + "0c7g35vn7r9rylhp0gj1yfslg7jybwrhpqpp7vdcd90xfccih24r")))) + (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 "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggeffects" version)) + (sha256 + (base32 + "070c3fxmzajq2fy816s5pfqdyjlnzkabj97z7fcsva4h5rnqi9d6")))) + (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 "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sessioninfo" version)) + (sha256 + (base32 + "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn")))) + (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 "2.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "remotes" version)) + (sha256 + (base32 + "0rsjxmhwpr51ilsdjfqn06mj8yr2d7nckcn3arv1ljn23qfkpcxa")))) + (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 "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rcmdcheck" version)) + (sha256 + (base32 + "0ys1nd7690mhwzslyzg8fq1wxr28nz8g6av5iykkrshb8lkxg7ly")))) + (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-sessioninfo" ,r-sessioninfo) + ("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 "0.6.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "pander" version)) + (sha256 + (base32 + "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi")))) + (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))) + +(define-public r-weights + (package + (name "r-weights") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "weights" version)) + (sha256 + (base32 + "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdata" ,r-gdata) + ("r-hmisc" ,r-hmisc) + ("r-mice" ,r-mice))) + (home-page + "https://cran.r-project.org/web/packages/weights/") + (synopsis "Weighting and weighted statistics") + (description "This package Provides a variety of functions for producing +simple weighted statistics, such as weighted Pearson's correlations, partial +correlations, Chi-Squared statistics, histograms, and t-tests. Also now +includes some software for quickly recoding survey data and plotting point +estimates from interaction terms in regressions (and multiply imputed +regressions). NOTE: Weighted partial correlation calculations pulled to +address a bug.") + (license license:gpl2+))) + +(define-public r-rcppannoy + (package + (name "r-rcppannoy") + (version "0.0.11") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppAnnoy" version)) + (sha256 + (base32 + "1ik50ancfgcvh03n4jsqwjk8lf056rbgd70q4l4didmvh5kcyjd1")))) + (properties `((upstream-name . "RcppAnnoy"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") + (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") + (description + "Annoy is a small C++ library for Approximate Nearest Neighbors written +for efficient memory usage as well an ability to load from and save to disk. +This package provides an R interface.") + ;; Annoy is released under ASL 2.0, but this wrapper is released under + ;; GPLv2+. + (license (list license:gpl2+ license:asl2.0)))) + +(define-public r-ncdf4 + (package + (name "r-ncdf4") + (version "1.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "ncdf4" version)) + (sha256 + (base32 + "0lwjjis0b83c4l3xvqai4ckzrskd6mychck1iwxcxgjvh0d77mgd")))) + (build-system r-build-system) + (inputs + `(("netcdf" ,netcdf) + ("zlib" ,zlib))) + (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") + (synopsis "R interface to Unidata netCDF format data files") + (description + "This package provides a high-level R interface to data files written +using Unidata's netCDF library (version 4 or earlier), which are binary data +files that are portable across platforms and include metadata information in +addition to the data sets. Using this package, netCDF files can be opened and +data sets read in easily. It is also easy to create new netCDF dimensions, +variables, and files, in either version 3 or 4 format, and manipulate existing +netCDF files.") + (license license:gpl3+))) + +(define-public r-biocmanager + (package + (name "r-biocmanager") + (version "1.30.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "BiocManager" version)) + (sha256 + (base32 + "0kxs76pixk1d2lpvkyrq6nnvv1rqf55ph5f7igkadyyqirf3y2ah")))) + (properties `((upstream-name . "BiocManager"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/BiocManager/") + (synopsis "Access the Bioconductor project package repository") + (description + "This package provides a convenient tool to install and update +Bioconductor packages.") + (license license:artistic2.0))) + +(define-public r-rgl + (package + (name "r-rgl") + (version "0.99.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "rgl" version)) + (sha256 + (base32 + "0q8sg8fr0140ilssqhscaxkjc29w1rpp6f4k50amw3zzs9g58ak9")))) + (build-system r-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("glu" ,glu) + ("libx11" ,libx11) + ("ghc-pandoc" ,ghc-pandoc) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-crosstalk" ,r-crosstalk) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-manipulatewidget" ,r-manipulatewidget) + ("r-shiny" ,r-shiny))) + (home-page "https://r-forge.r-project.org/projects/rgl/") + (synopsis "3D visualization using OpenGL") + (description + "This package provides medium to high level functions for 3D interactive graphics, +including functions modelled on base graphics (@code{plot3d()}, etc.) as well +as functions for constructing representations of geometric +objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to +various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D +image formats, including PNG, Postscript, SVG, PGF.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-multicool + (package + (name "r-multicool") + (version "0.1-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "multicool" version)) + (sha256 + (base32 + "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v")))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/multicool/") + (synopsis "Permutations of multisets in cool-lex order") + (description + "This package provides a set of tools to permute multisets without loops +or hash tables and to generate integer partitions. Cool-lex order is similar +to colexicographical order.") + (license license:gpl2))) + +(define-public r-misc3d + (package + (name "r-misc3d") + (version "0.8-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "misc3d" version)) + (sha256 + (base32 + "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/misc3d/") + (synopsis "Miscellaneous 3D Plots") + (description + "This package provides a collection of miscellaneous 3d plots, including +isosurfaces.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-ks + (package + (name "r-ks") + (version "1.11.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ks" version)) + (sha256 + (base32 + "0z749c3xzpf6n0g7xcfplrhap1di8k7kcfr7vigh95ywnigyhs8d")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fnn" ,r-fnn) + ("r-kernlab" ,r-kernlab) + ("r-kernsmooth" ,r-kernsmooth) + ("r-matrix" ,r-matrix) + ("r-mclust" ,r-mclust) + ("r-mgcv" ,r-mgcv) + ("r-misc3d" ,r-misc3d) + ("r-multicool" ,r-multicool) + ("r-mvtnorm" ,r-mvtnorm))) + (home-page "http://www.mvstat.net/tduong/") + (synopsis "Kernel smoothing") + (description + "This package provides kernel smoothers for univariate and multivariate +data, including density functions, density derivatives, cumulative +distributions, modal clustering, discriminant analysis, and two-sample +hypothesis testing.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-feature + (package + (name "r-feature") + (version "1.2.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "feature" version)) + (sha256 + (base32 + "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ks" ,r-ks) + ("r-misc3d" ,r-misc3d) + ("r-rgl" ,r-rgl))) + (home-page "http://www.mvstat.net/tduong/") + (synopsis "Inferential feature significance for kernel density estimation") + (description + "The feature package contains functions to display and compute kernel +density estimates, significant gradient and significant curvature regions. +Significant gradient and/or curvature regions often correspond to significant +features (e.g. local modes).") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-arm + (package + (name "r-arm") + (version "1.10-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "arm" version)) + (sha256 + (base32 + "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-coda" ,r-coda) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-nlme" ,r-nlme))) + (home-page "https://cran.r-project.org/web/packages/arm/") + (synopsis "Data analysis using regression and multilevel/hierarchical models") + (description + "This package provides functions to accompany A. Gelman and J. Hill, +Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge +University Press, 2007.") + (license license:gpl3+))) + +(define-public r-circular + (package + (name "r-circular") + (version "0.4-93") + (source + (origin + (method url-fetch) + (uri (cran-uri "circular" version)) + (sha256 + (base32 + "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-mvtnorm" ,r-mvtnorm))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/circular/") + (synopsis "Circular statistics") + (description + "This package provides tools for circular statistics, from \"Topics in +circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World +Scientific.") + (license license:gpl2+))) + +(define-public r-activity + (package + (name "r-activity") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "activity" version)) + (sha256 + (base32 + "1lqajgxfps2h6amz1791vp3f52rs9ghmanq1nqfxqd2jmk3idkrx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-circular" ,r-circular) + ("r-overlap" ,r-overlap) + ("r-pbapply" ,r-pbapply))) + (home-page "https://cran.r-project.org/web/packages/activity/") + (synopsis "Animal activity statistics") + (description + "This package provides functions to fit kernel density functions to +animal activity time data; plot activity distributions; quantify overall +levels of activity; statistically compare activity metrics through +bootstrapping; and evaluate variation in linear variables with time (or other +circular variables).") + (license license:gpl3))) + +(define-public r-ouch + (package + (name "r-ouch") + (version "2.11-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ouch" version)) + (sha256 + (base32 + "0xkwwi62vdahlcg3k32zb1nfwsx87zdssk79mvcxgfsw9bw4gahx")))) + (build-system r-build-system) + (propagated-inputs `(("r-subplex" ,r-subplex))) + (home-page "http://kingaa.github.io/ouch/") + (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") + (description + "This package provides tools to fit and compare Ornstein-Uhlenbeck models +for evolution along a phylogenetic tree.") + (license license:gpl2+))) |