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-rw-r--r--gnu/packages/cran.scm1709
1 files changed, 1614 insertions, 95 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index efcc2dccb5..423bb5b54f 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.
;;;
@@ -31,10 +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)
@@ -43,7 +49,8 @@
#: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
@@ -164,19 +171,19 @@ package is a port of the Python package @code{cssselect}.")
(define-public r-reprex
(package
(name "r-reprex")
- (version "0.2.0")
+ (version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "reprex" version))
(sha256
(base32
- "1l44pxjiz3g0jkk3v6rg5jps3llihfiah0qyv40s0bxvxa6gm8v9"))))
+ "1ws5gds453xgfili87r35rz1wn2i7jbqissq98csbiddpkgls8sx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
("r-clipr" ,r-clipr)
- ("r-knitr" ,r-knitr)
+ ("r-fs" ,r-fs)
("r-rlang" ,r-rlang)
("r-rmarkdown" ,r-rmarkdown)
("r-whisker" ,r-whisker)
@@ -318,14 +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)
@@ -490,13 +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")
@@ -508,19 +515,21 @@ processes. Most of its code is based on the @code{psutil} Python package.")
(define-public r-pkgbuild
(package
(name "r-pkgbuild")
- (version "1.0.0")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgbuild" version))
(sha256
(base32
- "10iz8057mixl9j73pq2cbp4ib6dadfsgi3fcsjjm7l3wwb9issd9"))))
+ "1i1rrax7x7r2bplig5cfc50lx85jc4n9a3qmvbdviaj22wr2lghs"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
+ ("r-cli" ,r-cli)
("r-crayon" ,r-crayon)
("r-desc" ,r-desc)
+ ("r-prettyunits" ,r-prettyunits)
("r-r6" ,r-r6)
("r-rprojroot" ,r-rprojroot)
("r-withr" ,r-withr)))
@@ -535,14 +544,14 @@ is configured appropriately so R can use them.")
(define-public r-pkgload
(package
(name "r-pkgload")
- (version "1.0.0")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgload" version))
(sha256
(base32
- "1rjj229nq9fsl4ki4m75ybsavjgpqqhsr1zjzapwicsrxv6212px"))))
+ "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
(build-system r-build-system)
(propagated-inputs
`(("r-desc" ,r-desc)
@@ -562,14 +571,16 @@ you to rapidly iterate while developing a package.")
(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
@@ -788,14 +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)
@@ -887,14 +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)
@@ -932,14 +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)
@@ -1346,17 +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")
@@ -1581,14 +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)))
@@ -1624,14 +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)))
@@ -1757,14 +1769,14 @@ provided.")
(define-public r-ipred
(package
(name "r-ipred")
- (version "0.9-7")
+ (version "0.9-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "ipred" version))
(sha256
(base32
- "0q53cqs46501wsd4cmfsmr78l8nv1hkbamk9m0ns5qy02df5r254"))))
+ "01xcg3c121ndfpz9dirqxszknh4yb1p222p7f1wbwwhdrg1i27cw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)
@@ -1784,14 +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)
@@ -1852,14 +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)
@@ -2037,17 +2049,18 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
(define-public r-jomo
(package
(name "r-jomo")
- (version "2.6-4")
+ (version "2.6-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "jomo" version))
(sha256
(base32
- "05g2rj9g7rgyb22b0gybw042nydyqsqsb31v05hifzavri8ij01x"))))
+ "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/")
@@ -2224,14 +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/")
@@ -2314,14 +2327,14 @@ training models for classification or ranking.")
(define-public r-xts
(package
(name "r-xts")
- (version "0.11-0")
+ (version "0.11-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "xts" version))
(sha256
(base32
- "1v50yn4bsjzdyk7r90isn6dxmpkapillrhpx3gqsshd180vwzqk9"))))
+ "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
(build-system r-build-system)
(propagated-inputs `(("r-zoo" ,r-zoo)))
(home-page "https://github.com/joshuaulrich/xts")
@@ -2499,14 +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)
@@ -2546,14 +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)
@@ -2701,20 +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
@@ -2761,14 +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")
@@ -2845,14 +2857,14 @@ terminals.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.8")
+ (version "0.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "1bgpr5i5399jf9n6pg2mm4aamisbhppg082ad0wv1j4g0rlxf1gy"))))
+ "08w5hyq3ysh631d5whgcfv1bb007cdc0bjhb83vwmhazs6rgvyjy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@@ -2960,14 +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
@@ -3067,6 +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")
@@ -3168,14 +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
@@ -3238,14 +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)))
@@ -3294,14 +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)))
@@ -3359,14 +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)
@@ -3448,6 +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")
@@ -3498,14 +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
@@ -3521,14 +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
@@ -3562,7 +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)))
@@ -4057,14 +4121,14 @@ simple method for converting between file types.")
(define-public r-maptools
(package
(name "r-maptools")
- (version "0.9-3")
+ (version "0.9-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "maptools" version))
(sha256
(base32
- "0hxbv01im9zk1qrwgigpc510w6x0kzdzip4gx2jzfqmmwr8m17r8"))))
+ "1753kgyc4kmbb5h6knz5wgvvvj8v77kzm8lz0kwz05m5k3spa24k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
@@ -4085,14 +4149,14 @@ exchanging spatial objects with other R packages.")
(define-public r-later
(package
(name "r-later")
- (version "0.7.4")
+ (version "0.7.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "later" version))
(sha256
(base32
- "125zc499gj702x2bch95lsfzk2qb4dzv3604x9afym2i3ylrmm64"))))
+ "0xhwn37makzm85zb6w5acc7svzibxcnz69rks0kxw22vapkxwz1i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
@@ -4234,14 +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)
@@ -4254,7 +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
@@ -4385,14 +4450,14 @@ and adds the annotation to the plot.")
(define-public r-ggpubr
(package
(name "r-ggpubr")
- (version "0.1.8")
+ (version "0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggpubr" version))
(sha256
(base32
- "0psl2zndm4wk6nnj1nv305islpxfvfgd87gjh2ph8yqn4mxpnfi1"))))
+ "0rkpcjb1x7lvhj68aam5airbi534jqyiq12x5xk40a25iifhghq6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cowplot" ,r-cowplot)
@@ -4534,14 +4599,14 @@ steps and provides ggplot2-based elegant data visualization.")
(define-public r-fansi
(package
(name "r-fansi")
- (version "0.3.0")
+ (version "0.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "fansi" version))
(sha256
(base32
- "135qj7bcc3mwn0vg55hiiadf66lx6zaxvkicfmfw9x0zr7ah2r6x"))))
+ "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr))) ; for vignettes
@@ -4576,14 +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)
@@ -4663,17 +4728,43 @@ 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 "0.9-0")
+ (version "0.10-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rdpack" version))
(sha256
(base32
- "067w0w6kza0hkzcnx58danl83yfvl9yjacr47mnid2bg856gdd1b"))))
+ "0bbjnw88h54v40hzim00i8yd3p4rk9i84zfdmgcbnylscwvsf0av"))))
(properties `((upstream-name . "Rdpack")))
(build-system r-build-system)
(propagated-inputs
@@ -4725,6 +4816,112 @@ 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")
@@ -4774,14 +4971,14 @@ other add-on packages.")
(define-public r-sjlabelled
(package
(name "r-sjlabelled")
- (version "1.0.13")
+ (version "1.0.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjlabelled" version))
(sha256
(base32
- "0xizj7mrhnbn8kwjgm076si9w68a7lgrx4vj1sbqmv9jx055h8wv"))))
+ "0ayfzhm9bwjfaarq5z0gvn9kapjwj3532azgin97nr5fnjdhvgaw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
@@ -4807,14 +5004,14 @@ vice versa), or to deal with multiple declared missing values.")
(define-public r-sjmisc
(package
(name "r-sjmisc")
- (version "2.7.4")
+ (version "2.7.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjmisc" version))
(sha256
(base32
- "11cy09k1d2y5wwqvafqxr01hzk4x68ji2pqlwj7fnpw27i3ap4q4"))))
+ "1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
@@ -4822,15 +5019,12 @@ vice versa), or to deal with multiple declared missing values.")
("r-dplyr" ,r-dplyr)
("r-haven" ,r-haven)
("r-magrittr" ,r-magrittr)
- ("r-pillar" ,r-pillar)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
("r-sjlabelled" ,r-sjlabelled)
("r-stringdist" ,r-stringdist)
("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-tidyselect" ,r-tidyselect)))
+ ("r-tidyr" ,r-tidyr)))
(home-page "https://github.com/strengejacke/sjmisc")
(synopsis "Data and variable transformation functions")
(description
@@ -4892,14 +5086,14 @@ functions.")
(define-public r-flextable
(package
(name "r-flextable")
- (version "0.4.5")
+ (version "0.4.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "flextable" version))
(sha256
(base32
- "09j2y0z7rkc0w1cl9pp1cpk6fnzzfr6245mxa3ca42z9k2cy2jfl"))))
+ "0fa42dvf0wyl91w4v0rywm3xgw9n03cfyl28ficrv8iabz4k4382"))))
(build-system r-build-system)
(propagated-inputs
`(("r-gdtools" ,r-gdtools)
@@ -5217,14 +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
@@ -5855,13 +6049,13 @@ detection.")
(define-public r-abps
(package
(name "r-abps")
- (version "0.2")
+ (version "0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ABPS" version))
(sha256
- (base32 "1k3f5i34f4w2khkszb4qhwwcpiy7gsfh82vjr6rypwg6rx5rjclq"))))
+ (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
(properties `((upstream-name . "ABPS")))
(build-system r-build-system)
(propagated-inputs `(("r-kernlab" ,r-kernlab)))
@@ -6160,6 +6354,52 @@ representing one simulated time step. Various mutation events are possible at
each time step, contributing to a diverse final repertoire.")
(license license:gpl2)))
+(define-public r-quic
+ (package
+ (name "r-quic")
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "QUIC" version))
+ (sha256
+ (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
+ (properties `((upstream-name . "QUIC")))
+ (build-system r-build-system)
+ (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
+ (synopsis "Regularized sparse inverse covariance matrix estimation")
+ (description
+ "This package implements the regularized Gaussian maximum likelihood
+estimation of the inverse of a covariance matrix. It uses Newton's method and
+coordinate descent to solve the regularized inverse covariance matrix
+estimation problem.")
+ ;; The project home page states that the release is under GPLv3 or later.
+ ;; The CRAN page only says GPL-3.
+ (license license:gpl3+)))
+
+(define-public r-abundant
+ (package
+ (name "r-abundant")
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "abundant" version))
+ (sha256
+ (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-quic" ,r-quic)))
+ (home-page "https://cran.r-project.org/web/packages/abundant/")
+ (synopsis "Abundant regression and high-dimensional principal fitted components")
+ (description
+ "This package provides tools to fit and predict with the high-dimensional
+principal fitted components model. This model is described by Cook, Forzani,
+and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
+ ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
+ ;; GPLv3+ package (QUIC) this likely means GPLv2+.
+ (license license:gpl2+)))
+
(define-public r-ac3net
(package
(name "r-ac3net")
@@ -6256,3 +6496,1282 @@ 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+)))
+
+(define-public r-fmsb
+ (package
+ (name "r-fmsb")
+ (version "0.6.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fmsb" version))
+ (sha256
+ (base32
+ "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
+ (build-system r-build-system)
+ (home-page "http://minato.sip21c.org/msb/")
+ (synopsis "Functions for medical statistics book with demographic data")
+ (description
+ "This package provides several utility functions for the book entitled
+\"Practices of Medical and Health Data Analysis using R\" (Pearson Education
+Japan, 2007) with Japanese demographic data and some demographic analysis
+related functions.")
+ (license license:gpl2+)))
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-19 04:45:28 +0000