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-rw-r--r--gnu/packages/cran.scm3176
1 files changed, 3076 insertions, 100 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ad8c6ebe67..dbc2b4614d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15,7 +15,7 @@
;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
-;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
+;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;;
@@ -73,6 +73,7 @@
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages statistics)
+ #:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
#:use-module (gnu packages xorg))
@@ -729,10 +730,34 @@ objects in HTML format.")
and vice-versa.")
(license license:gpl2+)))
+(define-public r-fastmap
+ (package
+ (name "r-fastmap")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fastmap" version))
+ (sha256
+ (base32
+ "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
+ (properties `((upstream-name . "fastmap")))
+ (build-system r-build-system)
+ (home-page "https://r-lib.github.io/fastmap/")
+ (synopsis "Fast implementation of a key-value store")
+ (description
+ "This package provides a fast implementation of a key-value store.
+Environments are commonly used as key-value stores, but every time a new key
+is used, it is added to R's global symbol table, causing a small amount of
+memory leakage. This can be problematic in cases where many different keys
+are used. Fastmap avoids this memory leak issue by implementing the map using
+data structures in C++.")
+ (license license:expat)))
+
(define-public r-shiny
(package
(name "r-shiny")
- (version "1.2.0")
+ (version "1.4.0")
(source
(origin
(method git-fetch)
@@ -742,7 +767,7 @@ and vice-versa.")
(file-name (git-file-name name version))
(sha256
(base32
- "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
+ "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7"))))
(build-system r-build-system)
(arguments
`(#:modules ((guix build r-build-system)
@@ -771,7 +796,7 @@ and vice-versa.")
"/share/javascript/html5shiv.min.js"))
(replace-file "json2-min.js"
(string-append (assoc-ref inputs "js-json2")
- "/share/javascript/json2.min.js"))
+ "/share/javascript/json2-min.js"))
(replace-file "strftime/strftime-min.js"
(string-append (assoc-ref inputs "js-strftime")
"/share/javascript/strftime.min.js"))
@@ -802,10 +827,15 @@ and vice-versa.")
("shiny.js" .
"shiny.min.js")
("jquery.js" .
- "jquery.min.js")))))
+ "jquery.min.js")
+ ("legacy/jquery.js" .
+ "legacy/jquery.min.js")
+ ("showdown/src/showdown.js" .
+ "showdown/compressed/showdown.js")))))
#t)))))
(propagated-inputs
`(("r-crayon" ,r-crayon)
+ ("r-fastmap" ,r-fastmap)
("r-httpuv" ,r-httpuv)
("r-mime" ,r-mime)
("r-jsonlite" ,r-jsonlite)
@@ -1262,14 +1292,14 @@ coordinates.")
(define-public r-rgooglemaps
(package
(name "r-rgooglemaps")
- (version "1.4.4")
+ (version "1.4.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "RgoogleMaps" version))
(sha256
(base32
- "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
+ "1acf0qc9597apcidjzrpvwhg9ihypr38jigc10jvqn33qbn1i9s7"))))
(properties `((upstream-name . "RgoogleMaps")))
(build-system r-build-system)
(propagated-inputs `(("r-png" ,r-png)))
@@ -1394,13 +1424,13 @@ embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
(define-public r-amap
(package
(name "r-amap")
- (version "0.8-17")
+ (version "0.8-18")
(source (origin
(method url-fetch)
(uri (cran-uri "amap" version))
(sha256
(base32
- "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
+ "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -2331,21 +2361,44 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
;; Any version of the LGPL.
(license license:lgpl3+)))
+(define-public r-bdsmatrix
+ (package
+ (name "r-bdsmatrix")
+ (version "1.3-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bdsmatrix" version))
+ (sha256
+ (base32
+ "17ddvz4gnih7rx0lr1gzk280xyh6x796cf2x794dvplpiiq83skh"))))
+ (properties `((upstream-name . "bdsmatrix")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
+ (synopsis "Routines for block diagonal symmetric matrices")
+ (description
+ "This package provides procedures to work with block diagonal symmetric
+matrices, a special case of sparse matrices.")
+ (license license:lgpl2.0)))
+
(define-public r-bbmle
(package
(name "r-bbmle")
- (version "1.0.20")
+ (version "1.0.22")
(source
(origin
(method url-fetch)
(uri (cran-uri "bbmle" version))
(sha256
(base32
- "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
+ "1idn55w5f3iw4r0ydyww8xyinninw07sxlwfqb565vmdrs87dwl4"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-lattice" ,r-lattice)
+ `(("r-bdsmatrix" ,r-bdsmatrix)
+ ("r-lattice" ,r-lattice)
("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-mvtnorm" ,r-mvtnorm)
("r-numderiv" ,r-numderiv)))
(home-page "https://cran.r-project.org/web/packages/bbmle")
(synopsis "Tools for General Maximum Likelihood Estimation")
@@ -2747,14 +2800,14 @@ dimensioned arrays.")
(define-public r-rmysql
(package
(name "r-rmysql")
- (version "0.10.17")
+ (version "0.10.18")
(source
(origin
(method url-fetch)
(uri (cran-uri "RMySQL" version))
(sha256
(base32
- "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
+ "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4"))))
(properties `((upstream-name . "RMySQL")))
(build-system r-build-system)
(inputs
@@ -2961,14 +3014,14 @@ problems as well as resampling based estimators of prediction error.")
(define-public r-psych
(package
(name "r-psych")
- (version "1.8.12")
+ (version "1.9.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "psych" version))
(sha256
(base32
- "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
+ "13r7fyjsl93m121awnwfhya8a0lw0l2byn60yqdbf9gp3lmb9ny0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
@@ -3015,14 +3068,14 @@ by base R methods related to model fitting.")
(define-public r-broom
(package
(name "r-broom")
- (version "0.5.2")
+ (version "0.5.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "broom" version))
(sha256
(base32
- "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
+ "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
@@ -3050,14 +3103,14 @@ provides a one-row summary of model-level statistics.")
(define-public r-recipes
(package
(name "r-recipes")
- (version "0.1.7")
+ (version "0.1.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "recipes" version))
(sha256
(base32
- "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98"))))
+ "1n32qc2a3n9cykm8dv9qcr77kdhqfsjiqf6kgfk9s0lnpx2zaldm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -3206,14 +3259,14 @@ with the package @code{optim}.")
(define-public r-ordinal
(package
(name "r-ordinal")
- (version "2019.4-25")
+ (version "2019.12-10")
(source
(origin
(method url-fetch)
(uri (cran-uri "ordinal" version))
(sha256
(base32
- "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
+ "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -3306,14 +3359,14 @@ analysis of multiply imputed data sets.")
(define-public r-mice
(package
(name "r-mice")
- (version "3.6.0")
+ (version "3.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mice" version))
(sha256
(base32
- "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
+ "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
@@ -3769,14 +3822,14 @@ rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
(define-public r-argparser
(package
(name "r-argparser")
- (version "0.4")
+ (version "0.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "argparser" version))
(sha256
(base32
- "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
+ "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
(build-system r-build-system)
(home-page "https://bitbucket.org/djhshih/argparser")
(synopsis "Command-line argument parser")
@@ -4017,14 +4070,14 @@ to variables on the left-hand side of the assignment.")
(define-public r-vctrs
(package
(name "r-vctrs")
- (version "0.2.0")
+ (version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "vctrs" version))
(sha256
(base32
- "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
+ "0rlwjfvvhv3s5mj4lqhwlqwddpizyp46i1qbcvw0mzb5q8b0nkz0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
@@ -4056,14 +4109,14 @@ to variables on the left-hand side of the assignment.")
(define-public r-pillar
(package
(name "r-pillar")
- (version "1.4.2")
+ (version "1.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
- "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
+ "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -4102,14 +4155,14 @@ terminals.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.17")
+ (version "0.18")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w"))))
+ "04mpbhadixbxmnazj0q6cj973cajchscvyh1k6a5b3qk26dp5krr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@@ -4195,14 +4248,14 @@ detect possible inconsistencies.")
(define-public r-sna
(package
(name "r-sna")
- (version "2.4")
+ (version "2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "sna" version))
(sha256
(base32
- "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
+ "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-network" ,r-network)
@@ -4248,14 +4301,14 @@ of these tests are also included.")
(define-public r-ttr
(package
(name "r-ttr")
- (version "0.23-5")
+ (version "0.23-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "TTR" version))
(sha256
(base32
- "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
+ "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
(properties `((upstream-name . "TTR")))
(build-system r-build-system)
(propagated-inputs
@@ -5598,14 +5651,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
(define-public r-renv
(package
(name "r-renv")
- (version "0.9.1")
+ (version "0.9.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "renv" version))
(sha256
(base32
- "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm"))))
+ "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr"))))
(properties `((upstream-name . "renv")))
(build-system r-build-system)
(home-page "https://rstudio.github.io/renv")
@@ -5691,18 +5744,19 @@ obtain a better initial configuration in non-metric MDS.")
(define-public r-reticulate
(package
(name "r-reticulate")
- (version "1.13")
+ (version "1.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "reticulate" version))
(sha256
(base32
- "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
+ "0icb9zl9zlx75njv7y1dr450k0yw2n3q2jkr4nicnphdyfn69gkn"))))
(build-system r-build-system)
(inputs `(("python" ,python)))
(propagated-inputs
- `(("r-jsonlite" ,r-jsonlite)
+ `(("r-rappdirs" ,r-rappdirs)
+ ("r-jsonlite" ,r-jsonlite)
("r-matrix" ,r-matrix)
("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/rstudio/reticulate")
@@ -5717,14 +5771,14 @@ Python to R they are converted back to R types.")
(define-public r-bibtex
(package
(name "r-bibtex")
- (version "0.4.2")
+ (version "0.4.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bibtex" version))
(sha256
(base32
- "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
+ "1ks1w59ldwmfd1sj8ap7smyhf8dhykv7xnwrl8z9xzkcfpv1rbc0"))))
(build-system r-build-system)
(propagated-inputs `(("r-stringr" ,r-stringr)))
(home-page "https://github.com/romainfrancois/bibtex")
@@ -6118,14 +6172,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
(define-public r-rdpack
(package
(name "r-rdpack")
- (version "0.11-0")
+ (version "0.11-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rdpack" version))
(sha256
(base32
- "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
+ "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
(properties `((upstream-name . "Rdpack")))
(build-system r-build-system)
(propagated-inputs
@@ -6686,14 +6740,14 @@ Group (Non-)Overlap considerations.")
(define-public r-deriv
(package
(name "r-deriv")
- (version "3.9.0")
+ (version "4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "Deriv" version))
(sha256
(base32
- "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw"))))
+ "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
(properties `((upstream-name . "Deriv")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/Deriv")
@@ -6841,14 +6895,14 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
(define-public r-rootsolve
(package
(name "r-rootsolve")
- (version "1.8.1")
+ (version "1.8.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "rootSolve" version))
(sha256
(base32
- "0skrspq7sd7gaq73w91km14v8znc8chncgy64hvjgcng2xw15phx"))))
+ "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
(properties `((upstream-name . "rootSolve")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@@ -6899,13 +6953,13 @@ the analyzed items.")
(define-public r-slam
(package
(name "r-slam")
- (version "0.1-46")
+ (version "0.1-47")
(source
(origin
(method url-fetch)
(uri (cran-uri "slam" version))
(sha256
- (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b"))))
+ (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/slam/")
(synopsis "Sparse lightweight arrays and matrices")
@@ -7821,16 +7875,68 @@ analysis.")
;; Either version of the GPL.
(license (list license:gpl2 license:gpl3))))
+(define-public r-gee
+ (package
+ (name "r-gee")
+ (version "4.13-20")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gee" version))
+ (sha256
+ (base32
+ "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
+ (properties `((upstream-name . "gee")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/gee/")
+ (synopsis "Generalized estimation equation solver")
+ (description
+ "This package provides a solver for generalized estimation equations.")
+ (license license:gpl2)))
+
+(define-public r-tab
+ (package
+ (name "r-tab")
+ (version "4.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tab" version))
+ (sha256
+ (base32
+ "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
+ (properties `((upstream-name . "tab")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-gee" ,r-gee)
+ ("r-knitr" ,r-knitr)
+ ("r-mass" ,r-mass)
+ ("r-survey" ,r-survey)
+ ("r-survival" ,r-survival)
+ ("r-xtable" ,r-xtable)))
+ (home-page "https://cran.r-project.org/web/packages/tab/")
+ (synopsis "Create summary tables for statistical reports")
+ (description
+ "This package contains functions for creating various types of summary
+tables, e.g. comparing characteristics across levels of a categorical variable
+and summarizing fitted generalized linear models, generalized estimating
+equations, and Cox proportional hazards models. Functions are available to
+handle data from simple random samples as well as complex surveys.")
+ (license license:gpl3+)))
+
(define-public r-dvmisc
(package
(name "r-dvmisc")
- (version "1.1.3")
+ (version "1.1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "dvmisc" version))
(sha256
- (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
+ (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cubature" ,r-cubature)
@@ -7840,10 +7946,10 @@ analysis.")
("r-mass" ,r-mass)
("r-mvtnorm" ,r-mvtnorm)
("r-pracma" ,r-pracma)
- ("r-purrr" ,r-purrr)
("r-rbenchmark" ,r-rbenchmark)
("r-rcpp" ,r-rcpp)
- ("r-survey" ,r-survey)))
+ ("r-survey" ,r-survey)
+ ("r-tab" ,r-tab)))
(home-page "https://cran.r-project.org/web/packages/dvmisc/")
(synopsis "Faster computation of common statistics and miscellaneous functions")
(description
@@ -8118,14 +8224,14 @@ packages maintained by Torsten Hothorn.")
(define-public r-multcomp
(package
(name "r-multcomp")
- (version "1.4-10")
+ (version "1.4-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "multcomp" version))
(sha256
(base32
- "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
+ "0jw9661hs4396wz9vflk3rak0ryzj1cg2pnndsn1gb4fjyf2vlhb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-codetools" ,r-codetools)
@@ -8403,14 +8509,14 @@ ROPE percentage and pd).")
(define-public r-performance
(package
(name "r-performance")
- (version "0.4.0")
+ (version "0.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0"))))
+ "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
@@ -8430,22 +8536,20 @@ effects models and Bayesian models.")
(define-public r-ggeffects
(package
(name "r-ggeffects")
- (version "0.13.0")
+ (version "0.14.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
- "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb"))))
+ "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-dplyr" ,r-dplyr)
- ("r-insight" ,r-insight)
+ `(("r-insight" ,r-insight)
("r-magrittr" ,r-magrittr)
("r-mass" ,r-mass)
("r-purrr" ,r-purrr)
- ("r-rlang" ,r-rlang)
("r-sjlabelled" ,r-sjlabelled)
("r-sjmisc" ,r-sjmisc)))
(home-page "https://github.com/strengejacke/ggeffects")
@@ -9011,14 +9115,14 @@ experiments using ANOVA or mixed models.")
(define-public r-lmertest
(package
(name "r-lmertest")
- (version "3.1-0")
+ (version "3.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "lmerTest" version))
(sha256
(base32
- "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
+ "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj"))))
(properties `((upstream-name . "lmerTest")))
(build-system r-build-system)
(propagated-inputs
@@ -9456,14 +9560,14 @@ for evolution along a phylogenetic tree.")
(define-public r-fmsb
(package
(name "r-fmsb")
- (version "0.6.3")
+ (version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "fmsb" version))
(sha256
(base32
- "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
+ "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
(build-system r-build-system)
(home-page "http://minato.sip21c.org/msb/")
(synopsis "Functions for medical statistics book with demographic data")
@@ -9637,14 +9741,14 @@ Processing.")
(define-public r-tm
(package
(name "r-tm")
- (version "0.7-6")
+ (version "0.7-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "tm" version))
(sha256
(base32
- "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
+ "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
(properties `((upstream-name . "tm")))
(build-system r-build-system)
(propagated-inputs
@@ -9733,13 +9837,13 @@ maps.")
(define-public r-tidytree
(package
(name "r-tidytree")
- (version "0.3.0")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidytree" version))
(sha256
- (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy"))))
+ (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ape" ,r-ape)
@@ -11053,13 +11157,13 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.")
(define-public r-spam
(package
(name "r-spam")
- (version "2.5-0")
+ (version "2.5-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "spam" version))
(sha256
- (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2"))))
+ (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dotcall64" ,r-dotcall64)))
@@ -12402,14 +12506,14 @@ compatible with @code{rzmq} are also provided.")
(define-public r-repr
(package
(name "r-repr")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "repr" version))
(sha256
(base32
- "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
+ "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
@@ -14805,18 +14909,17 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
(define-public r-sctransform
(package
(name "r-sctransform")
- (version "0.2.0")
+ (version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "sctransform" version))
(sha256
(base32
- "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
+ "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-future" ,r-future)
- ("r-future-apply" ,r-future-apply)
+ `(("r-future-apply" ,r-future-apply)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-mass" ,r-mass)
@@ -15092,14 +15195,14 @@ annotated biological functions.")
(define-public r-plot3d
(package
(name "r-plot3d")
- (version "1.1.1")
+ (version "1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "plot3D" version))
(sha256
(base32
- "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
+ "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
(properties `((upstream-name . "plot3D")))
(build-system r-build-system)
(propagated-inputs `(("r-misc3d" ,r-misc3d)))
@@ -15824,19 +15927,18 @@ PROJ.4 library.")
(define-public r-insol
(package
(name "r-insol")
- (version "1.2")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "insol" version))
(sha256
(base32
- "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
+ "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
(properties `((upstream-name . "insol")))
(build-system r-build-system)
(propagated-inputs
- `(("r-raster" ,r-raster)
- ("r-rgdal" ,r-rgdal)))
+ `(("r-raster" ,r-raster)))
(native-inputs
`(("gfortran" ,gfortran)))
(home-page "https://meteoexploration.com/R/insol/index.html")
@@ -15927,40 +16029,41 @@ programming problems.")
(define-public r-desolve
(package
(name "r-desolve")
- (version "1.25")
+ (version "1.27")
(source
(origin
(method url-fetch)
(uri (cran-uri "deSolve" version))
(sha256
- (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp"))))
+ (base32 "1qhjq4vxlxd9qmhf6i26x1k7bzhldlxzbby1zgcplicdvlqk951d"))))
(properties `((upstream-name . "deSolve")))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(home-page "https://desolve.r-forge.r-project.org/")
(synopsis "Solvers for initial value problems of differential equations")
- (description "This package provides functions that solve initial
-value problems of a system of first-order ordinary differential equations (ODE),
-of partial differential equations (PDE), of differential algebraic equations
-(DAE), and of delay differential equations. The functions provide an interface
-to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
-to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
-the Runge-Kutta family with fixed or variable time steps. The package contains
-routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
-differential equations (PDE) that have been converted to ODEs by numerical
-differencing.")
+ (description "This package provides functions that solve initial value
+problems of a system of first-order @dfn{ordinary differential
+equations} (ODE), of @dfn{partial differential equations} (PDE), of
+@dfn{differential algebraic equations} (DAE), and of delay differential
+equations. The functions provide an interface to the FORTRAN functions
+@code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
+collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
+C-implementation of solvers of the Runge-Kutta family with fixed or variable
+time steps. The package contains routines designed for solving ODEs resulting
+from 1-D, 2-D and 3-D partial differential equations that have been converted
+to ODEs by numerical differencing.")
(license license:gpl2+)))
(define-public r-pracma
(package
(name "r-pracma")
- (version "2.2.5")
+ (version "2.2.9")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
+ (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/pracma/")
(synopsis "Practical numerical math functions")
@@ -16012,3 +16115,2876 @@ graphics directly in the terminal window. This package provides a basic
plotting function (and equivalents of curve, density, acf and barplot) as well
as a boxplot function.")
(license license:lgpl3+)))
+
+(define-public r-bio3d
+ (package
+ (name "r-bio3d")
+ (version "2.4-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bio3d" version))
+ (sha256
+ (base32
+ "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
+ (properties `((upstream-name . "bio3d")))
+ (build-system r-build-system)
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+ (home-page "http://thegrantlab.org/bio3d/")
+ (synopsis "Biological structure analysis")
+ (description
+ "This package provides utilities to process, organize and explore protein
+structure, sequence and dynamics data. Features include the ability to read
+and write structure, sequence and dynamic trajectory data, perform sequence
+and structure database searches, data summaries, atom selection, alignment,
+superposition, rigid core identification, clustering, torsion analysis,
+distance matrix analysis, structure and sequence conservation analysis, normal
+mode analysis, principal component analysis of heterogeneous structure data,
+and correlation network analysis from normal mode and molecular dynamics data.
+In addition, various utility functions are provided to enable the statistical
+and graphical power of the R environment to work with biological sequence and
+structural data.")
+ (license license:gpl2+)))
+
+(define-public r-bios2cor
+ (package
+ (name "r-bios2cor")
+ (version "2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Bios2cor" version))
+ (sha256
+ (base32
+ "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n"))))
+ (properties `((upstream-name . "Bios2cor")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bigmemory" ,r-bigmemory)
+ ("r-bio3d" ,r-bio3d)
+ ("r-circular" ,r-circular)
+ ("r-igraph" ,r-igraph)))
+ (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
+ (synopsis "From biological sequences and simulations to correlation analysis")
+ (description
+ "This package provides utilities for computation and analysis of
+correlation/covariation in multiple sequence alignments and in side chain
+motions during molecular dynamics simulations. Features include the
+computation of correlation/covariation scores using a variety of scoring
+functions between either sequence positions in alignments or side chain
+dihedral angles in molecular dynamics simulations and utilities to analyze the
+correlation/covariation matrix through a variety of tools including network
+representation and principal components analysis. In addition, several
+utility functions are based on the R graphical environment to provide friendly
+tools for help in data interpretation.")
+ (license license:gpl2+)))
+
+;; This package includes minified JavaScript files. When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-networkd3
+ (package
+ (name "r-networkd3")
+ (version "0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "networkD3" version))
+ (sha256
+ (base32
+ "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
+ (snippet
+ '(begin
+ (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
+ #t))))
+ (properties `((upstream-name . "networkD3")))
+ (build-system r-build-system)
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build r-build-system)
+ (srfi srfi-1)
+ (ice-9 popen))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/htmlwidgets/lib/"
+ (call-with-values
+ (lambda ()
+ (unzip2
+ `((,(assoc-ref inputs "d3.v4.js")
+ "d3-4.5.0/d3.min.js"))))
+ (lambda (sources targets)
+ (for-each (lambda (source target)
+ (format #t "Processing ~a --> ~a~%"
+ source target)
+ (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (call-with-output-file target
+ (lambda (port)
+ (dump-port minified port)))))
+ sources targets))))
+ #t)))))
+ (native-inputs
+ `(("uglify-js" ,uglify-js)
+ ;; NOTE: Make sure that this version of d3 is still valid when
+ ;; upgrading the package.
+ ("d3.v4.js"
+ ,(origin
+ (method url-fetch)
+ (uri "https://d3js.org/d3.v4.js")
+ (sha256
+ (base32
+ "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
+ (propagated-inputs
+ `(("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)))
+ (home-page "https://cran.r-project.org/package=networkD3")
+ (synopsis "D3 JavaScript network graphs from R")
+ (description
+ "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
+graphs from R.")
+ (license license:gpl3+)))
+
+(define-public r-aasea
+ (package
+ (name "r-aasea")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "aaSEA" version))
+ (sha256
+ (base32
+ "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
+ (properties `((upstream-name . "aaSEA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bios2cor" ,r-bios2cor)
+ ("r-dt" ,r-dt)
+ ("r-hmisc" ,r-hmisc)
+ ("r-magrittr" ,r-magrittr)
+ ("r-networkd3" ,r-networkd3)
+ ("r-plotly" ,r-plotly)
+ ("r-seqinr" ,r-seqinr)
+ ("r-shiny" ,r-shiny)
+ ("r-shinydashboard" ,r-shinydashboard)))
+ (home-page "https://cran.r-project.org/web/packages/aaSEA/")
+ (synopsis "Amino acid substitution effect analyzer")
+ (description
+ "Given a protein multiple sequence alignment, it is a daunting task to
+assess the effects of substitutions along sequence length. The aaSEA package
+is intended to help researchers to rapidly analyze property changes caused by
+single, multiple and correlated amino acid substitutions in proteins.")
+ (license license:gpl3)))
+
+(define-public r-abacus
+ (package
+ (name "r-abacus")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ABACUS" version))
+ (sha256
+ (base32
+ "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
+ (properties `((upstream-name . "ABACUS")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-shiny" ,r-shiny)))
+ (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
+ (synopsis "Apps-based activities for communicating and understanding statistics")
+ (description
+ "This package provides a set of Shiny apps for effective communication
+and understanding in statistics. The current version includes properties of
+normal distribution, properties of sampling distribution, one-sample z and t
+tests, two samples independent (unpaired) t test and analysis of variance.")
+ (license license:gpl3)))
+
+(define-public r-abc-rap
+ (package
+ (name "r-abc-rap")
+ (version "0.9.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ABC.RAP" version))
+ (sha256
+ (base32
+ "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
+ (properties `((upstream-name . "ABC.RAP")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
+ (synopsis "Array-based CpG region analysis pipeline")
+ (description
+ "This package aims to identify candidate genes that are differentially
+methylated between cases and controls. It applies Student's t-test and delta
+beta analysis to identify candidate genes containing multiple CpG sites.")
+ (license license:gpl3)))
+
+(define-public r-abcadm
+ (package
+ (name "r-abcadm")
+ (version "1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "abcADM" version))
+ (sha256
+ (base32
+ "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
+ (properties `((upstream-name . "abcADM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://cran.r-project.org/web/packages/abcADM/")
+ (synopsis "Fit accumulated damage models and estimate reliability using ABC")
+ (description
+ "This package provides tools to estimate parameters of accumulated
+damage (load duration) models based on failure time data under a Bayesian
+framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
+long-term reliability under stochastic load profiles.")
+ (license license:gpl3)))
+
+(define-public r-rglpk
+ (package
+ (name "r-rglpk")
+ (version "0.6-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Rglpk" version))
+ (sha256
+ (base32
+ "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
+ (properties `((upstream-name . "Rglpk")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-slam" ,r-slam)))
+ (inputs
+ `(("glpk" ,glpk)))
+ (home-page "http://R-Forge.R-project.org/projects/rglp/")
+ (synopsis "R interface to the GNU Linear Programming Kit")
+ (description
+ "This package provides an R interface to the GNU Linear Programming Kit,
+software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
+integer linear programming} (MILP) and other related problems.")
+ ;; Either license
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-abcdefba
+ (package
+ (name "r-abcdefba")
+ (version "0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "abcdeFBA" version))
+ (sha256
+ (base32
+ "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
+ (properties `((upstream-name . "abcdeFBA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-corrplot" ,r-corrplot)
+ ("r-lattice" ,r-lattice)
+ ("r-rgl" ,r-rgl)
+ ("r-rglpk" ,r-rglpk)))
+ (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
+ (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
+ (description
+ "This package provides functions for Constraint Based Simulation using
+Flux Balance Analysis and informative analysis of the data generated during
+simulation.")
+ (license license:gpl2)))
+
+(define-public r-abcrlda
+ (package
+ (name "r-abcrlda")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "abcrlda" version))
+ (sha256
+ (base32
+ "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85"))))
+ (properties `((upstream-name . "abcrlda")))
+ (build-system r-build-system)
+ (home-page "https://ieeexplore.ieee.org/document/8720003/")
+ (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
+ (description
+ "This package offers methods to perform @dfn{asymptotically
+bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
+cost-sensitive binary classification. The bias-correction is an estimate of
+the bias term added to regularized discriminant analysis that minimizes the
+overall risk.")
+ (license license:gpl3)))
+
+(define-public r-abemus
+ (package
+ (name "r-abemus")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "abemus" version))
+ (sha256
+ (base32
+ "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
+ (properties `((upstream-name . "abemus")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)))
+ (home-page "https://cran.r-project.org/web/packages/abemus/")
+ (synopsis "Adaptive base error model in ultra-deep sequencing data")
+ (description
+ "This package provides an implementation of @dfn{Adaptive Base Error
+Model in Ultra-deep Sequencing data} (ABEMUS), which combines
+platform-specific genetic knowledge and empirical signal to readily detect and
+quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
+cell free DNA} (cfDNA).")
+ (license license:gpl3)))
+
+;; This package includes minified JavaScript files. When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-rintrojs
+ (package
+ (name "r-rintrojs")
+ (version "0.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rintrojs" version))
+ (sha256
+ (base32
+ "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
+ (properties `((upstream-name . "rintrojs")))
+ (build-system r-build-system)
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build r-build-system)
+ (srfi srfi-1)
+ (ice-9 popen))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/javascript/introjs/"
+ (call-with-values
+ (lambda ()
+ (unzip2
+ `((,(assoc-ref inputs "intro.js")
+ "intro.min.js"))))
+ (lambda (sources targets)
+ (for-each (lambda (source target)
+ (format #t "Processing ~a --> ~a~%"
+ source target)
+ (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (call-with-output-file target
+ (lambda (port)
+ (dump-port minified port)))))
+ sources targets))))
+ #t)))))
+ (native-inputs
+ `(("uglify-js" ,uglify-js)
+ ("intro.js"
+ ,(origin
+ (method url-fetch)
+ (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
+ (sha256
+ (base32
+ "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
+ (propagated-inputs
+ `(("r-jsonlite" ,r-jsonlite)
+ ("r-shiny" ,r-shiny)))
+ (home-page "https://github.com/carlganz/rintrojs")
+ (synopsis "Wrapper for the Intro.js library")
+ (description
+ "This package provides a wrapper for the @url{http://www.introjs.com,
+Intro.js} library. This package makes it easy to include step-by-step
+introductions, and clickable hints in a Shiny application. It supports both
+static introductions in the UI, and programmatic introductions from the
+server-side.")
+ (license license:agpl3+)))
+
+(define-public r-sysfonts
+ (package
+ (name "r-sysfonts")
+ (version "0.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sysfonts" version))
+ (sha256
+ (base32
+ "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
+ (properties `((upstream-name . "sysfonts")))
+ (build-system r-build-system)
+ (inputs
+ `(("freetype" ,freetype)
+ ("libpng" ,libpng)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "https://github.com/yixuan/sysfonts")
+ (synopsis "Loading fonts into R")
+ (description
+ "This is a package to simplify loading of system fonts and Google Fonts
+into R, in order to support other packages.")
+ (license license:gpl2)))
+
+(define-public r-showtextdb
+ (package
+ (name "r-showtextdb")
+ (version "2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "showtextdb" version))
+ (sha256
+ (base32
+ "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
+ (properties `((upstream-name . "showtextdb")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-sysfonts" ,r-sysfonts)))
+ (home-page "https://cran.r-project.org/web/packages/showtextdb/")
+ (synopsis "Font files for the 'showtext' package")
+ (description
+ "This package provides font files that can be used by the @code{showtext}
+package.")
+ (license license:asl2.0)))
+
+(define-public r-showtext
+ (package
+ (name "r-showtext")
+ (version "0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "showtext" version))
+ (sha256
+ (base32
+ "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73"))))
+ (properties `((upstream-name . "showtext")))
+ (build-system r-build-system)
+ (inputs
+ `(("freetype" ,freetype)
+ ("libpng" ,libpng)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-showtextdb" ,r-showtextdb)
+ ("r-sysfonts" ,r-sysfonts)))
+ (native-inputs `(("pkg-config" ,pkg-config)))
+ (home-page "https://github.com/yixuan/showtext")
+ (synopsis "Using fonts more easily in R graphs")
+ (description
+ "This package aims to make it easy to use various types of
+fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
+most output formats of R graphics including PNG, PDF and SVG. Text glyphs
+will be converted into polygons or raster images, hence after the plot has
+been created, it no longer relies on the font files. No external software
+such as Ghostscript is needed to use this package.")
+ (license license:asl2.0)))
+
+(define-public r-emojifont
+ (package
+ (name "r-emojifont")
+ (version "0.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "emojifont" version))
+ (sha256
+ (base32
+ "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
+ (properties `((upstream-name . "emojifont")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-proto" ,r-proto)
+ ("r-showtext" ,r-showtext)
+ ("r-sysfonts" ,r-sysfonts)))
+ (home-page "https://guangchuangyu.github.io/emojifont")
+ (synopsis "Emoji and Font Awesome in R graphics")
+ (description
+ "This package enables the use of emoji and the Font Awesome glyphs in
+both base and ggplot2 graphics.")
+ (license license:artistic2.0)))
+
+(define-public r-abstractr
+ (package
+ (name "r-abstractr")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "abstractr" version))
+ (sha256
+ (base32
+ "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
+ (properties `((upstream-name . "abstractr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-colourpicker" ,r-colourpicker)
+ ("r-emojifont" ,r-emojifont)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-rintrojs" ,r-rintrojs)
+ ("r-shiny" ,r-shiny)
+ ("r-shinythemes" ,r-shinythemes)))
+ (home-page "https://matt-kumar.shinyapps.io/portfolio")
+ (synopsis "R-Shiny application for creating visual abstracts")
+ (description
+ "This package provides an R Shiny application to create visual abstracts
+for original research. A variety of user defined options and formatting are
+included.")
+ (license license:gpl3)))
+
+(define-public r-abtest
+ (package
+ (name "r-abtest")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "abtest" version))
+ (sha256
+ (base32
+ "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
+ (properties `((upstream-name . "abtest")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrix" ,r-matrix)
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-plotrix" ,r-plotrix)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-sn" ,r-sn)
+ ("r-truncnorm" ,r-truncnorm)
+ ("r-vgam" ,r-vgam)))
+ (home-page "https://cran.r-project.org/web/packages/abtest/")
+ (synopsis "Bayesian A/B testing")
+ (description
+ "This package provides functions for Bayesian A/B testing including prior
+elicitation options based on Kass and Vaidyanathan (1992)
+@url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
+ (license license:gpl2+)))
+
+(define-public r-accept
+ (package
+ (name "r-accept")
+ (version "0.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "accept" version))
+ (sha256
+ (base32
+ "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx"))))
+ (properties `((upstream-name . "accept")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-extrafont" ,r-extrafont)
+ ("r-mass" ,r-mass)
+ ("r-plotly" ,r-plotly)
+ ("r-stringr" ,r-stringr)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://cran.r-project.org/web/packages/accept/")
+ (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
+ (description
+ "This package allows clinicians to predict the rate and severity of
+future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
+Disease} (COPD) patients, based on the clinical prediction model published in
+Adibi et al. (2019) @url{doi:10.1101/651901}.")
+ (license license:gpl3)))
+
+(define-public r-smpracticals
+ (package
+ (name "r-smpracticals")
+ (version "1.4-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "SMPracticals" version))
+ (sha256
+ (base32
+ "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
+ (properties `((upstream-name . "SMPracticals")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ellipse" ,r-ellipse)
+ ("r-mass" ,r-mass)
+ ("r-nlme" ,r-nlme)
+ ("r-survival" ,r-survival)))
+ (home-page "http://statwww.epfl.ch/davison/SM/")
+ (synopsis "Practicals for use with Davison (2003) Statistical Models")
+ (description
+ "This package contains the datasets and a few functions for use with the
+practicals outlined in Appendix A of the book Statistical Models (Davison,
+2003, Cambridge University Press). The practicals themselves can be found at
+@url{http://statwww.epfl.ch/davison/SM/}.")
+ (license license:gpl2+)))
+
+(define-public r-fgui
+ (package
+ (name "r-fgui")
+ (version "1.0-8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fgui" version))
+ (sha256
+ (base32
+ "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
+ (properties `((upstream-name . "fgui")))
+ (build-system r-build-system)
+ (home-page
+ "https://sites.google.com/site/thomashoffmannproject/software/fgui")
+ (synopsis "Create GUI for R functions")
+ (description
+ "Rapidly create a GUI for a function you created by automatically
+creating widgets for arguments of the function. This package automatically
+parses help routines for context-sensitive help to these arguments. The
+interface is essentially a wrapper to some Tcl/Tk routines to both simplify
+and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
+incorporated into the interface for greater customization for the more
+experienced.")
+ ;; Any version of the GPL.
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-tcltk2
+ (package
+ (name "r-tcltk2")
+ (version "1.2-11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tcltk2" version))
+ (sha256
+ (base32
+ "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
+ (properties `((upstream-name . "tcltk2")))
+ (build-system r-build-system)
+ (inputs
+ `(("tcl" ,tcl)
+ ("tk" ,tk)))
+ (home-page "http://www.sciviews.org/SciViews-R")
+ (synopsis "Tcl/Tk additions")
+ (description
+ "This package provides a series of additional Tcl commands and Tk widgets
+with style and various functions to supplement the tcltk package")
+ (license license:lgpl3)))
+
+(define-public r-accrual
+ (package
+ (name "r-accrual")
+ (version "1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "accrual" version))
+ (sha256
+ (base32
+ "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
+ (properties `((upstream-name . "accrual")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fgui" ,r-fgui)
+ ("r-smpracticals" ,r-smpracticals)
+ ("r-tcltk2" ,r-tcltk2)))
+ (home-page "https://cran.r-project.org/web/packages/accrual/")
+ (synopsis "Bayesian accrual prediction")
+ (description
+ "Subject recruitment for medical research is challenging. Slow patient
+accrual leads to delay in research. Accrual monitoring during the process of
+recruitment is critical. Researchers need reliable tools to manage the
+accrual rate. This package provides an implementation of a Bayesian method
+that integrates researcher's experience on previous trials and data from the
+current study, providing reliable prediction on accrual rate for clinical
+studies. It provides functions for Bayesian accrual prediction which can be
+easily used by statisticians and clinical researchers.")
+ (license license:gpl2)))
+
+(define-public r-accrued
+ (package
+ (name "r-accrued")
+ (version "1.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "accrued" version))
+ (sha256
+ (base32
+ "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
+ (properties `((upstream-name . "accrued")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/accrued/")
+ (synopsis "Data quality visualization tools for partially accruing data")
+ (description
+ "This is a package for visualizing data quality of partially accruing
+data.")
+ (license license:gpl3)))
+
+(define-public r-mda
+ (package
+ (name "r-mda")
+ (version "0.4-10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "mda" version))
+ (sha256
+ (base32
+ "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
+ (properties `((upstream-name . "mda")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-class" ,r-class)))
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/mda/")
+ (synopsis "Mixture and flexible discriminant analysis")
+ (description
+ "This is a package for mixture and flexible discriminant analysis,
+@dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
+ (license license:gpl2)))
+
+(define-public r-elasticnet
+ (package
+ (name "r-elasticnet")
+ (version "1.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "elasticnet" version))
+ (sha256
+ (base32
+ "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
+ (properties `((upstream-name . "elasticnet")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lars" ,r-lars)))
+ (home-page "http://www.stat.umn.edu/~hzou")
+ (synopsis "Elastic-Net for sparse estimation and sparse PCA")
+ (description
+ "This package provides functions for fitting the entire solution path of
+the Elastic-Net and also provides functions for estimating sparse Principal
+Components. The Lasso solution paths can be computed by the same function.")
+ (license license:gpl2+)))
+
+(define-public r-sparselda
+ (package
+ (name "r-sparselda")
+ (version "0.1-9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sparseLDA" version))
+ (sha256
+ (base32
+ "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
+ (properties `((upstream-name . "sparseLDA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-elasticnet" ,r-elasticnet)
+ ("r-mass" ,r-mass)
+ ("r-mda" ,r-mda)))
+ (home-page "http://www.imm.dtu.dk/~lhc")
+ (synopsis "Sparse discriminant analysis")
+ (description
+ "This package performs sparse linear discriminant analysis for Gaussians
+and mixture of Gaussian models.")
+ (license license:gpl2+)))
+
+(define-public r-accsda
+ (package
+ (name "r-accsda")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "accSDA" version))
+ (sha256
+ (base32
+ "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
+ (properties `((upstream-name . "accSDA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-ggthemes" ,r-ggthemes)
+ ("r-gridextra" ,r-gridextra)
+ ("r-mass" ,r-mass)
+ ("r-rarpack" ,r-rarpack)
+ ("r-sparselda" ,r-sparselda)))
+ (home-page "https://github.com/gumeo/accSDA/wiki")
+ (synopsis "Accelerated sparse discriminant analysis")
+ (description
+ "This package provides an implementation of sparse linear discriminant
+analysis, which is a supervised classification method for multiple classes.
+Various novel optimization approaches to this problem are implemented
+including @dfn{alternating direction method of multipliers} (ADMM),
+@dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
+Functions for performing cross validation are also supplied along with basic
+prediction and plotting functions. @dfn{Sparse zero variance
+discriminant} (SZVD) analysis is also included in the package.")
+ (license license:gpl2+)))
+
+(define-public r-ace2fastq
+ (package
+ (name "r-ace2fastq")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ace2fastq" version))
+ (sha256
+ (base32
+ "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
+ (properties `((upstream-name . "ace2fastq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-stringr" ,r-stringr)))
+ (home-page "https://github.com/c5sire/ace2fastq")
+ (synopsis "ACE file to FASTQ converter")
+ (description
+ "The ACE file format is used in genomics to store contigs from sequencing
+machines. This tools converts it into FASTQ format. Both formats contain the
+sequence characters and their corresponding quality information. Unlike the
+FASTQ file, the ACE file stores the quality values numerically. The
+conversion algorithm uses the standard Sanger formula. The package
+facilitates insertion into pipelines, and content inspection.")
+ (license license:gpl3)))
+
+(define-public r-rngwell
+ (package
+ (name "r-rngwell")
+ (version "0.10-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rngWELL" version))
+ (sha256
+ (base32
+ "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb"))))
+ (properties `((upstream-name . "rngWELL")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/rngWELL/")
+ (synopsis "Toolbox for WELL random number generators")
+ (description
+ "This is a dedicated package to WELL pseudo random generators, which were
+introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
+on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
+ (license license:bsd-3)))
+
+(define-public r-randtoolbox
+ (package
+ (name "r-randtoolbox")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "randtoolbox" version))
+ (sha256
+ (base32
+ "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd"))))
+ (properties `((upstream-name . "randtoolbox")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rngwell" ,r-rngwell)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
+ (synopsis "Toolbox for pseudo and quasi random number generation")
+ (description
+ "This package provides
+
+@enumerate
+@item pseudo random generators, such as general linear
+congruential generators, multiple recursive generators and generalized
+feedback shift register (SF-Mersenne Twister algorithm and WELL
+generators)
+
+@item quasi random generators, such as the Torus algorithm, the Sobol
+sequence, the Halton sequence (including the Van der Corput sequence), and
+
+@item some generator tests: the gap test, the serial test, the poker test.
+@end enumerate
+
+See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
+ (license license:bsd-3)))
+
+(define-public r-lhs
+ (package
+ (name "r-lhs")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "lhs" version))
+ (sha256
+ (base32
+ "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
+ (properties `((upstream-name . "lhs")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/bertcarnell/lhs")
+ (synopsis "Latin Hypercube Samples")
+ (description
+ "This package provides a number of methods for creating and augmenting
+Latin Hypercube Samples.")
+ (license license:gpl3)))
+
+(define-public r-acebayes
+ (package
+ (name "r-acebayes")
+ (version "1.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acebayes" version))
+ (sha256
+ (base32
+ "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln"))))
+ (properties `((upstream-name . "acebayes")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-compare" ,r-compare)
+ ("r-lhs" ,r-lhs)
+ ("r-randtoolbox" ,r-randtoolbox)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (home-page "https://cran.r-project.org/web/packages/acebayes/")
+ (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
+ (description
+ "Finding an optimal Bayesian experimental design involves maximizing an
+objective function given by the expectation of some appropriately chosen
+utility function with respect to the joint distribution of unknown
+quantities (including responses). This objective function is usually not
+available in closed form and the design space can be continuous and of high
+dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
+to maximise an approximation to the expectation of the utility function.")
+ (license license:gpl2)))
+
+(define-public r-acet
+ (package
+ (name "r-acet")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ACEt" version))
+ (sha256
+ (base32
+ "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
+ (properties `((upstream-name . "ACEt")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-mass" ,r-mass)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (home-page "https://cran.r-project.org/web/packages/ACEt/")
+ (synopsis "Estimating dynamic heritability and twin model comparison")
+ (description
+ "This package supports twin models that are able to estimate the dynamic
+behaviour of the variance components in the classical twin models with respect
+to age using B-splines and P-splines.")
+ (license license:gpl2+)))
+
+(define-public r-acfmperiod
+ (package
+ (name "r-acfmperiod")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acfMPeriod" version))
+ (sha256
+ (base32
+ "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
+ (properties `((upstream-name . "acfMPeriod")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mass" ,r-mass)))
+ (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
+ (synopsis "Estimation of the ACF from the M-periodogram")
+ (description
+ "This package support non-robust and robust computations of the sample
+autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
+univariate and multivariate processes. The methodology consists in reversing
+the diagonalization procedure involving the periodogram or the
+cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
+ACOVF or the ACF as discussed in Fuller (1995)
+@url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
+robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
+discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
+ (license license:gpl2+)))
+
+(define-public r-gamlss-data
+ (package
+ (name "r-gamlss-data")
+ (version "5.1-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gamlss.data" version))
+ (sha256
+ (base32
+ "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
+ (properties `((upstream-name . "gamlss.data")))
+ (build-system r-build-system)
+ (home-page "http://www.gamlss.org/")
+ (synopsis "GAMLSS data")
+ (description
+ "This package provides data used as examples to demonstrate GAMLSS
+models.")
+ ;; Either version of the license
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-gamlss
+ (package
+ (name "r-gamlss")
+ (version "5.1-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gamlss" version))
+ (sha256
+ (base32
+ "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc"))))
+ (properties `((upstream-name . "gamlss")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gamlss-data" ,r-gamlss-data)
+ ("r-gamlss-dist" ,r-gamlss-dist)
+ ("r-mass" ,r-mass)
+ ("r-nlme" ,r-nlme)
+ ("r-survival" ,r-survival)))
+ (home-page "http://www.gamlss.org/")
+ (synopsis "Generalized additive models for location scale and shape")
+ (description
+ "This package provides functions for fitting the generalized additive
+models for location scale and shape introduced by Rigby and
+Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
+use a distributional regression approach where all the parameters of the
+conditional distribution of the response variable are modelled using
+explanatory variables.")
+ ;; Either version of the license
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-acid
+ (package
+ (name "r-acid")
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acid" version))
+ (sha256
+ (base32
+ "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
+ (properties `((upstream-name . "acid")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gamlss" ,r-gamlss)
+ ("r-gamlss-dist" ,r-gamlss-dist)
+ ("r-hmisc" ,r-hmisc)))
+ (home-page "https://cran.r-project.org/web/packages/acid/")
+ (synopsis "Analysing conditional income distributions")
+ (description
+ "This package provides functions for the analysis of income distributions
+for subgroups of the population as defined by a set of variables like age,
+gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
+distribution as well as functions for moments, inequality measures, entropy
+measures and polarisation measures of income distributions. This package thus
+aides the analysis of income inequality by offering tools for the exploratory
+analysis of income distributions at the disaggregated level.")
+ (license license:gpl3)))
+
+(define-public r-acm4r
+ (package
+ (name "r-acm4r")
+ (version "1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acm4r" version))
+ (sha256
+ (base32
+ "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
+ (properties `((upstream-name . "acm4r")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-mass" ,r-mass)))
+ (home-page "https://cran.r-project.org/web/packages/acm4r/")
+ (synopsis "Align-and-count method comparisons of RFLP data")
+ (description
+ "This is a package to compare sequence fragment lengths or molecular
+weights from pairs of lanes. The number of matching bands in the
+@dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
+the align-and-count method.")
+ ;; Any version of the GPL
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-filematrix
+ (package
+ (name "r-filematrix")
+ (version "1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "filematrix" version))
+ (sha256
+ (base32
+ "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
+ (properties `((upstream-name . "filematrix")))
+ (build-system r-build-system)
+ ;; These inputs are needed for vignettes
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
+ (home-page "https://github.com/andreyshabalin/filematrix")
+ (synopsis "File-backed matrix class with convenient read and write access")
+ (description
+ "This package provides an interface for working with large matrices
+stored in files, not in computer memory. It supports multiple non-character
+data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
+byte real values). Access to parts of the matrix is done by indexing, exactly
+as with usual R matrices. It supports very large matrices; the package has
+been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
+columns, ad allows for quick addition of extra columns to a filematrix.")
+ (license license:lgpl3)))
+
+(define-public r-acmeeqtl
+ (package
+ (name "r-acmeeqtl")
+ (version "1.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ACMEeqtl" version))
+ (sha256
+ (base32
+ "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
+ (properties `((upstream-name . "ACMEeqtl")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-filematrix" ,r-filematrix)))
+ (home-page "https://github.com/andreyshabalin/ACMEeqtl")
+ (synopsis "Estimation of interpretable eQTL effect sizes")
+ (description
+ "This package provides a non-linear model, termed ACME, that reflects a
+parsimonious biological model for allelic contributions of cis-acting eQTLs.
+With non-linear least-squares algorithm the maximum likelihood parameters can
+be estimated. The ACME model provides interpretable effect size estimates and
+p-values with well controlled Type-I error.")
+ (license license:lgpl3)))
+
+(define-public r-acmer
+ (package
+ (name "r-acmer")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acmeR" version))
+ (sha256
+ (base32
+ "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
+ (properties `((upstream-name . "acmeR")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-foreign" ,r-foreign)))
+ (home-page "https://cran.r-project.org/web/packages/acmeR/")
+ (synopsis "ACME estimator of bird and bat mortality by wind turbines")
+ (description
+ "This package provides an implementation of the ACME estimator, described
+in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
+Mortality at Wind Turbines. Unlike most other models, this estimator supports
+decreasing-hazard Weibull model for persistence; decreasing search proficiency
+as carcasses age; variable bleed-through at successive searches; and interval
+mortality estimates. The package provides, based on search data, functions
+for estimating the mortality inflation factor in Frequentist and Bayesian
+settings.")
+ (license license:expat)))
+
+(define-public r-r-huge
+ (package
+ (name "r-r-huge")
+ (version "0.9.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "R.huge" version))
+ (sha256
+ (base32
+ "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
+ (properties `((upstream-name . "R.huge")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-r-methodss3" ,r-r-methodss3)
+ ("r-r-oo" ,r-r-oo)
+ ("r-r-utils" ,r-r-utils)))
+ (home-page "https://github.com/HenrikBengtsson/R.huge")
+ (synopsis "Methods for accessing huge amounts of data")
+ (description
+ "This is a deprecated package for accessing huge amounts of data.
+ Cross-platform alternatives are the following packages: bigmemory (CRAN),
+ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
+the @code{aroma.affymetrix} package.")
+ (license license:lgpl2.1+)))
+
+(define-public r-r-filesets
+ (package
+ (name "r-r-filesets")
+ (version "2.13.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "R.filesets" version))
+ (sha256
+ (base32
+ "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
+ (properties `((upstream-name . "R.filesets")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-digest" ,r-digest)
+ ("r-r-cache" ,r-r-cache)
+ ("r-r-methodss3" ,r-r-methodss3)
+ ("r-r-oo" ,r-r-oo)
+ ("r-r-utils" ,r-r-utils)))
+ (home-page "https://github.com/HenrikBengtsson/R.filesets")
+ (synopsis "Easy handling of and access to files")
+ (description
+ "This package provides classes and methods to locate, setup, subset,
+navigate and iterate file sets, i.e. sets of files located in one or more
+directories on the file system. The API is designed such that these classes
+can be extended via inheritance to provide a richer API for special file
+formats. Moreover, a specific name format is defined such that filenames and
+directories can be considered to have full names which consists of a name
+followed by comma-separated tags. This adds additional flexibility to
+identify file sets and individual files.")
+ (license license:lgpl2.1+)))
+
+(define-public r-r-devices
+ (package
+ (name "r-r-devices")
+ (version "2.16.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "R.devices" version))
+ (sha256
+ (base32
+ "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
+ (properties `((upstream-name . "R.devices")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-base64enc" ,r-base64enc)
+ ("r-r-methodss3" ,r-r-methodss3)
+ ("r-r-oo" ,r-r-oo)
+ ("r-r-utils" ,r-r-utils)))
+ (home-page "https://github.com/HenrikBengtsson/R.devices")
+ (synopsis "Unified handling of graphics devices")
+ (description
+ "This package provides functions for creating plots and image files in a
+unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
+Default device options as well as scales and aspect ratios are controlled in a
+uniform way across all device types. Switching output format requires minimal
+changes in code. This package is ideal for large-scale batch processing,
+because it will never leave open graphics devices or incomplete image files
+behind, even on errors or user interrupts.")
+ (license license:lgpl2.1+)))
+
+(define-public r-acnr
+ (package
+ (name "r-acnr")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acnr" version))
+ (sha256
+ (base32
+ "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
+ (properties `((upstream-name . "acnr")))
+ (build-system r-build-system)
+ (home-page "https://github.com/mpierrejean/acnr")
+ (synopsis "Annotated copy-number regions")
+ (description
+ "This package provides SNP array data from different types of copy-number
+regions. These regions were identified manually by the authors of the package
+and may be used to generate realistic data sets with known truth.")
+ (license license:lgpl2.1+)))
+
+(define-public r-acopula
+ (package
+ (name "r-acopula")
+ (version "0.9.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acopula" version))
+ (sha256
+ (base32
+ "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
+ (properties `((upstream-name . "acopula")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/acopula/")
+ (synopsis "Modelling dependence with multivariate Archimax copulas")
+ (description
+ "Archimax copulas are a mixture of Archimedean and EV copulas. This
+package provides definitions of several parametric families of generator and
+dependence function, computes CDF and PDF, estimates parameters, tests for
+goodness of fit, generates random sample and checks copula properties for
+custom constructs. In the 2-dimensional case explicit formulas for density
+are used, contrary to higher dimensions when all derivatives are linearly
+approximated. Several non-archimax families (normal, FGM, Plackett) are
+provided as well.")
+ (license license:gpl2)))
+
+(define-public r-tuner
+ (package
+ (name "r-tuner")
+ (version "1.3.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tuneR" version))
+ (sha256
+ (base32
+ "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
+ (properties `((upstream-name . "tuneR")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-signal" ,r-signal)))
+ (home-page "https://cran.r-project.org/web/packages/tuneR/")
+ (synopsis "Analysis of music and speech")
+ (description
+ "This is a package for the analysis of music and speech. Analyze music
+and speech, extract features like MFCCs, handle wave files and their
+representation in various ways, read MP3, read MIDI, perform steps of a
+transcription, ...")
+ ;; Either of these versions.
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-seewave
+ (package
+ (name "r-seewave")
+ (version "2.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "seewave" version))
+ (sha256
+ (base32
+ "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
+ (properties `((upstream-name . "seewave")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-tuner" ,r-tuner)))
+ (home-page "http://rug.mnhn.fr/seewave")
+ (synopsis "Sound analysis and synthesis")
+ (description
+ "This package provides functions for analysing, manipulating, displaying,
+editing and synthesizing time waves (particularly sound). This package
+processes time analysis (oscillograms and envelopes), spectral content,
+resonance quality factor, entropy, cross correlation and autocorrelation,
+zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
+and 3D spectrograms and many other analyses.")
+ (license license:gpl2+)))
+
+(define-public r-acousticndlcoder
+ (package
+ (name "r-acousticndlcoder")
+ (version "1.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "AcousticNDLCodeR" version))
+ (sha256
+ (base32
+ "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
+ (properties
+ `((upstream-name . "AcousticNDLCodeR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-seewave" ,r-seewave)
+ ("r-tuner" ,r-tuner)
+ ("r-zoo" ,r-zoo)))
+ (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
+ (synopsis "Coding sound files for use with NDL")
+ (description
+ "Make acoustic cues to use with the R package @code{ndl}.
+The package implements functions used in the PLoS ONE paper \"Words from
+spontaneous conversational speech can be recognized with human-like accuracy
+by an error-driven learning algorithm that discriminates between meanings
+straight from smart acoustic features, bypassing the phoneme as recognition
+unit.\" @url{doi:10.1371/journal.pone.0174623}")
+ (license license:gpl2+)))
+
+(define-public r-acp
+ (package
+ (name "r-acp")
+ (version "2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acp" version))
+ (sha256
+ (base32
+ "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
+ (properties `((upstream-name . "acp")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-quantmod" ,r-quantmod)
+ ("r-tseries" ,r-tseries)))
+ (home-page "https://cran.r-project.org/web/packages/acp/")
+ (synopsis "Autoregressive conditional Poisson")
+ (description
+ "This package supports the analysis of count data exhibiting
+autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
+model (ACP(p,q)) proposed by Heinen (2003).")
+ (license license:gpl2)))
+
+(define-public r-ada
+ (package
+ (name "r-ada")
+ (version "2.0-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ada" version))
+ (sha256
+ (base32
+ "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
+ (properties `((upstream-name . "ada")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-rpart" ,r-rpart)))
+ (home-page "https://cran.r-project.org/web/packages/ada/")
+ (synopsis "Stochastic boosting")
+ (description
+ "This package provides a straightforward, well-documented, and broad
+boosting routine for classification, ideally suited for small to
+moderate-sized data sets. It performs discrete, real, and gentle boost under
+both exponential and logistic loss on a given data set.")
+ ;; Any version of the GPL.
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-genalg
+ (package
+ (name "r-genalg")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "genalg" version))
+ (sha256
+ (base32
+ "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
+ (properties `((upstream-name . "genalg")))
+ (build-system r-build-system)
+ (home-page "https://github.com/egonw/genalg")
+ (synopsis "R based genetic algorithm")
+ (description
+ "This package provides an R based genetic algorithm for binary and
+floating point chromosomes.")
+ (license license:gpl2)))
+
+(define-public r-kernelfactory
+ (package
+ (name "r-kernelfactory")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "kernelFactory" version))
+ (sha256
+ (base32
+ "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
+ (properties `((upstream-name . "kernelFactory")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-auc" ,r-auc)
+ ("r-genalg" ,r-genalg)
+ ("r-kernlab" ,r-kernlab)
+ ("r-randomforest" ,r-randomforest)))
+ (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
+ (synopsis "Ensemble of kernel machines")
+ (description
+ "Kernel factory is an ensemble method where each base classifier (random
+forest) is fit on the kernel matrix of a subset of the training data.")
+ (license license:gpl2+)))
+
+(define-public r-dummies
+ (package
+ (name "r-dummies")
+ (version "1.5.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "dummies" version))
+ (sha256
+ (base32
+ "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
+ (properties `((upstream-name . "dummies")))
+ (build-system r-build-system)
+ (home-page "http://www.decisionpatterns.com")
+ (synopsis "Create dummy/indicator variables flexibly and efficiently")
+ (description
+ "This package lets you expand factors, characters and other eligible
+classes into dummy/indicator variables.")
+ (license license:gpl2+)))
+
+(define-public r-acrm
+ (package
+ (name "r-acrm")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "aCRM" version))
+ (sha256
+ (base32
+ "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
+ (properties `((upstream-name . "aCRM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ada" ,r-ada)
+ ("r-dummies" ,r-dummies)
+ ("r-kernelfactory" ,r-kernelfactory)
+ ("r-randomforest" ,r-randomforest)))
+ (home-page "https://cran.r-project.org/web/packages/aCRM/")
+ (synopsis "Convenience functions for analytical customer relationship management")
+ (description
+ "This package provides convenience functions for data preparation and
+modeling often used in @dfn{analytical customer relationship
+management} (aCRM).")
+ (license license:gpl2+)))
+
+(define-public r-treeclust
+ (package
+ (name "r-treeclust")
+ (version "1.1-7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "treeClust" version))
+ (sha256
+ (base32
+ "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
+ (properties `((upstream-name . "treeClust")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cluster" ,r-cluster)
+ ("r-rpart" ,r-rpart)))
+ (home-page "https://cran.r-project.org/web/packages/treeClust/")
+ (synopsis "Cluster distances through trees")
+ (description
+ "This package provides tools to create a measure of inter-point
+dissimilarity useful for clustering mixed data, and, optionally, perform the
+clustering.")
+ (license license:gpl2+)))
+
+(define-public r-acrosstic
+ (package
+ (name "r-acrosstic")
+ (version "1.0-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "AcrossTic" version))
+ (sha256
+ (base32
+ "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
+ (properties `((upstream-name . "AcrossTic")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lpsolve" ,r-lpsolve)
+ ("r-treeclust" ,r-treeclust)))
+ (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
+ (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
+ (description
+ "This is a package for constructing minimum-cost regular spanning
+subgraph as part of a non-parametric two-sample test for equality of
+distribution.")
+ (license license:gpl2+)))
+
+(define-public r-acrt
+ (package
+ (name "r-acrt")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acrt" version))
+ (sha256
+ (base32
+ "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
+ (properties `((upstream-name . "acrt")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-sandwich" ,r-sandwich)))
+ (home-page "https://cran.r-project.org/web/packages/acrt/")
+ (synopsis "Autocorrelation robust testing")
+ (description
+ "This package provides functions for testing affine hypotheses on the
+regression coefficient vector in regression models with autocorrelated
+errors.")
+ (license license:gpl2)))
+
+(define-public r-acs
+ (package
+ (name "r-acs")
+ (version "2.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acs" version))
+ (sha256
+ (base32
+ "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
+ (properties `((upstream-name . "acs")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-httr" ,r-httr)
+ ("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-stringr" ,r-stringr)
+ ("r-xml" ,r-xml)))
+ (home-page "http://dusp.mit.edu/faculty/ezra-glenn")
+ (synopsis "Work with data from the US Census")
+ (description
+ "This package provides a general toolkit for downloading, managing,
+analyzing, and presenting data from the
+@url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
+including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
+American Community Survey (ACS). Confidence intervals provided with ACS data
+are converted to standard errors to be bundled with estimates in complex
+@code{acs} objects. The package provides new methods to conduct standard
+operations on @code{acs} objects and present/plot data in statistically
+appropriate ways.")
+ (license license:gpl3)))
+
+(define-public r-acss-data
+ (package
+ (name "r-acss-data")
+ (version "1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acss.data" version))
+ (sha256
+ (base32
+ "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
+ (properties `((upstream-name . "acss.data")))
+ (build-system r-build-system)
+ (home-page "http://complexitycalculator.com/methodology.html")
+ (synopsis "Data for algorithmic complexity of short strings")
+ (description
+ "This is a data only package providing the algorithmic complexity of
+short strings, computed using the coding theorem method. For a given set of
+symbols in a string, all possible or a large number of random samples of
+Turing machines with a given number of states (e.g., 5) and number of symbols
+corresponding to the number of symbols in the strings were simulated until
+they reached a halting state or failed to end. This package contains data on
+4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
+4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
+distribution of the halting states.")
+ (license license:gpl2+)))
+
+(define-public r-acss
+ (package
+ (name "r-acss")
+ (version "0.2-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acss" version))
+ (sha256
+ (base32
+ "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
+ (properties `((upstream-name . "acss")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-acss-data" ,r-acss-data)
+ ("r-zoo" ,r-zoo)))
+ (home-page "http://complexitycalculator.com/methodology.html")
+ (synopsis "Algorithmic complexity for short strings")
+ (description
+ "The main purpose of this package is to provide the algorithmic
+complexity for short strings, an approximation of the Kolmogorov Complexity of
+a short string using the coding theorem method. While the database containing
+the complexity is provided in the data only package @code{acss.data}, this
+package provides functions accessing the data such as @code{prob_random}
+returning the posterior probability that a given string was produced by a
+random process. In addition, two traditional (but problematic) measures of
+complexity are also provided: entropy and change complexity.")
+ (license license:gpl2+)))
+
+(define-public r-acswr
+ (package
+ (name "r-acswr")
+ (version "1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ACSWR" version))
+ (sha256
+ (base32
+ "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
+ (properties `((upstream-name . "ACSWR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mass" ,r-mass)))
+ (home-page "https://cran.r-project.org/web/packages/ACSWR/")
+ (synopsis "Companion package for the book \"A Course in Statistics with R\"")
+ (description
+ "This is a companion package for the book \"A Course in Statistics with
+R\" (ISBN 978-1-119-15272-9.)")
+ (license license:gpl2)))
+
+(define-public r-alabama
+ (package
+ (name "r-alabama")
+ (version "2015.3-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "alabama" version))
+ (sha256
+ (base32
+ "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
+ (properties `((upstream-name . "alabama")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-numderiv" ,r-numderiv)))
+ (home-page "https://cran.r-project.org/web/packages/alabama/")
+ (synopsis "Constrained nonlinear optimization")
+ (description
+ "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
+Algorithm; it is used for optimizing smooth nonlinear objective functions with
+constraints. Linear or nonlinear equality and inequality constraints are
+allowed.")
+ (license license:gpl2+)))
+
+(define-public r-gdina
+ (package
+ (name "r-gdina")
+ (version "2.7.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "GDINA" version))
+ (sha256
+ (base32
+ "0875xfbm36gqzr0116xzlbm8rlff85rybr4s4hjzfflfvjdhgvfx"))))
+ (properties `((upstream-name . "GDINA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-alabama" ,r-alabama)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-mass" ,r-mass)
+ ("r-nloptr" ,r-nloptr)
+ ("r-numderiv" ,r-numderiv)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-rsolnp" ,r-rsolnp)
+ ("r-shiny" ,r-shiny)
+ ("r-shinydashboard" ,r-shinydashboard)))
+ (home-page "https://github.com/Wenchao-Ma/GDINA")
+ (synopsis "Generalized DINA model framework")
+ (description
+ "This package provides a set of psychometric tools for cognitive
+diagnosis modeling based on the generalized deterministic inputs, noisy and
+gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
+and its extensions, including the sequential G-DINA model by Ma and de la
+Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
+polytomous G-DINA model by Chen and de la Torre
+@url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
+distribution can be independent, saturated, higher-order, loglinear smoothed
+or structured. Q-matrix validation, item and model fit statistics, model
+comparison at test and item level and differential item functioning can also
+be conducted. A graphical user interface is also provided.")
+ (license license:gpl3)))
+
+(define-public r-actcd
+ (package
+ (name "r-actcd")
+ (version "1.2-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ACTCD" version))
+ (sha256
+ (base32
+ "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
+ (properties `((upstream-name . "ACTCD")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gdina" ,r-gdina)
+ ("r-r-methodss3" ,r-r-methodss3)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/ACTCD/")
+ (synopsis "Asymptotic classification theory for cognitive diagnosis")
+ (description
+ "This is a package supporting cluster analysis for cognitive diagnosis
+based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
+@url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
+sum-scores, cluster analysis techniques can be used to classify examinees into
+latent classes based on their attribute patterns. In addition to the
+algorithms used to classify data, three labeling approaches are proposed to
+label clusters so that examinees' attribute profiles can be obtained.")
+ (license license:gpl2+)))
+
+(define-public r-ineq
+ (package
+ (name "r-ineq")
+ (version "0.2-13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ineq" version))
+ (sha256
+ (base32
+ "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
+ (properties `((upstream-name . "ineq")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/ineq/")
+ (synopsis "Measuring inequality, concentration, and poverty")
+ (description
+ "This package provides tools for measuring inequality, concentration, and
+poverty measures. It provides both empirical and theoretical Lorenz curves.")
+ ;; Either of these two versions.
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-actfrag
+ (package
+ (name "r-actfrag")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ActFrag" version))
+ (sha256
+ (base32
+ "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d"))))
+ (properties `((upstream-name . "ActFrag")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-accelerometry" ,r-accelerometry)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ineq" ,r-ineq)
+ ("r-survival" ,r-survival)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "https://github.com/junruidi/ActFrag")
+ (synopsis "Activity fragmentation metrics extraction")
+ (description
+ "This package provides functions to extract commonly used fragmentation
+metrics to quantify time accumulation strategies based on minute level
+actigraphy-measured activity counts data.")
+ (license license:gpl3)))
+
+(define-public r-fda
+ (package
+ (name "r-fda")
+ (version "2.4.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fda" version))
+ (sha256
+ (base32
+ "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2"))))
+ (properties `((upstream-name . "fda")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrix" ,r-matrix)))
+ (home-page "http://www.functionaldata.org")
+ (synopsis "Functional data analysis")
+ (description
+ "These functions were developed to support functional data analysis as
+described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
+Analysis. The package includes data sets and script files working many
+examples.")
+ (license license:gpl2+)))
+
+(define-public r-actigraphy
+ (package
+ (name "r-actigraphy")
+ (version "1.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Actigraphy" version))
+ (sha256
+ (base32
+ "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574"))))
+ (properties `((upstream-name . "Actigraphy")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fda" ,r-fda)
+ ("r-sdmtools" ,r-sdmtools)))
+ (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
+ (synopsis "Actigraphy data analysis")
+ (description
+ "This package provides tools for functional linear modeling and analysis
+of actigraphy data.")
+ (license license:asl2.0)))
+
+(define-public r-activedriver
+ (package
+ (name "r-activedriver")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ActiveDriver" version))
+ (sha256
+ (base32
+ "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
+ (properties `((upstream-name . "ActiveDriver")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mass" ,r-mass)))
+ (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
+ (synopsis "Tools for finding cancer driver proteins")
+ (description
+ "This package provides a mutation analysis tool that discovers cancer
+driver genes with frequent mutations in protein signalling sites such as
+post-translational modifications (phosphorylation, ubiquitination, etc). The
+Poisson generalized linear regression model identifies genes where cancer
+mutations in signalling sites are more frequent than expected from the
+sequence of the entire gene. Integration of mutations with signalling
+information helps find new driver genes and propose candidate mechanisms to
+known drivers.")
+ (license license:gpl2+)))
+
+(define-public r-activitycounts
+ (package
+ (name "r-activitycounts")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "activityCounts" version))
+ (sha256
+ (base32
+ "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
+ (properties
+ `((upstream-name . "activityCounts")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lubridate" ,r-lubridate)
+ ("r-magrittr" ,r-magrittr)
+ ("r-seewave" ,r-seewave)
+ ("r-signal" ,r-signal)
+ ("r-tibble" ,r-tibble)))
+ (home-page "https://github.com/walkabillylab/activityCounts")
+ (synopsis "Generate ActiLife counts")
+ (description
+ "ActiLife generates activity counts from data collected by Actigraph
+accelerometers. Actigraph is one of the most common research-grade
+accelerometers. There is considerable research validating and developing
+algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
+counts are proprietary and difficult to implement if researchers use different
+accelerometer brands. The code creates ActiLife counts from raw acceleration
+data for different accelerometer brands.")
+ (license license:gpl3)))
+
+(define-public r-activityindex
+ (package
+ (name "r-activityindex")
+ (version "0.3.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ActivityIndex" version))
+ (sha256
+ (base32
+ "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
+ (properties `((upstream-name . "ActivityIndex")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-r-utils" ,r-r-utils)))
+ (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
+ (synopsis "Activity Index calculation using raw accelerometry data")
+ (description
+ "This is a package to read raw accelerometry from GT3X+ accelerometry
+data and plain table data to calculate the Activity Index from Bai et
+al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
+ (license license:gpl3)))
+
+(define-public r-activpal
+ (package
+ (name "r-activpal")
+ (version "0.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "activPAL" version))
+ (sha256
+ (base32
+ "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
+ (properties `((upstream-name . "activPAL")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-devtools" ,r-devtools)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-lubridate" ,r-lubridate)
+ ("r-magrittr" ,r-magrittr)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "https://cran.r-project.org/web/packages/activPAL")
+ (synopsis "Processing and chart generation from activPAL events files")
+ (description
+ "This package contains functions to generate pre-defined summary
+statistics from activPAL events files. The package also contains functions to
+produce informative graphics that visualize physical activity behaviour and
+trends. This includes generating graphs that align physical activity
+behaviour with additional time based observations described by other data
+sets, such as sleep diaries and continuous glucose monitoring data.")
+ (license license:gpl3)))
+
+(define-public r-activpalprocessing
+ (package
+ (name "r-activpalprocessing")
+ (version "1.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "activpalProcessing" version))
+ (sha256
+ (base32
+ "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
+ (properties
+ `((upstream-name . "activpalProcessing")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-chron" ,r-chron)))
+ (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
+ (synopsis "Process activPAL events files")
+ (description
+ "This package performs estimation of physical activity and sedentary
+behavior variables from activPAL events files.")
+ ;; Either version of the GPL.
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-actogrammr
+ (package
+ (name "r-actogrammr")
+ (version "0.2.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "actogrammr" version))
+ (sha256
+ (base32
+ "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
+ (properties `((upstream-name . "actogrammr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-lubridate" ,r-lubridate)
+ ("r-readr" ,r-readr)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "https://cran.r-project.org/web/packages/actogrammr/")
+ (synopsis "Read in activity data and plot actograms")
+ (description
+ "Read in activity measurements from standard file formats used by
+circadian rhythm researchers, currently only ClockLab format, and process and
+plot the data. The central type of plot is the actogram, as first described
+in \"Activity and distribution of certain wild mice in relation to biotic
+communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
+ (license license:gpl3)))
+
+(define-public r-expint
+ (package
+ (name "r-expint")
+ (version "0.1-6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "expint" version))
+ (sha256
+ (base32
+ "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
+ (properties `((upstream-name . "expint")))
+ (build-system r-build-system)
+ (home-page "https://gitlab.com/vigou3/expint")
+ (synopsis "Exponential integral and incomplete Gamma function")
+ (description
+ "This package provides the exponential integrals @code{E_1(x)},
+@code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
+function @code{G(a, x)} defined for negative values of its first argument.
+The package also gives easy access to the underlying C routines through an
+API; see the package vignette for details.")
+ (license license:gpl2+)))
+
+(define-public r-actuar
+ (package
+ (name "r-actuar")
+ (version "2.3-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "actuar" version))
+ (sha256
+ (base32
+ "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
+ (properties `((upstream-name . "actuar")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-expint" ,r-expint)))
+ (home-page "https://gitlab.com/vigou3/actuar")
+ (synopsis "Actuarial functions and heavy tailed distributions")
+ (description
+ "This package provides functions and data sets for actuarial science:
+modeling of loss distributions; risk theory and ruin theory; simulation of
+compound models, discrete mixtures and compound hierarchical models;
+credibility theory. It boasts support for many additional probability
+distributions to model insurance loss amounts and loss frequency: 19
+continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
+distribution; zero-truncated and zero-modified extensions of the standard
+discrete distributions. It also supports phase-type distributions commonly
+used to compute ruin probabilities.")
+ (license license:gpl2+)))
+
+(define-public r-bmp
+ (package
+ (name "r-bmp")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bmp" version))
+ (sha256
+ (base32
+ "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
+ (properties `((upstream-name . "bmp")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/bmp/")
+ (synopsis "Read Bitmap (BMP) images")
+ (description
+ "This package provides pure R tools to read BMP format images. It is
+currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
+ (license license:gpl2+)))
+
+(define-public r-readbitmap
+ (package
+ (name "r-readbitmap")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "readbitmap" version))
+ (sha256
+ (base32
+ "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
+ (properties `((upstream-name . "readbitmap")))
+ (build-system r-build-system)
+ (inputs
+ `(("libjpeg" ,libjpeg)
+ ("libpng" ,libpng)))
+ (propagated-inputs
+ `(("r-bmp" ,r-bmp)
+ ("r-jpeg" ,r-jpeg)
+ ("r-png" ,r-png)
+ ("r-tiff" ,r-tiff)))
+ (home-page "https://github.com/jefferis/readbitmap")
+ (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
+ (description
+ "This package provides tools to identify and read BMP, JPEG, PNG, and
+TIFF format bitmap images. Identification defaults to the use of the magic
+number embedded in the file rather than the file extension.")
+ (license license:gpl2+)))
+
+(define-public r-imager
+ (package
+ (name "r-imager")
+ (version "0.41.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "imager" version))
+ (sha256
+ (base32
+ "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v"))))
+ (properties `((upstream-name . "imager")))
+ (build-system r-build-system)
+ (inputs
+ `(("fftw" ,fftw)
+ ("libtiff" ,libtiff)
+ ("libx11" ,libx11)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-cairo" ,r-cairo)
+ ("r-downloader" ,r-downloader)
+ ("r-igraph" ,r-igraph)
+ ("r-jpeg" ,r-jpeg)
+ ("r-magrittr" ,r-magrittr)
+ ("r-plyr" ,r-plyr)
+ ("r-png" ,r-png)
+ ("r-purrr" ,r-purrr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-readbitmap" ,r-readbitmap)
+ ("r-stringr" ,r-stringr)))
+ (native-inputs `(("pkg-config" ,pkg-config)))
+ (home-page "http://dahtah.github.io/imager")
+ (synopsis "Image processing library")
+ (description
+ "This is a package for fast image processing for images in up to 4
+dimensions (two spatial dimensions, one time/depth dimension, one color
+dimension). It provides most traditional image processing tools (filtering,
+morphology, transformations, etc.) as well as various functions for easily
+analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
+simple, modern C++ library for image processing.")
+ (license license:lgpl3)))
+
+(define-public r-acuityview
+ (package
+ (name "r-acuityview")
+ (version "0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "AcuityView" version))
+ (sha256
+ (base32
+ "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
+ (properties `((upstream-name . "AcuityView")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fftwtools" ,r-fftwtools)
+ ("r-imager" ,r-imager)
+ ("r-plotrix" ,r-plotrix)))
+ (home-page "https://cran.r-project.org/web/packages/AcuityView/")
+ (synopsis "Display scenes as seen by an animal with less acute vision")
+ (description
+ "This package provides a simple method for representing a visual scene as
+it may be seen by an animal with less acute vision.")
+ (license license:gpl2+)))
+
+(define-public r-adabag
+ (package
+ (name "r-adabag")
+ (version "4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "adabag" version))
+ (sha256
+ (base32
+ "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
+ (properties `((upstream-name . "adabag")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-caret" ,r-caret)
+ ("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-rpart" ,r-rpart)))
+ (home-page "https://cran.r-project.org/web/packages/adabag/")
+ (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
+ (description
+ "This package implements Freund and Schapire's Adaboost.M1 algorithm and
+Breiman's Bagging algorithm using classification trees as individual
+classifiers. Once these classifiers have been trained, they can be used to
+predict on new data. Also, cross validation estimation of the error can be
+done.")
+ (license license:gpl2+)))
+
+(define-public r-adagio
+ (package
+ (name "r-adagio")
+ (version "0.7.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "adagio" version))
+ (sha256
+ (base32
+ "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
+ (properties `((upstream-name . "adagio")))
+ (build-system r-build-system)
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/adagio/")
+ (synopsis "Discrete and global optimization routines")
+ (description
+ "This package provides methods and algorithms for discrete optimization,
+e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
+Hooke-Jeeves minimization, and some (evolutionary) global optimization
+functions.")
+ (license license:gpl3+)))
+
+(define-public r-univoutl
+ (package
+ (name "r-univoutl")
+ (version "0.1-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "univOutl" version))
+ (sha256
+ (base32
+ "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
+ (properties `((upstream-name . "univOutl")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-hmisc" ,r-hmisc)
+ ("r-robustbase" ,r-robustbase)))
+ (home-page "https://github.com/marcellodo/univOutl")
+ (synopsis "Detection of univariate outliers")
+ (description
+ "This package provides well-known outlier detection techniques in the
+univariate case. Methods to deal with skewed distribution are included too.
+The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
+historical data is implemented as well. When available, survey weights can be
+used in outliers detection.")
+ (license license:gpl2+)))
+
+(define-public r-tolerance
+ (package
+ (name "r-tolerance")
+ (version "1.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tolerance" version))
+ (sha256
+ (base32
+ "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86"))))
+ (properties `((upstream-name . "tolerance")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rgl" ,r-rgl)))
+ (home-page "https://cran.r-project.org/web/packages/tolerance/")
+ (synopsis "Statistical tolerance intervals and regions")
+ (description
+ "This package provides functions for estimating tolerance
+limits (intervals) for various univariate distributions (binomial, Cauchy,
+discrete Pareto, exponential, two-parameter exponential, extreme value,
+hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
+normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
+Bayesian normal tolerance limits, multivariate normal tolerance regions,
+nonparametric tolerance intervals, tolerance bands for regression
+settings (linear regression, nonlinear regression, nonparametric regression,
+and multivariate regression), and analysis of variance tolerance intervals.
+Visualizations are also available for most of these settings.")
+ (license license:gpl2+)))
+
+(define-public r-additivitytests
+ (package
+ (name "r-additivitytests")
+ (version "1.1-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "additivityTests" version))
+ (sha256
+ (base32
+ "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
+ (properties
+ `((upstream-name . "additivityTests")))
+ (build-system r-build-system)
+ (home-page "https://github.com/simecek/additivityTests")
+ (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
+ (description
+ "This package provides an implementation of the Tukey, Mandel,
+Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
+ (license license:gpl3)))
+
+(define-public r-flexclust
+ (package
+ (name "r-flexclust")
+ (version "1.4-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "flexclust" version))
+ (sha256
+ (base32
+ "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
+ (properties `((upstream-name . "flexclust")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-class" ,r-class)
+ ("r-lattice" ,r-lattice)
+ ("r-modeltools" ,r-modeltools)))
+ (home-page "https://cran.r-project.org/web/packages/flexclust/")
+ (synopsis "Flexible cluster algorithms")
+ (description
+ "The main function @code{kcca} implements a general framework for
+k-centroids cluster analysis supporting arbitrary distance measures and
+centroid computation. Further cluster methods include hard competitive
+learning, neural gas, and QT clustering. There are numerous visualization
+methods for cluster results (neighborhood graphs, convex cluster hulls,
+barcharts of centroids, ...), and bootstrap methods for the analysis of
+cluster stability.")
+ (license license:gpl2)))
+
+(define-public r-biclust
+ (package
+ (name "r-biclust")
+ (version "2.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "biclust" version))
+ (sha256
+ (base32
+ "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0"))))
+ (properties `((upstream-name . "biclust")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-additivitytests" ,r-additivitytests)
+ ("r-colorspace" ,r-colorspace)
+ ("r-flexclust" ,r-flexclust)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "https://cran.r-project.org/web/packages/biclust/")
+ (synopsis "BiCluster algorithms")
+ (description
+ "The main function @code{biclust()} provides several algorithms to find
+biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
+In addition, the package provides methods for data
+preprocessing (normalization and discretization), visualization, and
+validation of bicluster solutions.")
+ (license license:gpl3)))
+
+(define-public r-icge
+ (package
+ (name "r-icge")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ICGE" version))
+ (sha256
+ (base32
+ "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
+ (properties `((upstream-name . "ICGE")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cluster" ,r-cluster)
+ ("r-mass" ,r-mass)))
+ (home-page "https://cran.r-project.org/web/packages/ICGE/")
+ (synopsis "Cluster estimation and identification of atypical units")
+ (description
+ "ICGE is a package that helps to estimate the number of real clusters in
+data as well as to identify atypical units. The underlying methods are based
+on distances rather than on unit x variables.")
+ (license license:gpl2+)))
+
+(define-public r-depth
+ (package
+ (name "r-depth")
+ (version "2.1-1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "depth" version))
+ (sha256
+ (base32
+ "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
+ (properties `((upstream-name . "depth")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abind" ,r-abind)
+ ("r-circular" ,r-circular)
+ ("r-rgl" ,r-rgl)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/depth/")
+ (synopsis "Nonparametric depth functions for multivariate analysis")
+ (description
+ "This package provides tools for depth functions methodology applied to
+multivariate analysis. Besides allowing calculation of depth values and
+depth-based location estimators, the package includes functions or drawing
+contour plots and perspective plots of depth functions. Euclidian and
+spherical depths are supported.")
+ (license license:gpl2)))
+
+(define-public r-archetypes
+ (package
+ (name "r-archetypes")
+ (version "2.2-0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "archetypes" version))
+ (sha256
+ (base32
+ "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
+ (properties `((upstream-name . "archetypes")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-modeltools" ,r-modeltools)
+ ("r-nnls" ,r-nnls)))
+ (home-page "https://cran.r-project.org/web/packages/archetypes")
+ (synopsis "Archetypal analysis")
+ (description
+ "The main function @code{archetypes} implements a framework for
+archetypal analysis supporting arbitrary problem solving mechanisms for the
+different conceptual parts of the algorithm.")
+ (license license:gpl2+)))
+
+(define-public r-shapes
+ (package
+ (name "r-shapes")
+ (version "1.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "shapes" version))
+ (sha256
+ (base32
+ "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
+ (properties `((upstream-name . "shapes")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mass" ,r-mass)
+ ("r-minpack-lm" ,r-minpack-lm)
+ ("r-rgl" ,r-rgl)
+ ("r-scatterplot3d" ,r-scatterplot3d)))
+ (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
+ (synopsis "Statistical shape analysis")
+ (description
+ "This package provides routines for the statistical analysis of landmark
+shapes, including Procrustes analysis, graphical displays, principal
+components analysis, permutation and bootstrap tests, thin-plate spline
+transformation grids and comparing covariance matrices. See Dryden, I.L. and
+Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
+Edition), John Wiley and Sons.")
+ (license license:gpl2)))
+
+(define-public r-anthropometry
+ (package
+ (name "r-anthropometry")
+ (version "1.13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Anthropometry" version))
+ (sha256
+ (base32
+ "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8"))))
+ (properties `((upstream-name . "Anthropometry")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-archetypes" ,r-archetypes)
+ ("r-biclust" ,r-biclust)
+ ("r-cluster" ,r-cluster)
+ ("r-depth" ,r-depth)
+ ("r-fnn" ,r-fnn)
+ ("r-icge" ,r-icge)
+ ("r-nnls" ,r-nnls)
+ ("r-rgl" ,r-rgl)
+ ("r-shapes" ,r-shapes)))
+ (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
+ (synopsis "Statistical methods for anthropometric data")
+ (description
+ "This package provides statistical methods especially developed to
+analyze anthropometric data. These methods are aimed at providing effective
+solutions to some commons problems related to Ergonomics and Anthropometry.
+They are based on clustering, the statistical concept of data depth,
+statistical shape analysis and archetypal analysis.")
+ (license license:gpl2+)))
+
+(define-public r-adamethods
+ (package
+ (name "r-adamethods")
+ (version "1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "adamethods" version))
+ (sha256
+ (base32
+ "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
+ (properties `((upstream-name . "adamethods")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-anthropometry" ,r-anthropometry)
+ ("r-archetypes" ,r-archetypes)
+ ("r-fnn" ,r-fnn)
+ ("r-foreach" ,r-foreach)
+ ("r-nnls" ,r-nnls)
+ ("r-tolerance" ,r-tolerance)
+ ("r-univoutl" ,r-univoutl)))
+ (home-page "https://cran.r-project.org/web/packages/adamethods/")
+ (synopsis "Archetypoid algorithms and anomaly detection")
+ (description
+ "This package is a collection of several algorithms to obtain
+archetypoids with small and large databases and with both classical
+multivariate data and functional data (univariate and multivariate). Some of
+these algorithms also allow to detect anomalies (outliers).")
+ (license license:gpl2+)))
+
+(define-public r-idpmisc
+ (package
+ (name "r-idpmisc")
+ (version "1.1.19")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "IDPmisc" version))
+ (sha256
+ (base32
+ "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd"))))
+ (properties `((upstream-name . "IDPmisc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)))
+ (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
+ (synopsis "Functions for data analyses and visualization")
+ (description
+ "This package provides different high-level graphics functions for
+displaying large datasets, displaying circular data in a very flexible way,
+finding local maxima, brewing color ramps, drawing nice arrows, zooming
+2D-plots, creating figures with differently colored margin and plot region.
+In addition, the package contains auxiliary functions for data manipulation
+like omitting observations with irregular values or selecting data by logical
+vectors, which include NAs. Other functions are especially useful in
+spectroscopy and analyses of environmental data: robust baseline fitting,
+finding peaks in spectra, converting humidity measures.")
+ (license license:gpl3+)))
+
+(define-public r-qqman
+ (package
+ (name "r-qqman")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "qqman" version))
+ (sha256
+ (base32
+ "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
+ (properties `((upstream-name . "qqman")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-calibrate" ,r-calibrate)))
+ (home-page "https://cran.r-project.org/web/packages/qqman/")
+ (synopsis "Q-Q and Manhattan plots for GWAS data")
+ (description
+ "This package allows you to create Q-Q and Manhattan plots for GWAS data
+from PLINK results.")
+ (license license:gpl3)))
+
+(define-public r-ggplot-multistats
+ (package
+ (name "r-ggplot-multistats")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ggplot.multistats" version))
+ (sha256
+ (base32
+ "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
+ (properties
+ `((upstream-name . "ggplot.multistats")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-hexbin" ,r-hexbin)
+ ("r-rlang" ,r-rlang)
+ ("r-scales" ,r-scales)))
+ (home-page "https://github.com/flying-sheep/ggplot.multistats")
+ (synopsis "Multiple summary statistics for binned stats/geometries")
+ (description
+ "This package provides the ggplot binning layer @code{stat_summaries_hex()},
+which functions similar to its singular form, but allows the use of multiple
+statistics per bin. Those statistics can be mapped to multiple bin
+aesthetics.")
+ (license license:gpl3)))
+
+(define-public r-knn-covertree
+ (package
+ (name "r-knn-covertree")
+ (version "1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "knn.covertree" version))
+ (sha256
+ (base32
+ "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
+ (properties `((upstream-name . "knn.covertree")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)))
+ (home-page "https://github.com/flying-sheep/knn.covertree")
+ (synopsis "Accurate kNN Implementation with multiple distance measures")
+ (description
+ "Similarly to the FNN package, this package allows calculation of the k
+nearest neighbors (kNN) of a data matrix. The implementation is based on
+cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
+Langford (2006) @url{doi:10.1145/1143844.1143857}.")
+ (license license:agpl3+)))
+
+(define-public r-poibin
+ (package
+ (name "r-poibin")
+ (version "1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "poibin" version))
+ (sha256
+ (base32
+ "1rllgmk7yanb5amysl33kmi11lx86q5kqblyb8qqb3ckj2w4jhm2"))))
+ (properties `((upstream-name . "poibin")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/poibin/")
+ (synopsis "Poisson binomial distribution")
+ (description
+ "This package provides an implementation of both the exact and
+approximation methods for computing the @dfn{cumulative distribution
+function} (CDF) of the Poisson binomial distribution. It also provides the
+@dfn{probability mass function} (PMF), quantile function, and random number
+generation for the Poisson binomial distribution.")
+ (license license:gpl2)))
+
+(define-public r-diagram
+ (package
+ (name "r-diagram")
+ (version "1.6.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diagram" version))
+ (sha256
+ (base32
+ "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
+ (properties `((upstream-name . "diagram")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-shape" ,r-shape)))
+ (home-page "https://cran.r-project.org/web/packages/diagram/")
+ (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
+ (description
+ "This package provides tools to visualize simple graphs (networks) based
+on a transition matrix, utilities to plot flow diagrams, visualizing webs,
+electrical networks, etc. It also includes supporting material for the book
+\"A practical guide to ecological modelling - using R as a simulation
+platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
+\"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
+Francesca Mazzia (2012).")
+ (license license:gpl2+)))
+
+(define-public r-lim
+ (package
+ (name "r-lim")
+ (version "1.4.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "LIM" version))
+ (sha256
+ (base32
+ "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
+ (properties `((upstream-name . "LIM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-diagram" ,r-diagram)
+ ("r-limsolve" ,r-limsolve)))
+ (home-page "https://cran.r-project.org/web/packages/LIM/")
+ (synopsis "Linear inverse model examples and solution methods")
+ (description
+ "This package provides functions that read and solve linear inverse
+problems (food web problems, linear programming problems).")
+ (license license:gpl2+)))
+
+(define-public r-shinycssloaders
+ (package
+ (name "r-shinycssloaders")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "shinycssloaders" version))
+ (sha256
+ (base32
+ "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4"))))
+ (properties
+ `((upstream-name . "shinycssloaders")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-digest" ,r-digest)
+ ("r-glue" ,r-glue)
+ ("r-shiny" ,r-shiny)))
+ (home-page "https://github.com/andrewsali/shinycssloaders")
+ (synopsis "Add CSS loading animations to Shiny outputs")
+ (description
+ "This package provides tools to create a lightweight Shiny wrapper for
+the css-loaders created by Luke Hass
+@url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
+automatically show a loader when the output is (re)calculating.")
+ (license license:gpl3)))
+
+(define-public r-rsvg
+ (package
+ (name "r-rsvg")
+ (version "1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rsvg" version))
+ (sha256
+ (base32
+ "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
+ (properties `((upstream-name . "rsvg")))
+ (build-system r-build-system)
+ (inputs
+ `(("librsvg" ,librsvg)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "https://github.com/jeroen/rsvg#readme")
+ (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
+ (description
+ "This package allows you to render vector-based SVG images into
+high-quality custom-size bitmap arrays using the librsvg2 library. The
+resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
+addition, the package can convert images directly to various formats such as
+PDF or PostScript.")
+ (license license:expat)))
+
+(define-public r-influencer
+ (package
+ (name "r-influencer")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "influenceR" version))
+ (sha256
+ (base32
+ "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
+ (properties `((upstream-name . "influenceR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)))
+ (home-page "https://github.com/rcc-uchicago/influenceR")
+ (synopsis "Tools to quantify structural importance of nodes in a network")
+ (description
+ "This package provides functionality to compute various node centrality
+measures on networks. Included are functions to compute betweenness
+centrality (by utilizing Madduri and Bader's SNAP library), implementations of
+Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
+algorithm to identify key players, and Valente's bridging metric. The
+betweenness, Key Players, and bridging implementations are parallelized with
+OpenMP.")
+ (license license:gpl2)))