Commit | Line | Data |
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cb7e4867 | 1 | ;;; GNU Guix --- Functional package management for GNU |
35cf4874 | 2 | ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
ed6094fc | 3 | ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com> |
f4cd2cea | 4 | ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> |
fcf40039 | 5 | ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> |
b70fa3c7 | 6 | ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> |
82047474 | 7 | ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> |
0947698c | 8 | ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> |
37337699 | 9 | ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> |
4c77abc4 | 10 | ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com> |
cd4b2e78 | 11 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
576e74ee RW |
12 | ;;; Copyright © 2017 Alex Kost <alezost@gmail.com> |
13 | ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com> | |
cb7e4867 RW |
14 | ;;; |
15 | ;;; This file is part of GNU Guix. | |
16 | ;;; | |
17 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
18 | ;;; under the terms of the GNU General Public License as published by | |
19 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
20 | ;;; your option) any later version. | |
21 | ;;; | |
22 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
23 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
24 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
25 | ;;; GNU General Public License for more details. | |
26 | ;;; | |
27 | ;;; You should have received a copy of the GNU General Public License | |
28 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
29 | ||
30 | (define-module (gnu packages statistics) | |
31 | #:use-module ((guix licenses) #:prefix license:) | |
32 | #:use-module (guix packages) | |
33 | #:use-module (guix download) | |
7941d1ed | 34 | #:use-module (guix hg-download) |
5f1bb222 | 35 | #:use-module (guix git-download) |
cb7e4867 | 36 | #:use-module (guix utils) |
dbb35813 | 37 | #:use-module (guix build-system ant) |
cb7e4867 | 38 | #:use-module (guix build-system gnu) |
b12636e6 | 39 | #:use-module (guix build-system r) |
9bc08aa0 | 40 | #:use-module (guix build-system python) |
f1fe5283 | 41 | #:use-module (guix build-system trivial) |
cb7e4867 | 42 | #:use-module (gnu packages) |
dbb35813 | 43 | #:use-module (gnu packages algebra) |
ed33049c | 44 | #:use-module (gnu packages autotools) |
9a7b5784 | 45 | #:use-module (gnu packages bash) |
ac257f12 | 46 | #:use-module (gnu packages check) |
cb7e4867 | 47 | #:use-module (gnu packages compression) |
056468dc | 48 | #:use-module (gnu packages cran) |
cefaa79c | 49 | #:use-module (gnu packages curl) |
576e74ee | 50 | #:use-module (gnu packages emacs) |
eeb883cb | 51 | #:use-module (gnu packages emacs-xyz) |
cb7e4867 RW |
52 | #:use-module (gnu packages gcc) |
53 | #:use-module (gnu packages gtk) | |
0b65f1a0 JD |
54 | #:use-module (gnu packages gettext) |
55 | #:use-module (gnu packages glib) | |
77bdb276 | 56 | #:use-module (gnu packages haskell) |
cb7e4867 RW |
57 | #:use-module (gnu packages icu4c) |
58 | #:use-module (gnu packages image) | |
59 | #:use-module (gnu packages java) | |
2d21d44d | 60 | #:use-module (gnu packages machine-learning) |
cb7e4867 | 61 | #:use-module (gnu packages maths) |
07f911ba | 62 | #:use-module (gnu packages multiprecision) |
cb7e4867 RW |
63 | #:use-module (gnu packages pcre) |
64 | #:use-module (gnu packages perl) | |
65 | #:use-module (gnu packages pkg-config) | |
9bc08aa0 | 66 | #:use-module (gnu packages python) |
44d10b1f | 67 | #:use-module (gnu packages python-xyz) |
cb7e4867 | 68 | #:use-module (gnu packages readline) |
035711f1 | 69 | #:use-module (gnu packages ssh) |
3146aab7 | 70 | #:use-module (gnu packages tcl) |
cb7e4867 | 71 | #:use-module (gnu packages texinfo) |
33dc54b0 | 72 | #:use-module (gnu packages time) |
035711f1 | 73 | #:use-module (gnu packages tls) |
ce0614dd | 74 | #:use-module (gnu packages base) |
6140747f | 75 | #:use-module (gnu packages web) |
67a167fd | 76 | #:use-module (gnu packages xml) |
9bc08aa0 | 77 | #:use-module (gnu packages xorg) |
9bc08aa0 | 78 | #:use-module (srfi srfi-1)) |
cb7e4867 | 79 | |
0b65f1a0 JD |
80 | |
81 | (define-public pspp | |
82 | (package | |
83 | (name "pspp") | |
ed33049c | 84 | (version "1.2.0") |
0b65f1a0 JD |
85 | (source |
86 | (origin | |
87 | (method url-fetch) | |
88 | (uri (string-append "mirror://gnu/pspp/pspp-" | |
89 | version ".tar.gz")) | |
90 | (sha256 | |
91 | (base32 | |
ed33049c | 92 | "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5")))) |
0b65f1a0 JD |
93 | (build-system gnu-build-system) |
94 | (inputs | |
95 | `(("cairo" ,cairo) | |
b94a6ca0 | 96 | ("gettext" ,gettext-minimal) |
0b65f1a0 JD |
97 | ("gsl" ,gsl) |
98 | ("libxml2" ,libxml2) | |
99 | ("pango" ,pango) | |
100 | ("readline" ,readline) | |
101 | ("gtk" ,gtk+) | |
102 | ("gtksourceview" ,gtksourceview) | |
ed33049c | 103 | ("spread-sheet-widget" ,spread-sheet-widget) |
0b65f1a0 JD |
104 | ("zlib" ,zlib))) |
105 | (native-inputs | |
ed33049c KK |
106 | `(("autoconf" ,autoconf) ;for tests |
107 | ("glib" ,glib "bin") ;for glib-genmarshal | |
0b65f1a0 | 108 | ("perl" ,perl) |
ed33049c KK |
109 | ("pkg-config" ,pkg-config) |
110 | ("python" ,python-2) ;for tests | |
111 | ("texinfo" ,texinfo))) | |
6fd52309 | 112 | (home-page "https://www.gnu.org/software/pspp/") |
0b65f1a0 JD |
113 | (synopsis "Statistical analysis") |
114 | (description | |
115 | "GNU PSPP is a statistical analysis program. It can perform | |
116 | descriptive statistics, T-tests, linear regression and non-parametric tests. | |
117 | It features both a graphical interface as well as command-line input. PSPP | |
118 | is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data | |
119 | can be imported from spreadsheets, text files and database sources and it can | |
120 | be output in text, PostScript, PDF or HTML.") | |
121 | (license license:gpl3+))) | |
122 | ||
0bca8643 RW |
123 | (define-public jags |
124 | (package | |
125 | (name "jags") | |
126 | (version "4.3.0") | |
127 | (source (origin | |
128 | (method url-fetch) | |
129 | (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/" | |
130 | (version-major version) ".x/Source/" | |
131 | "JAGS-" version ".tar.gz")) | |
132 | (sha256 | |
133 | (base32 | |
134 | "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica")))) | |
135 | (build-system gnu-build-system) | |
136 | (home-page "http://mcmc-jags.sourceforge.net/") | |
137 | (native-inputs | |
138 | `(("gfortran" ,gfortran) | |
139 | ("lapack" ,lapack))) | |
140 | (synopsis "Gibbs sampler") | |
141 | (description "JAGS is Just Another Gibbs Sampler. It is a program for | |
142 | analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) | |
143 | simulation not wholly unlike BUGS. JAGS was written with three aims in mind: | |
144 | ||
145 | @enumerate | |
146 | @item To have a cross-platform engine for the BUGS language; | |
147 | @item To be extensible, allowing users to write their own functions, | |
148 | distributions and samplers; | |
149 | @item To be a platform for experimentation with ideas in Bayesian modelling. | |
150 | @end enumerate\n") | |
151 | (license license:gpl2))) | |
152 | ||
cd4b2e78 TGR |
153 | (define-public libxls |
154 | (package | |
155 | (name "libxls") | |
156 | (version "1.5.0") | |
157 | (source | |
158 | (origin | |
159 | (method url-fetch) | |
160 | (uri (string-append "https://github.com/libxls/libxls/releases/download/" | |
161 | "v" version "/libxls-" version ".tar.gz")) | |
162 | (sha256 | |
163 | (base32 "00j2lrcvvhclmh3z9vy7myqq1br1jnnqkz2wzgk4a1gbg8c5afn5")))) | |
164 | (build-system gnu-build-system) | |
165 | (home-page "https://github.com/libxls/libxls") | |
166 | (synopsis "Read binary (.xls) Excel spreadsheet files") | |
167 | (description | |
168 | "libxls is a C library to read .xls spreadsheet files in the binary OLE | |
169 | BIFF8 format as created by Excel 97 and later versions. It cannot write them. | |
170 | ||
171 | This package also provides @command{xls2csv} to export Excel files to CSV.") | |
172 | (license license:bsd-2))) | |
173 | ||
aeb64f3c RW |
174 | ;; Update this package together with the set of recommended packages: r-boot, |
175 | ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, | |
176 | ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. | |
d22546cf | 177 | (define r-with-tests |
cb7e4867 | 178 | (package |
d22546cf | 179 | (name "r-with-tests") |
cee9ab24 | 180 | (version "3.5.1") |
cb7e4867 RW |
181 | (source (origin |
182 | (method url-fetch) | |
183 | (uri (string-append "mirror://cran/src/base/R-" | |
9cf5f134 | 184 | (version-major version) "/R-" |
cb7e4867 RW |
185 | version ".tar.gz")) |
186 | (sha256 | |
187 | (base32 | |
cee9ab24 | 188 | "1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4")))) |
cb7e4867 RW |
189 | (build-system gnu-build-system) |
190 | (arguments | |
f9c3bd2e | 191 | `(#:disallowed-references (,tzdata-for-tests) |
3ffaec13 | 192 | #:make-flags |
ff2b1c17 RW |
193 | (list (string-append "LDFLAGS=-Wl,-rpath=" |
194 | (assoc-ref %outputs "out") | |
4621acfd RW |
195 | "/lib/R/lib") |
196 | ;; This affects the embedded timestamp of only the core packages. | |
197 | "PKG_BUILT_STAMP=1970-01-01") | |
ff2b1c17 | 198 | #:phases |
f4f4ced8 | 199 | (modify-phases %standard-phases |
bd3a1846 | 200 | (add-before 'configure 'do-not-compress-serialized-files |
a8cd3523 | 201 | (lambda* (#:key inputs #:allow-other-keys) |
bd3a1846 RW |
202 | ;; This ensures that Guix can detect embedded store references; |
203 | ;; see bug #28157 for details. | |
204 | (substitute* "src/library/base/makebasedb.R" | |
205 | (("compress = TRUE") "compress = FALSE")) | |
a8cd3523 | 206 | #t)) |
b5ce25cc RJ |
207 | (add-before 'configure 'patch-uname |
208 | (lambda* (#:key inputs #:allow-other-keys) | |
209 | (let ((uname-bin (string-append (assoc-ref inputs "coreutils") | |
210 | "/bin/uname"))) | |
211 | (substitute* "src/scripts/R.sh.in" | |
212 | (("uname") uname-bin))) | |
213 | #t)) | |
aeb64f3c | 214 | (add-after 'unpack 'build-reproducibly |
4621acfd | 215 | (lambda _ |
60c9190e RW |
216 | ;; The documentation contains time stamps to demonstrate |
217 | ;; documentation generation in different phases. | |
218 | (substitute* "src/library/tools/man/Rd2HTML.Rd" | |
219 | (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S") | |
220 | "(removed for reproducibility)")) | |
221 | ||
222 | ;; Remove timestamp from tracing environment. This fixes | |
223 | ;; reproducibility of "methods.rd{b,x}". | |
224 | (substitute* "src/library/methods/R/trace.R" | |
225 | (("dateCreated = Sys.time\\(\\)") | |
226 | "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")")) | |
227 | ||
228 | ;; Ensure that gzipped files are reproducible. | |
beaa026a RW |
229 | (substitute* '("src/library/grDevices/Makefile.in" |
230 | "doc/manual/Makefile.in") | |
231 | (("R_GZIPCMD\\)" line) | |
232 | (string-append line " -n"))) | |
60c9190e RW |
233 | |
234 | ;; The "srcfile" procedure in "src/library/base/R/srcfile.R" | |
235 | ;; queries the mtime of a given file and records it in an object. | |
236 | ;; This is acceptable at runtime to detect stale source files, | |
237 | ;; but it destroys reproducibility at build time. | |
0fa4702c RW |
238 | |
239 | ;; Similarly, the "srcfilecopy" procedure records the current | |
240 | ;; time. We change both of them to respect SOURCE_DATE_EPOCH. | |
241 | (substitute* "src/library/base/R/srcfile.R" | |
242 | (("timestamp <- (timestamp.*|file.mtime.*)" _ time) | |
243 | (string-append "timestamp <- \ | |
244 | as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ | |
245 | as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\ | |
246 | } else { " time "}, origin=\"1970-01-01\")\n"))) | |
60c9190e | 247 | |
beaa026a RW |
248 | ;; This library is installed using "install_package_description", |
249 | ;; so we need to pass the "builtStamp" argument. | |
250 | (substitute* "src/library/tools/Makefile.in" | |
251 | (("(install_package_description\\(.*\"')\\)\"" line prefix) | |
252 | (string-append prefix ", builtStamp='1970-01-01')\""))) | |
174fbd5f RW |
253 | |
254 | ;; R bundles an older version of help2man, which does not respect | |
255 | ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man, | |
256 | ;; because that breaks a test. | |
257 | (with-fluids ((%default-port-encoding "ISO-8859-1")) | |
258 | (substitute* "tools/help2man.pl" | |
259 | (("my \\$date = strftime \"%B %Y\", localtime" line) | |
260 | (string-append line " 1")))) | |
4621acfd RW |
261 | #t)) |
262 | (add-before 'configure 'set-default-pager | |
f4f4ced8 RW |
263 | ;; Set default pager to "cat", because otherwise it is "false", |
264 | ;; making "help()" print nothing at all. | |
265 | (lambda _ (setenv "PAGER" "cat") #t)) | |
e42eb908 | 266 | (add-before 'check 'set-timezone |
a71d769d RW |
267 | ;; Some tests require the timezone to be set. However, the |
268 | ;; timezone may not just be "UTC", or else a brittle regression | |
269 | ;; test in reg-tests-1d will fail. | |
270 | (lambda* (#:key inputs #:allow-other-keys) | |
271 | (setenv "TZ" "UTC+1") | |
272 | (setenv "TZDIR" | |
273 | (string-append (assoc-ref inputs "tzdata") | |
274 | "/share/zoneinfo")) | |
275 | #t)) | |
af23b6e9 | 276 | (add-after 'build 'make-info |
aaaede49 | 277 | (lambda _ (invoke "make" "info"))) |
af23b6e9 | 278 | (add-after 'build 'install-info |
aaaede49 | 279 | (lambda _ (invoke "make" "install-info")))) |
cb7e4867 | 280 | #:configure-flags |
d22546cf RW |
281 | `(;; We build the recommended packages here, because they are needed in |
282 | ;; order to run the test suite. We disable them in the r-minimal | |
283 | ;; package. | |
aeb64f3c | 284 | "--with-cairo" |
71e98ca5 | 285 | "--with-blas=-lopenblas" |
cb7e4867 RW |
286 | "--with-libpng" |
287 | "--with-jpeglib" | |
288 | "--with-libtiff" | |
289 | "--with-ICU" | |
3146aab7 RW |
290 | "--with-tcltk" |
291 | ,(string-append "--with-tcl-config=" | |
292 | (assoc-ref %build-inputs "tcl") | |
293 | "/lib/tclConfig.sh") | |
294 | ,(string-append "--with-tk-config=" | |
295 | (assoc-ref %build-inputs "tk") | |
296 | "/lib/tkConfig.sh") | |
cb7e4867 RW |
297 | "--enable-R-shlib" |
298 | "--enable-BLAS-shlib" | |
f2ac9379 | 299 | "--with-system-tre"))) |
5e9738b7 RW |
300 | ;; R has some support for Java. When the JDK is available at configure |
301 | ;; time environment variables pointing to the JDK will be recorded under | |
302 | ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R | |
303 | ;; CMD javareconf". "R CMD javareconf" appears to only be used to update | |
304 | ;; the recorded environment variables in $R_HOME/etc. Refer to | |
305 | ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support | |
306 | ;; for additional information. | |
307 | ||
308 | ;; As the JDK is a rather large input with only very limited effects on R, | |
309 | ;; we decided to drop it. | |
cb7e4867 RW |
310 | (native-inputs |
311 | `(("bzip2" ,bzip2) | |
312 | ("perl" ,perl) | |
313 | ("pkg-config" ,pkg-config) | |
cb7e4867 | 314 | ("texinfo" ,texinfo) ; for building HTML manuals |
f9c3bd2e | 315 | ("tzdata" ,tzdata-for-tests) |
cb7e4867 RW |
316 | ("xz" ,xz))) |
317 | (inputs | |
05e9f30f RW |
318 | `(;; We need not only cairo here, but pango to ensure that tests for the |
319 | ;; "cairo" bitmapType plotting backend succeed. | |
320 | ("pango" ,pango) | |
b5ce25cc | 321 | ("coreutils" ,coreutils) |
e42eb908 | 322 | ("curl" ,curl) |
71e98ca5 | 323 | ("openblas" ,openblas) |
19afbea1 | 324 | ("gfortran" ,gfortran) |
cb7e4867 | 325 | ("icu4c" ,icu4c) |
cb7e4867 RW |
326 | ("libjpeg" ,libjpeg) |
327 | ("libpng" ,libpng) | |
328 | ("libtiff" ,libtiff) | |
329 | ("libxt" ,libxt) | |
330 | ("pcre" ,pcre) | |
331 | ("readline" ,readline) | |
9a7b5784 RW |
332 | ;; This avoids a reference to the ungraftable static bash. R uses the |
333 | ;; detected shell for the "system" procedure. | |
334 | ("bash" ,bash-minimal) | |
3146aab7 RW |
335 | ("tcl" ,tcl) |
336 | ("tk" ,tk) | |
bd3a1846 | 337 | ("which" ,which) |
cb7e4867 | 338 | ("zlib" ,zlib))) |
12a9f4af RW |
339 | (native-search-paths |
340 | (list (search-path-specification | |
341 | (variable "R_LIBS_SITE") | |
342 | (files (list "site-library/"))))) | |
d062957a | 343 | (home-page "https://www.r-project.org/") |
cb7e4867 RW |
344 | (synopsis "Environment for statistical computing and graphics") |
345 | (description | |
346 | "R is a language and environment for statistical computing and graphics. | |
347 | It provides a variety of statistical techniques, such as linear and nonlinear | |
348 | modeling, classical statistical tests, time-series analysis, classification | |
349 | and clustering. It also provides robust support for producing | |
350 | publication-quality data plots. A large amount of 3rd-party packages are | |
351 | available, greatly increasing its breadth and scope.") | |
352 | (license license:gpl3+))) | |
b12636e6 | 353 | |
d22546cf RW |
354 | (define-public r-minimal |
355 | (package (inherit r-with-tests) | |
356 | (name "r-minimal") | |
357 | (arguments | |
358 | `(#:tests? #f | |
359 | ,@(substitute-keyword-arguments (package-arguments r-with-tests) | |
360 | ((#:configure-flags flags) | |
361 | ;; Do not build the recommended packages. The build system creates | |
362 | ;; random temporary directories and embeds their names in some | |
363 | ;; package files. We build these packages with the r-build-system | |
364 | ;; instead. | |
365 | `(cons "--without-recommended-packages" ,flags))))))) | |
366 | ||
6be54a87 RW |
367 | (define-public rmath-standalone |
368 | (package (inherit r-minimal) | |
369 | (name "rmath-standalone") | |
370 | (arguments | |
371 | '(#:phases | |
372 | (modify-phases %standard-phases | |
373 | (add-after 'configure 'chdir | |
374 | (lambda _ (chdir "src/nmath/standalone/") #t))))) | |
375 | (synopsis "Standalone R math library") | |
376 | (description | |
377 | "This package provides the R math library as an independent package."))) | |
378 | ||
8f006917 RW |
379 | (define-public r-boot |
380 | (package | |
381 | (name "r-boot") | |
af1eeabe | 382 | (version "1.3-20") |
8f006917 RW |
383 | (source |
384 | (origin | |
385 | (method url-fetch) | |
386 | (uri (cran-uri "boot" version)) | |
387 | (sha256 | |
388 | (base32 | |
af1eeabe | 389 | "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd")))) |
8f006917 | 390 | (build-system r-build-system) |
e9960d8c | 391 | (home-page "https://cran.r-project.org/web/packages/boot") |
8f006917 RW |
392 | (synopsis "Bootstrap functions for R") |
393 | (description | |
394 | "This package provides functions and datasets for bootstrapping from the | |
395 | book \"Bootstrap Methods and Their Application\" by A.C. Davison and | |
396 | D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") | |
397 | ;; Unlimited distribution | |
398 | (license (license:non-copyleft "file://R/bootfuns.q")))) | |
399 | ||
c7e80a7e RW |
400 | (define-public r-mass |
401 | (package | |
402 | (name "r-mass") | |
600a25eb | 403 | (version "7.3-51.1") |
c7e80a7e RW |
404 | (source |
405 | (origin | |
406 | (method url-fetch) | |
407 | (uri (cran-uri "MASS" version)) | |
408 | (sha256 | |
409 | (base32 | |
600a25eb | 410 | "14907ia8418mp3p1rs1i2f1x5b6kk5z998dk353a29j3xqf3ybyq")))) |
c7e80a7e RW |
411 | (properties `((upstream-name . "MASS"))) |
412 | (build-system r-build-system) | |
413 | (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") | |
414 | (synopsis "Support functions and datasets for Venables and Ripley's MASS") | |
415 | (description | |
416 | "This package provides functions and datasets for the book \"Modern | |
417 | Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") | |
418 | ;; Either version may be picked. | |
419 | (license (list license:gpl2 license:gpl3)))) | |
420 | ||
74892587 RW |
421 | (define-public r-class |
422 | (package | |
423 | (name "r-class") | |
3dbd87f5 | 424 | (version "7.3-15") |
74892587 RW |
425 | (source |
426 | (origin | |
427 | (method url-fetch) | |
428 | (uri (cran-uri "class" version)) | |
429 | (sha256 | |
430 | (base32 | |
3dbd87f5 | 431 | "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn")))) |
74892587 RW |
432 | (build-system r-build-system) |
433 | (propagated-inputs | |
434 | `(("r-mass" ,r-mass))) | |
435 | (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") | |
436 | (synopsis "R functions for classification") | |
437 | (description | |
438 | "This package provides various functions for classification, including | |
439 | k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") | |
440 | ;; Either of the two versions can be picked. | |
441 | (license (list license:gpl2 license:gpl3)))) | |
442 | ||
a27bfb84 RW |
443 | (define-public r-cluster |
444 | (package | |
445 | (name "r-cluster") | |
ac6672d5 | 446 | (version "2.0.7-1") |
a27bfb84 RW |
447 | (source |
448 | (origin | |
449 | (method url-fetch) | |
450 | (uri (cran-uri "cluster" version)) | |
451 | (sha256 | |
452 | (base32 | |
ac6672d5 | 453 | "1grxbifbc4nwig25dmjgkympnbzb4al0w6k1c0ibdhpk1h4l20di")))) |
a27bfb84 | 454 | (build-system r-build-system) |
9ef9c648 RW |
455 | (inputs |
456 | `(("gfortran" ,gfortran))) | |
e9960d8c | 457 | (home-page "https://cran.r-project.org/web/packages/cluster") |
a27bfb84 RW |
458 | (synopsis "Methods for cluster analysis") |
459 | (description | |
460 | "This package provides methods for cluster analysis. It is a much | |
461 | extended version of the original from Peter Rousseeuw, Anja Struyf and Mia | |
462 | Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") | |
463 | (license license:gpl2+))) | |
464 | ||
c1999c59 RW |
465 | (define-public r-codetools |
466 | (package | |
467 | (name "r-codetools") | |
60f1bce0 | 468 | (version "0.2-16") |
c1999c59 RW |
469 | (source |
470 | (origin | |
471 | (method url-fetch) | |
472 | (uri (cran-uri "codetools" version)) | |
473 | (sha256 | |
474 | (base32 | |
60f1bce0 | 475 | "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn")))) |
c1999c59 | 476 | (build-system r-build-system) |
e9960d8c | 477 | (home-page "https://cran.r-project.org/web/packages/codetools") |
c1999c59 | 478 | (synopsis "Code analysis tools for R") |
9ef9c648 RW |
479 | (description "This package provides code analysis tools for R to check R |
480 | code for possible problems.") | |
c1999c59 RW |
481 | ;; Any version of the GPL. |
482 | (license (list license:gpl2+ license:gpl3+)))) | |
483 | ||
69fddd2d RW |
484 | (define-public r-foreign |
485 | (package | |
486 | (name "r-foreign") | |
43708816 | 487 | (version "0.8-71") |
69fddd2d RW |
488 | (source |
489 | (origin | |
490 | (method url-fetch) | |
491 | (uri (cran-uri "foreign" version)) | |
492 | (sha256 | |
493 | (base32 | |
43708816 | 494 | "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv")))) |
69fddd2d | 495 | (build-system r-build-system) |
e9960d8c | 496 | (home-page "https://cran.r-project.org/web/packages/foreign") |
69fddd2d RW |
497 | (synopsis "Read data stored by other statistics software") |
498 | (description | |
499 | "This package provides functions for reading and writing data stored by | |
500 | some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and | |
501 | for reading and writing some dBase files.") | |
502 | (license license:gpl2+))) | |
503 | ||
e88bad6d RW |
504 | (define-public r-kernsmooth |
505 | (package | |
506 | (name "r-kernsmooth") | |
507 | (version "2.23-15") | |
508 | (source | |
509 | (origin | |
510 | (method url-fetch) | |
511 | (uri (cran-uri "KernSmooth" version)) | |
512 | (sha256 | |
513 | (base32 | |
514 | "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) | |
515 | (properties `((upstream-name . "KernSmooth"))) | |
516 | (build-system r-build-system) | |
9ef9c648 RW |
517 | (inputs |
518 | `(("gfortran" ,gfortran))) | |
e9960d8c | 519 | (home-page "https://cran.r-project.org/web/packages/KernSmooth") |
e88bad6d RW |
520 | (synopsis "Functions for kernel smoothing") |
521 | (description | |
522 | "This package provides functions for kernel smoothing (and density | |
523 | estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) | |
524 | \"Kernel Smoothing\".") | |
9ef9c648 | 525 | ;; Unlimited use and distribution |
e88bad6d RW |
526 | (license (license:non-copyleft "file://LICENCE.note")))) |
527 | ||
060c1286 RW |
528 | (define-public r-lattice |
529 | (package | |
530 | (name "r-lattice") | |
1966d8ff | 531 | (version "0.20-38") |
060c1286 RW |
532 | (source (origin |
533 | (method url-fetch) | |
534 | (uri (cran-uri "lattice" version)) | |
535 | (sha256 | |
536 | (base32 | |
1966d8ff | 537 | "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx")))) |
060c1286 RW |
538 | (build-system r-build-system) |
539 | (home-page "http://lattice.r-forge.r-project.org/") | |
540 | (synopsis "High-level data visualization system") | |
541 | (description | |
542 | "The lattice package provides a powerful and elegant high-level data | |
543 | visualization system inspired by Trellis graphics, with an emphasis on | |
544 | multivariate data. Lattice is sufficient for typical graphics needs, and is | |
545 | also flexible enough to handle most nonstandard requirements.") | |
546 | (license license:gpl2+))) | |
547 | ||
69e14f9e RW |
548 | (define-public r-matrix |
549 | (package | |
550 | (name "r-matrix") | |
83ca17d8 | 551 | (version "1.2-15") |
69e14f9e RW |
552 | (source |
553 | (origin | |
554 | (method url-fetch) | |
555 | (uri (cran-uri "Matrix" version)) | |
556 | (sha256 | |
557 | (base32 | |
83ca17d8 | 558 | "1mshhyia6imh939p8labxi0wv21lal7csmccxi42klpgdh1j89kv")))) |
69e14f9e RW |
559 | (properties `((upstream-name . "Matrix"))) |
560 | (build-system r-build-system) | |
561 | (propagated-inputs | |
562 | `(("r-lattice" ,r-lattice))) | |
563 | (home-page "http://Matrix.R-forge.R-project.org/") | |
564 | (synopsis "Sparse and dense matrix classes and methods") | |
565 | (description | |
566 | "This package provides classes and methods for dense and sparse matrices | |
567 | and operations on them using LAPACK and SuiteSparse.") | |
568 | (license license:gpl2+))) | |
569 | ||
248f6526 RW |
570 | (define-public r-nlme |
571 | (package | |
572 | (name "r-nlme") | |
6fa9cf1a | 573 | (version "3.1-137") |
248f6526 RW |
574 | (source |
575 | (origin | |
576 | (method url-fetch) | |
577 | (uri (cran-uri "nlme" version)) | |
578 | (sha256 | |
579 | (base32 | |
6fa9cf1a | 580 | "11vyxxc0n36vb8d8g02zr0402ymicvbifwdsqm7gy9iqqnwrn101")))) |
248f6526 RW |
581 | (build-system r-build-system) |
582 | (propagated-inputs | |
583 | `(("r-lattice" ,r-lattice))) | |
584 | (native-inputs | |
585 | `(("gfortran" ,gfortran))) | |
e9960d8c | 586 | (home-page "https://cran.r-project.org/web/packages/nlme") |
248f6526 RW |
587 | (synopsis "Linear and nonlinear mixed effects models") |
588 | (description | |
589 | "This package provides tools to fit and compare Gaussian linear and | |
590 | nonlinear mixed-effects models.") | |
591 | (license license:gpl2+))) | |
592 | ||
ac8d738b RW |
593 | (define-public r-mgcv |
594 | (package | |
595 | (name "r-mgcv") | |
48a4b775 | 596 | (version "1.8-27") |
ac8d738b RW |
597 | (source |
598 | (origin | |
599 | (method url-fetch) | |
600 | (uri (cran-uri "mgcv" version)) | |
601 | (sha256 | |
602 | (base32 | |
48a4b775 | 603 | "06vx1z52gcdmji0phmphfa0sg62gwxkw590prplxgv4da7xrk2y8")))) |
ac8d738b RW |
604 | (build-system r-build-system) |
605 | (propagated-inputs | |
606 | `(("r-matrix" ,r-matrix) | |
607 | ("r-nlme" ,r-nlme))) | |
e9960d8c | 608 | (home-page "https://cran.r-project.org/web/packages/mgcv") |
ac8d738b RW |
609 | (synopsis "Mixed generalised additive model computation") |
610 | (description | |
611 | "GAMs, GAMMs and other generalized ridge regression with multiple smoothing | |
612 | parameter estimation by GCV, REML or UBRE/AIC. The library includes a | |
613 | @code{gam()} function, a wide variety of smoothers, JAGS support and | |
614 | distributions beyond the exponential family.") | |
615 | (license license:gpl2+))) | |
616 | ||
a5a34365 RW |
617 | (define-public r-nnet |
618 | (package | |
619 | (name "r-nnet") | |
620 | (version "7.3-12") | |
621 | (source | |
622 | (origin | |
623 | (method url-fetch) | |
624 | (uri (cran-uri "nnet" version)) | |
625 | (sha256 | |
626 | (base32 | |
627 | "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7")))) | |
628 | (build-system r-build-system) | |
629 | (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") | |
630 | (synopsis "Feed-forward neural networks and multinomial log-linear models") | |
631 | (description | |
632 | "This package provides functions for feed-forward neural networks with a | |
633 | single hidden layer, and for multinomial log-linear models.") | |
634 | (license (list license:gpl2+ license:gpl3+)))) | |
635 | ||
567b154f RW |
636 | (define-public r-rpart |
637 | (package | |
638 | (name "r-rpart") | |
e24ccf46 | 639 | (version "4.1-13") |
567b154f RW |
640 | (source |
641 | (origin | |
642 | (method url-fetch) | |
643 | (uri (cran-uri "rpart" version)) | |
644 | (sha256 | |
645 | (base32 | |
e24ccf46 | 646 | "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf")))) |
567b154f | 647 | (build-system r-build-system) |
e9960d8c | 648 | (home-page "https://cran.r-project.org/web/packages/rpart") |
567b154f RW |
649 | (synopsis "Recursive partitioning and regression trees") |
650 | (description | |
651 | "This package provides recursive partitioning functions for | |
652 | classification, regression and survival trees.") | |
653 | (license (list license:gpl2+ license:gpl3+)))) | |
654 | ||
4b005c7a RW |
655 | (define-public r-spatial |
656 | (package | |
657 | (name "r-spatial") | |
658 | (version "7.3-11") | |
659 | (source | |
660 | (origin | |
661 | (method url-fetch) | |
662 | (uri (cran-uri "spatial" version)) | |
663 | (sha256 | |
664 | (base32 | |
665 | "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32")))) | |
666 | (build-system r-build-system) | |
667 | (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") | |
668 | (synopsis "Functions for kriging and point pattern analysis") | |
669 | (description | |
670 | "This package provides functions for kriging and point pattern | |
671 | analysis.") | |
672 | ;; Either version may be picked. | |
673 | (license (list license:gpl2 license:gpl3)))) | |
674 | ||
6eaa9bfb RW |
675 | (define-public r-survival |
676 | (package | |
677 | (name "r-survival") | |
35cf4874 | 678 | (version "2.43-3") |
6eaa9bfb RW |
679 | (source |
680 | (origin | |
681 | (method url-fetch) | |
682 | (uri (cran-uri "survival" version)) | |
683 | (sha256 | |
684 | (base32 | |
35cf4874 | 685 | "0ldrjja1dj4n1ic0lbggm7jvk52sl5h85i8m23nrgndi60acsv4r")))) |
6eaa9bfb RW |
686 | (build-system r-build-system) |
687 | (propagated-inputs | |
688 | `(("r-matrix" ,r-matrix))) | |
689 | (home-page "https://github.com/therneau/survival") | |
690 | (synopsis "Survival analysis") | |
691 | (description | |
692 | "This package contains the core survival analysis routines, including | |
693 | definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) | |
694 | curves, Cox models, and parametric accelerated failure time models.") | |
695 | (license license:lgpl2.0+))) | |
696 | ||
2d7c4ae3 RW |
697 | (define-public r |
698 | (package (inherit r-minimal) | |
699 | (name "r") | |
f1fe5283 RW |
700 | (source #f) |
701 | (build-system trivial-build-system) | |
e3cfef22 | 702 | (arguments '(#:builder (begin (mkdir %output) #t))) |
f1fe5283 | 703 | (propagated-inputs |
2d7c4ae3 | 704 | `(("r-minimal" ,r-minimal) |
f1fe5283 RW |
705 | ("r-boot" ,r-boot) |
706 | ("r-class" ,r-class) | |
707 | ("r-cluster" ,r-cluster) | |
708 | ("r-codetools" ,r-codetools) | |
709 | ("r-foreign" ,r-foreign) | |
710 | ("r-kernsmooth" ,r-kernsmooth) | |
711 | ("r-lattice" ,r-lattice) | |
712 | ("r-mass" ,r-mass) | |
713 | ("r-matrix" ,r-matrix) | |
714 | ("r-mgcv" ,r-mgcv) | |
715 | ("r-nlme" ,r-nlme) | |
716 | ("r-nnet" ,r-nnet) | |
717 | ("r-rpart" ,r-rpart) | |
718 | ("r-spatial" ,r-spatial) | |
719 | ("r-survival" ,r-survival))))) | |
720 | ||
42066e6b BW |
721 | (define-public r-bit |
722 | (package | |
723 | (name "r-bit") | |
99b225f3 | 724 | (version "1.1-14") |
42066e6b BW |
725 | (source |
726 | (origin | |
727 | (method url-fetch) | |
728 | (uri (cran-uri "bit" version)) | |
729 | (sha256 | |
730 | (base32 | |
99b225f3 | 731 | "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw")))) |
42066e6b BW |
732 | (build-system r-build-system) |
733 | (home-page "http://ff.r-forge.r-project.org") | |
734 | (synopsis "Class for vectors of 1-bit booleans") | |
735 | (description | |
736 | "This package provides bitmapped vectors of booleans (no @code{NA}s), | |
737 | coercion from and to logicals, integers and integer subscripts, fast boolean | |
738 | operators and fast summary statistics. With @code{bit} class vectors of true | |
739 | binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") | |
740 | (license license:gpl2))) | |
741 | ||
ce3f92e7 BW |
742 | (define-public r-bit64 |
743 | (package | |
744 | (name "r-bit64") | |
831858a7 | 745 | (version "0.9-7") |
ce3f92e7 BW |
746 | (source |
747 | (origin | |
748 | (method url-fetch) | |
749 | (uri (cran-uri "bit64" version)) | |
750 | (sha256 | |
751 | (base32 | |
831858a7 | 752 | "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv")))) |
ce3f92e7 BW |
753 | (build-system r-build-system) |
754 | (propagated-inputs | |
755 | `(("r-bit" ,r-bit))) | |
756 | (home-page "http://ff.r-forge.r-project.org/") | |
757 | (synopsis "S3 class for vectors of 64 bit integers") | |
758 | (description | |
759 | "The bit64 package provides serializable S3 atomic 64 bit (signed) | |
760 | integers that can be used in vectors, matrices, arrays and @code{data.frames}. | |
761 | Methods are available for coercion from and to logicals, integers, doubles, | |
762 | characters and factors as well as many elementwise and summary functions. | |
763 | Many fast algorithmic operations such as @code{match} and @code{order} support | |
764 | interactive data exploration and manipulation and optionally leverage | |
765 | caching.") | |
766 | (license license:gpl2))) | |
767 | ||
3587effb RW |
768 | (define-public r-dichromat |
769 | (package | |
770 | (name "r-dichromat") | |
771 | (version "2.0-0") | |
772 | (source | |
773 | (origin | |
774 | (method url-fetch) | |
9cda3622 | 775 | (uri (cran-uri "dichromat" version)) |
3587effb RW |
776 | (sha256 |
777 | (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i")))) | |
778 | (build-system r-build-system) | |
e9960d8c | 779 | (home-page "https://cran.r-project.org/web/packages/dichromat") |
3587effb RW |
780 | (synopsis "Color schemes for dichromats") |
781 | (description | |
782 | "Dichromat collapses red-green or green-blue distinctions to simulate the | |
783 | effects of different types of color-blindness.") | |
784 | (license license:gpl2+))) | |
177f38c7 RW |
785 | |
786 | (define-public r-digest | |
787 | (package | |
788 | (name "r-digest") | |
05839496 | 789 | (version "0.6.18") |
177f38c7 RW |
790 | (source |
791 | (origin | |
792 | (method url-fetch) | |
9cda3622 | 793 | (uri (cran-uri "digest" version)) |
177f38c7 | 794 | (sha256 |
05839496 | 795 | (base32 "0k3iv0r8wy8w7zchmgrnrqv3bc149075j4817kf0q521vi4f6vbj")))) |
177f38c7 | 796 | (build-system r-build-system) |
fe2087cc RW |
797 | ;; Vignettes require r-knitr, which requires r-digest, so we have to |
798 | ;; disable them and the tests. | |
799 | (arguments | |
800 | `(#:tests? #f | |
801 | #:configure-flags (list "--no-build-vignettes"))) | |
177f38c7 RW |
802 | (home-page "http://dirk.eddelbuettel.com/code/digest.html") |
803 | (synopsis "Create cryptographic hash digests of R objects") | |
804 | (description | |
805 | "This package contains an implementation of a function 'digest()' for the | |
806 | creation of hash digests of arbitrary R objects (using the md5, sha-1, | |
807 | sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison | |
808 | of R language objects, as well as a function 'hmac()' to create hash-based | |
809 | message authentication code. | |
810 | ||
811 | Please note that this package is not meant to be deployed for cryptographic | |
812 | purposes for which more comprehensive (and widely tested) libraries such as | |
813 | OpenSSL should be used.") | |
814 | (license license:gpl2+))) | |
112bb3c0 | 815 | |
52ad9cb6 RJ |
816 | (define-public r-estimability |
817 | (package | |
818 | (name "r-estimability") | |
d222070a | 819 | (version "1.3") |
52ad9cb6 RJ |
820 | (source (origin |
821 | (method url-fetch) | |
822 | (uri (cran-uri "estimability" version)) | |
823 | (sha256 | |
824 | (base32 | |
d222070a | 825 | "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3")))) |
52ad9cb6 | 826 | (build-system r-build-system) |
e9960d8c | 827 | (home-page "https://cran.r-project.org/web/packages/estimability") |
52ad9cb6 RJ |
828 | (synopsis "Tools for assessing estimability of linear predictions") |
829 | (description "Provides tools for determining estimability of linear | |
830 | functions of regression coefficients, and 'epredict' methods that handle | |
831 | non-estimable cases correctly.") | |
832 | (license license:gpl2+))) | |
833 | ||
0c77fd50 RW |
834 | (define-public r-pheatmap |
835 | (package | |
836 | (name "r-pheatmap") | |
b6e27673 | 837 | (version "1.0.12") |
0c77fd50 RW |
838 | (source |
839 | (origin | |
840 | (method url-fetch) | |
841 | (uri (cran-uri "pheatmap" version)) | |
842 | (sha256 | |
843 | (base32 | |
b6e27673 | 844 | "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) |
0c77fd50 RW |
845 | (build-system r-build-system) |
846 | (propagated-inputs | |
847 | `(("r-gtable" ,r-gtable) | |
848 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
849 | ("r-scales" ,r-scales))) | |
850 | (home-page | |
e9960d8c | 851 | "https://cran.r-project.org/web/packages/pheatmap") |
0c77fd50 RW |
852 | (synopsis "Pretty heatmaps") |
853 | (description | |
854 | "This package provides an implementation of heatmaps that offers more | |
855 | control over dimensions and appearance.") | |
856 | (license license:gpl2+))) | |
857 | ||
b7eee9fc RW |
858 | (define-public r-labeling |
859 | (package | |
860 | (name "r-labeling") | |
861 | (version "0.3") | |
862 | (source | |
863 | (origin | |
864 | (method url-fetch) | |
9cda3622 | 865 | (uri (cran-uri "labeling" version)) |
b7eee9fc RW |
866 | (sha256 |
867 | (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d")))) | |
868 | (build-system r-build-system) | |
e9960d8c | 869 | (home-page "https://cran.r-project.org/web/packages/labeling") |
b7eee9fc RW |
870 | (synopsis "Axis labeling algorithms") |
871 | (description "The labeling package provides a range of axis labeling | |
872 | algorithms.") | |
873 | (license license:expat))) | |
d69c4b04 RW |
874 | |
875 | (define-public r-magrittr | |
876 | (package | |
877 | (name "r-magrittr") | |
878 | (version "1.5") | |
879 | (source | |
880 | (origin | |
881 | (method url-fetch) | |
9cda3622 | 882 | (uri (cran-uri "magrittr" version)) |
d69c4b04 RW |
883 | (sha256 |
884 | (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05")))) | |
885 | (build-system r-build-system) | |
e9960d8c | 886 | (home-page "https://cran.r-project.org/web/packages/magrittr/index.html") |
d69c4b04 RW |
887 | (synopsis "A forward-pipe operator for R") |
888 | (description | |
889 | "Magrittr provides a mechanism for chaining commands with a new | |
890 | forward-pipe operator, %>%. This operator will forward a value, or the result | |
891 | of an expression, into the next function call/expression. There is flexible | |
892 | support for the type of right-hand side expressions. For more information, | |
893 | see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") | |
894 | (license license:expat))) | |
44373339 RW |
895 | |
896 | (define-public r-munsell | |
897 | (package | |
898 | (name "r-munsell") | |
3399dc97 | 899 | (version "0.5.0") |
44373339 RW |
900 | (source |
901 | (origin | |
902 | (method url-fetch) | |
9cda3622 | 903 | (uri (cran-uri "munsell" version)) |
44373339 | 904 | (sha256 |
3399dc97 | 905 | (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh")))) |
44373339 RW |
906 | (build-system r-build-system) |
907 | (propagated-inputs | |
908 | `(("r-colorspace" ,r-colorspace))) | |
e9960d8c | 909 | (home-page "https://cran.r-project.org/web/packages/munsell") |
44373339 RW |
910 | (synopsis "Munsell colour system") |
911 | (description | |
912 | "The Munsell package contains Functions for exploring and using the | |
913 | Munsell colour system.") | |
914 | (license license:expat))) | |
ea69e2f8 | 915 | |
de682e6f BW |
916 | (define-public r-permute |
917 | (package | |
918 | (name "r-permute") | |
8b2f96e7 | 919 | (version "0.9-4") |
de682e6f BW |
920 | (source |
921 | (origin | |
922 | (method url-fetch) | |
923 | (uri (cran-uri "permute" version)) | |
924 | (sha256 | |
925 | (base32 | |
8b2f96e7 | 926 | "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5")))) |
de682e6f BW |
927 | (build-system r-build-system) |
928 | ;; Tests do not run correctly, but running them properly would entail a | |
929 | ;; circular dependency with vegan. | |
930 | (home-page "https://github.com/gavinsimpson/permute") | |
931 | (synopsis "Functions for Generating Restricted Permutations of Data") | |
932 | (description | |
933 | "This package provides a set of restricted permutation designs for freely | |
934 | exchangeable, line transects (time series), spatial grid designs and permutation | |
935 | of blocks (groups of samples). @code{permute} also allows split-plot designs, | |
936 | in which the whole-plots or split-plots or both can be freely exchangeable.") | |
937 | (license license:gpl2+))) | |
938 | ||
7e10056b RW |
939 | (define-public r-plyr |
940 | (package | |
941 | (name "r-plyr") | |
deb265a7 | 942 | (version "1.8.4") |
7e10056b RW |
943 | (source |
944 | (origin | |
945 | (method url-fetch) | |
9cda3622 | 946 | (uri (cran-uri "plyr" version)) |
7e10056b | 947 | (sha256 |
deb265a7 | 948 | (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0")))) |
7e10056b RW |
949 | (build-system r-build-system) |
950 | (native-inputs `(("r-rcpp" ,r-rcpp))) | |
951 | (home-page "http://had.co.nz/plyr") | |
952 | (synopsis "Tools for Splitting, Applying and Combining Data") | |
953 | (description | |
954 | "Plyr is a set of tools that solves a common set of problems: you need to | |
955 | break a big problem down into manageable pieces, operate on each piece and | |
956 | then put all the pieces back together. For example, you might want to fit a | |
957 | model to each spatial location or time point in your study, summarise data by | |
958 | panels or collapse high-dimensional arrays to simpler summary statistics.") | |
959 | (license license:expat))) | |
9a4d8968 RW |
960 | |
961 | (define-public r-proto | |
962 | (package | |
963 | (name "r-proto") | |
d13a4e25 | 964 | (version "1.0.0") |
9a4d8968 RW |
965 | (source |
966 | (origin | |
967 | (method url-fetch) | |
9cda3622 | 968 | (uri (cran-uri "proto" version)) |
9a4d8968 | 969 | (sha256 |
d13a4e25 | 970 | (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j")))) |
9a4d8968 | 971 | (build-system r-build-system) |
73ea83f5 | 972 | (home-page "https://github.com/hadley/proto") |
9a4d8968 RW |
973 | (synopsis "Prototype object-based programming") |
974 | (description | |
975 | "Proto is an object oriented system using object-based, also called | |
976 | prototype-based, rather than class-based object oriented ideas.") | |
977 | (license license:gpl2+))) | |
a45ba127 RW |
978 | |
979 | (define-public r-rcolorbrewer | |
980 | (package | |
981 | (name "r-rcolorbrewer") | |
982 | (version "1.1-2") | |
983 | (source | |
984 | (origin | |
985 | (method url-fetch) | |
9cda3622 | 986 | (uri (cran-uri "RColorBrewer" version)) |
a45ba127 RW |
987 | (sha256 |
988 | (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk")))) | |
989 | (build-system r-build-system) | |
e9960d8c | 990 | (home-page "https://cran.r-project.org/web/packages/RColorBrewer") |
a45ba127 RW |
991 | (synopsis "ColorBrewer palettes") |
992 | (description | |
993 | "This package provides color schemes for maps (and other graphics) | |
994 | designed by Cynthia Brewer as described at http://colorbrewer2.org") | |
995 | ;; Includes code licensed under bsd-4 | |
996 | (license license:asl2.0))) | |
4dca98dc | 997 | |
8e1bfc7e RW |
998 | (define-public r-sendmailr |
999 | (package | |
1000 | (name "r-sendmailr") | |
1001 | (version "1.2-1") | |
1002 | (source | |
1003 | (origin | |
1004 | (method url-fetch) | |
1005 | (uri (cran-uri "sendmailR" version)) | |
1006 | (sha256 | |
1007 | (base32 | |
1008 | "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4")))) | |
1009 | (properties `((upstream-name . "sendmailR"))) | |
1010 | (build-system r-build-system) | |
1011 | (propagated-inputs | |
1012 | `(("r-base64enc" ,r-base64enc))) | |
1013 | (home-page | |
e9960d8c | 1014 | "https://cran.r-project.org/web/packages/sendmailR") |
8e1bfc7e RW |
1015 | (synopsis "Send email using R") |
1016 | (description | |
1017 | "This package contains a simple SMTP client which provides a portable | |
1018 | solution for sending email, including attachments, from within R.") | |
1019 | (license license:gpl2+))) | |
1020 | ||
4dca98dc RW |
1021 | (define-public r-stringi |
1022 | (package | |
1023 | (name "r-stringi") | |
71fe7f9d | 1024 | (version "1.3.1") |
4dca98dc RW |
1025 | (source |
1026 | (origin | |
1027 | (method url-fetch) | |
9cda3622 | 1028 | (uri (cran-uri "stringi" version)) |
4dca98dc RW |
1029 | (sha256 |
1030 | (base32 | |
71fe7f9d | 1031 | "0qn3xy6vnz11vv2prbm55vkbgxr6dl8w5vk5q8d7wlp9nqxndprj")))) |
4dca98dc RW |
1032 | (build-system r-build-system) |
1033 | (inputs `(("icu4c" ,icu4c))) | |
1034 | (native-inputs `(("pkg-config" ,pkg-config))) | |
1035 | (home-page "http://stringi.rexamine.com/") | |
1036 | (synopsis "Character string processing facilities") | |
1037 | (description | |
1038 | "This package allows for fast, correct, consistent, portable, as well as | |
1039 | convenient character string/text processing in every locale and any native | |
1040 | encoding. Owing to the use of the ICU library, the package provides R users | |
1041 | with platform-independent functions known to Java, Perl, Python, PHP, and Ruby | |
1042 | programmers. Among available features there are: pattern searching | |
1043 | (e.g. via regular expressions), random string generation, string collation, | |
1044 | transliteration, concatenation, date-time formatting and parsing, etc.") | |
1045 | (license license:bsd-3))) | |
d5cd5c15 RW |
1046 | |
1047 | (define-public r-stringr | |
1048 | (package | |
1049 | (name "r-stringr") | |
605fcf8a | 1050 | (version "1.4.0") |
d5cd5c15 RW |
1051 | (source |
1052 | (origin | |
1053 | (method url-fetch) | |
9cda3622 | 1054 | (uri (cran-uri "stringr" version)) |
d5cd5c15 | 1055 | (sha256 |
605fcf8a | 1056 | (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47")))) |
d5cd5c15 RW |
1057 | (build-system r-build-system) |
1058 | (propagated-inputs | |
b4c6f4ca RW |
1059 | `(("r-glue" ,r-glue) |
1060 | ("r-magrittr" ,r-magrittr) | |
d5cd5c15 | 1061 | ("r-stringi" ,r-stringi))) |
718a2bde | 1062 | (home-page "https://github.com/hadley/stringr") |
d5cd5c15 RW |
1063 | (synopsis "Simple, consistent wrappers for common string operations") |
1064 | (description | |
1065 | "Stringr is a consistent, simple and easy to use set of wrappers around | |
1066 | the fantastic 'stringi' package. All function and argument names (and | |
1067 | positions) are consistent, all functions deal with \"NA\"'s and zero length | |
1068 | vectors in the same way, and the output from one function is easy to feed into | |
1069 | the input of another.") | |
1070 | (license license:gpl2+))) | |
9ca731ba RW |
1071 | |
1072 | (define-public r-reshape2 | |
1073 | (package | |
1074 | (name "r-reshape2") | |
de3fd925 | 1075 | (version "1.4.3") |
9ca731ba RW |
1076 | (source |
1077 | (origin | |
1078 | (method url-fetch) | |
9cda3622 | 1079 | (uri (cran-uri "reshape2" version)) |
9ca731ba | 1080 | (sha256 |
de3fd925 | 1081 | (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa")))) |
9ca731ba RW |
1082 | (build-system r-build-system) |
1083 | (propagated-inputs | |
1084 | `(("r-plyr" ,r-plyr) | |
1085 | ("r-rcpp" ,r-rcpp) | |
1086 | ("r-stringr" ,r-stringr))) | |
1087 | (home-page "https://github.com/hadley/reshape") | |
1088 | (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package") | |
1089 | (description | |
1090 | "Reshape2 is an R library to flexibly restructure and aggregate data | |
1091 | using just two functions: melt and dcast (or acast).") | |
1092 | (license license:expat))) | |
a11ee478 RW |
1093 | |
1094 | (define-public r-scales | |
1095 | (package | |
1096 | (name "r-scales") | |
3bf39027 | 1097 | (version "1.0.0") |
a11ee478 RW |
1098 | (source |
1099 | (origin | |
1100 | (method url-fetch) | |
9cda3622 | 1101 | (uri (cran-uri "scales" version)) |
a11ee478 | 1102 | (sha256 |
3bf39027 | 1103 | (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc")))) |
a11ee478 RW |
1104 | (build-system r-build-system) |
1105 | (propagated-inputs | |
3bf39027 | 1106 | `(("r-labeling" ,r-labeling) |
a11ee478 | 1107 | ("r-munsell" ,r-munsell) |
a11ee478 | 1108 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
b93881b9 RW |
1109 | ("r-rcpp" ,r-rcpp) |
1110 | ("r-r6" ,r-r6) | |
1111 | ("r-viridislite" ,r-viridislite))) | |
a11ee478 RW |
1112 | (home-page "https://github.com/hadley/scales") |
1113 | (synopsis "Scale functions for visualization") | |
1114 | (description | |
1115 | "This package provides graphical scales that map data to aesthetics, and | |
1116 | provides methods for automatically determining breaks and labels for axes and | |
1117 | legends.") | |
1118 | (license license:expat))) | |
d11b808f RW |
1119 | |
1120 | (define-public r-ggplot2 | |
1121 | (package | |
1122 | (name "r-ggplot2") | |
9413424d | 1123 | (version "3.1.0") |
d11b808f RW |
1124 | (source |
1125 | (origin | |
1126 | (method url-fetch) | |
9cda3622 | 1127 | (uri (cran-uri "ggplot2" version)) |
d11b808f | 1128 | (sha256 |
9413424d | 1129 | (base32 "1msy36r21nlmnpyaw2m9k0ykmnd19b9il01b65w457pfw75prrs9")))) |
d11b808f RW |
1130 | (build-system r-build-system) |
1131 | (propagated-inputs | |
1132 | `(("r-digest" ,r-digest) | |
1133 | ("r-gtable" ,r-gtable) | |
1134 | ("r-plyr" ,r-plyr) | |
ab01f1cd | 1135 | ("r-lazyeval" ,r-lazyeval) |
aeb64f3c | 1136 | ("r-mass" ,r-mass) |
f236d998 | 1137 | ("r-mgcv" ,r-mgcv) |
ab01f1cd | 1138 | ("r-tibble" ,r-tibble) |
d11b808f | 1139 | ("r-reshape2" ,r-reshape2) |
f236d998 | 1140 | ("r-rlang" ,r-rlang) |
e4b6c565 | 1141 | ("r-scales" ,r-scales) |
f236d998 AB |
1142 | ("r-svglite" ,r-svglite) ; Needed for 'ggsave' |
1143 | ("r-viridislite" ,r-viridislite) | |
1144 | ("r-withr" ,r-withr))) | |
1145 | (home-page "https://ggplot2.tidyverse.org") | |
d11b808f RW |
1146 | (synopsis "An implementation of the grammar of graphics") |
1147 | (description | |
1148 | "Ggplot2 is an implementation of the grammar of graphics in R. It | |
1149 | combines the advantages of both base and lattice graphics: conditioning and | |
1150 | shared axes are handled automatically, and you can still build up a plot step | |
1151 | by step from multiple data sources. It also implements a sophisticated | |
1152 | multidimensional conditioning system and a consistent interface to map data to | |
1153 | aesthetic attributes.") | |
1154 | (license license:gpl2+))) | |
ed6094fc | 1155 | |
6de897ac RJ |
1156 | (define-public r-ggdendro |
1157 | (package | |
1158 | (name "r-ggdendro") | |
1159 | (version "0.1-20") | |
1160 | (source (origin | |
1161 | (method url-fetch) | |
1162 | (uri (cran-uri "ggdendro" version)) | |
1163 | (sha256 | |
1164 | (base32 | |
1165 | "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j")))) | |
1166 | (build-system r-build-system) | |
1167 | (propagated-inputs | |
1168 | `(("r-ggplot2" ,r-ggplot2) | |
1169 | ("r-mass" ,r-mass) | |
1170 | ("r-knitr" ,r-knitr))) | |
1171 | (home-page "https://github.com/andrie/ggdendro") | |
1172 | (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2") | |
1173 | (description "This is a set of tools for dendrograms and tree plots using | |
1174 | ggplot2. The ggplot2 philosophy is to clearly separate data from the | |
1175 | presentation. Unfortunately the plot method for dendrograms plots directly | |
1176 | to a plot device with out exposing the data. The ggdendro package resolves | |
1177 | this by making available functions that extract the dendrogram plot data. | |
1178 | The package provides implementations for tree, rpart, as well as diana and | |
1179 | agnes cluster diagrams.") | |
1180 | (license license:gpl2+))) | |
1181 | ||
c5940b15 BW |
1182 | (define-public r-gdtools |
1183 | (package | |
1184 | (name "r-gdtools") | |
e3ddb563 | 1185 | (version "0.1.7") |
c5940b15 BW |
1186 | (source |
1187 | (origin | |
1188 | (method url-fetch) | |
1189 | (uri (cran-uri "gdtools" version)) | |
1190 | (sha256 | |
1191 | (base32 | |
e3ddb563 | 1192 | "122k9spymawfnfyksxyapwq9cigydy5nrjwhrwrhy3qkax3aycf6")))) |
c5940b15 BW |
1193 | (build-system r-build-system) |
1194 | (native-inputs | |
1195 | `(("r-rcpp" ,r-rcpp) | |
1196 | ("pkg-config" ,pkg-config))) | |
1197 | (inputs | |
e3ddb563 RW |
1198 | `(("cairo" ,cairo) |
1199 | ("zlib" ,zlib))) | |
054a9a78 RW |
1200 | (propagated-inputs |
1201 | `(("r-withr" ,r-withr))) | |
e9960d8c | 1202 | (home-page "https://cran.r-project.org/web/packages/gdtools") |
c5940b15 BW |
1203 | (synopsis "Utilities for graphical rendering") |
1204 | (description | |
1205 | "The @code{gdtools} package provides functionalities to get font metrics | |
1206 | and to generate base64 encoded string from raster matrix.") | |
1207 | (license license:gpl3))) | |
1208 | ||
3aebedcc BW |
1209 | (define-public r-svglite |
1210 | (package | |
1211 | (name "r-svglite") | |
ea008095 | 1212 | (version "1.2.1") |
3aebedcc BW |
1213 | (source |
1214 | (origin | |
1215 | (method url-fetch) | |
1216 | (uri (cran-uri "svglite" version)) | |
1217 | (sha256 | |
1218 | (base32 | |
ea008095 | 1219 | "1bws3lc4hlhln11zd7lalhiyc43yk6c6vrzy41fkxk1dkjazfx51")))) |
3aebedcc BW |
1220 | (build-system r-build-system) |
1221 | (native-inputs `(("r-rcpp" ,r-rcpp))) | |
1222 | (propagated-inputs | |
1223 | `(("r-bh" ,r-bh) | |
1224 | ("r-gdtools" ,r-gdtools))) | |
1225 | (home-page "https://github.com/hadley/svglite") | |
1226 | (synopsis "SVG graphics device") | |
1227 | (description | |
1228 | "@code{svglite} is a graphics device that produces clean | |
1229 | @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or | |
1230 | hand editing. Compared to the built-in @code{svg()}, @code{svglite} is | |
1231 | considerably faster, produces smaller files, and leaves text as is.") | |
1232 | (license license:gpl2+))) | |
1233 | ||
ed6094fc VVP |
1234 | (define-public r-assertthat |
1235 | (package | |
1236 | (name "r-assertthat") | |
958d0ee4 | 1237 | (version "0.2.0") |
ed6094fc VVP |
1238 | (source (origin |
1239 | (method url-fetch) | |
9cda3622 | 1240 | (uri (cran-uri "assertthat" version)) |
ed6094fc VVP |
1241 | (sha256 |
1242 | (base32 | |
958d0ee4 | 1243 | "1wp5znk3xy338x6hknppk702jn596yr735d9i7c3wabm3sdzfgnp")))) |
ed6094fc VVP |
1244 | (build-system r-build-system) |
1245 | (home-page "https://github.com/hadley/assertthat") | |
1246 | (synopsis "Easy pre and post assertions") | |
1247 | (description | |
1248 | "Assertthat is an extension to stopifnot() that makes it easy to declare | |
1249 | the pre and post conditions that your code should satisfy, while also | |
1250 | producing friendly error messages so that your users know what they've done | |
1251 | wrong.") | |
1252 | (license license:gpl3+))) | |
6af48134 VVP |
1253 | |
1254 | (define-public r-lazyeval | |
1255 | (package | |
1256 | (name "r-lazyeval") | |
bc409c8d | 1257 | (version "0.2.1") |
6af48134 VVP |
1258 | (source (origin |
1259 | (method url-fetch) | |
9cda3622 | 1260 | (uri (cran-uri "lazyeval" version)) |
6af48134 VVP |
1261 | (sha256 |
1262 | (base32 | |
bc409c8d | 1263 | "0q9zx78ncy2ffzrf9sh053069kd3w1xn1ss3gsbyf3y4jhza9cw3")))) |
6af48134 VVP |
1264 | (build-system r-build-system) |
1265 | (home-page "https://github.com/hadley/lazyeval") | |
1266 | (synopsis "Lazy (non-standard) evaluation in R") | |
1267 | (description | |
1268 | "This package provides the tools necessary to do non-standard | |
1269 | evaluation (NSE) in R.") | |
1270 | (license license:gpl3+))) | |
8ea6b30f VVP |
1271 | |
1272 | (define-public r-dbi | |
1273 | (package | |
1274 | (name "r-dbi") | |
c5324315 | 1275 | (version "1.0.0") |
8ea6b30f VVP |
1276 | (source (origin |
1277 | (method url-fetch) | |
9cda3622 | 1278 | (uri (cran-uri "DBI" version)) |
8ea6b30f VVP |
1279 | (sha256 |
1280 | (base32 | |
c5324315 | 1281 | "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz")))) |
8ea6b30f VVP |
1282 | (build-system r-build-system) |
1283 | (home-page "https://github.com/rstats-db/DBI") | |
1284 | (synopsis "R database interface") | |
1285 | (description | |
1286 | "The DBI package provides a database interface (DBI) definition for | |
1287 | communication between R and relational database management systems. All | |
1288 | classes in this package are virtual and need to be extended by the various | |
1289 | R/DBMS implementations.") | |
1290 | (license license:lgpl2.0+))) | |
675c9f44 VVP |
1291 | |
1292 | (define-public r-bh | |
1293 | (package | |
1294 | (name "r-bh") | |
eae93bd3 | 1295 | (version "1.69.0-1") |
675c9f44 VVP |
1296 | (source (origin |
1297 | (method url-fetch) | |
1298 | (uri (cran-uri "BH" version)) | |
1299 | (sha256 | |
1300 | (base32 | |
eae93bd3 | 1301 | "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0")))) |
675c9f44 VVP |
1302 | (build-system r-build-system) |
1303 | (home-page "https://github.com/eddelbuettel/bh") | |
1304 | (synopsis "R package providing subset of Boost headers") | |
1305 | (description | |
1306 | "This package aims to provide the most useful subset of Boost libraries | |
1307 | for template use among CRAN packages.") | |
1308 | (license license:boost1.0))) | |
256ccc92 VVP |
1309 | |
1310 | (define-public r-evaluate | |
1311 | (package | |
1312 | (name "r-evaluate") | |
aa995686 | 1313 | (version "0.12") |
256ccc92 VVP |
1314 | (source (origin |
1315 | (method url-fetch) | |
1316 | (uri (cran-uri "evaluate" version)) | |
1317 | (sha256 | |
1318 | (base32 | |
aa995686 | 1319 | "11rpn40153kcvqqrfhg2ldqfs68frg6yzsl0k3rxnlnv4c0v008g")))) |
256ccc92 | 1320 | (build-system r-build-system) |
256ccc92 VVP |
1321 | (home-page "https://github.com/hadley/evaluate") |
1322 | (synopsis "Parsing and evaluation tools for R") | |
1323 | (description | |
1324 | "This package provides tools that allow you to recreate the parsing, | |
1325 | evaluation and display of R code, with enough information that you can | |
1326 | accurately recreate what happens at the command line. The tools can easily be | |
1327 | adapted for other output formats, such as HTML or LaTeX.") | |
1328 | (license license:gpl3+))) | |
c5bf3abe VVP |
1329 | |
1330 | (define-public r-formatr | |
1331 | (package | |
1332 | (name "r-formatr") | |
6dc86e8d | 1333 | (version "1.5") |
c5bf3abe VVP |
1334 | (source (origin |
1335 | (method url-fetch) | |
1336 | (uri (cran-uri "formatR" version)) | |
1337 | (sha256 | |
1338 | (base32 | |
6dc86e8d | 1339 | "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47")))) |
c5bf3abe VVP |
1340 | (build-system r-build-system) |
1341 | (home-page "http://yihui.name/formatR") | |
1342 | (synopsis "Format R code automatically") | |
1343 | (description | |
1344 | "This package provides a function to format R source code. Spaces and | |
1345 | indent will be added to the code automatically, and comments will be preserved | |
1346 | under certain conditions, so that R code will be more human-readable and tidy. | |
1347 | There is also a Shiny app as a user interface in this package.") | |
1348 | (license license:gpl3+))) | |
ad3f005b VVP |
1349 | |
1350 | (define-public r-highr | |
1351 | (package | |
1352 | (name "r-highr") | |
d086829d | 1353 | (version "0.7") |
ad3f005b VVP |
1354 | (source (origin |
1355 | (method url-fetch) | |
1356 | (uri (cran-uri "highr" version)) | |
1357 | (sha256 | |
1358 | (base32 | |
d086829d | 1359 | "1dzknqk4x7iiiq1jkh9bqm5qcvs7mbqxbkn5955050payavabfya")))) |
ad3f005b VVP |
1360 | (build-system r-build-system) |
1361 | (home-page "https://github.com/yihui/highr") | |
1362 | (synopsis "Syntax highlighting for R source code") | |
1363 | (description | |
1364 | "This package provides syntax highlighting for R source code. Currently | |
1365 | it supports LaTeX and HTML output. Source code of other languages is | |
1366 | supported via Andre Simon's highlight package.") | |
1367 | (license license:gpl3+))) | |
acbb40fa VVP |
1368 | |
1369 | (define-public r-mime | |
1370 | (package | |
1371 | (name "r-mime") | |
9f743835 | 1372 | (version "0.6") |
acbb40fa VVP |
1373 | (source (origin |
1374 | (method url-fetch) | |
1375 | (uri (cran-uri "mime" version)) | |
1376 | (sha256 | |
1377 | (base32 | |
9f743835 | 1378 | "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7")))) |
acbb40fa VVP |
1379 | (build-system r-build-system) |
1380 | (home-page "https://github.com/yihui/mime") | |
1381 | (synopsis "R package to map filenames to MIME types") | |
1382 | (description | |
1383 | "This package guesses the MIME type from a filename extension using the | |
1384 | data derived from /etc/mime.types in UNIX-type systems.") | |
1385 | (license license:gpl2))) | |
3f8ac353 VVP |
1386 | |
1387 | (define-public r-markdown | |
1388 | (package | |
1389 | (name "r-markdown") | |
bf3aded0 | 1390 | (version "0.9") |
3f8ac353 VVP |
1391 | (source (origin |
1392 | (method url-fetch) | |
1393 | (uri (cran-uri "markdown" version)) | |
1394 | (sha256 | |
1395 | (base32 | |
bf3aded0 | 1396 | "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h")))) |
3f8ac353 VVP |
1397 | (build-system r-build-system) |
1398 | ;; Skip check phase because the tests require the r-knitr package to be | |
1399 | ;; installed. This prevents installation failures. Knitr normally | |
1400 | ;; shouldn't be available since r-markdown is a dependency of the r-knitr | |
1401 | ;; package. | |
1402 | (arguments `(#:tests? #f)) | |
1403 | (propagated-inputs | |
1404 | `(("r-mime" ,r-mime))) | |
1405 | (home-page "https://github.com/rstudio/markdown") | |
1406 | (synopsis "Markdown rendering for R") | |
1407 | (description | |
1408 | "This package provides R bindings to the Sundown Markdown rendering | |
1409 | library (https://github.com/vmg/sundown). Markdown is a plain-text formatting | |
1410 | syntax that can be converted to XHTML or other formats.") | |
1411 | (license license:gpl2))) | |
ea3a8095 VVP |
1412 | |
1413 | (define-public r-yaml | |
1414 | (package | |
1415 | (name "r-yaml") | |
3299bc1c | 1416 | (version "2.2.0") |
ea3a8095 VVP |
1417 | (source (origin |
1418 | (method url-fetch) | |
1419 | (uri (cran-uri "yaml" version)) | |
1420 | (sha256 | |
1421 | (base32 | |
3299bc1c | 1422 | "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m")))) |
ea3a8095 VVP |
1423 | (build-system r-build-system) |
1424 | (home-page "https://cran.r-project.org/web/packages/yaml/") | |
1425 | (synopsis "Methods to convert R data to YAML and back") | |
1426 | (description | |
1427 | "This package implements the libyaml YAML 1.1 parser and | |
1428 | emitter (http://pyyaml.org/wiki/LibYAML) for R.") | |
1429 | (license license:bsd-3))) | |
213656b9 VVP |
1430 | |
1431 | (define-public r-knitr | |
1432 | (package | |
1433 | (name "r-knitr") | |
495866a9 | 1434 | (version "1.21") |
213656b9 VVP |
1435 | (source (origin |
1436 | (method url-fetch) | |
1437 | (uri (cran-uri "knitr" version)) | |
1438 | (sha256 | |
1439 | (base32 | |
495866a9 | 1440 | "0xzymi4gkilqaa5b2ay9zk1advavzkwxf7mb064bqfb09y8rak0j")))) |
213656b9 VVP |
1441 | (build-system r-build-system) |
1442 | (propagated-inputs | |
1443 | `(("r-evaluate" ,r-evaluate) | |
213656b9 VVP |
1444 | ("r-highr" ,r-highr) |
1445 | ("r-markdown" ,r-markdown) | |
1446 | ("r-stringr" ,r-stringr) | |
495866a9 | 1447 | ("r-xfun" ,r-xfun) |
213656b9 VVP |
1448 | ("r-yaml" ,r-yaml))) |
1449 | (home-page "http://yihui.name/knitr/") | |
1450 | (synopsis "General-purpose package for dynamic report generation in R") | |
1451 | (description | |
1452 | "This package provides a general-purpose tool for dynamic report | |
1453 | generation in R using Literate Programming techniques.") | |
1454 | ;; The code is released under any version of the GPL. As it is used by | |
1455 | ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+ | |
1456 | ;; here. | |
1457 | (license license:gpl2+))) | |
4f0e8484 | 1458 | |
4ce3c287 RW |
1459 | (define-public r-knitrbootstrap |
1460 | (package | |
1461 | (name "r-knitrbootstrap") | |
624283a1 | 1462 | (version "1.0.2") |
4ce3c287 RW |
1463 | (source |
1464 | (origin | |
1465 | (method url-fetch) | |
1466 | (uri (cran-uri "knitrBootstrap" version)) | |
1467 | (sha256 | |
1468 | (base32 | |
624283a1 | 1469 | "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3")))) |
4ce3c287 RW |
1470 | (properties `((upstream-name . "knitrBootstrap"))) |
1471 | (build-system r-build-system) | |
1472 | (propagated-inputs | |
1473 | `(("r-knitr" ,r-knitr) | |
624283a1 RW |
1474 | ("r-rmarkdown" ,r-rmarkdown) |
1475 | ("r-markdown" ,r-markdown))) | |
4ce3c287 RW |
1476 | (home-page "https://github.com/jimhester/knitrBootstrap") |
1477 | (synopsis "Knitr bootstrap framework") | |
1478 | (description | |
1479 | "This package provides a framework to create Bootstrap 3 HTML reports | |
1480 | from knitr Rmarkdown.") | |
1481 | (license license:expat))) | |
1482 | ||
4f0e8484 VVP |
1483 | (define-public r-microbenchmark |
1484 | (package | |
1485 | (name "r-microbenchmark") | |
cb448dd2 | 1486 | (version "1.4-6") |
4f0e8484 VVP |
1487 | (source (origin |
1488 | (method url-fetch) | |
1489 | (uri (cran-uri "microbenchmark" version)) | |
1490 | (sha256 | |
1491 | (base32 | |
cb448dd2 | 1492 | "1sn1fxgzakm5iqbgc35g3k4yi0iqrkmwz33cvdrphrzh1lxnmi3s")))) |
4f0e8484 | 1493 | (build-system r-build-system) |
4f0e8484 VVP |
1494 | (home-page "https://cran.r-project.org/web/packages/microbenchmark/") |
1495 | (synopsis "Accurate timing functions for R") | |
1496 | (description | |
1497 | "This package provides infrastructure to accurately measure and compare | |
1498 | the execution time of R expressions.") | |
1499 | (license license:bsd-2))) | |
1cf1cbb0 | 1500 | |
0661b4db VVP |
1501 | (define-public r-pryr |
1502 | (package | |
1503 | (name "r-pryr") | |
1e898bba | 1504 | (version "0.1.4") |
0661b4db VVP |
1505 | (source (origin |
1506 | (method url-fetch) | |
1507 | (uri (cran-uri "pryr" version)) | |
1508 | (sha256 | |
1509 | (base32 | |
1e898bba | 1510 | "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k")))) |
0661b4db VVP |
1511 | (build-system r-build-system) |
1512 | (propagated-inputs | |
1513 | `(("r-stringr" ,r-stringr) | |
1514 | ("r-codetools" ,r-codetools))) | |
1515 | (native-inputs | |
1516 | `(("r-rcpp" ,r-rcpp))) | |
1517 | (home-page "https://github.com/hadley/pryr") | |
1518 | (synopsis "Tools for computing on the R language") | |
1519 | (description | |
1520 | "This package provides useful tools to pry back the covers of R and | |
1521 | understand the language at a deeper level.") | |
1522 | (license license:gpl2))) | |
b668a95c VVP |
1523 | |
1524 | (define-public r-memoise | |
1525 | (package | |
1526 | (name "r-memoise") | |
050d41ca | 1527 | (version "1.1.0") |
b668a95c VVP |
1528 | (source (origin |
1529 | (method url-fetch) | |
1530 | (uri (cran-uri "memoise" version)) | |
1531 | (sha256 | |
1532 | (base32 | |
050d41ca | 1533 | "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj")))) |
b668a95c VVP |
1534 | (build-system r-build-system) |
1535 | (propagated-inputs | |
1536 | `(("r-digest" ,r-digest))) | |
7bf837fd | 1537 | (home-page "https://github.com/hadley/memoise") |
b668a95c VVP |
1538 | (synopsis "Memoise functions for R") |
1539 | (description | |
1540 | "This R package allows to cache the results of a function so that when | |
1541 | you call it again with the same arguments it returns the pre-computed value.") | |
1542 | (license license:expat))) | |
834f7ff3 VVP |
1543 | |
1544 | (define-public r-crayon | |
1545 | (package | |
1546 | (name "r-crayon") | |
b0c8cba4 | 1547 | (version "1.3.4") |
834f7ff3 VVP |
1548 | (source (origin |
1549 | (method url-fetch) | |
1550 | (uri (cran-uri "crayon" version)) | |
1551 | (sha256 | |
1552 | (base32 | |
b0c8cba4 | 1553 | "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw")))) |
834f7ff3 VVP |
1554 | (build-system r-build-system) |
1555 | (propagated-inputs | |
1556 | `(("r-memoise" ,r-memoise))) | |
1557 | (home-page "https://github.com/gaborcsardi/crayon") | |
1558 | (synopsis "Colored terminal output for R") | |
1559 | (description | |
1560 | "Colored terminal output on terminals that support ANSI color and | |
1561 | highlight codes. It also works in Emacs ESS. ANSI color support is | |
1562 | automatically detected. Colors and highlighting can be combined and nested. | |
1563 | New styles can also be created easily. This package was inspired by the | |
1564 | \"chalk\" JavaScript project.") | |
1565 | (license license:expat))) | |
5b9789a6 | 1566 | |
35b2001a RW |
1567 | (define-public r-praise |
1568 | (package | |
1569 | (name "r-praise") | |
1570 | (version "1.0.0") | |
1571 | (source | |
1572 | (origin | |
1573 | (method url-fetch) | |
1574 | (uri (cran-uri "praise" version)) | |
1575 | (sha256 | |
1576 | (base32 | |
1577 | "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw")))) | |
1578 | (build-system r-build-system) | |
1579 | (home-page "https://github.com/gaborcsardi/praise") | |
1580 | (synopsis "Functions to praise users") | |
1581 | (description | |
1582 | "This package provides template functions to assist in building friendly | |
1583 | R packages that praise their users.") | |
1584 | (license license:expat))) | |
1585 | ||
5b9789a6 VVP |
1586 | (define-public r-testthat |
1587 | (package | |
1588 | (name "r-testthat") | |
3a83251c | 1589 | (version "2.0.1") |
5b9789a6 VVP |
1590 | (source (origin |
1591 | (method url-fetch) | |
1592 | (uri (cran-uri "testthat" version)) | |
1593 | (sha256 | |
1594 | (base32 | |
3a83251c | 1595 | "1cafy5xsjx6m08s45456mjsal7mfxzwpbrds0p4z3gwam948gpzy")))) |
5b9789a6 VVP |
1596 | (build-system r-build-system) |
1597 | (propagated-inputs | |
aead9e1b | 1598 | `(("r-cli" ,r-cli) |
99eca2b1 | 1599 | ("r-crayon" ,r-crayon) |
aead9e1b | 1600 | ("r-digest" ,r-digest) |
99eca2b1 RW |
1601 | ("r-magrittr" ,r-magrittr) |
1602 | ("r-praise" ,r-praise) | |
aead9e1b RW |
1603 | ("r-r6" ,r-r6) |
1604 | ("r-rlang" ,r-rlang) | |
1605 | ("r-withr" ,r-withr))) | |
5b9789a6 VVP |
1606 | (home-page "https://github.com/hadley/testthat") |
1607 | (synopsis "Unit testing for R") | |
1608 | (description | |
1609 | "This package provides a unit testing system for R designed to be fun, | |
1610 | flexible and easy to set up.") | |
1611 | (license license:expat))) | |
ffd4b478 VVP |
1612 | |
1613 | (define-public r-r6 | |
1614 | (package | |
1615 | (name "r-r6") | |
822863f8 | 1616 | (version "2.3.0") |
ffd4b478 VVP |
1617 | (source (origin |
1618 | (method url-fetch) | |
1619 | (uri (cran-uri "R6" version)) | |
1620 | (sha256 | |
1621 | (base32 | |
822863f8 | 1622 | "1jgshp0x8a65rwyvk31slnfp7l153dk5826y2rxcd5lpclby3d85")))) |
ffd4b478 | 1623 | (build-system r-build-system) |
ffd4b478 VVP |
1624 | (home-page "https://github.com/wch/R6/") |
1625 | (synopsis "Classes with reference semantics in R") | |
1626 | (description | |
1627 | "The R6 package allows the creation of classes with reference semantics, | |
1628 | similar to R's built-in reference classes. Compared to reference classes, R6 | |
1629 | classes are simpler and lighter-weight, and they are not built on S4 classes | |
1630 | so they do not require the methods package. These classes allow public and | |
1631 | private members, and they support inheritance, even when the classes are | |
1632 | defined in different packages.") | |
1633 | (license license:expat))) | |
2a3a8ae7 | 1634 | |
2f06dc04 RJ |
1635 | (define-public r-rlang |
1636 | (package | |
1637 | (name "r-rlang") | |
c668a958 | 1638 | (version "0.3.1") |
2f06dc04 RJ |
1639 | (source (origin |
1640 | (method url-fetch) | |
1641 | (uri (cran-uri "rlang" version)) | |
1642 | (sha256 | |
1643 | (base32 | |
c668a958 | 1644 | "0lbi66bavca866k26dnpkxj3l106xr4a6khcsfn8i3i8w8mpnhih")))) |
2f06dc04 RJ |
1645 | (build-system r-build-system) |
1646 | (home-page "http://rlang.tidyverse.org") | |
1647 | (synopsis "Functions for base types, core R and Tidyverse features") | |
1648 | (description "This package provides a toolbox for working with base types, | |
1649 | core R features like the condition system, and core @code{Tidyverse} features | |
1650 | like tidy evaluation.") | |
1651 | (license license:gpl3))) | |
1652 | ||
a589acfb RW |
1653 | (define-public r-tibble |
1654 | (package | |
1655 | (name "r-tibble") | |
3fe45dda | 1656 | (version "2.0.1") |
a589acfb RW |
1657 | (source |
1658 | (origin | |
1659 | (method url-fetch) | |
1660 | (uri (cran-uri "tibble" version)) | |
1661 | (sha256 | |
1662 | (base32 | |
3fe45dda | 1663 | "04rxf5x9awwa9c00v9p7d3a2lqnn7j2rjg4r219hmw7cbqlwrcks")))) |
a589acfb RW |
1664 | (build-system r-build-system) |
1665 | (propagated-inputs | |
f12ed366 | 1666 | `(("r-cli" ,r-cli) |
59b62f19 | 1667 | ("r-crayon" ,r-crayon) |
f12ed366 RW |
1668 | ("r-fansi" ,r-fansi) |
1669 | ("r-pkgconfig" ,r-pkgconfig) | |
1670 | ("r-pillar" ,r-pillar) | |
1671 | ("r-rlang" ,r-rlang))) | |
a589acfb RW |
1672 | (home-page "https://github.com/hadley/tibble") |
1673 | (synopsis "Simple data frames") | |
1674 | (description | |
1675 | "This package provides a @code{tbl_df} class that offers better checking | |
1676 | and printing capabilities than traditional data frames.") | |
1677 | (license license:expat))) | |
1678 | ||
2a3a8ae7 VVP |
1679 | (define-public r-dplyr |
1680 | (package | |
1681 | (name "r-dplyr") | |
441cf11d | 1682 | (version "0.7.8") |
2a3a8ae7 VVP |
1683 | (source (origin |
1684 | (method url-fetch) | |
1685 | (uri (cran-uri "dplyr" version)) | |
1686 | (sha256 | |
1687 | (base32 | |
441cf11d | 1688 | "06p59nhli8c1sarghzxq0y4pk6lyyz3xwkarp55b252dfg2rly9p")))) |
2a3a8ae7 VVP |
1689 | (build-system r-build-system) |
1690 | (propagated-inputs | |
1691 | `(("r-assertthat" ,r-assertthat) | |
1692 | ("r-r6" ,r-r6) | |
1693 | ("r-magrittr" ,r-magrittr) | |
a40b2c21 RW |
1694 | ("r-rlang" ,r-rlang) |
1695 | ("r-plogr" ,r-plogr) | |
1696 | ("r-glue" ,r-glue) | |
1697 | ("r-pkgconfig" ,r-pkgconfig) | |
1698 | ("r-bindrcpp" ,r-bindrcpp) | |
512f22f9 TGR |
1699 | ("r-tibble" ,r-tibble) |
1700 | ("r-tidyselect" ,r-tidyselect))) | |
2a3a8ae7 VVP |
1701 | (native-inputs |
1702 | `(("r-rcpp" ,r-rcpp) | |
1703 | ("r-bh" ,r-bh))) | |
1704 | (home-page "https://github.com/hadley/dplyr") | |
1705 | (synopsis "Tools for working with data frames in R") | |
1706 | (description | |
1707 | "dplyr is the next iteration of plyr. It is focussed on tools for | |
1708 | working with data frames. It has three main goals: 1) identify the most | |
1709 | important data manipulation tools needed for data analysis and make them easy | |
1710 | to use in R; 2) provide fast performance for in-memory data by writing key | |
1711 | pieces of code in C++; 3) use the same code interface to work with data no | |
1712 | matter where it is stored, whether in a data frame, a data table or | |
1713 | database.") | |
1714 | (license license:expat))) | |
91312ebe | 1715 | |
caa4e796 RW |
1716 | (define-public r-dbplyr |
1717 | (package | |
1718 | (name "r-dbplyr") | |
23347dc3 | 1719 | (version "1.3.0") |
caa4e796 RW |
1720 | (source |
1721 | (origin | |
1722 | (method url-fetch) | |
1723 | (uri (cran-uri "dbplyr" version)) | |
1724 | (sha256 | |
1725 | (base32 | |
23347dc3 | 1726 | "07p23vyvi7s4abldhkyir05kcf7xnfc18igfryq12j67xd0jql0m")))) |
caa4e796 RW |
1727 | (build-system r-build-system) |
1728 | (propagated-inputs | |
1729 | `(("r-assertthat" ,r-assertthat) | |
1730 | ("r-dbi" ,r-dbi) | |
1731 | ("r-dplyr" ,r-dplyr) | |
1732 | ("r-glue" ,r-glue) | |
1733 | ("r-purrr" ,r-purrr) | |
1734 | ("r-r6" ,r-r6) | |
1735 | ("r-rlang" ,r-rlang) | |
172b63e4 RW |
1736 | ("r-tibble" ,r-tibble) |
1737 | ("r-tidyselect" ,r-tidyselect))) | |
caa4e796 RW |
1738 | (home-page "https://github.com/tidyverse/dbplyr") |
1739 | (synopsis "Dplyr back end for databases") | |
1740 | (description | |
1741 | "This package provides a dplyr back end for databases that allows you to | |
1742 | work with remote database tables as if they are in-memory data frames. Basic | |
1743 | features works with any database that has a @code{DBI} back end; more advanced | |
1744 | features require SQL translation to be provided by the package author.") | |
1745 | (license license:expat))) | |
1746 | ||
b4d6f408 RW |
1747 | (define-public r-acepack |
1748 | (package | |
1749 | (name "r-acepack") | |
572e1a0c | 1750 | (version "1.4.1") |
b4d6f408 RW |
1751 | (source |
1752 | (origin | |
1753 | (method url-fetch) | |
1754 | (uri (cran-uri "acepack" version)) | |
1755 | (sha256 | |
1756 | (base32 | |
572e1a0c | 1757 | "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2")))) |
b4d6f408 RW |
1758 | (build-system r-build-system) |
1759 | (inputs | |
1760 | `(("gfortran" ,gfortran))) | |
e9960d8c | 1761 | (home-page "https://cran.r-project.org/web/packages/acepack") |
b4d6f408 RW |
1762 | (synopsis "Functions for regression transformations") |
1763 | (description | |
1764 | "This package provides ACE and AVAS methods for choosing regression | |
1765 | transformations.") | |
1766 | (license license:expat))) | |
1767 | ||
b1acb445 RW |
1768 | (define-public r-formula |
1769 | (package | |
1770 | (name "r-formula") | |
54d557e2 | 1771 | (version "1.2-3") |
b1acb445 RW |
1772 | (source |
1773 | (origin | |
1774 | (method url-fetch) | |
1775 | (uri (cran-uri "Formula" version)) | |
1776 | (sha256 | |
1777 | (base32 | |
54d557e2 | 1778 | "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l")))) |
b1acb445 RW |
1779 | (properties `((upstream-name . "Formula"))) |
1780 | (build-system r-build-system) | |
e9960d8c | 1781 | (home-page "https://cran.r-project.org/web/packages/Formula") |
b1acb445 RW |
1782 | (synopsis "Extended model formulas") |
1783 | (description | |
1784 | "This package provides a new class @code{Formula}, which extends the base | |
1785 | class @code{formula}. It supports extended formulas with multiple parts of | |
1786 | regressors on the right-hand side and/or multiple responses on the left-hand | |
1787 | side.") | |
1788 | (license (list license:gpl2+ license:gpl3+)))) | |
1789 | ||
97ee973d RW |
1790 | (define-public r-locfit |
1791 | (package | |
1792 | (name "r-locfit") | |
1793 | (version "1.5-9.1") | |
1794 | (source | |
1795 | (origin | |
1796 | (method url-fetch) | |
1797 | (uri (cran-uri "locfit" version)) | |
1798 | (sha256 | |
1799 | (base32 | |
1800 | "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m")))) | |
1801 | (build-system r-build-system) | |
aeb64f3c RW |
1802 | (propagated-inputs |
1803 | `(("r-lattice" ,r-lattice))) | |
e9960d8c | 1804 | (home-page "https://cran.r-project.org/web/packages/locfit") |
97ee973d RW |
1805 | (synopsis "Local regression, likelihood and density estimation") |
1806 | (description | |
1807 | "This package provides functions used for local regression, likelihood | |
1808 | and density estimation.") | |
1809 | (license (list license:gpl2+ license:gpl3+)))) | |
1810 | ||
91312ebe VVP |
1811 | (define-public r-chron |
1812 | (package | |
1813 | (name "r-chron") | |
45350539 | 1814 | (version "2.3-53") |
91312ebe VVP |
1815 | (source (origin |
1816 | (method url-fetch) | |
1817 | (uri (cran-uri "chron" version)) | |
1818 | (sha256 | |
1819 | (base32 | |
45350539 | 1820 | "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j")))) |
91312ebe | 1821 | (build-system r-build-system) |
e9960d8c | 1822 | (home-page "https://cran.r-project.org/web/packages/chron") |
91312ebe VVP |
1823 | (synopsis "Chronological R objects which can handle dates and times") |
1824 | (description | |
1825 | "This package provides chronological R objects which can handle dates and | |
1826 | times.") | |
1827 | (license license:gpl2))) | |
0e4e03f8 | 1828 | |
62141c07 | 1829 | (define-public r-data-table |
0e4e03f8 | 1830 | (package |
62141c07 | 1831 | (name "r-data-table") |
d0fb25d9 | 1832 | (version "1.12.0") |
0e4e03f8 VVP |
1833 | (source (origin |
1834 | (method url-fetch) | |
1835 | (uri (cran-uri "data.table" version)) | |
1836 | (sha256 | |
1837 | (base32 | |
d0fb25d9 | 1838 | "1xz388khklqqc39r1cmjvqm65azambgzqw0743aypm6v4chi26v1")))) |
0e4e03f8 | 1839 | (build-system r-build-system) |
0e4e03f8 VVP |
1840 | (home-page "https://github.com/Rdatatable/data.table/wiki") |
1841 | (synopsis "Enhanced version of data.frame R object") | |
1842 | (description | |
62141c07 RW |
1843 | "The R package @code{data.table} is an extension of @code{data.frame} |
1844 | providing functions for fast aggregation of large data (e.g. 100GB in RAM), | |
1845 | fast ordered joins, fast add/modify/delete of columns by group, column listing | |
1846 | and fast file reading.") | |
1847 | (license license:gpl3+))) | |
9bc08aa0 | 1848 | |
a73f4cd1 RW |
1849 | (define-public r-xtable |
1850 | (package | |
1851 | (name "r-xtable") | |
7f38b31e | 1852 | (version "1.8-3") |
a73f4cd1 RW |
1853 | (source |
1854 | (origin | |
1855 | (method url-fetch) | |
1856 | (uri (cran-uri "xtable" version)) | |
1857 | (sha256 | |
1858 | (base32 | |
7f38b31e | 1859 | "09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk")))) |
a73f4cd1 RW |
1860 | (build-system r-build-system) |
1861 | (native-inputs | |
7f38b31e | 1862 | `(("r-knitr" ,r-knitr))) ; for vignettes |
a73f4cd1 RW |
1863 | (home-page "http://xtable.r-forge.r-project.org/") |
1864 | (synopsis "Export R tables to LaTeX or HTML") | |
1865 | (description | |
1866 | "This package provides tools to export R data as LaTeX and HTML tables.") | |
1867 | (license license:gpl2+))) | |
1868 | ||
9bc08aa0 RW |
1869 | (define-public python-patsy |
1870 | (package | |
1871 | (name "python-patsy") | |
f4cd2cea | 1872 | (version "0.4.1") |
9bc08aa0 RW |
1873 | (source (origin |
1874 | (method url-fetch) | |
f4cd2cea | 1875 | (uri (pypi-uri "patsy" version ".zip")) |
9bc08aa0 RW |
1876 | (sha256 |
1877 | (base32 | |
f4cd2cea | 1878 | "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w")))) |
9bc08aa0 RW |
1879 | (build-system python-build-system) |
1880 | (arguments | |
1881 | `(#:phases | |
1882 | (modify-phases %standard-phases | |
9cbd819a TGR |
1883 | (replace 'check |
1884 | (lambda _ (invoke "nosetests" "-v")))))) | |
9bc08aa0 RW |
1885 | (propagated-inputs |
1886 | `(("python-numpy" ,python-numpy) | |
1887 | ("python-scipy" ,python-scipy) | |
1888 | ("python-six" ,python-six))) | |
1889 | (native-inputs | |
1890 | `(("python-nose" ,python-nose) | |
1891 | ("unzip" ,unzip))) | |
1892 | (home-page "https://github.com/pydata/patsy") | |
1893 | (synopsis "Describe statistical models and build design matrices") | |
1894 | (description | |
1895 | "Patsy is a Python package for describing statistical models and for | |
1896 | building design matrices.") | |
1897 | ;; The majority of the code is distributed under BSD-2. The module | |
1898 | ;; patsy.compat contains code derived from the Python standard library, | |
1899 | ;; and is covered by the PSFL. | |
5c31f4aa | 1900 | (license (list license:bsd-2 license:psfl)))) |
9bc08aa0 RW |
1901 | |
1902 | (define-public python2-patsy | |
5c31f4aa | 1903 | (package-with-python2 python-patsy)) |
37fdba7e RW |
1904 | |
1905 | (define-public python-statsmodels | |
1906 | (package | |
1907 | (name "python-statsmodels") | |
cee3d713 | 1908 | (version "0.9.0") |
37fdba7e RW |
1909 | (source |
1910 | (origin | |
1911 | (method url-fetch) | |
6cb74776 | 1912 | (uri (pypi-uri "statsmodels" version)) |
37fdba7e RW |
1913 | (sha256 |
1914 | (base32 | |
cee3d713 | 1915 | "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4")))) |
37fdba7e RW |
1916 | (build-system python-build-system) |
1917 | (arguments | |
4eeed444 RW |
1918 | `(;; The test suite is very large and rather brittle. Tests often fail |
1919 | ;; because of minor changes in dependencies that upstream hasn't fixed | |
1920 | ;; in a new release. | |
1921 | #:tests? #f | |
1922 | #:phases | |
37fdba7e | 1923 | (modify-phases %standard-phases |
37fdba7e RW |
1924 | (add-after 'unpack 'set-matplotlib-backend-to-agg |
1925 | (lambda _ | |
1926 | ;; Set the matplotlib backend to Agg to avoid problems using the | |
1927 | ;; GTK backend without a display. | |
6cb74776 MB |
1928 | (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py") |
1929 | '("statsmodels/tsa/vector_ar/tests/test_var.py" | |
1930 | "statsmodels/duration/tests/test_survfunc.py")) | |
37fdba7e RW |
1931 | (("import matplotlib\\.pyplot as plt" line) |
1932 | (string-append "import matplotlib;matplotlib.use('Agg');" | |
1933 | line))) | |
cee3d713 | 1934 | #t))))) |
37fdba7e RW |
1935 | (propagated-inputs |
1936 | `(("python-numpy" ,python-numpy) | |
1937 | ("python-scipy" ,python-scipy) | |
1938 | ("python-pandas" ,python-pandas) | |
1939 | ("python-patsy" ,python-patsy) | |
1940 | ("python-matplotlib" ,python-matplotlib))) | |
1941 | (native-inputs | |
1942 | `(("python-cython" ,python-cython) | |
1943 | ("python-nose" ,python-nose) | |
1944 | ("python-sphinx" ,python-sphinx))) | |
1945 | (home-page "http://statsmodels.sourceforge.net/") | |
1946 | (synopsis "Statistical modeling and econometrics in Python") | |
1947 | (description | |
1948 | "Statsmodels is a Python package that provides a complement to scipy for | |
1949 | statistical computations including descriptive statistics and estimation and | |
1950 | inference for statistical models.") | |
1951 | (license license:bsd-3))) | |
1952 | ||
1953 | (define-public python2-statsmodels | |
1954 | (let ((stats (package-with-python2 python-statsmodels))) | |
1955 | (package (inherit stats) | |
1956 | (propagated-inputs | |
8b52167e RW |
1957 | `(("python2-pytz" ,python2-pytz) |
1958 | ("python2-numpy" ,python2-numpy) | |
37fdba7e RW |
1959 | ("python2-scipy" ,python2-scipy) |
1960 | ("python2-pandas" ,python2-pandas) | |
1961 | ("python2-patsy" ,python2-patsy) | |
00e10c6e | 1962 | ("python2-matplotlib" ,python2-matplotlib)))))) |
67a167fd | 1963 | |
82047474 RJ |
1964 | (define-public r-coda |
1965 | (package | |
1966 | (name "r-coda") | |
e028eaa9 | 1967 | (version "0.19-2") |
82047474 RJ |
1968 | (source (origin |
1969 | (method url-fetch) | |
1970 | (uri (cran-uri "coda" version)) | |
1971 | (sha256 | |
1972 | (base32 | |
e028eaa9 | 1973 | "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7")))) |
82047474 | 1974 | (build-system r-build-system) |
aeb64f3c RW |
1975 | (propagated-inputs |
1976 | `(("r-lattice" ,r-lattice))) | |
e9960d8c | 1977 | (home-page "https://cran.r-project.org/web/packages/coda") |
82047474 RJ |
1978 | (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") |
1979 | (description "This package provides functions for summarizing and plotting | |
1980 | the output from Markov Chain Monte Carlo (MCMC) simulations, as well as | |
1981 | diagnostic tests of convergence to the equilibrium distribution of the Markov | |
1982 | chain.") | |
1983 | (license license:gpl2+))) | |
1984 | ||
fdd0f7b2 RW |
1985 | (define-public r-ade4 |
1986 | (package | |
1987 | (name "r-ade4") | |
9b7e8df8 | 1988 | (version "1.7-13") |
fdd0f7b2 RW |
1989 | (source |
1990 | (origin | |
1991 | (method url-fetch) | |
1992 | (uri (cran-uri "ade4" version)) | |
1993 | (sha256 | |
1994 | (base32 | |
9b7e8df8 | 1995 | "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m")))) |
fdd0f7b2 | 1996 | (build-system r-build-system) |
f9f1291b RW |
1997 | (propagated-inputs |
1998 | `(("r-mass" ,r-mass))) | |
fdd0f7b2 RW |
1999 | (home-page "http://pbil.univ-lyon1.fr/ADE-4") |
2000 | (synopsis "Multivariate data analysis and graphical display") | |
2001 | (description | |
2002 | "The ade4 package contains data analysis functions to analyze ecological | |
2003 | and environmental data in the framework of Euclidean exploratory methods.") | |
2004 | (license license:gpl2+))) | |
2005 | ||
67a167fd RW |
2006 | (define-public r-xml2 |
2007 | (package | |
2008 | (name "r-xml2") | |
78e03a76 | 2009 | (version "1.2.0") |
67a167fd RW |
2010 | (source |
2011 | (origin | |
2012 | (method url-fetch) | |
2013 | (uri (cran-uri "xml2" version)) | |
2014 | (sha256 | |
2015 | (base32 | |
78e03a76 | 2016 | "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha")))) |
67a167fd RW |
2017 | (build-system r-build-system) |
2018 | (inputs | |
78e03a76 RW |
2019 | `(("libxml2" ,libxml2) |
2020 | ("zlib" ,zlib))) | |
2021 | (native-inputs | |
2022 | `(("pkg-config" ,pkg-config))) | |
67a167fd | 2023 | (propagated-inputs |
78e03a76 | 2024 | `(("r-rcpp" ,r-rcpp))) |
67a167fd RW |
2025 | (home-page "https://github.com/hadley/xml2") |
2026 | (synopsis "Parse XML with R") | |
2027 | (description | |
2028 | "This package provides a simple, consistent interface to working with XML | |
2029 | files in R. It is built on top of the libxml2 C library.") | |
2030 | (license license:gpl2+))) | |
6140747f | 2031 | |
9003957e RW |
2032 | (define-public r-multitaper |
2033 | (package | |
2034 | (name "r-multitaper") | |
fde66e30 | 2035 | (version "1.0-14") |
9003957e RW |
2036 | (source |
2037 | (origin | |
2038 | (method url-fetch) | |
2039 | (uri (cran-uri "multitaper" version)) | |
2040 | (sha256 | |
2041 | (base32 | |
fde66e30 | 2042 | "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68")))) |
9003957e RW |
2043 | (build-system r-build-system) |
2044 | (native-inputs | |
2045 | `(("gfortran" ,gfortran))) | |
7bf837fd | 2046 | (home-page "https://github.com/wesleyburr/multitaper/") |
9003957e RW |
2047 | (synopsis "Multitaper spectral analysis tools") |
2048 | (description | |
2049 | "This package implements multitaper spectral estimation | |
2050 | techniques using prolate spheroidal sequences (Slepians) and sine | |
2051 | tapers for time series analysis. It includes an adaptive weighted | |
2052 | multitaper spectral estimate, a coherence estimate, Thomson's Harmonic | |
2053 | F-test, and complex demodulation. The Slepians sequences are | |
2054 | generated efficiently using a tridiagonal matrix solution, and | |
2055 | jackknifed confidence intervals are available for most estimates.") | |
2056 | (license license:gpl2+))) | |
2057 | ||
6140747f RW |
2058 | (define-public r-rversions |
2059 | (package | |
2060 | (name "r-rversions") | |
81147fe8 | 2061 | (version "1.0.3") |
6140747f RW |
2062 | (source (origin |
2063 | (method url-fetch) | |
2064 | (uri (cran-uri "rversions" version)) | |
2065 | (sha256 | |
2066 | (base32 | |
81147fe8 | 2067 | "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11")))) |
6140747f RW |
2068 | (build-system r-build-system) |
2069 | (propagated-inputs | |
2070 | `(("r-curl" ,r-curl) | |
2071 | ("r-xml2" ,r-xml2))) | |
2072 | (home-page "https://github.com/metacran/rversions") | |
2073 | (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") | |
2074 | (description | |
2075 | "This package provides functions to query the main R repository to find | |
2076 | the versions that @code{r-release} and @code{r-oldrel} refer to, and also all | |
2077 | previous R versions and their release dates.") | |
2078 | (license license:expat))) | |
1a77eccd RW |
2079 | |
2080 | (define-public r-whisker | |
2081 | (package | |
2082 | (name "r-whisker") | |
2083 | (version "0.3-2") | |
2084 | (source (origin | |
2085 | (method url-fetch) | |
2086 | (uri (cran-uri "whisker" version)) | |
2087 | (sha256 | |
2088 | (base32 | |
2089 | "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28")))) | |
2090 | (build-system r-build-system) | |
7bf837fd | 2091 | (home-page "https://github.com/edwindj/whisker") |
1a77eccd RW |
2092 | (synopsis "Logicless mustache templating for R") |
2093 | (description | |
2094 | "This package provides logicless templating, with a syntax that is not | |
2095 | limited to R.") | |
2096 | (license license:gpl3+))) | |
13d083af | 2097 | |
0d90462f RW |
2098 | (define-public r-backports |
2099 | (package | |
2100 | (name "r-backports") | |
ca4861c6 | 2101 | (version "1.1.3") |
0d90462f RW |
2102 | (source |
2103 | (origin | |
2104 | (method url-fetch) | |
2105 | (uri (cran-uri "backports" version)) | |
2106 | (sha256 | |
2107 | (base32 | |
ca4861c6 | 2108 | "1hac46xaawnqajlsfb5k7pfkc2ya9h76s5qv9ycj3jafh93d26z4")))) |
0d90462f | 2109 | (build-system r-build-system) |
e9960d8c | 2110 | (home-page "https://cran.r-project.org/web/packages/backports") |
0d90462f RW |
2111 | (synopsis "Reimplementations of functions introduced since R 3.0.0") |
2112 | (description | |
2113 | "Provides implementations of functions which have been introduced in R | |
2114 | since version 3.0.0. The backports are conditionally exported which results | |
2115 | in R resolving the function names to the version shipped with R (if available) | |
2116 | and uses the implemented backports as fallback. This way package developers | |
2117 | can make use of the new functions without worrying about the minimum required | |
2118 | R version.") | |
2119 | (license license:gpl2+))) | |
2120 | ||
929d4aae RW |
2121 | (define-public r-checkmate |
2122 | (package | |
2123 | (name "r-checkmate") | |
0550c2bf | 2124 | (version "1.9.1") |
929d4aae RW |
2125 | (source |
2126 | (origin | |
2127 | (method url-fetch) | |
2128 | (uri (cran-uri "checkmate" version)) | |
2129 | (sha256 | |
2130 | (base32 | |
0550c2bf | 2131 | "1y4ylzn55kpyfpzcx9rxb9413d3ck6hair36ldl0ak61ia5kc75p")))) |
929d4aae RW |
2132 | (build-system r-build-system) |
2133 | (propagated-inputs | |
2134 | `(("r-backports" ,r-backports))) | |
2135 | (home-page "https://github.com/mllg/checkmate") | |
2136 | (synopsis "Fast and versatile argument checks") | |
2137 | (description | |
2138 | "This package provides tests and assertions to perform frequent argument | |
2139 | checks. A substantial part of the package was written in C to minimize any | |
2140 | worries about execution time overhead.") | |
2141 | (license license:bsd-3))) | |
2142 | ||
cd26ec3b RW |
2143 | (define-public r-bbmisc |
2144 | (package | |
2145 | (name "r-bbmisc") | |
ac5e8102 | 2146 | (version "1.11") |
cd26ec3b RW |
2147 | (source |
2148 | (origin | |
2149 | (method url-fetch) | |
2150 | (uri (cran-uri "BBmisc" version)) | |
2151 | (sha256 | |
2152 | (base32 | |
ac5e8102 | 2153 | "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y")))) |
cd26ec3b RW |
2154 | (properties `((upstream-name . "BBmisc"))) |
2155 | (build-system r-build-system) | |
2156 | (propagated-inputs | |
2157 | `(("r-checkmate" ,r-checkmate))) | |
2158 | (home-page "https://github.com/berndbischl/BBmisc") | |
2159 | (synopsis "Miscellaneous functions for R package development") | |
2160 | (description | |
2161 | "This package provides miscellaneous helper functions for the development | |
2162 | of R packages.") | |
2163 | (license license:bsd-3))) | |
2164 | ||
dc4fb16d RW |
2165 | (define-public r-fail |
2166 | (package | |
2167 | (name "r-fail") | |
2168 | (version "1.3") | |
2169 | (source | |
2170 | (origin | |
2171 | (method url-fetch) | |
2172 | (uri (cran-uri "fail" version)) | |
2173 | (sha256 | |
2174 | (base32 | |
2175 | "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d")))) | |
2176 | (build-system r-build-system) | |
2177 | (propagated-inputs | |
2178 | `(("r-bbmisc" ,r-bbmisc) | |
2179 | ("r-checkmate" ,r-checkmate))) | |
2180 | (home-page "https://github.com/mllg/fail") | |
2181 | (synopsis "File abstraction interface layer (FAIL)") | |
2182 | (description | |
2183 | "This package provides a more comfortable interface to work with R data | |
2184 | or source files in a key-value fashion.") | |
2185 | (license license:bsd-3))) | |
2186 | ||
9e330278 RW |
2187 | (define-public r-batchjobs |
2188 | (package | |
2189 | (name "r-batchjobs") | |
e35cac95 | 2190 | (version "1.7") |
9e330278 RW |
2191 | (source |
2192 | (origin | |
2193 | (method url-fetch) | |
2194 | (uri (cran-uri "BatchJobs" version)) | |
2195 | (sha256 | |
2196 | (base32 | |
e35cac95 | 2197 | "035658marnw57p4f38g99rwmvmb6hpbq0fhlxp3qbw22zfnnkvs9")))) |
9e330278 RW |
2198 | (properties `((upstream-name . "BatchJobs"))) |
2199 | (build-system r-build-system) | |
2200 | (propagated-inputs | |
e35cac95 RW |
2201 | `(("r-backports" ,r-backports) |
2202 | ("r-bbmisc" ,r-bbmisc) | |
9e330278 RW |
2203 | ("r-brew" ,r-brew) |
2204 | ("r-checkmate" ,r-checkmate) | |
e35cac95 | 2205 | ("r-data-table" ,r-data-table) |
9e330278 RW |
2206 | ("r-dbi" ,r-dbi) |
2207 | ("r-digest" ,r-digest) | |
9e330278 RW |
2208 | ("r-rsqlite" ,r-rsqlite) |
2209 | ("r-sendmailr" ,r-sendmailr) | |
e35cac95 | 2210 | ("r-stringi" ,r-stringi))) |
9e330278 RW |
2211 | (home-page "https://github.com/tudo-r/BatchJobs") |
2212 | (synopsis "Batch computing with R") | |
2213 | (description | |
2214 | "This package provides @code{Map}, @code{Reduce} and @code{Filter} | |
2215 | variants to generate jobs on batch computing systems like PBS/Torque, LSF, | |
2216 | SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") | |
2217 | (license license:bsd-2))) | |
2218 | ||
13d083af RW |
2219 | (define-public r-brew |
2220 | (package | |
2221 | (name "r-brew") | |
2222 | (version "1.0-6") | |
2223 | (source (origin | |
2224 | (method url-fetch) | |
2225 | (uri (cran-uri "brew" version)) | |
2226 | (sha256 | |
2227 | (base32 | |
2228 | "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp")))) | |
2229 | (build-system r-build-system) | |
e9960d8c | 2230 | (home-page "https://cran.r-project.org/web/packages/brew") |
13d083af RW |
2231 | (synopsis "Templating framework for report generation") |
2232 | (description | |
2233 | "The brew package implements a templating framework for mixing text and R | |
2234 | code for report generation. The template syntax is similar to PHP, Ruby's erb | |
2235 | module, Java Server Pages, and Python's psp module.") | |
2236 | (license license:gpl2+))) | |
167c9882 | 2237 | |
1cbb07a8 RW |
2238 | (define-public r-desc |
2239 | (package | |
2240 | (name "r-desc") | |
b2aeb2a5 | 2241 | (version "1.2.0") |
1cbb07a8 RW |
2242 | (source |
2243 | (origin | |
2244 | (method url-fetch) | |
2245 | (uri (cran-uri "desc" version)) | |
2246 | (sha256 | |
2247 | (base32 | |
b2aeb2a5 | 2248 | "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6")))) |
1cbb07a8 RW |
2249 | (build-system r-build-system) |
2250 | (propagated-inputs | |
2251 | `(("r-assertthat" ,r-assertthat) | |
2252 | ("r-crayon" ,r-crayon) | |
2253 | ("r-r6" ,r-r6) | |
2254 | ("r-rprojroot" ,r-rprojroot))) | |
2255 | (home-page "https://github.com/r-pkgs/desc") | |
2256 | (synopsis "Manipulate DESCRIPTION Files") | |
2257 | (description | |
2258 | "This package provides tools to read, write, create, and manipulate | |
2259 | DESCRIPTION files. It is intended for packages that create or manipulate | |
2260 | other packages.") | |
2261 | (license license:expat))) | |
2262 | ||
bf6dcf59 RW |
2263 | (define-public r-commonmark |
2264 | (package | |
2265 | (name "r-commonmark") | |
02c89c58 | 2266 | (version "1.7") |
bf6dcf59 RW |
2267 | (source |
2268 | (origin | |
2269 | (method url-fetch) | |
2270 | (uri (cran-uri "commonmark" version)) | |
2271 | (sha256 | |
2272 | (base32 | |
02c89c58 | 2273 | "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni")))) |
bf6dcf59 | 2274 | (build-system r-build-system) |
e9960d8c | 2275 | (home-page "https://cran.r-project.org/web/packages/commonmark") |
bf6dcf59 RW |
2276 | (synopsis "CommonMark and Github Markdown Rendering in R") |
2277 | (description | |
2278 | "The CommonMark specification defines a rationalized version of markdown | |
2279 | syntax. This package uses the 'cmark' reference implementation for converting | |
2280 | markdown text into various formats including HTML, LaTeX and groff man. In | |
2281 | addition, it exposes the markdown parse tree in XML format. The latest | |
2282 | version of this package also adds support for Github extensions including | |
2283 | tables, autolinks and strikethrough text.") | |
2284 | (license license:bsd-2))) | |
2285 | ||
167c9882 RW |
2286 | (define-public r-roxygen2 |
2287 | (package | |
2288 | (name "r-roxygen2") | |
9094eb89 | 2289 | (version "6.1.1") |
167c9882 RW |
2290 | (source (origin |
2291 | (method url-fetch) | |
2292 | (uri (cran-uri "roxygen2" version)) | |
2293 | (sha256 | |
2294 | (base32 | |
9094eb89 | 2295 | "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd")))) |
167c9882 RW |
2296 | (build-system r-build-system) |
2297 | (propagated-inputs | |
2298 | `(("r-brew" ,r-brew) | |
1db29375 RW |
2299 | ("r-commonmark" ,r-commonmark) |
2300 | ("r-desc" ,r-desc) | |
167c9882 | 2301 | ("r-digest" ,r-digest) |
2848c52c RW |
2302 | ("r-pkgload" ,r-pkgload) |
2303 | ("r-purrr" ,r-purrr) | |
1db29375 | 2304 | ("r-r6" ,r-r6) |
167c9882 RW |
2305 | ("r-rcpp" ,r-rcpp) |
2306 | ("r-stringi" ,r-stringi) | |
1db29375 RW |
2307 | ("r-stringr" ,r-stringr) |
2308 | ("r-xml2" ,r-xml2))) | |
2848c52c RW |
2309 | (native-inputs |
2310 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
167c9882 RW |
2311 | (home-page "https://github.com/klutometis/roxygen") |
2312 | (synopsis "In-source documentation system for R") | |
2313 | (description | |
2314 | "Roxygen2 is a Doxygen-like in-source documentation system for Rd, | |
2315 | collation, and NAMESPACE files.") | |
2316 | (license license:gpl2+))) | |
681e03c1 | 2317 | |
c26c0628 RW |
2318 | (define-public r-openssl |
2319 | (package | |
2320 | (name "r-openssl") | |
9066534d | 2321 | (version "1.2.2") |
c26c0628 RW |
2322 | (source |
2323 | (origin | |
2324 | (method url-fetch) | |
2325 | (uri (cran-uri "openssl" version)) | |
2326 | (sha256 | |
2327 | (base32 | |
9066534d | 2328 | "0jfkna9zzhy2m5qd8501ija5jnpxzjn8wi3wjw0kr2fm4sl7qynz")))) |
c26c0628 RW |
2329 | (build-system r-build-system) |
2330 | (inputs | |
0dc3b4d4 | 2331 | `(("libressl" ,libressl))) |
6d1db050 RW |
2332 | (native-inputs |
2333 | `(("pkg-config" ,pkg-config))) | |
2334 | (propagated-inputs | |
2335 | `(("r-askpass" ,r-askpass))) | |
c26c0628 RW |
2336 | (home-page "https://github.com/jeroenooms/openssl") |
2337 | (synopsis "Toolkit for encryption, signatures and certificates") | |
2338 | (description | |
2339 | "This package provides R bindings to OpenSSL libssl and libcrypto, plus | |
2340 | custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 | |
2341 | and P-521. Cryptographic signatures can either be created and verified | |
2342 | manually or via x509 certificates. AES block cipher is used in CBC mode for | |
2343 | symmetric encryption; RSA for asymmetric (public key) encryption. High-level | |
2344 | envelope functions combine RSA and AES for encrypting arbitrary sized data. | |
2345 | Other utilities include key generators, hash functions (md5, sha1, sha256, | |
2346 | etc), base64 encoder, a secure random number generator, and @code{bignum} math | |
2347 | methods for manually performing crypto calculations on large multibyte | |
2348 | integers.") | |
2349 | (license license:expat))) | |
2350 | ||
681e03c1 RW |
2351 | (define-public r-httr |
2352 | (package | |
2353 | (name "r-httr") | |
c12e4293 | 2354 | (version "1.4.0") |
681e03c1 RW |
2355 | (source (origin |
2356 | (method url-fetch) | |
2357 | (uri (cran-uri "httr" version)) | |
2358 | (sha256 | |
2359 | (base32 | |
c12e4293 | 2360 | "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn")))) |
681e03c1 RW |
2361 | (build-system r-build-system) |
2362 | (propagated-inputs | |
2363 | `(("r-curl" ,r-curl) | |
681e03c1 | 2364 | ("r-jsonlite" ,r-jsonlite) |
59bf9f4e | 2365 | ("r-openssl" ,r-openssl) |
681e03c1 | 2366 | ("r-mime" ,r-mime) |
7d60652e | 2367 | ("r-r6" ,r-r6))) |
681e03c1 RW |
2368 | (home-page "https://github.com/hadley/httr") |
2369 | (synopsis "Tools for working with URLs and HTTP") | |
2370 | (description | |
2371 | "The aim of httr is to provide a wrapper for RCurl customised to the | |
2372 | demands of modern web APIs. It provides useful tools for working with HTTP | |
2373 | organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration | |
2374 | functions make it easy to control additional request components.") | |
2375 | (license license:expat))) | |
035711f1 RW |
2376 | |
2377 | (define-public r-git2r | |
2378 | (package | |
2379 | (name "r-git2r") | |
8f49d99a | 2380 | (version "0.24.0") |
035711f1 RW |
2381 | (source (origin |
2382 | (method url-fetch) | |
2383 | (uri (cran-uri "git2r" version)) | |
2384 | (sha256 | |
2385 | (base32 | |
8f49d99a | 2386 | "0vfc25z4j53pc49cnp3zjwzjb72kvc0aq96wgyg10xpgvhl3z0gg")))) |
035711f1 RW |
2387 | (build-system r-build-system) |
2388 | ;; This R package contains modified sources of libgit2. This modified | |
2389 | ;; version of libgit2 is built as the package is built. Hence libgit2 is | |
2390 | ;; not among the inputs of this package. | |
2391 | (inputs | |
8f49d99a | 2392 | `(("libssh2" ,libssh2) ; for SSH transport |
035711f1 RW |
2393 | ("openssl" ,openssl) |
2394 | ("zlib" ,zlib))) | |
19cb93be RW |
2395 | (native-inputs |
2396 | `(("pkg-config" ,pkg-config))) | |
035711f1 RW |
2397 | (home-page "https://github.com/ropensci/git2r") |
2398 | (synopsis "Access Git repositories with R") | |
2399 | (description | |
2400 | "This package provides an R interface to the libgit2 library, which is a | |
2401 | pure C implementation of the Git core methods.") | |
2402 | ;; GPLv2 only with linking exception. | |
2403 | (license license:gpl2))) | |
81a4228b RW |
2404 | |
2405 | (define-public r-rstudioapi | |
2406 | (package | |
2407 | (name "r-rstudioapi") | |
fb459342 | 2408 | (version "0.9.0") |
81a4228b RW |
2409 | (source (origin |
2410 | (method url-fetch) | |
2411 | (uri (cran-uri "rstudioapi" version)) | |
2412 | (sha256 | |
2413 | (base32 | |
fb459342 | 2414 | "0gn1pvaxfh2gh2ikvxcr8f6k97ygcfr68iz6dhwlq4z71a1s4jai")))) |
81a4228b | 2415 | (build-system r-build-system) |
e9960d8c | 2416 | (home-page "https://cran.r-project.org/web/packages/rstudioapi") |
81a4228b RW |
2417 | (synopsis "Safely access the RStudio API") |
2418 | (description | |
2419 | "This package provides functions to access the RStudio API and provide | |
2420 | informative error messages when it's not available.") | |
2421 | (license license:expat))) | |
d6e21589 RW |
2422 | |
2423 | (define-public r-devtools | |
2424 | (package | |
2425 | (name "r-devtools") | |
c5bd8a7c | 2426 | (version "2.0.1") |
d6e21589 RW |
2427 | (source (origin |
2428 | (method url-fetch) | |
2429 | (uri (cran-uri "devtools" version)) | |
2430 | (sha256 | |
2431 | (base32 | |
c5bd8a7c | 2432 | "1nyspqicn9zd1rgq3k07b3179i8w5ys6jbd65g9q8qczrb7z3x8f")))) |
d6e21589 RW |
2433 | (build-system r-build-system) |
2434 | (propagated-inputs | |
c5bd8a7c RW |
2435 | `(("r-callr" ,r-callr) |
2436 | ("r-cli" ,r-cli) | |
2437 | ("r-digest" ,r-digest) | |
d6e21589 RW |
2438 | ("r-git2r" ,r-git2r) |
2439 | ("r-httr" ,r-httr) | |
2440 | ("r-jsonlite" ,r-jsonlite) | |
2441 | ("r-memoise" ,r-memoise) | |
c5bd8a7c RW |
2442 | ("r-pkgbuild" ,r-pkgbuild) |
2443 | ("r-pkgload" ,r-pkgload) | |
2444 | ("r-rcmdcheck" ,r-rcmdcheck) | |
2445 | ("r-remotes" ,r-remotes) | |
d6e21589 | 2446 | ("r-rstudioapi" ,r-rstudioapi) |
c5bd8a7c RW |
2447 | ("r-sessioninfo" ,r-sessioninfo) |
2448 | ("r-usethis" ,r-usethis) | |
fa9f0e6c | 2449 | ("r-withr" ,r-withr))) |
d6e21589 RW |
2450 | (home-page "https://github.com/hadley/devtools") |
2451 | (synopsis "Tools to make developing R packages easier") | |
2452 | (description "The devtools package is a collection of package development | |
2453 | tools to simplify the devolpment of R packages.") | |
2454 | (license license:gpl2+))) | |
03af370f | 2455 | |
a080e50c RJ |
2456 | (define-public r-withr |
2457 | (package | |
2458 | (name "r-withr") | |
bae598d6 | 2459 | (version "2.1.2") |
a080e50c RJ |
2460 | (source (origin |
2461 | (method url-fetch) | |
2462 | (uri (cran-uri "withr" version)) | |
2463 | (sha256 | |
2464 | (base32 | |
bae598d6 | 2465 | "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1")))) |
a080e50c RJ |
2466 | (build-system r-build-system) |
2467 | (home-page "https://github.com/jimhester/withr") | |
2468 | (synopsis "Run code with temporarily modified global state") | |
2469 | (description | |
2470 | "This package provides a set of functions to run R code in an environment | |
2471 | in which global state has been temporarily modified. Many of these functions | |
2472 | were originally a part of the r-devtools package.") | |
2473 | (license license:gpl2+))) | |
2474 | ||
b90314b4 RW |
2475 | (define-public r-hms |
2476 | (package | |
2477 | (name "r-hms") | |
361cee71 | 2478 | (version "0.4.2") |
b90314b4 RW |
2479 | (source |
2480 | (origin | |
2481 | (method url-fetch) | |
2482 | (uri (cran-uri "hms" version)) | |
2483 | (sha256 | |
2484 | (base32 | |
361cee71 | 2485 | "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55")))) |
b90314b4 | 2486 | (build-system r-build-system) |
09c0107f RW |
2487 | (propagated-inputs |
2488 | `(("r-rlang" ,r-rlang) | |
2489 | ("r-pkgconfig" ,r-pkgconfig))) | |
b90314b4 RW |
2490 | (home-page "https://github.com/rstats-db/hms") |
2491 | (synopsis "Pretty time of day") | |
2492 | (description | |
2493 | "This package implements an S3 class for storing and formatting | |
2494 | time-of-day values, based on the @code{difftime} class.") | |
2495 | (license license:gpl3+))) | |
2496 | ||
03af370f RW |
2497 | (define-public r-readr |
2498 | (package | |
2499 | (name "r-readr") | |
ef915303 | 2500 | (version "1.3.1") |
03af370f RW |
2501 | (source (origin |
2502 | (method url-fetch) | |
2503 | (uri (cran-uri "readr" version)) | |
2504 | (sha256 | |
2505 | (base32 | |
ef915303 | 2506 | "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k")))) |
03af370f RW |
2507 | (build-system r-build-system) |
2508 | (propagated-inputs | |
ef915303 RW |
2509 | `(("r-clipr" ,r-clipr) |
2510 | ("r-crayon" ,r-crayon) | |
2511 | ("r-rcpp" ,r-rcpp) | |
8c6e2b84 RW |
2512 | ("r-hms" ,r-hms) |
2513 | ("r-tibble" ,r-tibble) | |
2514 | ("r-r6" ,r-r6) | |
03af370f RW |
2515 | ("r-bh" ,r-bh))) |
2516 | (home-page "https://github.com/hadley/readr") | |
2517 | (synopsis "Read tabular data") | |
2518 | (description | |
2519 | "This package provides functions to read flat or tabular text files from | |
2520 | disk (or a connection).") | |
2521 | (license license:gpl2+))) | |
60a9d3d0 RW |
2522 | |
2523 | (define-public r-plotrix | |
2524 | (package | |
2525 | (name "r-plotrix") | |
62a7492c | 2526 | (version "3.7-4") |
60a9d3d0 RW |
2527 | (source (origin |
2528 | (method url-fetch) | |
2529 | (uri (cran-uri "plotrix" version)) | |
2530 | (sha256 | |
2531 | (base32 | |
62a7492c | 2532 | "1hs0zwaqs34559girinvysjfbvznyn8znp9cwvkqx6k2cqvcjinj")))) |
60a9d3d0 | 2533 | (build-system r-build-system) |
e9960d8c | 2534 | (home-page "https://cran.r-project.org/web/packages/plotrix") |
60a9d3d0 RW |
2535 | (synopsis "Various plotting functions") |
2536 | (description | |
2537 | "This package provides lots of plotting, various labeling, axis and color | |
2538 | scaling functions for R.") | |
2539 | (license license:gpl2+))) | |
2a40f763 RW |
2540 | |
2541 | (define-public r-gridbase | |
2542 | (package | |
2543 | (name "r-gridbase") | |
2544 | (version "0.4-7") | |
2545 | (source (origin | |
2546 | (method url-fetch) | |
2547 | (uri (cran-uri "gridBase" version)) | |
2548 | (sha256 | |
2549 | (base32 | |
2550 | "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy")))) | |
2551 | (build-system r-build-system) | |
e9960d8c | 2552 | (home-page "https://cran.r-project.org/web/packages/gridBase") |
2a40f763 RW |
2553 | (synopsis "Integration of base and grid graphics") |
2554 | (description | |
2555 | "This package provides an integration of base and grid graphics for R.") | |
2556 | (license license:gpl2+))) | |
ca3476cd | 2557 | |
b20abbcd RW |
2558 | (define-public r-latticeextra |
2559 | (package | |
2560 | (name "r-latticeextra") | |
2561 | (version "0.6-28") | |
2562 | (source | |
2563 | (origin | |
2564 | (method url-fetch) | |
2565 | (uri (cran-uri "latticeExtra" version)) | |
2566 | (sha256 | |
2567 | (base32 | |
2568 | "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq")))) | |
2569 | (properties `((upstream-name . "latticeExtra"))) | |
2570 | (build-system r-build-system) | |
2571 | (propagated-inputs | |
2572 | `(("r-lattice" ,r-lattice) | |
2573 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
2574 | (home-page "http://latticeextra.r-forge.r-project.org/") | |
2575 | (synopsis "Extra graphical utilities based on lattice") | |
2576 | (description | |
2577 | "Building on the infrastructure provided by the lattice package, this | |
2578 | package provides several new high-level graphics functions and methods, as | |
2579 | well as additional utilities such as panel and axis annotation functions.") | |
2580 | (license license:gpl2+))) | |
2581 | ||
e22d4ca4 RW |
2582 | (define-public r-rcpparmadillo |
2583 | (package | |
2584 | (name "r-rcpparmadillo") | |
82dad63e | 2585 | (version "0.9.200.7.0") |
e22d4ca4 RW |
2586 | (source (origin |
2587 | (method url-fetch) | |
2588 | (uri (cran-uri "RcppArmadillo" version)) | |
2589 | (sha256 | |
2590 | (base32 | |
82dad63e | 2591 | "11m04yvdh6086567dzzxchbf68fl5hxf2y32acf3f43bjqgwbv2p")))) |
e22d4ca4 RW |
2592 | (properties `((upstream-name . "RcppArmadillo"))) |
2593 | (build-system r-build-system) | |
c43db8da RW |
2594 | (native-inputs |
2595 | `(("r-knitr" ,r-knitr))) ; needed for vignettes | |
e22d4ca4 | 2596 | (propagated-inputs |
0685fe3c | 2597 | `(("r-rcpp" ,r-rcpp))) |
e22d4ca4 RW |
2598 | (home-page "https://github.com/RcppCore/RcppArmadillo") |
2599 | (synopsis "Rcpp integration for the Armadillo linear algebra library") | |
2600 | (description | |
2601 | "Armadillo is a templated C++ linear algebra library that aims towards a | |
2602 | good balance between speed and ease of use. Integer, floating point and | |
2603 | complex numbers are supported, as well as a subset of trigonometric and | |
2604 | statistics functions. Various matrix decompositions are provided through | |
2605 | optional integration with LAPACK and ATLAS libraries. This package includes | |
2606 | the header files from the templated Armadillo library.") | |
2607 | ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp | |
2608 | ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or | |
2609 | ;; later, as is the rest of 'Rcpp'. | |
2610 | (license license:gpl2+))) | |
bb6d2dad RW |
2611 | |
2612 | (define-public r-bitops | |
2613 | (package | |
2614 | (name "r-bitops") | |
2615 | (version "1.0-6") | |
2616 | (source (origin | |
2617 | (method url-fetch) | |
2618 | (uri (cran-uri "bitops" version)) | |
2619 | (sha256 | |
2620 | (base32 | |
2621 | "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv")))) | |
2622 | (build-system r-build-system) | |
e9960d8c | 2623 | (home-page "https://cran.r-project.org/web/packages/bitops") |
bb6d2dad RW |
2624 | (synopsis "Bitwise operations") |
2625 | (description | |
2626 | "This package provides functions for bitwise operations on integer | |
2627 | vectors.") | |
2628 | (license license:gpl2+))) | |
4c1f2705 RW |
2629 | |
2630 | (define-public r-catools | |
2631 | (package | |
2632 | (name "r-catools") | |
a1d9387d | 2633 | (version "1.17.1.2") |
4c1f2705 RW |
2634 | (source (origin |
2635 | (method url-fetch) | |
2636 | (uri (cran-uri "caTools" version)) | |
2637 | (sha256 | |
2638 | (base32 | |
a1d9387d | 2639 | "0svj31y7h8vimvliygmmbl7pk850qk80k1vn38mlcxsnmcpm9k39")))) |
4c1f2705 RW |
2640 | (properties `((upstream-name . "caTools"))) |
2641 | (build-system r-build-system) | |
2642 | (propagated-inputs | |
2643 | `(("r-bitops" ,r-bitops))) | |
e9960d8c | 2644 | (home-page "https://cran.r-project.org/web/packages/caTools") |
4c1f2705 RW |
2645 | (synopsis "Various tools including functions for moving window statistics") |
2646 | (description | |
2647 | "This package contains several basic utility functions including: | |
2648 | moving (rolling, running) window statistic functions, read/write for GIF and | |
2649 | ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 | |
2650 | encoder/decoder, round-off-error-free sum and cumsum, etc.") | |
2651 | (license license:gpl3+))) | |
77bdb276 | 2652 | |
046e27e3 RW |
2653 | (define-public r-rprojroot |
2654 | (package | |
2655 | (name "r-rprojroot") | |
1324f85b | 2656 | (version "1.3-2") |
046e27e3 RW |
2657 | (source |
2658 | (origin | |
2659 | (method url-fetch) | |
2660 | (uri (cran-uri "rprojroot" version)) | |
2661 | (sha256 | |
2662 | (base32 | |
1324f85b | 2663 | "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz")))) |
046e27e3 RW |
2664 | (build-system r-build-system) |
2665 | (propagated-inputs | |
2666 | `(("r-backports" ,r-backports))) | |
2667 | (home-page "https://github.com/krlmlr/rprojroot") | |
2668 | (synopsis "Finding files in project subdirectories") | |
2669 | (description | |
2670 | "This package helps accessing files relative to a project root. It | |
2671 | provides helpers for robust, reliable and flexible paths to files below a | |
2672 | project root. The root of a project is defined as a directory that matches a | |
2673 | certain criterion, e.g., it contains a certain regular file.") | |
2674 | (license license:gpl3))) | |
2675 | ||
77bdb276 RW |
2676 | (define-public r-rmarkdown |
2677 | (package | |
2678 | (name "r-rmarkdown") | |
54ebdf6f | 2679 | (version "1.11") |
77bdb276 RW |
2680 | (source |
2681 | (origin | |
2682 | (method url-fetch) | |
2683 | (uri (cran-uri "rmarkdown" version)) | |
2684 | (sha256 | |
2685 | (base32 | |
54ebdf6f | 2686 | "0yyjbh891mdqzpjkblz8510ng71i7mxmyiqr69x3rwlwk2vakk79")))) |
77bdb276 RW |
2687 | (properties `((upstream-name . "rmarkdown"))) |
2688 | (build-system r-build-system) | |
2689 | (propagated-inputs | |
0382d377 | 2690 | `(("r-base64enc" ,r-base64enc) |
8e1369f1 | 2691 | ("r-evaluate" ,r-evaluate) |
77bdb276 | 2692 | ("r-htmltools" ,r-htmltools) |
87a7c55e | 2693 | ("r-jsonlite" ,r-jsonlite) |
77bdb276 | 2694 | ("r-knitr" ,r-knitr) |
0382d377 | 2695 | ("r-mime" ,r-mime) |
0382d377 | 2696 | ("r-stringr" ,r-stringr) |
6221de18 | 2697 | ("r-tinytex" ,r-tinytex) |
77bdb276 | 2698 | ("r-yaml" ,r-yaml) |
78f2c08c | 2699 | ("ghc-pandoc" ,ghc-pandoc))) |
77bdb276 RW |
2700 | (home-page "http://rmarkdown.rstudio.com") |
2701 | (synopsis "Convert R Markdown documents into a variety of formats") | |
2702 | (description | |
2703 | "This package provides tools to convert R Markdown documents into a | |
2704 | variety of formats.") | |
2705 | (license license:gpl3+))) | |
b73751c8 RW |
2706 | |
2707 | (define-public r-gtable | |
2708 | (package | |
2709 | (name "r-gtable") | |
810e4195 | 2710 | (version "0.2.0") |
b73751c8 RW |
2711 | (source (origin |
2712 | (method url-fetch) | |
2713 | (uri (cran-uri "gtable" version)) | |
2714 | (sha256 | |
2715 | (base32 | |
810e4195 | 2716 | "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0")))) |
b73751c8 RW |
2717 | (properties `((upstream-name . "gtable"))) |
2718 | (build-system r-build-system) | |
9c53993f TGR |
2719 | (home-page "https://cran.r-project.org/web/packages/gtable") |
2720 | (synopsis "R library to arrange grobs in tables") | |
b73751c8 | 2721 | (description |
9c53993f TGR |
2722 | "Gtable is a collection of tools to make it easier to work with |
2723 | \"tables\" of grobs.") | |
b73751c8 | 2724 | (license license:gpl2+))) |
9e47f30b RW |
2725 | |
2726 | (define-public r-gridextra | |
2727 | (package | |
2728 | (name "r-gridextra") | |
9f14fffe | 2729 | (version "2.3") |
9e47f30b RW |
2730 | (source (origin |
2731 | (method url-fetch) | |
2732 | (uri (cran-uri "gridExtra" version)) | |
2733 | (sha256 | |
2734 | (base32 | |
9f14fffe | 2735 | "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1")))) |
9e47f30b RW |
2736 | (properties `((upstream-name . "gridExtra"))) |
2737 | (build-system r-build-system) | |
2738 | (propagated-inputs | |
2739 | `(("r-gtable" ,r-gtable))) | |
2740 | (native-inputs | |
2741 | `(("r-knitr" ,r-knitr))) ;for building vignettes | |
2742 | (home-page "https://github.com/baptiste/gridextra") | |
2743 | (synopsis "Miscellaneous functions for \"Grid\" graphics") | |
2744 | (description | |
2745 | "This package provides a number of user-level functions to work with | |
2746 | @code{grid} graphics, notably to arrange multiple grid-based plots on a page, | |
2747 | and draw tables.") | |
2748 | (license license:gpl2+))) | |
2749 | ||
aa184803 RJ |
2750 | (define-public r-pkgconfig |
2751 | (package | |
2752 | (name "r-pkgconfig") | |
eb668d5c | 2753 | (version "2.0.2") |
aa184803 RJ |
2754 | (source (origin |
2755 | (method url-fetch) | |
2756 | (uri (cran-uri "pkgconfig" version)) | |
2757 | (sha256 | |
2758 | (base32 | |
eb668d5c | 2759 | "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695")))) |
aa184803 RJ |
2760 | (build-system r-build-system) |
2761 | (home-page "https://github.com/gaborcsardi/pkgconfig") | |
2762 | (synopsis "Private configuration for R packages") | |
2763 | (description "This package provides the functionality to set configuration | |
2764 | options on a per-package basis. Options set by a given package only apply to | |
2765 | that package, other packages are unaffected.") | |
2766 | (license license:expat))) | |
2767 | ||
796237a9 RJ |
2768 | (define-public r-blob |
2769 | (package | |
2770 | (name "r-blob") | |
917378f7 | 2771 | (version "1.1.1") |
796237a9 RJ |
2772 | (source (origin |
2773 | (method url-fetch) | |
2774 | (uri (cran-uri "blob" version)) | |
2775 | (sha256 | |
2776 | (base32 | |
917378f7 | 2777 | "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc")))) |
796237a9 RJ |
2778 | (build-system r-build-system) |
2779 | (propagated-inputs | |
917378f7 TGR |
2780 | `(("r-prettyunits" ,r-prettyunits) |
2781 | ("r-tibble" ,r-tibble))) | |
796237a9 RJ |
2782 | (home-page "https://github.com/hadley/blob") |
2783 | (synopsis "Simple S3 Class for representing vectors of binary data") | |
2784 | (description "Raw vectors in R are useful for storing a single binary | |
2785 | object. What if you want to put a vector of them in a data frame? The blob | |
2786 | package provides the blob object, a list of raw vectors, suitable for use as | |
2787 | a column in data frame.") | |
2788 | (license license:gpl3+))) | |
2789 | ||
21e4d6a9 RW |
2790 | (define-public r-rsqlite |
2791 | (package | |
2792 | (name "r-rsqlite") | |
067fb62a | 2793 | (version "2.1.1") |
21e4d6a9 RW |
2794 | (source (origin |
2795 | (method url-fetch) | |
2796 | (uri (cran-uri "RSQLite" version)) | |
2797 | (sha256 | |
2798 | (base32 | |
067fb62a | 2799 | "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z")))) |
21e4d6a9 RW |
2800 | (properties `((upstream-name . "RSQLite"))) |
2801 | (build-system r-build-system) | |
2802 | (propagated-inputs | |
35bb2ff8 RW |
2803 | `(("r-dbi" ,r-dbi) |
2804 | ("r-bh" ,r-bh) | |
2805 | ("r-memoise" ,r-memoise) | |
2806 | ("r-plogr" ,r-plogr) | |
8060a617 RJ |
2807 | ("r-rcpp" ,r-rcpp) |
2808 | ("r-bit64" ,r-bit64) | |
2809 | ("r-blob" ,r-blob) | |
2810 | ("r-pkgconfig" ,r-pkgconfig))) | |
21e4d6a9 RW |
2811 | (home-page "https://github.com/rstats-db/RSQLite") |
2812 | (synopsis "SQLite interface for R") | |
2813 | (description | |
2814 | "This package embeds the SQLite database engine in R and provides an | |
2815 | interface compliant with the DBI package. The source for the SQLite | |
8060a617 | 2816 | engine (version 3.8.8.2) is included.") |
21e4d6a9 RW |
2817 | (license license:lgpl2.0+))) |
2818 | ||
cefaa79c RW |
2819 | (define-public r-rcurl |
2820 | (package | |
2821 | (name "r-rcurl") | |
2822 | (version "1.95-0.1.2") | |
2823 | (source (origin | |
2824 | (method url-fetch) | |
5713bbf1 | 2825 | (uri (string-append "https://www.bioconductor.org/packages/" |
cefaa79c RW |
2826 | "release/extra/src/" |
2827 | "contrib/RCurl_" version ".tar.gz")) | |
2828 | (sha256 | |
2829 | (base32 | |
2830 | "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc")))) | |
2831 | (properties `((upstream-name . "RCurl"))) | |
2832 | (build-system r-build-system) | |
8d3dda02 RW |
2833 | (arguments |
2834 | `(#:phases | |
2835 | (modify-phases %standard-phases | |
2836 | (add-after 'unpack 'respect-CURL_CA_BUNDLE | |
2837 | (lambda _ | |
2838 | (substitute* "R/options.S" | |
2839 | (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m) | |
2840 | (string-append "\ | |
2841 | certs = Sys.getenv(\"CURL_CA_BUNDLE\") | |
2842 | if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) } | |
2843 | " m))) | |
2844 | #t))))) | |
cefaa79c RW |
2845 | (inputs |
2846 | `(("libcurl" ,curl))) | |
2847 | (propagated-inputs | |
2848 | `(("r-bitops" ,r-bitops))) | |
2849 | (home-page "http://www.omegahat.org/RCurl") | |
2850 | (synopsis "General network client interface for R") | |
2851 | (description | |
2852 | "The package allows one to compose general HTTP requests and provides | |
2853 | convenient functions to fetch URIs, GET and POST forms, etc. and process the | |
2854 | results returned by the Web server. This provides a great deal of control | |
2855 | over the HTTP/FTP/... connection and the form of the request while providing a | |
2856 | higher-level interface than is available just using R socket connections. | |
2857 | Additionally, the underlying implementation is robust and extensive, | |
2858 | supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, | |
2859 | ldap, and also supports cookies, redirects, authentication, etc.") | |
2860 | (license license:bsd-3))) | |
2861 | ||
543ded36 RW |
2862 | (define-public r-xml |
2863 | (package | |
2864 | (name "r-xml") | |
4fadef3b | 2865 | (version "3.98-1.19") |
543ded36 RW |
2866 | (source (origin |
2867 | (method url-fetch) | |
2868 | (uri (cran-uri "XML" version)) | |
2869 | (sha256 | |
2870 | (base32 | |
4fadef3b | 2871 | "1axyfa56q45x7z4zd56aasdn9hz9niv2vv5qm1zp9i94vyic9cc1")))) |
543ded36 RW |
2872 | (properties |
2873 | `((upstream-name . "XML"))) | |
2874 | (build-system r-build-system) | |
2875 | (inputs | |
e5e56cc9 RW |
2876 | `(("libxml2" ,libxml2) |
2877 | ("zlib" ,zlib))) | |
2878 | (native-inputs | |
2879 | `(("pkg-config" ,pkg-config))) | |
543ded36 RW |
2880 | (home-page "http://www.omegahat.org/RSXML") |
2881 | (synopsis "Tools for parsing and generating XML within R") | |
2882 | (description | |
2883 | "Many approaches for both reading and creating XML (and HTML) | |
2884 | documents (including DTDs), both local and accessible via HTTP or FTP. Also | |
2885 | offers access to an XPath \"interpreter\".") | |
2886 | (license license:bsd-2))) | |
2887 | ||
b74f64a9 RW |
2888 | (define-public r-xnomial |
2889 | (package | |
2890 | (name "r-xnomial") | |
2891 | (version "1.0.4") | |
2892 | (source | |
2893 | (origin (method url-fetch) | |
2894 | (uri (cran-uri "XNomial" version)) | |
2895 | (sha256 | |
2896 | (base32 | |
2897 | "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6")))) | |
2898 | (properties (quasiquote ((upstream-name . "XNomial")))) | |
2899 | (build-system r-build-system) | |
e9960d8c | 2900 | (home-page "https://cran.r-project.org/web/packages/XNomial") |
b74f64a9 RW |
2901 | (synopsis "Goodness-of-Fit test for multinomial data") |
2902 | (description | |
2903 | "This package provides an exact Goodness-of-Fit test for | |
2904 | multinomial data with fixed probabilities. It can be used to | |
2905 | determine whether a set of counts fits a given expected ratio. To see | |
2906 | whether a set of observed counts fits an expectation, one can examine | |
2907 | all possible outcomes with @code{xmulti()} or a random sample of them | |
2908 | with @code{xmonte()} and find the probability of an observation | |
2909 | deviating from the expectation by at least as much as the observed. | |
2910 | As a measure of deviation from the expected, one can use the | |
2911 | log-likelihood ratio, the multinomial probability, or the classic | |
2912 | chi-square statistic. A histogram of the test statistic can also be | |
2913 | plotted and compared with the asymptotic curve.") | |
2914 | (license (list license:gpl2+ license:gpl3+)))) | |
2915 | ||
ca65d387 RW |
2916 | (define-public r-lambda-r |
2917 | (package | |
2918 | (name "r-lambda-r") | |
b4ca0076 | 2919 | (version "1.2.3") |
ca65d387 RW |
2920 | (source (origin |
2921 | (method url-fetch) | |
2922 | (uri (cran-uri "lambda.r" version)) | |
2923 | (sha256 | |
2924 | (base32 | |
b4ca0076 | 2925 | "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c")))) |
ca65d387 RW |
2926 | (properties `((upstream-name . "lambda.r"))) |
2927 | (build-system r-build-system) | |
6ab97ed5 RW |
2928 | (propagated-inputs |
2929 | `(("r-formatr" ,r-formatr))) | |
e9960d8c | 2930 | (home-page "https://cran.r-project.org/web/packages/lambda.r") |
ca65d387 RW |
2931 | (synopsis "Functional programming extension for R") |
2932 | (description | |
2933 | "This package provides a language extension to efficiently write | |
2934 | functional programs in R. Syntax extensions include multi-part function | |
2935 | definitions, pattern matching, guard statements, built-in (optional) type | |
2936 | safety.") | |
2937 | (license license:lgpl3+))) | |
2938 | ||
b9ff33b5 RW |
2939 | (define-public r-futile-options |
2940 | (package | |
2941 | (name "r-futile-options") | |
30d76d44 | 2942 | (version "1.0.1") |
b9ff33b5 RW |
2943 | (source (origin |
2944 | (method url-fetch) | |
2945 | (uri (cran-uri "futile.options" version)) | |
2946 | (sha256 | |
2947 | (base32 | |
30d76d44 | 2948 | "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s")))) |
b9ff33b5 RW |
2949 | (properties |
2950 | `((upstream-name . "futile.options"))) | |
2951 | (build-system r-build-system) | |
e9960d8c | 2952 | (home-page "https://cran.r-project.org/web/packages/futile.options") |
b9ff33b5 RW |
2953 | (synopsis "Options management framework") |
2954 | (description | |
2955 | "The futile.options subsystem provides an easy user-defined options | |
2956 | management system that is properly scoped. This means that options created | |
2957 | via @code{futile.options} are fully self-contained and will not collide with | |
2958 | options defined in other packages.") | |
2959 | (license license:lgpl3+))) | |
2960 | ||
6b82f56c RW |
2961 | (define-public r-futile-logger |
2962 | (package | |
2963 | (name "r-futile-logger") | |
27f10d3d | 2964 | (version "1.4.3") |
6b82f56c RW |
2965 | (source (origin |
2966 | (method url-fetch) | |
2967 | (uri (cran-uri "futile.logger" version)) | |
2968 | (sha256 | |
2969 | (base32 | |
27f10d3d | 2970 | "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy")))) |
6b82f56c RW |
2971 | (properties `((upstream-name . "futile.logger"))) |
2972 | (build-system r-build-system) | |
2973 | (propagated-inputs | |
2974 | `(("r-futile-options" ,r-futile-options) | |
2975 | ("r-lambda-r" ,r-lambda-r))) | |
e9960d8c | 2976 | (home-page "https://cran.r-project.org/web/packages/futile.logger") |
6b82f56c RW |
2977 | (synopsis "Logging utility for R") |
2978 | (description | |
2979 | "This package provides a simple yet powerful logging utility. Based | |
2980 | loosely on log4j, futile.logger takes advantage of R idioms to make logging a | |
2981 | convenient and easy to use replacement for @code{cat} and @code{print} | |
2982 | statements.") | |
2983 | (license license:lgpl3+))) | |
2984 | ||
3e4c0c66 RW |
2985 | (define-public r-segmented |
2986 | (package | |
2987 | (name "r-segmented") | |
4a1945da | 2988 | (version "0.5-3.0") |
3e4c0c66 RW |
2989 | (source |
2990 | (origin | |
2991 | (method url-fetch) | |
2992 | (uri (cran-uri "segmented" version)) | |
2993 | (sha256 | |
2994 | (base32 | |
4a1945da | 2995 | "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq")))) |
3e4c0c66 | 2996 | (build-system r-build-system) |
e9960d8c | 2997 | (home-page "https://cran.r-project.org/web/packages/segmented") |
3e4c0c66 RW |
2998 | (synopsis "Regression models with breakpoints estimation") |
2999 | (description | |
3000 | "Given a regression model, segmented updates the model by adding one or | |
3001 | more segmented (i.e., piecewise-linear) relationships. Several variables with | |
3002 | multiple breakpoints are allowed.") | |
3003 | (license (list license:gpl2+ license:gpl3+)))) | |
3004 | ||
bc899123 RW |
3005 | (define-public r-snow |
3006 | (package | |
3007 | (name "r-snow") | |
3ea7aefd | 3008 | (version "0.4-3") |
bc899123 RW |
3009 | (source (origin |
3010 | (method url-fetch) | |
3011 | (uri (cran-uri "snow" version)) | |
3012 | (sha256 | |
3013 | (base32 | |
3ea7aefd | 3014 | "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5")))) |
bc899123 | 3015 | (build-system r-build-system) |
e9960d8c | 3016 | (home-page "https://cran.r-project.org/web/packages/snow") |
bc899123 RW |
3017 | (synopsis "Support for simple parallel computing in R") |
3018 | (description | |
3019 | "The snow package provides support for simple parallel computing on a | |
3020 | network of workstations using R. A master R process calls @code{makeCluster} | |
3021 | to start a cluster of worker processes; the master process then uses functions | |
3022 | such as @code{clusterCall} and @code{clusterApply} to execute R code on the | |
3023 | worker processes and collect and return the results on the master.") | |
3024 | (license (list license:gpl2+ license:gpl3+)))) | |
3025 | ||
d706257b RW |
3026 | (define-public r-sparsem |
3027 | (package | |
3028 | (name "r-sparsem") | |
81c057ce | 3029 | (version "1.77") |
d706257b RW |
3030 | (source (origin |
3031 | (method url-fetch) | |
3032 | (uri (cran-uri "SparseM" version)) | |
3033 | (sha256 | |
3034 | (base32 | |
81c057ce | 3035 | "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9")))) |
d706257b RW |
3036 | (properties |
3037 | `((upstream-name . "SparseM"))) | |
d7786ce9 RW |
3038 | (inputs |
3039 | `(("gfortran" ,gfortran))) | |
d706257b RW |
3040 | (build-system r-build-system) |
3041 | (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") | |
3042 | (synopsis "Sparse linear algebra") | |
3043 | (description | |
3044 | "This package provides some basic linear algebra functionality for sparse | |
3045 | matrices. It includes Cholesky decomposition and backsolving as well as | |
3046 | standard R subsetting and Kronecker products.") | |
3047 | (license license:gpl2+))) | |
3048 | ||
264df1a4 RW |
3049 | (define-public r-iterators |
3050 | (package | |
3051 | (name "r-iterators") | |
93f9e0d9 | 3052 | (version "1.0.10") |
264df1a4 RW |
3053 | (source |
3054 | (origin | |
3055 | (method url-fetch) | |
3056 | (uri (cran-uri "iterators" version)) | |
3057 | (sha256 | |
3058 | (base32 | |
93f9e0d9 | 3059 | "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9")))) |
264df1a4 | 3060 | (build-system r-build-system) |
e9960d8c | 3061 | (home-page "https://cran.r-project.org/web/packages/iterators") |
264df1a4 RW |
3062 | (synopsis "Iterator construct for R") |
3063 | (description | |
3064 | "This package provides support for iterators, which allow a programmer to | |
3065 | traverse through all the elements of a vector, list, or other collection of | |
3066 | data.") | |
3067 | (license license:asl2.0))) | |
3068 | ||
b2cdb027 RW |
3069 | (define-public r-foreach |
3070 | (package | |
3071 | (name "r-foreach") | |
6bc862c1 | 3072 | (version "1.4.4") |
b2cdb027 RW |
3073 | (source |
3074 | (origin | |
3075 | (method url-fetch) | |
3076 | (uri (cran-uri "foreach" version)) | |
3077 | (sha256 | |
3078 | (base32 | |
6bc862c1 | 3079 | "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0")))) |
b2cdb027 RW |
3080 | (build-system r-build-system) |
3081 | (propagated-inputs | |
3082 | `(("r-codetools" ,r-codetools) | |
3083 | ("r-iterators" ,r-iterators))) | |
e9960d8c | 3084 | (home-page "https://cran.r-project.org/web/packages/foreach") |
b2cdb027 RW |
3085 | (synopsis "Foreach looping construct for R") |
3086 | (description | |
3087 | "This package provides support for the @code{foreach} looping construct. | |
3088 | @code{foreach} is an idiom that allows for iterating over elements in a | |
3089 | collection, without the use of an explicit loop counter. This package in | |
3090 | particular is intended to be used for its return value, rather than for its | |
3091 | side effects. In that sense, it is similar to the standard @code{lapply} | |
3092 | function, but doesn't require the evaluation of a function. Using | |
3093 | @code{foreach} without side effects also facilitates executing the loop in | |
3094 | parallel.") | |
3095 | (license license:asl2.0))) | |
3096 | ||
71cafa04 RW |
3097 | (define-public r-doparallel |
3098 | (package | |
3099 | (name "r-doparallel") | |
33fb92aa | 3100 | (version "1.0.14") |
71cafa04 RW |
3101 | (source |
3102 | (origin | |
3103 | (method url-fetch) | |
3104 | (uri (cran-uri "doParallel" version)) | |
3105 | (sha256 | |
3106 | (base32 | |
33fb92aa | 3107 | "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb")))) |
71cafa04 RW |
3108 | (properties `((upstream-name . "doParallel"))) |
3109 | (build-system r-build-system) | |
3110 | (propagated-inputs | |
3111 | `(("r-foreach" ,r-foreach) | |
3112 | ("r-iterators" ,r-iterators))) | |
e9960d8c | 3113 | (home-page "https://cran.r-project.org/web/packages/doParallel") |
71cafa04 RW |
3114 | (synopsis "Foreach parallel adaptor for the 'parallel' package") |
3115 | (description | |
3116 | "This package provides a parallel backend for the @code{%dopar%} function | |
3117 | using the parallel package.") | |
3118 | (license license:gpl2+))) | |
3119 | ||
66cf0f05 RW |
3120 | (define-public r-domc |
3121 | (package | |
3122 | (name "r-domc") | |
5ac4bd9c | 3123 | (version "1.3.5") |
66cf0f05 RW |
3124 | (source |
3125 | (origin | |
3126 | (method url-fetch) | |
3127 | (uri (cran-uri "doMC" version)) | |
3128 | (sha256 | |
3129 | (base32 | |
5ac4bd9c | 3130 | "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr")))) |
66cf0f05 RW |
3131 | (properties `((upstream-name . "doMC"))) |
3132 | (build-system r-build-system) | |
3133 | (propagated-inputs | |
3134 | `(("r-foreach" ,r-foreach) | |
3135 | ("r-iterators" ,r-iterators))) | |
e9960d8c | 3136 | (home-page "https://cran.r-project.org/web/packages/doMC") |
66cf0f05 RW |
3137 | (synopsis "Foreach parallel adaptor for the 'parallel' package") |
3138 | (description | |
3139 | "This package provides a parallel backend for the @code{%dopar%} function | |
3140 | using the multicore functionality of the parallel package.") | |
3141 | (license license:gpl2+))) | |
3142 | ||
a8227e4a RW |
3143 | (define-public r-dt |
3144 | (package | |
3145 | (name "r-dt") | |
466397c3 | 3146 | (version "0.5") |
a8227e4a RW |
3147 | (source (origin |
3148 | (method url-fetch) | |
3149 | (uri (cran-uri "DT" version)) | |
3150 | (sha256 | |
3151 | (base32 | |
466397c3 | 3152 | "1s5d3sld4l8zygpkvprvlbqa0pm2cv1bm7h7p999wxlap28vnnqf")))) |
a8227e4a RW |
3153 | (properties |
3154 | `((upstream-name . "DT"))) | |
3155 | (build-system r-build-system) | |
3156 | (propagated-inputs | |
a63117c8 RW |
3157 | `(("r-crosstalk" ,r-crosstalk) |
3158 | ("r-htmltools" ,r-htmltools) | |
a8227e4a | 3159 | ("r-htmlwidgets" ,r-htmlwidgets) |
466397c3 RW |
3160 | ("r-magrittr" ,r-magrittr) |
3161 | ("r-promises" ,r-promises))) | |
a8227e4a RW |
3162 | (home-page "http://rstudio.github.io/DT") |
3163 | (synopsis "R wrapper of the DataTables JavaScript library") | |
3164 | (description | |
3165 | "This package allows for data objects in R to be rendered as HTML tables | |
3166 | using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). | |
3167 | The 'DataTables' library has been included in this R package.") | |
3168 | ;; The DT package as a whole is distributed under GPLv3. The DT package | |
3169 | ;; inludes other software components under different licenses: | |
3170 | ;; | |
3171 | ;; * Expat: jQuery, jquery.highlight.js, DataTables | |
3172 | ;; * ASL2.0: selectize.js | |
3173 | ;; * WTFPL: noUiSlider | |
3174 | (license (list license:gpl3 | |
3175 | license:expat | |
3176 | license:asl2.0 | |
3177 | (license:non-copyleft "http://www.wtfpl.net/txt/copying/"))))) | |
3178 | ||
a69a5935 RW |
3179 | (define-public r-base64enc |
3180 | (package | |
3181 | (name "r-base64enc") | |
3182 | (version "0.1-3") | |
3183 | (source (origin | |
3184 | (method url-fetch) | |
3185 | (uri (cran-uri "base64enc" version)) | |
3186 | (sha256 | |
3187 | (base32 | |
3188 | "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd")))) | |
3189 | (build-system r-build-system) | |
3190 | (home-page "http://www.rforge.net/base64enc") | |
3191 | (synopsis "Tools for Base64 encoding") | |
3192 | (description | |
3193 | "This package provides tools for handling Base64 encoding. It is more | |
3194 | flexible than the orphaned \"base64\" package.") | |
3195 | (license license:gpl2+))) | |
3196 | ||
dada39aa RW |
3197 | (define-public r-irlba |
3198 | (package | |
3199 | (name "r-irlba") | |
6be62a5a | 3200 | (version "2.3.3") |
dada39aa RW |
3201 | (source |
3202 | (origin | |
3203 | (method url-fetch) | |
3204 | (uri (cran-uri "irlba" version)) | |
3205 | (sha256 | |
3206 | (base32 | |
6be62a5a | 3207 | "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf")))) |
dada39aa | 3208 | (build-system r-build-system) |
aeb64f3c RW |
3209 | (propagated-inputs |
3210 | `(("r-matrix" ,r-matrix))) | |
e9960d8c | 3211 | (home-page "https://cran.r-project.org/web/packages/irlba") |
dada39aa RW |
3212 | (synopsis "Methods for eigendecomposition of large matrices") |
3213 | (description | |
3214 | "This package provides fast and memory efficient methods for truncated | |
3215 | singular and eigenvalue decompositions, as well as for principal component | |
3216 | analysis of large sparse or dense matrices.") | |
3217 | (license (list license:gpl2+ license:gpl3+)))) | |
3218 | ||
c7f04517 BW |
3219 | (define-public r-glmnet |
3220 | (package | |
3221 | (name "r-glmnet") | |
4c44dd7a | 3222 | (version "2.0-16") |
c7f04517 BW |
3223 | (source |
3224 | (origin | |
3225 | (method url-fetch) | |
3226 | (uri (cran-uri "glmnet" version)) | |
3227 | (sha256 | |
3228 | (base32 | |
4c44dd7a | 3229 | "1brr51z1fzbpyj6myyir4g6dhbp6xwl7nx4xnvrjarnf5y0csk55")))) |
c7f04517 | 3230 | (build-system r-build-system) |
aeb64f3c RW |
3231 | (inputs |
3232 | `(("gfortran" ,gfortran))) | |
c7f04517 | 3233 | (propagated-inputs |
aeb64f3c RW |
3234 | `(("r-foreach" ,r-foreach) |
3235 | ("r-matrix" ,r-matrix))) | |
c7f04517 BW |
3236 | (home-page "http://www.jstatsoft.org/v33/i01") |
3237 | (synopsis "Lasso and elastic-net regularized generalized linear models") | |
3238 | (description | |
3239 | "The glmnet package provides efficient procedures for fitting the entire | |
3240 | lasso or elastic-net regularization path for linear and Poisson regression, as | |
3241 | well as logistic, multinomial, Cox, multiple-response Gaussian and grouped | |
3242 | multinomial models. The algorithm uses cyclical coordinate descent in a | |
3243 | path-wise fashion.") | |
3244 | (license license:gpl2+))) | |
3245 | ||
3a6607f0 RW |
3246 | (define-public r-pkgmaker |
3247 | (package | |
3248 | (name "r-pkgmaker") | |
3a605165 | 3249 | (version "0.27") |
3a6607f0 RW |
3250 | (source |
3251 | (origin | |
3252 | (method url-fetch) | |
3253 | (uri (cran-uri "pkgmaker" version)) | |
3254 | (sha256 | |
3255 | (base32 | |
3a605165 | 3256 | "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp")))) |
3a6607f0 RW |
3257 | (build-system r-build-system) |
3258 | (propagated-inputs | |
3a605165 RW |
3259 | `(("r-bibtex" ,r-bibtex) |
3260 | ("r-codetools" ,r-codetools) | |
3a6607f0 | 3261 | ("r-digest" ,r-digest) |
3a605165 | 3262 | ("r-magrittr" ,r-magrittr) |
3a6607f0 | 3263 | ("r-registry" ,r-registry) |
3a605165 | 3264 | ("r-stringi" ,r-stringi) |
3a6607f0 | 3265 | ("r-stringr" ,r-stringr) |
3a605165 | 3266 | ("r-withr" ,r-withr) |
3a6607f0 RW |
3267 | ("r-xtable" ,r-xtable))) |
3268 | (home-page "https://renozao.github.io/pkgmaker") | |
3269 | (synopsis "Package development utilities") | |
3270 | (description | |
3271 | "This package provides some low-level utilities to use for R package | |
3272 | development. It currently provides managers for multiple package specific | |
3273 | options and registries, vignette, unit test and bibtex related utilities.") | |
3274 | (license license:gpl2+))) | |
3275 | ||
2d0f7d80 RW |
3276 | (define-public r-registry |
3277 | (package | |
3278 | (name "r-registry") | |
b22a2040 | 3279 | (version "0.5-1") |
2d0f7d80 RW |
3280 | (source |
3281 | (origin | |
3282 | (method url-fetch) | |
3283 | (uri (cran-uri "registry" version)) | |
3284 | (sha256 | |
3285 | (base32 | |
b22a2040 | 3286 | "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz")))) |
2d0f7d80 | 3287 | (build-system r-build-system) |
e9960d8c | 3288 | (home-page "https://cran.r-project.org/web/packages/registry") |
2d0f7d80 RW |
3289 | (synopsis "Infrastructure for R package registries") |
3290 | (description | |
3291 | "This package provides a generic infrastructure for creating and using R | |
3292 | package registries.") | |
3293 | (license license:gpl2+))) | |
3294 | ||
790034bd RW |
3295 | (define-public r-rngtools |
3296 | (package | |
3297 | (name "r-rngtools") | |
7da0790e | 3298 | (version "1.3.1") |
790034bd RW |
3299 | (source |
3300 | (origin | |
3301 | (method url-fetch) | |
3302 | (uri (cran-uri "rngtools" version)) | |
3303 | (sha256 | |
3304 | (base32 | |
7da0790e | 3305 | "097215qcfw6ybllpzmp1532r59h2srvch3aca4z4s6l2rf9w8gvn")))) |
790034bd RW |
3306 | (build-system r-build-system) |
3307 | (propagated-inputs | |
3308 | `(("r-digest" ,r-digest) | |
3309 | ("r-pkgmaker" ,r-pkgmaker) | |
3310 | ("r-stringr" ,r-stringr))) | |
3311 | (home-page "https://renozao.github.io/rngtools") | |
3312 | (synopsis "Utility functions for working with random number generators") | |
3313 | (description | |
3314 | "This package contains a set of functions for working with Random Number | |
3315 | Generators (RNGs). In particular, it defines a generic S4 framework for | |
3316 | getting/setting the current RNG, or RNG data that are embedded into objects | |
3317 | for reproducibility. Notably, convenient default methods greatly facilitate | |
3318 | the way current RNG settings can be changed.") | |
3319 | (license license:gpl3+))) | |
3320 | ||
c72c1249 RW |
3321 | (define-public r-rtsne |
3322 | (package | |
3323 | (name "r-rtsne") | |
23dd886a | 3324 | (version "0.15") |
c72c1249 RW |
3325 | (source |
3326 | (origin | |
3327 | (method url-fetch) | |
3328 | (uri (cran-uri "Rtsne" version)) | |
3329 | (sha256 | |
3330 | (base32 | |
23dd886a | 3331 | "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn")))) |
c72c1249 RW |
3332 | (properties `((upstream-name . "Rtsne"))) |
3333 | (build-system r-build-system) | |
3334 | (propagated-inputs | |
3335 | `(("r-rcpp" ,r-rcpp))) | |
3336 | (home-page "https://github.com/jkrijthe/Rtsne") | |
3337 | (synopsis "T-distributed stochastic neighbor embedding") | |
3338 | (description | |
3339 | "This package provides an R wrapper around the fast T-distributed | |
3340 | Stochastic Neighbor Embedding using a Barnes-Hut implementation.") | |
3341 | ;; The declared license for this package is BSD-3, but it also includes | |
3342 | ;; code licensed under BSD-4. | |
3343 | (license (list license:bsd-3 license:bsd-4)))) | |
3344 | ||
c533589c RW |
3345 | (define-public r-e1071 |
3346 | (package | |
3347 | (name "r-e1071") | |
c21c5188 | 3348 | (version "1.7-0.1") |
c533589c RW |
3349 | (source |
3350 | (origin | |
3351 | (method url-fetch) | |
3352 | (uri (cran-uri "e1071" version)) | |
3353 | (sha256 | |
3354 | (base32 | |
c21c5188 | 3355 | "11fqm4shmksalkazcwvzfknp3amigw7fr8wdwanqa5v5kx7ihyq9")))) |
c533589c | 3356 | (build-system r-build-system) |
aeb64f3c RW |
3357 | (propagated-inputs |
3358 | `(("r-class" ,r-class))) | |
e9960d8c | 3359 | (home-page "https://cran.r-project.org/web/packages/e1071") |
c533589c RW |
3360 | (synopsis "Miscellaneous functions for probability theory") |
3361 | (description | |
3362 | "This package provides functions for latent class analysis, short time | |
3363 | Fourier transform, fuzzy clustering, support vector machines, shortest path | |
3364 | computation, bagged clustering, naive Bayes classifier, and more.") | |
3365 | (license license:gpl2+))) | |
3366 | ||
c6105d69 RJ |
3367 | (define-public r-bigmemory-sri |
3368 | (package | |
3369 | (name "r-bigmemory-sri") | |
3370 | (version "0.1.3") | |
3371 | (source | |
3372 | (origin | |
3373 | (method url-fetch) | |
3374 | (uri (cran-uri "bigmemory.sri" version)) | |
3375 | (sha256 | |
3376 | (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m")))) | |
3377 | (properties | |
3378 | `((upstream-name . "bigmemory.sri"))) | |
3379 | (build-system r-build-system) | |
e9960d8c | 3380 | (home-page "https://cran.r-project.org/web/packages/bigmemory.sri") |
c6105d69 RJ |
3381 | (synopsis "Shared resource interface for the bigmemory package") |
3382 | (description "This package provides a shared resource interface for the | |
3383 | bigmemory and synchronicity packages.") | |
3384 | ;; Users can choose either LGPLv3 or ASL2.0. | |
3385 | (license (list license:lgpl3 license:asl2.0)))) | |
4a838652 RJ |
3386 | |
3387 | (define-public r-synchronicity | |
3388 | (package | |
3389 | (name "r-synchronicity") | |
6d83cd1f | 3390 | (version "1.3.5") |
4a838652 RJ |
3391 | (source |
3392 | (origin | |
3393 | (method url-fetch) | |
3394 | (uri (cran-uri "synchronicity" version)) | |
3395 | (sha256 | |
3396 | (base32 | |
6d83cd1f | 3397 | "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx")))) |
4a838652 RJ |
3398 | (build-system r-build-system) |
3399 | (propagated-inputs | |
3400 | `(("r-bh" ,r-bh) | |
3401 | ("r-bigmemory-sri" ,r-bigmemory-sri) | |
a566b3f9 RW |
3402 | ("r-rcpp" ,r-rcpp) |
3403 | ("r-uuid" ,r-uuid))) | |
4a838652 RJ |
3404 | (home-page "http://www.bigmemory.org") |
3405 | (synopsis "Boost mutex functionality in R") | |
3406 | (description "This package provides support for synchronization | |
3407 | via mutexes and may eventually support interprocess communication and | |
3408 | message passing.") | |
3409 | ;; Users can choose either LGPLv3 or ASL2.0. | |
3410 | (license (list license:lgpl3 license:asl2.0)))) | |
59523c4c RJ |
3411 | |
3412 | (define-public r-bigmemory | |
3413 | (package | |
3414 | (name "r-bigmemory") | |
48237fde | 3415 | (version "4.5.33") |
59523c4c RJ |
3416 | (source |
3417 | (origin | |
3418 | (method url-fetch) | |
3419 | (uri (cran-uri "bigmemory" version)) | |
3420 | (sha256 | |
3421 | (base32 | |
48237fde | 3422 | "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj")))) |
59523c4c RJ |
3423 | (build-system r-build-system) |
3424 | (propagated-inputs | |
3425 | `(("r-bh" ,r-bh) | |
3426 | ("r-rcpp" ,r-rcpp) | |
f1b90a2b | 3427 | ("r-bigmemory-sri" ,r-bigmemory-sri))) |
59523c4c RJ |
3428 | (home-page "http://www.bigmemory.org") |
3429 | (synopsis "Manage large matrices with shared memory or memory-mapped files") | |
3430 | (description "This package provides methods to create, store, access, and | |
3431 | manipulate large matrices. Matrices are allocated to shared memory and may use | |
3432 | memory-mapped files.") | |
3433 | ;; Users can choose either LGPLv3 or ASL2.0. | |
3434 | (license (list license:lgpl3 license:asl2.0)))) | |
c6105d69 | 3435 | |
b783ff78 RW |
3436 | (define-public r-nmf |
3437 | (package | |
3438 | (name "r-nmf") | |
69c38faa | 3439 | (version "0.21.0") |
b783ff78 RW |
3440 | (source |
3441 | (origin | |
3442 | (method url-fetch) | |
3443 | (uri (cran-uri "NMF" version)) | |
3444 | (sha256 | |
3445 | (base32 | |
69c38faa | 3446 | "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v")))) |
b783ff78 RW |
3447 | (properties `((upstream-name . "NMF"))) |
3448 | (build-system r-build-system) | |
3449 | (propagated-inputs | |
3450 | `(("r-cluster" ,r-cluster) | |
69c38faa RW |
3451 | ("r-bigmemory" ,r-bigmemory) ; suggested |
3452 | ("r-synchronicity" ,r-synchronicity) ; suggested | |
b783ff78 RW |
3453 | ("r-colorspace" ,r-colorspace) |
3454 | ("r-digest" ,r-digest) | |
3455 | ("r-doparallel" ,r-doparallel) | |
3456 | ("r-foreach" ,r-foreach) | |
3457 | ("r-ggplot2" ,r-ggplot2) | |
3458 | ("r-gridbase" ,r-gridbase) | |
3459 | ("r-pkgmaker" ,r-pkgmaker) | |
3460 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
3461 | ("r-registry" ,r-registry) | |
3462 | ("r-reshape2" ,r-reshape2) | |
3463 | ("r-rngtools" ,r-rngtools) | |
3464 | ("r-stringr" ,r-stringr))) | |
3465 | (home-page "http://renozao.github.io/NMF") | |
3466 | (synopsis "Algorithms and framework for nonnegative matrix factorization") | |
3467 | (description | |
3468 | "This package provides a framework to perform Non-negative Matrix | |
3469 | Factorization (NMF). The package implements a set of already published | |
3470 | algorithms and seeding methods, and provides a framework to test, develop and | |
3471 | plug new or custom algorithms. Most of the built-in algorithms have been | |
3472 | optimized in C++, and the main interface function provides an easy way of | |
3473 | performing parallel computations on multicore machines.") | |
3474 | (license license:gpl2+))) | |
3475 | ||
8bfe007c RW |
3476 | (define-public r-r-methodss3 |
3477 | (package | |
3478 | (name "r-r-methodss3") | |
887d45d4 | 3479 | (version "1.7.1") |
8bfe007c RW |
3480 | (source (origin |
3481 | (method url-fetch) | |
3482 | (uri (cran-uri "R.methodsS3" version)) | |
3483 | (sha256 | |
3484 | (base32 | |
887d45d4 | 3485 | "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24")))) |
8bfe007c RW |
3486 | (properties `((upstream-name . "R.methodsS3"))) |
3487 | (build-system r-build-system) | |
e9960d8c | 3488 | (home-page "https://cran.r-project.org/web/packages/R.methodsS3") |
8bfe007c RW |
3489 | (synopsis "S3 methods simplified") |
3490 | (description | |
3491 | "This package provides methods that simplify the setup of S3 generic | |
3492 | functions and S3 methods. Major effort has been made in making definition of | |
3493 | methods as simple as possible with a minimum of maintenance for package | |
3494 | developers. For example, generic functions are created automatically, if | |
3495 | missing, and naming conflict are automatically solved, if possible. The | |
3496 | method @code{setMethodS3()} is a good start for those who in the future may | |
3497 | want to migrate to S4.") | |
3498 | (license license:lgpl2.1+))) | |
3499 | ||
c8c75a8d RW |
3500 | (define-public r-r-oo |
3501 | (package | |
3502 | (name "r-r-oo") | |
5ce901d5 | 3503 | (version "1.22.0") |
c8c75a8d RW |
3504 | (source (origin |
3505 | (method url-fetch) | |
3506 | (uri (cran-uri "R.oo" version)) | |
3507 | (sha256 | |
3508 | (base32 | |
5ce901d5 | 3509 | "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0")))) |
c8c75a8d RW |
3510 | (properties `((upstream-name . "R.oo"))) |
3511 | (build-system r-build-system) | |
3512 | (propagated-inputs | |
3513 | `(("r-r-methodss3" ,r-r-methodss3))) | |
3514 | (home-page "https://github.com/HenrikBengtsson/R.oo") | |
3515 | (synopsis "R object-oriented programming with or without references") | |
3516 | (description | |
3517 | "This package provides methods and classes for object-oriented | |
3518 | programming in R with or without references. Large effort has been made on | |
3519 | making definition of methods as simple as possible with a minimum of | |
3520 | maintenance for package developers.") | |
3521 | (license license:lgpl2.1+))) | |
3522 | ||
9c94b53b RW |
3523 | (define-public r-r-utils |
3524 | (package | |
3525 | (name "r-r-utils") | |
3db71d06 | 3526 | (version "2.8.0") |
9c94b53b RW |
3527 | (source (origin |
3528 | (method url-fetch) | |
3529 | (uri (cran-uri "R.utils" version)) | |
3530 | (sha256 | |
3531 | (base32 | |
3db71d06 | 3532 | "1jaarld1jgpzh18kh9g3rlzcrk51vdgn2n1d1y28szzxlz94vifg")))) |
9c94b53b RW |
3533 | (properties `((upstream-name . "R.utils"))) |
3534 | (build-system r-build-system) | |
3535 | (propagated-inputs | |
3536 | `(("r-r-methodss3" ,r-r-methodss3) | |
3537 | ("r-r-oo" ,r-r-oo))) | |
3538 | (home-page "https://github.com/HenrikBengtsson/R.utils") | |
3539 | (synopsis "Various programming utilities") | |
3540 | (description | |
3541 | "This package provides utility functions useful when programming and | |
3542 | developing R packages.") | |
3543 | (license license:lgpl2.1+))) | |
3544 | ||
a63efbb4 RW |
3545 | (define-public r-r-cache |
3546 | (package | |
3547 | (name "r-r-cache") | |
2cd6bb5d | 3548 | (version "0.13.0") |
a63efbb4 RW |
3549 | (source (origin |
3550 | (method url-fetch) | |
3551 | (uri (cran-uri "R.cache" version)) | |
3552 | (sha256 | |
3553 | (base32 | |
2cd6bb5d | 3554 | "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k")))) |
a63efbb4 RW |
3555 | (properties `((upstream-name . "R.cache"))) |
3556 | (build-system r-build-system) | |
3557 | (propagated-inputs | |
3558 | `(("r-digest" ,r-digest) | |
3559 | ("r-r-methodss3" ,r-r-methodss3) | |
3560 | ("r-r-oo" ,r-r-oo) | |
3561 | ("r-r-utils" ,r-r-utils))) | |
3562 | (home-page "https://github.com/HenrikBengtsson/R.cache") | |
3563 | (synopsis "Light-weight caching of objects and results") | |
3564 | (description | |
3565 | "This package provides methods for caching or memoization of objects and | |
3566 | results. With this package, any R object can be cached in a key-value storage | |
3567 | where the key can be an arbitrary set of R objects. The cache memory is | |
3568 | persistent (on the file system).") | |
3569 | (license license:lgpl2.1+))) | |
3570 | ||
3703ffb4 RW |
3571 | (define-public r-r-rsp |
3572 | (package | |
3573 | (name "r-r-rsp") | |
21886e73 | 3574 | (version "0.43.1") |
3703ffb4 RW |
3575 | (source (origin |
3576 | (method url-fetch) | |
3577 | (uri (cran-uri "R.rsp" version)) | |
3578 | (sha256 | |
3579 | (base32 | |
21886e73 | 3580 | "0i01p8jxc4j4zl2v2ykvvpfnm5hv650zj1wi1dh8hq0c98xi2yfr")))) |
3703ffb4 RW |
3581 | (properties `((upstream-name . "R.rsp"))) |
3582 | (build-system r-build-system) | |
3583 | (propagated-inputs | |
f7d7dd41 RW |
3584 | `(("r-digest" ,r-digest) |
3585 | ("r-r-cache" ,r-r-cache) | |
3703ffb4 RW |
3586 | ("r-r-methodss3" ,r-r-methodss3) |
3587 | ("r-r-oo" ,r-r-oo) | |
3588 | ("r-r-utils" ,r-r-utils))) | |
3589 | (home-page "https://github.com/HenrikBengtsson/R.rsp") | |
3590 | (synopsis "Dynamic generation of scientific reports") | |
3591 | (description | |
3592 | "The RSP markup language provides a powerful markup for controlling the | |
3593 | content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr | |
3594 | documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary | |
3595 | to many other literate programming languages, with RSP it is straightforward | |
3596 | to loop over mixtures of code and text sections, e.g. in month-by-month | |
3597 | summaries. RSP has also several preprocessing directives for incorporating | |
3598 | static and dynamic contents of external files (local or online) among other | |
3599 | things. RSP is ideal for self-contained scientific reports and R package | |
3600 | vignettes.") | |
3601 | (license license:lgpl2.1+))) | |
3602 | ||
b5f13fdb RJ |
3603 | (define-public r-mvtnorm |
3604 | (package | |
3605 | (name "r-mvtnorm") | |
ed4100dc | 3606 | (version "1.0-10") |
b5f13fdb RJ |
3607 | (source (origin |
3608 | (method url-fetch) | |
3609 | (uri (cran-uri "mvtnorm" version)) | |
3610 | (sha256 | |
3611 | (base32 | |
ed4100dc | 3612 | "04md0wmqgif24g0a4hx19ifn4kk8nx10986vf2d9vascig6ikpri")))) |
b5f13fdb RJ |
3613 | (build-system r-build-system) |
3614 | (inputs | |
3615 | `(("gfortran" ,gfortran))) | |
3616 | (home-page "http://mvtnorm.R-forge.R-project.org") | |
3617 | (synopsis "Package for multivariate normal and t-distributions") | |
3618 | (description "This package can compute multivariate normal and | |
3619 | t-probabilities, quantiles, random deviates and densities.") | |
3620 | (license license:gpl2))) | |
3621 | ||
e05c37da RW |
3622 | (define-public r-matrixstats |
3623 | (package | |
3624 | (name "r-matrixstats") | |
195eec73 | 3625 | (version "0.54.0") |
e05c37da RW |
3626 | (source (origin |
3627 | (method url-fetch) | |
3628 | (uri (cran-uri "matrixStats" version)) | |
3629 | (sha256 | |
3630 | (base32 | |
195eec73 | 3631 | "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg")))) |
e05c37da RW |
3632 | (properties `((upstream-name . "matrixStats"))) |
3633 | (build-system r-build-system) | |
3634 | (native-inputs | |
3635 | `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes | |
3636 | (home-page "https://github.com/HenrikBengtsson/matrixStats") | |
3637 | (synopsis "Methods applying to vectors and matrix rows and columns") | |
3638 | (description | |
3639 | "This package provides methods operating on rows and columns of matrices, | |
3640 | e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are | |
3641 | also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and | |
3642 | @code{weightedMedians()}. All methods have been optimized for speed and | |
3643 | memory usage.") | |
3644 | (license license:artistic2.0))) | |
3645 | ||
a28d646b RW |
3646 | (define-public r-viridis |
3647 | (package | |
3648 | (name "r-viridis") | |
0cb4fb81 | 3649 | (version "0.5.1") |
a28d646b RW |
3650 | (source (origin |
3651 | (method url-fetch) | |
3652 | (uri (cran-uri "viridis" version)) | |
3653 | (sha256 | |
3654 | (base32 | |
0cb4fb81 | 3655 | "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx")))) |
a28d646b RW |
3656 | (build-system r-build-system) |
3657 | (propagated-inputs | |
3658 | `(("r-ggplot2" ,r-ggplot2) | |
7a8efc81 RW |
3659 | ("r-gridextra" ,r-gridextra) |
3660 | ("r-viridislite" ,r-viridislite))) | |
a28d646b RW |
3661 | (home-page "https://github.com/sjmgarnier/viridis") |
3662 | (synopsis "Matplotlib default color map") | |
3663 | (description | |
3664 | "This package is a port of the new @url{matplotlib, | |
3665 | http://matplotlib.org/} color maps (@code{viridis}--the default--, | |
3666 | @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are | |
3667 | designed in such a way that they will analytically be perfectly | |
3668 | perceptually-uniform, both in regular form and also when converted to | |
3669 | black-and-white. They are also designed to be perceived by readers with the | |
3670 | most common form of color blindness.") | |
3671 | (license license:x11))) | |
3672 | ||
c6ab73e8 RW |
3673 | (define-public r-viridislite |
3674 | (package | |
3675 | (name "r-viridislite") | |
be8db0a0 | 3676 | (version "0.3.0") |
c6ab73e8 RW |
3677 | (source |
3678 | (origin | |
3679 | (method url-fetch) | |
3680 | (uri (cran-uri "viridisLite" version)) | |
3681 | (sha256 | |
3682 | (base32 | |
be8db0a0 | 3683 | "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq")))) |
c6ab73e8 RW |
3684 | (properties `((upstream-name . "viridisLite"))) |
3685 | (build-system r-build-system) | |
3686 | (home-page "https://github.com/sjmgarnier/viridisLite") | |
3687 | (synopsis "Default color maps from matplotlib") | |
3688 | (description | |
3689 | "This package is a port of the new @code{matplotlib} color maps ('viridis', | |
3690 | 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting | |
3691 | library for Python. These color maps are designed in such a way that they | |
3692 | will analytically be perfectly perceptually-uniform, both in regular form and | |
3693 | also when converted to black-and-white. They are also designed to be | |
3694 | perceived by readers with the most common form of color blindness. This is | |
3695 | the 'lite' version of the more complete @code{viridis} package.") | |
3696 | (license license:expat))) | |
3697 | ||
c4a4ef39 RW |
3698 | (define-public r-tidyselect |
3699 | (package | |
3700 | (name "r-tidyselect") | |
834f203c | 3701 | (version "0.2.5") |
c4a4ef39 RW |
3702 | (source |
3703 | (origin | |
3704 | (method url-fetch) | |
3705 | (uri (cran-uri "tidyselect" version)) | |
3706 | (sha256 | |
3707 | (base32 | |
834f203c | 3708 | "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw")))) |
c4a4ef39 RW |
3709 | (build-system r-build-system) |
3710 | (propagated-inputs | |
3711 | `(("r-glue" ,r-glue) | |
3712 | ("r-purrr" ,r-purrr) | |
3713 | ("r-rcpp" ,r-rcpp) | |
3714 | ("r-rlang" ,r-rlang))) | |
e9960d8c | 3715 | (home-page "https://cran.r-project.org/web/packages/tidyselect") |
c4a4ef39 RW |
3716 | (synopsis "Select from a set of strings") |
3717 | (description | |
3718 | "This package provides a backend for the selecting functions of the | |
3719 | tidyverse. It makes it easy to implement select-like functions in your own | |
3720 | packages in a way that is consistent with other tidyverse interfaces for | |
3721 | selection.") | |
3722 | (license license:gpl3))) | |
3723 | ||
94b7e9b7 RW |
3724 | (define-public r-tidyr |
3725 | (package | |
3726 | (name "r-tidyr") | |
ebd37b49 | 3727 | (version "0.8.3") |
94b7e9b7 RW |
3728 | (source |
3729 | (origin | |
3730 | (method url-fetch) | |
3731 | (uri (cran-uri "tidyr" version)) | |
3732 | (sha256 | |
3733 | (base32 | |
ebd37b49 | 3734 | "0dyc4b03wi65bk7j0ma0y188syh37h57wgxji82i0h8j6pn593x1")))) |
94b7e9b7 RW |
3735 | (build-system r-build-system) |
3736 | (propagated-inputs | |
3737 | `(("r-dplyr" ,r-dplyr) | |
94b7e9b7 | 3738 | ("r-magrittr" ,r-magrittr) |
89b620e7 RW |
3739 | ("r-glue" ,r-glue) |
3740 | ("r-purrr" ,r-purrr) | |
3741 | ("r-rlang" ,r-rlang) | |
3742 | ("r-tidyselect" ,r-tidyselect) | |
94b7e9b7 | 3743 | ("r-rcpp" ,r-rcpp) |
d51f05f7 RW |
3744 | ("r-stringi" ,r-stringi) |
3745 | ("r-tibble" ,r-tibble))) | |
94b7e9b7 RW |
3746 | (home-page "https://github.com/hadley/tidyr") |
3747 | (synopsis "Tidy data with `spread()` and `gather()` functions") | |
3748 | (description | |
3749 | "tidyr is a reframing of the reshape2 package designed to accompany the | |
3750 | tidy data framework, and to work hand-in-hand with magrittr and dplyr to build | |
3751 | a solid pipeline for data analysis. It is designed specifically for tidying | |
3752 | data, not the general reshaping that reshape2 does, or the general aggregation | |
3753 | that reshape did. In particular, built-in methods only work for data frames, | |
3754 | and tidyr provides no margins or aggregation.") | |
3755 | (license license:expat))) | |
3756 | ||
bae79538 RW |
3757 | (define-public r-hexbin |
3758 | (package | |
3759 | (name "r-hexbin") | |
e30b878e | 3760 | (version "1.27.2") |
bae79538 RW |
3761 | (source |
3762 | (origin | |
3763 | (method url-fetch) | |
e30b878e | 3764 | (uri (cran-uri "hexbin" version)) |
bae79538 RW |
3765 | (sha256 |
3766 | (base32 | |
e30b878e | 3767 | "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26")))) |
bae79538 RW |
3768 | (build-system r-build-system) |
3769 | (propagated-inputs | |
3770 | `(("r-lattice" ,r-lattice))) | |
3771 | (native-inputs | |
3772 | `(("gfortran" ,gfortran))) | |
7bf837fd | 3773 | (home-page "https://github.com/edzer/hexbin") |
bae79538 RW |
3774 | (synopsis "Hexagonal binning routines") |
3775 | (description | |
3776 | "This package provides binning and plotting functions for hexagonal bins. | |
3777 | It uses and relies on grid graphics and formal (S4) classes and methods.") | |
3778 | (license license:gpl2+))) | |
a3c6445b RW |
3779 | |
3780 | (define-public r-purrr | |
3781 | (package | |
3782 | (name "r-purrr") | |
84840deb | 3783 | (version "0.3.1") |
a3c6445b RW |
3784 | (source |
3785 | (origin | |
3786 | (method url-fetch) | |
3787 | (uri (cran-uri "purrr" version)) | |
3788 | (sha256 | |
3789 | (base32 | |
84840deb | 3790 | "0fw8nyrwf009fpj3457binw5s02si226yrvn96hdivwj268ck8y2")))) |
a3c6445b RW |
3791 | (build-system r-build-system) |
3792 | (propagated-inputs | |
19fdd77c | 3793 | `(("r-magrittr" ,r-magrittr) |
2267e4d3 | 3794 | ("r-rlang" ,r-rlang))) |
a3c6445b RW |
3795 | (home-page "https://github.com/hadley/purrr") |
3796 | (synopsis "Functional programming tools") | |
3797 | (description | |
3798 | "This package completes R's functional programming tools with missing | |
3799 | features present in other programming languages.") | |
3800 | (license license:gpl3+))) | |
bae79538 | 3801 | |
fbf6045e RW |
3802 | (define-public r-plotly |
3803 | (package | |
3804 | (name "r-plotly") | |
88cb7aa9 | 3805 | (version "4.8.0") |
fbf6045e RW |
3806 | (source (origin |
3807 | (method url-fetch) | |
3808 | (uri (cran-uri "plotly" version)) | |
3809 | (sha256 | |
3810 | (base32 | |
88cb7aa9 | 3811 | "19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq")))) |
fbf6045e RW |
3812 | (build-system r-build-system) |
3813 | (propagated-inputs | |
3814 | `(("r-base64enc" ,r-base64enc) | |
f9b37606 | 3815 | ("r-crosstalk" ,r-crosstalk) |
fbf6045e | 3816 | ("r-digest" ,r-digest) |
f9b37606 | 3817 | ("r-data-table" ,r-data-table) |
88cf917b | 3818 | ("r-dplyr" ,r-dplyr) |
fbf6045e | 3819 | ("r-ggplot2" ,r-ggplot2) |
2c81794e | 3820 | ("r-hexbin" ,r-hexbin) |
f9b37606 | 3821 | ("r-htmltools" ,r-htmltools) |
fbf6045e RW |
3822 | ("r-htmlwidgets" ,r-htmlwidgets) |
3823 | ("r-httr" ,r-httr) | |
3824 | ("r-jsonlite" ,r-jsonlite) | |
88cf917b | 3825 | ("r-lazyeval" ,r-lazyeval) |
fbf6045e | 3826 | ("r-magrittr" ,r-magrittr) |
88cb7aa9 | 3827 | ("r-promises" ,r-promises) |
88cf917b | 3828 | ("r-purrr" ,r-purrr) |
f9b37606 | 3829 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
88cb7aa9 | 3830 | ("r-rlang" ,r-rlang) |
2c81794e | 3831 | ("r-scales" ,r-scales) |
88cf917b | 3832 | ("r-tibble" ,r-tibble) |
2c81794e | 3833 | ("r-tidyr" ,r-tidyr) |
88cf917b | 3834 | ("r-viridislite" ,r-viridislite))) |
fbf6045e RW |
3835 | (home-page "https://plot.ly/r") |
3836 | (synopsis "Create interactive web graphics") | |
3837 | (description | |
3838 | "This package enables the translation of ggplot2 graphs to an interactive | |
3839 | web-based version and/or the creation of custom web-based visualizations | |
3840 | directly from R. Once uploaded to a plotly account, plotly graphs (and the | |
3841 | data behind them) can be viewed and modified in a web browser.") | |
3842 | (license license:x11))) | |
3843 | ||
0947698c BW |
3844 | (define-public r-biased-urn |
3845 | (package | |
3846 | (name "r-biased-urn") | |
3847 | (version "1.07") | |
3848 | (source | |
3849 | (origin | |
3850 | (method url-fetch) | |
3851 | (uri (cran-uri "BiasedUrn" version)) | |
3852 | (sha256 | |
3853 | (base32 | |
3854 | "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) | |
3855 | (properties `((upstream-name . "BiasedUrn"))) | |
3856 | (build-system r-build-system) | |
3857 | (home-page "http://www.agner.org/random/") | |
3858 | (synopsis "Biased urn model distributions") | |
3859 | (description | |
3860 | "This package provides statistical models of biased sampling in the form | |
3861 | of univariate and multivariate noncentral hypergeometric distributions, | |
3862 | including Wallenius' noncentral hypergeometric distribution and Fisher's | |
3863 | noncentral hypergeometric distribution (also called extended hypergeometric | |
3864 | distribution).") | |
3865 | (license license:gpl3+))) | |
6499b70e | 3866 | |
58612fd2 RW |
3867 | (define-public r-rematch |
3868 | (package | |
3869 | (name "r-rematch") | |
3870 | (version "1.0.1") | |
3871 | (source | |
3872 | (origin | |
3873 | (method url-fetch) | |
3874 | (uri (cran-uri "rematch" version)) | |
3875 | (sha256 | |
3876 | (base32 | |
3877 | "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4")))) | |
3878 | (build-system r-build-system) | |
3879 | (home-page "https://github.com/MangoTheCat/rematch") | |
3880 | (synopsis "Match regular expressions with a nicer API") | |
3881 | (description | |
3882 | "This package provides a small wrapper on @code{regexpr} to extract the | |
3883 | matches and captured groups from the match of a regular expression to a | |
3884 | character vector.") | |
3885 | (license license:expat))) | |
3886 | ||
d427e03e RW |
3887 | (define-public r-cellranger |
3888 | (package | |
3889 | (name "r-cellranger") | |
3890 | (version "1.1.0") | |
3891 | (source | |
3892 | (origin | |
3893 | (method url-fetch) | |
3894 | (uri (cran-uri "cellranger" version)) | |
3895 | (sha256 | |
3896 | (base32 | |
3897 | "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x")))) | |
3898 | (build-system r-build-system) | |
3899 | (propagated-inputs | |
3900 | `(("r-rematch" ,r-rematch) | |
3901 | ("r-tibble" ,r-tibble))) | |
3902 | (home-page "https://github.com/rsheets/cellranger") | |
3903 | (synopsis "Translate spreadsheet cell ranges to rows and columns") | |
3904 | (description | |
3905 | "This package provides helper functions to work with spreadsheets and the | |
3906 | @code{A1:D10} style of cell range specification.") | |
3907 | (license license:expat))) | |
3908 | ||
9f5435d9 RW |
3909 | (define-public r-googlesheets |
3910 | (package | |
3911 | (name "r-googlesheets") | |
5dbe7aa9 | 3912 | (version "0.3.0") |
9f5435d9 RW |
3913 | (source |
3914 | (origin | |
3915 | (method url-fetch) | |
3916 | (uri (cran-uri "googlesheets" version)) | |
3917 | (sha256 | |
3918 | (base32 | |
5dbe7aa9 | 3919 | "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8")))) |
9f5435d9 RW |
3920 | (build-system r-build-system) |
3921 | (propagated-inputs | |
3922 | `(("r-cellranger" ,r-cellranger) | |
3923 | ("r-dplyr" ,r-dplyr) | |
3924 | ("r-httr" ,r-httr) | |
3925 | ("r-jsonlite" ,r-jsonlite) | |
3926 | ("r-purrr" ,r-purrr) | |
3927 | ("r-readr" ,r-readr) | |
3928 | ("r-stringr" ,r-stringr) | |
5dbe7aa9 | 3929 | ("r-tibble" ,r-tibble) |
9f5435d9 RW |
3930 | ("r-tidyr" ,r-tidyr) |
3931 | ("r-xml2" ,r-xml2))) | |
3932 | (home-page "https://github.com/jennybc/googlesheets") | |
3933 | (synopsis "Manage Google spreadsheets from R") | |
3934 | (description "This package provides tools to interact with Google Sheets | |
3935 | from within R.") | |
3936 | (license license:expat))) | |
3937 | ||
e7d16ad1 RW |
3938 | (define-public r-spams |
3939 | (package | |
3940 | (name "r-spams") | |
fcf40039 | 3941 | (version "2.6-2017-03-22") |
e7d16ad1 RW |
3942 | (source |
3943 | (origin | |
3944 | (method url-fetch) | |
ef8b9a77 TGR |
3945 | ;; Use the ‘Latest version’ link for a stable URI across releases. |
3946 | (uri (string-append "https://gforge.inria.fr/frs/download.php/" | |
3947 | "latestfile/4531/spams-R-v" version ".tar.gz")) | |
e7d16ad1 RW |
3948 | (sha256 |
3949 | (base32 | |
fcf40039 | 3950 | "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx")))) |
e7d16ad1 RW |
3951 | (build-system r-build-system) |
3952 | (arguments | |
3953 | `(#:phases | |
3954 | (modify-phases %standard-phases | |
3955 | (add-after 'unpack 'chdir | |
3956 | (lambda _ (chdir "spams") #t)) | |
ef8b9a77 | 3957 | ;; Don't tune for the building machine. |
fcf40039 | 3958 | (add-after 'chdir 'no-mtune |
e7d16ad1 | 3959 | (lambda _ |
fcf40039 EF |
3960 | (substitute* "src/Makevars" |
3961 | (("-mtune=native") "")) | |
e7d16ad1 | 3962 | #t))))) |
aeb64f3c RW |
3963 | (propagated-inputs |
3964 | `(("r-lattice" ,r-lattice) | |
3965 | ("r-matrix" ,r-matrix))) | |
e7d16ad1 RW |
3966 | (home-page "http://spams-devel.gforge.inria.fr") |
3967 | (synopsis "Toolbox for solving sparse estimation problems") | |
3968 | (description "SPAMS (SPArse Modeling Software) is an optimization toolbox | |
3969 | for solving various sparse estimation problems. It includes tools for the | |
3970 | following problems: | |
3971 | ||
3972 | @enumerate | |
3973 | @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle | |
3974 | component analysis} (PCA), ...) | |
3975 | @item Solving sparse decomposition problems with LARS, coordinate descent, | |
3976 | OMP, SOMP, proximal methods | |
3977 | @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse | |
3978 | group lasso, tree-structured regularization, structured sparsity with | |
3979 | overlapping groups,...). | |
3980 | @end enumerate\n") | |
3981 | (license license:gpl3+))) | |
3982 | ||
0811f0f9 RW |
3983 | (define-public r-base64 |
3984 | (package | |
3985 | (name "r-base64") | |
3986 | (version "2.0") | |
3987 | (source | |
3988 | (origin | |
3989 | (method url-fetch) | |
3990 | (uri (cran-uri "base64" version)) | |
3991 | (sha256 | |
3992 | (base32 | |
3993 | "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf")))) | |
3994 | (build-system r-build-system) | |
3995 | (propagated-inputs | |
3996 | `(("r-openssl" ,r-openssl))) | |
e9960d8c | 3997 | (home-page "https://cran.r-project.org/web/packages/base64") |
0811f0f9 RW |
3998 | (synopsis "Base64 encoder and decoder") |
3999 | (description | |
4000 | "This package is a compatibility wrapper to replace the orphaned package | |
4001 | by Romain Francois. New applications should use the openssl or base64enc | |
4002 | package instead.") | |
4003 | (license license:expat))) | |
4004 | ||
2d21d44d RW |
4005 | (define-public r-hmisc |
4006 | (package | |
4007 | (name "r-hmisc") | |
69e9899a | 4008 | (version "4.2-0") |
2d21d44d RW |
4009 | (source |
4010 | (origin | |
4011 | (method url-fetch) | |
4012 | (uri (cran-uri "Hmisc" version)) | |
4013 | (sha256 | |
4014 | (base32 | |
69e9899a | 4015 | "1n8i2jhc308hd6bvys9cd7nrz7pwjszs03r5bwlh1pc869ki95ly")))) |
2d21d44d RW |
4016 | (properties `((upstream-name . "Hmisc"))) |
4017 | (build-system r-build-system) | |
4018 | (native-inputs | |
4019 | `(("gfortran" ,gfortran))) | |
4020 | (propagated-inputs | |
4021 | `(("r-acepack" ,r-acepack) | |
807db78f | 4022 | ("r-base64enc" ,r-base64enc) |
aeb64f3c | 4023 | ("r-cluster" ,r-cluster) |
2d21d44d | 4024 | ("r-data-table" ,r-data-table) |
aeb64f3c | 4025 | ("r-foreign" ,r-foreign) |
2d21d44d RW |
4026 | ("r-formula" ,r-formula) |
4027 | ("r-ggplot2" ,r-ggplot2) | |
4028 | ("r-gridextra" ,r-gridextra) | |
4029 | ("r-gtable" ,r-gtable) | |
aeb64f3c | 4030 | ("r-lattice" ,r-lattice) |
2d21d44d | 4031 | ("r-latticeextra" ,r-latticeextra) |
e7165916 RW |
4032 | ("r-htmltable" ,r-htmltable) |
4033 | ("r-htmltools" ,r-htmltools) | |
aeb64f3c RW |
4034 | ("r-nnet" ,r-nnet) |
4035 | ("r-rpart" ,r-rpart) | |
4036 | ("r-survival" ,r-survival) | |
ab607061 | 4037 | ("r-viridis" ,r-viridis))) |
2d21d44d RW |
4038 | (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") |
4039 | (synopsis "Miscellaneous data analysis and graphics functions") | |
4040 | (description | |
4041 | "This package contains many functions useful for data analysis, | |
4042 | high-level graphics, utility operations, functions for computing sample size | |
4043 | and power, importing and annotating datasets, imputing missing values, | |
4044 | advanced table making, variable clustering, character string manipulation, | |
4045 | conversion of R objects to LaTeX code, and recoding variables.") | |
4046 | (license license:gpl2+))) | |
4047 | ||
aa3b3910 RW |
4048 | (define-public r-runit |
4049 | (package | |
4050 | (name "r-runit") | |
366dd8d7 | 4051 | (version "0.4.32") |
aa3b3910 RW |
4052 | (source |
4053 | (origin | |
4054 | (method url-fetch) | |
4055 | (uri (cran-uri "RUnit" version)) | |
4056 | (sha256 | |
4057 | (base32 | |
366dd8d7 | 4058 | "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3")))) |
aa3b3910 RW |
4059 | (properties `((upstream-name . "RUnit"))) |
4060 | (build-system r-build-system) | |
e9960d8c | 4061 | (home-page "https://cran.r-project.org/web/packages/RUnit") |
aa3b3910 RW |
4062 | (synopsis "R unit test framework") |
4063 | (description | |
4064 | "This package provides R functions implementing a standard unit testing | |
4065 | framework, with additional code inspection and report generation tools.") | |
4066 | (license license:gpl2+))) | |
4067 | ||
c9a66714 RW |
4068 | (define-public r-dynamictreecut |
4069 | (package | |
4070 | (name "r-dynamictreecut") | |
4071 | (version "1.63-1") | |
4072 | (source | |
4073 | (origin | |
4074 | (method url-fetch) | |
4075 | (uri (cran-uri "dynamicTreeCut" version)) | |
4076 | (sha256 | |
4077 | (base32 | |
4078 | "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3")))) | |
4079 | (properties `((upstream-name . "dynamicTreeCut"))) | |
4080 | (build-system r-build-system) | |
4081 | (home-page | |
4082 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/") | |
4083 | (synopsis "Detect clusters in hierarchical clustering dendrograms") | |
4084 | (description | |
4085 | "This package contains methods for the detection of clusters in | |
4086 | hierarchical clustering dendrograms.") | |
4087 | (license license:gpl2+))) | |
4088 | ||
c4708783 RW |
4089 | (define-public r-preprocesscore |
4090 | (package | |
4091 | (name "r-preprocesscore") | |
9bd78484 | 4092 | (version "1.44.0") |
c4708783 RW |
4093 | (source |
4094 | (origin | |
4095 | (method url-fetch) | |
4096 | (uri (bioconductor-uri "preprocessCore" version)) | |
4097 | (sha256 | |
4098 | (base32 | |
9bd78484 | 4099 | "0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j")))) |
c4708783 RW |
4100 | (properties |
4101 | `((upstream-name . "preprocessCore"))) | |
4102 | (build-system r-build-system) | |
4103 | (home-page "https://github.com/bmbolstad/preprocessCore") | |
4104 | (synopsis "Collection of pre-processing functions") | |
4105 | (description | |
4106 | "This package provides a library of core pre-processing and normalization | |
4107 | routines.") | |
4108 | (license license:lgpl2.0+))) | |
4109 | ||
1bd46f55 RW |
4110 | (define-public r-fastcluster |
4111 | (package | |
4112 | (name "r-fastcluster") | |
d2a48984 | 4113 | (version "1.1.25") |
1bd46f55 RW |
4114 | (source |
4115 | (origin | |
4116 | (method url-fetch) | |
4117 | (uri (cran-uri "fastcluster" version)) | |
4118 | (sha256 | |
4119 | (base32 | |
d2a48984 | 4120 | "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk")))) |
1bd46f55 RW |
4121 | (build-system r-build-system) |
4122 | (home-page "http://danifold.net/fastcluster.html") | |
4123 | (synopsis "Fast hierarchical clustering routines") | |
4124 | (description | |
4125 | "This package implements fast hierarchical, agglomerative clustering | |
4126 | routines. Part of the functionality is designed as drop-in replacement for | |
4127 | existing routines: @code{linkage()} in the SciPy package | |
4128 | @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package, | |
4129 | and the @code{flashClust} package. It provides the same functionality with | |
4130 | the benefit of a much faster implementation. Moreover, there are | |
4131 | memory-saving routines for clustering of vector data, which go beyond what the | |
4132 | existing packages provide.") | |
4133 | (license license:bsd-2))) | |
4134 | ||
6335bf1c RW |
4135 | (define-public r-sfsmisc |
4136 | (package | |
4137 | (name "r-sfsmisc") | |
2c8594d9 | 4138 | (version "1.1-3") |
6335bf1c RW |
4139 | (source |
4140 | (origin | |
4141 | (method url-fetch) | |
4142 | (uri (cran-uri "sfsmisc" version)) | |
4143 | (sha256 | |
4144 | (base32 | |
2c8594d9 | 4145 | "1y25nnw09qfm66523w1z4q766lv15a6ykvsq30r154n7m7aggvsq")))) |
6335bf1c | 4146 | (build-system r-build-system) |
e9960d8c | 4147 | (home-page "https://cran.r-project.org/web/packages/sfsmisc") |
6335bf1c RW |
4148 | (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") |
4149 | (description | |
4150 | "This package provides useful utilities from Seminar fuer Statistik ETH | |
4151 | Zurich, including many that are related to graphics.") | |
4152 | (license license:gpl2+))) | |
4153 | ||
1571f90e RW |
4154 | (define-public r-gtools |
4155 | (package | |
4156 | (name "r-gtools") | |
8da236a3 | 4157 | (version "3.8.1") |
1571f90e RW |
4158 | (source |
4159 | (origin | |
4160 | (method url-fetch) | |
4161 | (uri (cran-uri "gtools" version)) | |
4162 | (sha256 | |
4163 | (base32 | |
8da236a3 | 4164 | "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505")))) |
1571f90e | 4165 | (build-system r-build-system) |
08ddb98a RW |
4166 | (arguments |
4167 | `(#:phases | |
4168 | (modify-phases %standard-phases | |
4169 | (add-after 'unpack 'make-deterministic | |
4170 | (lambda _ | |
4171 | (substitute* "R/checkReverseDependencies.R" | |
4172 | (("tempdir\\(\\)") "\"/tmp\"")) | |
4173 | #t))))) | |
e9960d8c | 4174 | (home-page "https://cran.r-project.org/web/packages/gtools") |
1571f90e RW |
4175 | (synopsis "Various R programming tools") |
4176 | (description | |
4177 | "This package contains a collection of various functions to assist in R | |
4178 | programming, such as tools to assist in developing, updating, and maintaining | |
4179 | R and R packages, calculating the logit and inverse logit transformations, | |
4180 | tests for whether a value is missing, empty or contains only @code{NA} and | |
4181 | @code{NULL} values, and many more.") | |
4182 | (license license:gpl2))) | |
4183 | ||
6034cd90 RW |
4184 | (define-public r-gdata |
4185 | (package | |
4186 | (name "r-gdata") | |
80d11850 | 4187 | (version "2.18.0") |
6034cd90 RW |
4188 | (source |
4189 | (origin | |
4190 | (method url-fetch) | |
4191 | (uri (cran-uri "gdata" version)) | |
4192 | (sha256 | |
4193 | (base32 | |
80d11850 | 4194 | "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b")))) |
6034cd90 RW |
4195 | (build-system r-build-system) |
4196 | (inputs | |
4197 | `(("perl" ,perl))) | |
4198 | (propagated-inputs | |
4199 | `(("r-gtools" ,r-gtools))) | |
e9960d8c | 4200 | (home-page "https://cran.r-project.org/web/packages/gdata") |
6034cd90 RW |
4201 | (synopsis "Various R programming tools for data manipulation") |
4202 | (description | |
4203 | "This package provides various R programming tools for data manipulation, | |
4204 | including: | |
4205 | ||
4206 | @itemize | |
4207 | @item medical unit conversions | |
4208 | @item combining objects | |
4209 | @item character vector operations | |
4210 | @item factor manipulation | |
4211 | @item obtaining information about R objects | |
4212 | @item manipulating MS-Excel formatted files | |
4213 | @item generating fixed-width format files | |
4214 | @item extricating components of date and time objects | |
4215 | @item operations on columns of data frames | |
4216 | @item matrix operations | |
4217 | @item operations on vectors and data frames | |
4218 | @item value of last evaluated expression | |
4219 | @item wrapper for @code{sample} that ensures consistent behavior for | |
4220 | both scalar and vector arguments | |
4221 | @end itemize\n") | |
4222 | (license license:gpl2+))) | |
4223 | ||
0cfe0570 RW |
4224 | (define-public r-gplots |
4225 | (package | |
4226 | (name "r-gplots") | |
f308d426 | 4227 | (version "3.0.1.1") |
0cfe0570 RW |
4228 | (source |
4229 | (origin | |
4230 | (method url-fetch) | |
4231 | (uri (cran-uri "gplots" version)) | |
4232 | (sha256 | |
4233 | (base32 | |
f308d426 | 4234 | "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx")))) |
0cfe0570 RW |
4235 | (build-system r-build-system) |
4236 | (propagated-inputs | |
4237 | `(("r-catools" ,r-catools) | |
4238 | ("r-gdata" ,r-gdata) | |
4239 | ("r-gtools" ,r-gtools) | |
4240 | ("r-kernsmooth" ,r-kernsmooth))) | |
e9960d8c | 4241 | (home-page "https://cran.r-project.org/web/packages/gplots") |
0cfe0570 RW |
4242 | (synopsis "Various R programming tools for plotting data") |
4243 | (description | |
4244 | "This package provides various R programming tools for plotting data, | |
4245 | including: | |
4246 | ||
4247 | @itemize | |
4248 | @item calculating and plotting locally smoothed summary function | |
4249 | @item enhanced versions of standard plots | |
4250 | @item manipulating colors | |
4251 | @item calculating and plotting two-dimensional data summaries | |
4252 | @item enhanced regression diagnostic plots | |
4253 | @item formula-enabled interface to @code{stats::lowess} function | |
4254 | @item displaying textual data in plots | |
4255 | @item baloon plots | |
4256 | @item plotting \"Venn\" diagrams | |
4257 | @item displaying Open-Office style plots | |
4258 | @item plotting multiple data on same region, with separate axes | |
4259 | @item plotting means and confidence intervals | |
4260 | @item spacing points in an x-y plot so they don't overlap | |
4261 | @end itemize\n") | |
4262 | (license license:gpl2+))) | |
4263 | ||
419a8a18 RW |
4264 | (define-public r-rocr |
4265 | (package | |
4266 | (name "r-rocr") | |
4267 | (version "1.0-7") | |
4268 | (source | |
4269 | (origin | |
4270 | (method url-fetch) | |
4271 | (uri (cran-uri "ROCR" version)) | |
4272 | (sha256 | |
4273 | (base32 | |
4274 | "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7")))) | |
4275 | (properties `((upstream-name . "ROCR"))) | |
4276 | (build-system r-build-system) | |
4277 | (propagated-inputs | |
4278 | `(("r-gplots" ,r-gplots))) | |
4279 | (home-page "http://rocr.bioinf.mpi-sb.mpg.de/") | |
4280 | (synopsis "Visualizing the performance of scoring classifiers") | |
4281 | (description | |
4282 | "ROCR is a flexible tool for creating cutoff-parameterized 2D performance | |
4283 | curves by freely combining two from over 25 performance measures (new | |
4284 | performance measures can be added using a standard interface). Curves from | |
4285 | different cross-validation or bootstrapping runs can be averaged by different | |
4286 | methods, and standard deviations, standard errors or box plots can be used to | |
4287 | visualize the variability across the runs. The parameterization can be | |
4288 | visualized by printing cutoff values at the corresponding curve positions, or | |
4289 | by coloring the curve according to cutoff. All components of a performance | |
4290 | plot can be quickly adjusted using a flexible parameter dispatching | |
4291 | mechanism.") | |
4292 | (license license:gpl2+))) | |
4293 | ||
031cf6b6 RJ |
4294 | (define-public r-zoo |
4295 | (package | |
4296 | (name "r-zoo") | |
98a4b9d0 | 4297 | (version "1.8-4") |
031cf6b6 RJ |
4298 | (source (origin |
4299 | (method url-fetch) | |
4300 | (uri (cran-uri "zoo" version)) | |
4301 | (sha256 | |
4302 | (base32 | |
98a4b9d0 | 4303 | "1pywcp86kqijdrvl42qwdy75szrag9pzj0p88zbrj2r1klb8rn5i")))) |
031cf6b6 | 4304 | (build-system r-build-system) |
aeb64f3c RW |
4305 | (propagated-inputs |
4306 | `(("r-lattice" ,r-lattice))) | |
031cf6b6 RJ |
4307 | (home-page "http://zoo.R-Forge.R-project.org/") |
4308 | (synopsis "S3 infrastructure for regular and irregular time series") | |
4309 | (description "This package contains an S3 class with methods for totally | |
4310 | ordered indexed observations. It is particularly aimed at irregular time | |
4311 | series of numeric vectors/matrices and factors.") | |
4312 | (license license:gpl2+))) | |
4313 | ||
6499b70e RW |
4314 | (define-public r-ztable |
4315 | (package | |
4316 | (name "r-ztable") | |
e5db6890 | 4317 | (version "0.2.0") |
6499b70e RW |
4318 | (source (origin |
4319 | (method url-fetch) | |
4320 | (uri (cran-uri "ztable" version)) | |
4321 | (sha256 | |
4322 | (base32 | |
e5db6890 | 4323 | "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy")))) |
6499b70e | 4324 | (build-system r-build-system) |
e5db6890 RW |
4325 | (propagated-inputs |
4326 | `(("r-flextable" ,r-flextable) | |
4327 | ("r-magrittr" ,r-magrittr) | |
4328 | ("r-moonbook" ,r-moonbook) | |
4329 | ("r-officer" ,r-officer) | |
4330 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4331 | ("r-scales" ,r-scales) | |
4332 | ("r-stringr" ,r-stringr))) | |
e9960d8c | 4333 | (home-page "https://cran.r-project.org/web/packages/ztable") |
6499b70e RW |
4334 | (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") |
4335 | (description | |
4336 | "This package provides functions to make zebra-striped tables (tables | |
4337 | with alternating row colors) in LaTeX and HTML formats easily from | |
4338 | @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova}, | |
4339 | @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and | |
4340 | @code{cbind.mytable} objects.") | |
4341 | (license license:gpl2+))) | |
06958135 RJPB |
4342 | |
4343 | (define-public r-vipor | |
4344 | (package | |
4345 | (name "r-vipor") | |
4c7ab030 | 4346 | (version "0.4.5") |
06958135 RJPB |
4347 | (source (origin |
4348 | (method url-fetch) | |
4349 | (uri (cran-uri "vipor" version)) | |
4350 | (sha256 | |
4351 | (base32 | |
4c7ab030 | 4352 | "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx")))) |
06958135 | 4353 | (build-system r-build-system) |
e9960d8c | 4354 | (home-page "https://cran.r-project.org/web/packages/vipor") |
06958135 RJPB |
4355 | (synopsis "Plot categorical data using noise and density estimates") |
4356 | (description | |
4357 | "This package provides tools to generate a violin point plot, a | |
4358 | combination of a violin/histogram plot and a scatter plot by offsetting points | |
4359 | within a category based on their density using quasirandom noise.") | |
4360 | (license license:gpl2+))) | |
6ba27985 RJPB |
4361 | |
4362 | (define-public r-beeswarm | |
4363 | (package | |
4364 | (name "r-beeswarm") | |
4365 | (version "0.2.3") | |
4366 | (source (origin | |
4367 | (method url-fetch) | |
4368 | (uri (cran-uri "beeswarm" version)) | |
4369 | (sha256 | |
4370 | (base32 | |
4371 | "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581")))) | |
4372 | (build-system r-build-system) | |
4373 | (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/") | |
4374 | (synopsis "Implementation of bee swarm plots") | |
4375 | (description | |
4376 | "This package provides an implementation of bee swarm plots. The bee | |
4377 | swarm plot is a one-dimensional scatter plot like stripchart, but with | |
4378 | closely-packed, non-overlapping points.") | |
4379 | (license license:artistic2.0))) | |
649d0c48 RJPB |
4380 | |
4381 | (define-public r-sourcetools | |
4382 | (package | |
4383 | (name "r-sourcetools") | |
442ce03a | 4384 | (version "0.1.7") |
649d0c48 RJPB |
4385 | (source |
4386 | (origin | |
4387 | (method url-fetch) | |
4388 | (uri (cran-uri "sourcetools" version)) | |
4389 | (sha256 | |
4390 | (base32 | |
442ce03a | 4391 | "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627")))) |
649d0c48 | 4392 | (build-system r-build-system) |
e9960d8c | 4393 | (home-page "https://cran.r-project.org/web/packages/sourcetools") |
649d0c48 RJPB |
4394 | (synopsis "Tools for reading, tokenizing and parsing R code") |
4395 | (description | |
4396 | "The sourcetools package provides both an R and C++ interface for the | |
4397 | tokenization of R code, and helpers for interacting with the tokenized | |
4398 | representation of R code.") | |
4399 | (license license:expat))) | |
29430416 RJPB |
4400 | |
4401 | (define-public r-ggbeeswarm | |
4402 | (package | |
4403 | (name "r-ggbeeswarm") | |
c3317cd9 | 4404 | (version "0.6.0") |
29430416 RJPB |
4405 | (source (origin |
4406 | (method url-fetch) | |
4407 | (uri (cran-uri "ggbeeswarm" version)) | |
4408 | (sha256 | |
4409 | (base32 | |
c3317cd9 | 4410 | "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v")))) |
29430416 RJPB |
4411 | (build-system r-build-system) |
4412 | (propagated-inputs | |
4413 | `(("r-beeswarm" ,r-beeswarm) | |
4414 | ("r-ggplot2" ,r-ggplot2) | |
4415 | ("r-vipor" ,r-vipor))) | |
4416 | (home-page "https://github.com/eclarke/ggbeeswarm") | |
4417 | (synopsis "Categorical scatter (violin point) plots") | |
4418 | (description | |
4419 | "This package provides two methods of plotting categorical scatter plots | |
4420 | such that the arrangement of points within a category reflects the density of | |
4421 | data at that region, and avoids over-plotting.") | |
4422 | (license license:gpl2+))) | |
2fd261a3 | 4423 | |
ac1f1e4e RJ |
4424 | (define-public r-ggthemes |
4425 | (package | |
4426 | (name "r-ggthemes") | |
aeb11b75 | 4427 | (version "4.1.0") |
ac1f1e4e RJ |
4428 | (source (origin |
4429 | (method url-fetch) | |
4430 | (uri (cran-uri "ggthemes" version)) | |
4431 | (sha256 | |
4432 | (base32 | |
aeb11b75 | 4433 | "1a6r384v72hb91qkg9rz2m7s3qskbl9haxynf2vzz6v1ak9xd4c5")))) |
ac1f1e4e RJ |
4434 | (build-system r-build-system) |
4435 | (propagated-inputs | |
314e8e76 RW |
4436 | `(("r-ggplot2" ,r-ggplot2) |
4437 | ("r-purrr" ,r-purrr) | |
4438 | ("r-scales" ,r-scales) | |
4439 | ("r-stringr" ,r-stringr) | |
4440 | ("r-tibble" ,r-tibble))) | |
ac1f1e4e RJ |
4441 | (home-page "https://cran.rstudio.com/web/packages/ggthemes") |
4442 | (synopsis "Extra themes, scales and geoms for @code{ggplot2}") | |
4443 | (description "This package provides extra themes and scales for | |
4444 | @code{ggplot2} that replicate the look of plots by Edward Tufte and | |
4445 | Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The | |
4446 | Wall Street Journal, among others. This package also provides | |
4447 | @code{geoms} for Tufte's box plot and range frame.") | |
4448 | (license license:gpl2))) | |
4449 | ||
2fd261a3 RJPB |
4450 | (define-public r-statmod |
4451 | (package | |
4452 | (name "r-statmod") | |
a8c2706d | 4453 | (version "1.4.30") |
2fd261a3 RJPB |
4454 | (source (origin |
4455 | (method url-fetch) | |
4456 | (uri (cran-uri "statmod" version)) | |
4457 | (sha256 | |
4458 | (base32 | |
a8c2706d | 4459 | "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x")))) |
2fd261a3 | 4460 | (build-system r-build-system) |
e9960d8c | 4461 | (home-page "https://cran.r-project.org/web/packages/statmod") |
2fd261a3 RJPB |
4462 | (native-inputs |
4463 | `(("gfortran" ,gfortran))) | |
4464 | (synopsis "Statistical modeling") | |
4465 | (description | |
4466 | "This package provides a collection of algorithms and functions to aid | |
4467 | statistical modeling. It includes growth curve comparisons, limiting dilution | |
4468 | analysis (aka ELDA), mixed linear models, heteroscedastic regression, | |
4469 | inverse-Gaussian probability calculations, Gauss quadrature and a secure | |
4470 | convergence algorithm for nonlinear models. It also includes advanced | |
4471 | generalized linear model functions that implement secure convergence, | |
4472 | dispersion modeling and Tweedie power-law families.") | |
4473 | ;; Statmod is distributed under either license | |
4474 | (license (list license:gpl2 license:gpl3)))) | |
5f764dd7 | 4475 | |
c6dced88 RJPB |
4476 | (define-public r-rann |
4477 | (package | |
4478 | (name "r-rann") | |
7213ef07 | 4479 | (version "2.6.1") |
c6dced88 RJPB |
4480 | (source (origin |
4481 | (method url-fetch) | |
4482 | (uri (cran-uri "RANN" version)) | |
4483 | (sha256 | |
4484 | (base32 | |
7213ef07 | 4485 | "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj")))) |
c6dced88 RJPB |
4486 | (properties |
4487 | `((upstream-name . "RANN"))) | |
4488 | (build-system r-build-system) | |
4489 | (home-page "https://github.com/jefferis/RANN") | |
4490 | (synopsis "Fast nearest neighbour search") | |
4491 | (description | |
4492 | "This package finds the k nearest neighbours for every point in a given | |
4493 | dataset in O(N log N) time using Arya and Mount's ANN library. Provides | |
4494 | approximate, exact searches, fixed radius searches, bd and kb trees.") | |
4495 | (license license:gpl3+))) | |
4496 | ||
5f764dd7 RW |
4497 | (define-public r-fivethirtyeight |
4498 | (package | |
4499 | (name "r-fivethirtyeight") | |
4500 | (version "0.1.0") | |
4501 | (source | |
4502 | (origin | |
4503 | (method url-fetch) | |
4504 | (uri (string-append "https://mran.microsoft.com/src/contrib/" | |
4505 | "fivethirtyeight_" version ".tar.gz")) | |
4506 | (sha256 | |
4507 | (base32 | |
4508 | "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl")))) | |
4509 | (build-system r-build-system) | |
4510 | (propagated-inputs | |
4511 | `(("r-knitr" ,r-knitr) | |
4512 | ("r-rmarkdown" ,r-rmarkdown) | |
4513 | ("r-dplyr" ,r-dplyr) | |
4514 | ("r-readr" ,r-readr) | |
4515 | ("r-ggplot2" ,r-ggplot2) | |
4516 | ("r-magrittr" ,r-magrittr) | |
4517 | ("r-stringr" ,r-stringr))) | |
4518 | (home-page "https://mran.microsoft.com/package/fivethirtyeight/") | |
4519 | (synopsis "Data and code behind the stories at FiveThirtyEight") | |
4520 | (description "This R package provides access to the code and data sets | |
4521 | published by the statistics blog FiveThirtyEight.") | |
4522 | (license license:expat))) | |
26a281ef RW |
4523 | |
4524 | (define-public r-compquadform | |
4525 | (package | |
4526 | (name "r-compquadform") | |
f1a313df | 4527 | (version "1.4.3") |
26a281ef RW |
4528 | (source |
4529 | (origin | |
4530 | (method url-fetch) | |
4531 | (uri (cran-uri "CompQuadForm" version)) | |
4532 | (sha256 | |
4533 | (base32 | |
f1a313df | 4534 | "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4")))) |
26a281ef RW |
4535 | (properties `((upstream-name . "CompQuadForm"))) |
4536 | (build-system r-build-system) | |
e9960d8c | 4537 | (home-page "https://cran.r-project.org/web/packages/CompQuadForm") |
26a281ef RW |
4538 | (synopsis "Distribution function of quadratic forms in normal variables") |
4539 | (description | |
4540 | "This package provides functions to compute the distribution function of | |
4541 | quadratic forms in normal variables using Imhof's method, Davies's algorithm, | |
4542 | Farebrother's algorithm or Liu et al.'s algorithm.") | |
4543 | (license license:gpl2+))) | |
c6017f72 RJPB |
4544 | |
4545 | (define-public r-cowplot | |
4546 | (package | |
4547 | (name "r-cowplot") | |
70ee5ab1 | 4548 | (version "0.9.4") |
c6017f72 RJPB |
4549 | (source |
4550 | (origin | |
4551 | (method url-fetch) | |
4552 | (uri (cran-uri "cowplot" version)) | |
4553 | (sha256 | |
4554 | (base32 | |
70ee5ab1 | 4555 | "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv")))) |
c6017f72 RJPB |
4556 | (build-system r-build-system) |
4557 | (propagated-inputs | |
4558 | `(("r-ggplot2" ,r-ggplot2) | |
4559 | ("r-gtable" ,r-gtable) | |
b50a4b13 RW |
4560 | ("r-plyr" ,r-plyr) |
4561 | ("r-scales" ,r-scales))) | |
c6017f72 RJPB |
4562 | (home-page "https://github.com/wilkelab/cowplot") |
4563 | (synopsis "Streamlined plot theme and plot annotations for ggplot2") | |
4564 | (description | |
4565 | "This package provides some helpful extensions and modifications to the | |
4566 | ggplot2 package to combine multiple ggplot2 plots into one and label them with | |
4567 | letters, as is often required for scientific publications.") | |
4568 | (license license:gpl2))) | |
efba686c RJPB |
4569 | |
4570 | (define-public r-mixtools | |
4571 | (package | |
4572 | (name "r-mixtools") | |
2f44ef97 | 4573 | (version "1.1.0") |
efba686c RJPB |
4574 | (source |
4575 | (origin | |
4576 | (method url-fetch) | |
4577 | (uri (cran-uri "mixtools" version)) | |
4578 | (sha256 | |
4579 | (base32 | |
2f44ef97 | 4580 | "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl")))) |
efba686c RJPB |
4581 | (build-system r-build-system) |
4582 | (propagated-inputs | |
2f44ef97 RW |
4583 | `(("r-mass" ,r-mass) |
4584 | ("r-segmented" ,r-segmented) | |
4585 | ("r-survival" ,r-survival))) | |
e9960d8c | 4586 | (home-page "https://cran.r-project.org/web/packages/mixtools") |
efba686c RJPB |
4587 | (synopsis "Tools for analyzing finite mixture models") |
4588 | (description | |
4589 | "This package provides a collection of R functions for analyzing finite | |
4590 | mixture models.") | |
4591 | (license license:gpl2+))) | |
793f2edb RJPB |
4592 | |
4593 | (define-public r-lars | |
4594 | (package | |
4595 | (name "r-lars") | |
4596 | (version "1.2") | |
4597 | (source | |
4598 | (origin | |
4599 | (method url-fetch) | |
4600 | (uri (cran-uri "lars" version)) | |
4601 | (sha256 | |
4602 | (base32 | |
4603 | "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34")))) | |
4604 | (build-system r-build-system) | |
4605 | (inputs | |
4606 | `(("gfortran" ,gfortran))) | |
4607 | (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS") | |
4608 | (synopsis "Least angle regression software") | |
4609 | (description | |
4610 | "Least Angle Regression (\"LAR\") is a model selection algorithm; a | |
4611 | useful and less greedy version of traditional forward selection methods. A | |
4612 | simple modification of the LAR algorithm implements Tibshirani's Lasso; the | |
4613 | Lasso modification of LARS calculates the entire Lasso path of coefficients | |
4614 | for a given problem at the cost of a single least squares fit. Another LARS | |
4615 | modification efficiently implements epsilon Forward Stagewise linear | |
4616 | regression.") | |
4617 | (license license:gpl2))) | |
e431eb67 RJPB |
4618 | |
4619 | (define-public r-fastica | |
4620 | (package | |
4621 | (name "r-fastica") | |
62d3afc3 | 4622 | (version "1.2-1") |
e431eb67 RJPB |
4623 | (source |
4624 | (origin | |
4625 | (method url-fetch) | |
4626 | (uri (cran-uri "fastICA" version)) | |
4627 | (sha256 | |
4628 | (base32 | |
62d3afc3 | 4629 | "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg")))) |
e431eb67 RJPB |
4630 | (properties `((upstream-name . "fastICA"))) |
4631 | (build-system r-build-system) | |
e9960d8c | 4632 | (home-page "https://cran.r-project.org/web/packages/fastICA") |
e431eb67 RJPB |
4633 | (synopsis "FastICA algorithms to perform ICA and projection pursuit") |
4634 | (description | |
4635 | "This package provides an implementation of the FastICA algorithm to | |
4636 | perform @dfn{independent component analysis} (ICA) and projection pursuit.") | |
4637 | ;; Any GPL version. | |
4638 | (license license:gpl3+))) | |
37337699 RJPB |
4639 | |
4640 | (define-public r-randomforest | |
4641 | (package | |
4642 | (name "r-randomforest") | |
6e54870f | 4643 | (version "4.6-14") |
37337699 RJPB |
4644 | (source |
4645 | (origin | |
4646 | (method url-fetch) | |
4647 | (uri (cran-uri "randomForest" version)) | |
4648 | (sha256 | |
4649 | (base32 | |
6e54870f | 4650 | "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l")))) |
37337699 RJPB |
4651 | (properties `((upstream-name . "randomForest"))) |
4652 | (build-system r-build-system) | |
4653 | (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/") | |
4654 | (native-inputs | |
4655 | `(("gfortran" ,gfortran))) | |
4656 | (synopsis "Breiman and Cutler's random forests for classification and regression") | |
4657 | (description | |
4658 | "This package provides the Breiman and Cutler's random forests algorithm, based on a | |
4659 | forest of trees using random inputs, for classification and regression.") | |
4660 | (license license:gpl2+))) | |
d5eca4f9 RJPB |
4661 | |
4662 | (define-public r-diptest | |
4663 | (package | |
4664 | (name "r-diptest") | |
4665 | (version "0.75-7") | |
4666 | (source | |
4667 | (origin | |
4668 | (method url-fetch) | |
4669 | (uri (cran-uri "diptest" version)) | |
4670 | (sha256 | |
4671 | (base32 | |
4672 | "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6")))) | |
4673 | (build-system r-build-system) | |
e9960d8c | 4674 | (home-page "https://cran.r-project.org/web/packages/diptest") |
d5eca4f9 RJPB |
4675 | (synopsis "Hartigan's dip test statistic for unimodality") |
4676 | (description | |
4677 | "This package computes Hartigan's dip test statistic for unimodality, | |
4678 | multimodality and provides a test with simulation based p-values, where the | |
4679 | original public code has been corrected.") | |
4680 | (license license:gpl2+))) | |
1721fb4f RJPB |
4681 | |
4682 | (define-public r-modeltools | |
4683 | (package | |
4684 | (name "r-modeltools") | |
4481004f | 4685 | (version "0.2-22") |
1721fb4f RJPB |
4686 | (source |
4687 | (origin | |
4688 | (method url-fetch) | |
4689 | (uri (cran-uri "modeltools" version)) | |
4690 | (sha256 | |
4691 | (base32 | |
4481004f | 4692 | "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5")))) |
1721fb4f | 4693 | (build-system r-build-system) |
e9960d8c | 4694 | (home-page "https://cran.r-project.org/web/packages/modeltools") |
1721fb4f RJPB |
4695 | (synopsis "Tools and classes for statistical models") |
4696 | (description | |
4697 | "This package provides a collection of tools to deal with statistical | |
4698 | models. The functionality is experimental and the user interface is likely | |
4699 | to change in the future.") | |
4700 | (license license:gpl2))) | |
a1f2668e RJPB |
4701 | |
4702 | (define-public r-flexmix | |
4703 | (package | |
4704 | (name "r-flexmix") | |
bc7895e1 | 4705 | (version "2.3-15") |
a1f2668e RJPB |
4706 | (source |
4707 | (origin | |
4708 | (method url-fetch) | |
4709 | (uri (cran-uri "flexmix" version)) | |
4710 | (sha256 | |
4711 | (base32 | |
bc7895e1 | 4712 | "0hrz2axp2c9548b1r0bmrl57219nn030qndb83a8garkzq5lqi5s")))) |
a1f2668e RJPB |
4713 | (build-system r-build-system) |
4714 | (propagated-inputs | |
aeb64f3c RW |
4715 | `(("r-lattice" ,r-lattice) |
4716 | ("r-modeltools" ,r-modeltools) | |
4717 | ("r-nnet" ,r-nnet))) | |
e9960d8c | 4718 | (home-page "https://cran.r-project.org/web/packages/flexmix") |
a1f2668e RJPB |
4719 | (synopsis "Flexible mixture modeling") |
4720 | (description | |
4721 | "This package implements a general framework for finite mixtures of | |
4722 | regression models using the EM algorithm. FlexMix provides the E-step and | |
4723 | all data handling, while the M-step can be supplied by the user to easily | |
4724 | define new models. Existing drivers implement mixtures of standard linear | |
4725 | models, generalized linear models and model-based clustering.") | |
4726 | (license license:gpl2+))) | |
5638e154 RJPB |
4727 | |
4728 | (define-public r-mclust | |
4729 | (package | |
4730 | (name "r-mclust") | |
0adf04a2 | 4731 | (version "5.4.2") |
5638e154 RJPB |
4732 | (source |
4733 | (origin | |
4734 | (method url-fetch) | |
4735 | (uri (cran-uri "mclust" version)) | |
4736 | (sha256 | |
4737 | (base32 | |
0adf04a2 | 4738 | "09152swfpa3fzhmrq5cwb5kxgvrxvigv1m4v6rhcibrdhfd1x8x4")))) |
5638e154 RJPB |
4739 | (build-system r-build-system) |
4740 | (native-inputs | |
4741 | `(("gfortran" ,gfortran))) | |
4742 | (home-page "http://www.stat.washington.edu/mclust/") | |
4743 | (synopsis "Gaussian mixture modelling for model-based clustering etc.") | |
4744 | (description | |
4745 | "This package provides Gaussian finite mixture models fitted via EM | |
4746 | algorithm for model-based clustering, classification, and density estimation, | |
4747 | including Bayesian regularization, dimension reduction for visualisation, | |
4748 | and resampling-based inference.") | |
4749 | (license license:gpl2+))) | |
4750 | ||
c962816d RJPB |
4751 | (define-public r-prabclus |
4752 | (package | |
4753 | (name "r-prabclus") | |
56daae7b | 4754 | (version "2.2-7") |
c962816d RJPB |
4755 | (source |
4756 | (origin | |
4757 | (method url-fetch) | |
4758 | (uri (cran-uri "prabclus" version)) | |
4759 | (sha256 | |
4760 | (base32 | |
56daae7b | 4761 | "0h2nml8ri27mhfs2p6ngb6kfd6lyq30sc6813yybpskkrb6gs1pb")))) |
c962816d RJPB |
4762 | (build-system r-build-system) |
4763 | (propagated-inputs | |
aeb64f3c RW |
4764 | `(("r-mass" ,r-mass) |
4765 | ("r-mclust" ,r-mclust))) | |
c962816d RJPB |
4766 | (home-page "https://cran.r-project.org/web/packages/prabclus") |
4767 | (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") | |
4768 | (description | |
2e648d2b RW |
4769 | "This package provides distance-based parametric bootstrap tests for |
4770 | clustering with spatial neighborhood information. It implements some distance | |
4771 | measures, clustering of presence-absence, abundance and multilocus genetical | |
4772 | data for species delimitation, nearest neighbor based noise detection.") | |
c962816d | 4773 | (license license:gpl2+))) |
cda07208 RJPB |
4774 | |
4775 | (define-public r-deoptimr | |
4776 | (package | |
4777 | (name "r-deoptimr") | |
4778 | (version "1.0-8") | |
4779 | (source | |
4780 | (origin | |
4781 | (method url-fetch) | |
4782 | (uri (cran-uri "DEoptimR" version)) | |
4783 | (sha256 | |
4784 | (base32 | |
4785 | "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4")))) | |
4786 | (properties `((upstream-name . "DEoptimR"))) | |
4787 | (build-system r-build-system) | |
e9960d8c | 4788 | (home-page "https://cran.r-project.org/web/packages/DEoptimR") |
cda07208 RJPB |
4789 | (synopsis "Differential evolution optimization in pure R") |
4790 | (description | |
4791 | "This package provides a differential evolution (DE) stochastic | |
4792 | algorithms for global optimization of problems with and without constraints. | |
4793 | The aim is to curate a collection of its state-of-the-art variants that (1) do | |
4794 | not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) | |
4795 | can be efficiently implemented directly in the R language.") | |
4796 | (license license:gpl2+))) | |
c0cab38e RJPB |
4797 | |
4798 | (define-public r-robustbase | |
4799 | (package | |
4800 | (name "r-robustbase") | |
60aac7ec | 4801 | (version "0.93-3") |
c0cab38e RJPB |
4802 | (source |
4803 | (origin | |
4804 | (method url-fetch) | |
4805 | (uri (cran-uri "robustbase" version)) | |
4806 | (sha256 | |
4807 | (base32 | |
60aac7ec | 4808 | "1nqh1qg1qd1qrxl1w585dqx7ql55qzjny1r4f9hqxpwd7lml07cc")))) |
c0cab38e RJPB |
4809 | (build-system r-build-system) |
4810 | (inputs | |
4811 | `(("gfortran" ,gfortran))) | |
4812 | (propagated-inputs | |
4813 | `(("r-deoptimr" ,r-deoptimr))) | |
4814 | (home-page "http://robustbase.r-forge.r-project.org/") | |
4815 | (synopsis "Basic robust statistics") | |
4816 | (description | |
4817 | "This packages allows to analyze data with robust methods such as | |
4818 | regression methodology including model selections and multivariate statistics.") | |
4819 | (license license:gpl2+))) | |
5da4f84f | 4820 | |
23841b25 RW |
4821 | (define-public r-pcapp |
4822 | (package | |
4823 | (name "r-pcapp") | |
23fb6047 | 4824 | (version "1.9-73") |
23841b25 RW |
4825 | (source |
4826 | (origin | |
4827 | (method url-fetch) | |
4828 | (uri (cran-uri "pcaPP" version)) | |
4829 | (sha256 | |
4830 | (base32 | |
23fb6047 | 4831 | "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa")))) |
23841b25 RW |
4832 | (properties `((upstream-name . "pcaPP"))) |
4833 | (build-system r-build-system) | |
4834 | (propagated-inputs | |
4835 | `(("r-mvtnorm" ,r-mvtnorm))) | |
e9960d8c | 4836 | (home-page "https://cran.r-project.org/web/packages/pcaPP") |
23841b25 RW |
4837 | (synopsis "Robust PCA by projection pursuit") |
4838 | (description | |
4839 | "This package provides functions for robust @dfn{principal component | |
4840 | analysis} (PCA) by projection pursuit.") | |
4841 | (license license:gpl3+))) | |
4842 | ||
0bae5fd6 RW |
4843 | (define-public r-rrcov |
4844 | (package | |
4845 | (name "r-rrcov") | |
bcc17f7f | 4846 | (version "1.4-7") |
0bae5fd6 RW |
4847 | (source |
4848 | (origin | |
4849 | (method url-fetch) | |
4850 | (uri (cran-uri "rrcov" version)) | |
4851 | (sha256 | |
4852 | (base32 | |
bcc17f7f | 4853 | "14zjyqcdiqx6js99nx5s8hmyx564ixy2d8s6i7wa50xmx368rl6b")))) |
0bae5fd6 RW |
4854 | (build-system r-build-system) |
4855 | (propagated-inputs | |
4856 | `(("r-cluster" ,r-cluster) | |
4857 | ("r-lattice" ,r-lattice) | |
4858 | ("r-mvtnorm" ,r-mvtnorm) | |
4859 | ("r-pcapp" ,r-pcapp) | |
4860 | ("r-robustbase" ,r-robustbase))) | |
4861 | (native-inputs | |
4862 | `(("gfortran" ,gfortran))) | |
e9960d8c | 4863 | (home-page "https://cran.r-project.org/web/packages/rrcov") |
0bae5fd6 RW |
4864 | (synopsis "Scalable robust estimators with high breakdown Point") |
4865 | (description | |
4866 | "This package provides an implementation of robust location and scatter | |
4867 | estimation and robust multivariate analysis with high breakdown point.") | |
4868 | (license license:gpl2+))) | |
4869 | ||
5d0afe88 RW |
4870 | (define-public r-fit-models |
4871 | (package | |
4872 | (name "r-fit-models") | |
4873 | (version "0.5-14") | |
4874 | (source | |
4875 | (origin | |
4876 | (method url-fetch) | |
4877 | (uri (cran-uri "fit.models" version)) | |
4878 | (sha256 | |
4879 | (base32 | |
4880 | "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck")))) | |
4881 | (properties `((upstream-name . "fit.models"))) | |
4882 | (build-system r-build-system) | |
4883 | (propagated-inputs | |
4884 | `(("r-lattice" ,r-lattice))) | |
e9960d8c | 4885 | (home-page "https://cran.r-project.org/web/packages/fit.models") |
5d0afe88 RW |
4886 | (synopsis "Compare fitted models") |
4887 | (description | |
4888 | "The @code{fit.models} function and its associated methods (coefficients, print, | |
4889 | summary, plot, etc.) were originally provided in the @code{robust} package to | |
4890 | compare robustly and classically fitted model objects. The aim of the | |
4891 | @code{fit.models} package is to separate this fitted model object comparison | |
4892 | functionality from the robust package and to extend it to support fitting | |
4893 | methods (e.g., classical, robust, Bayesian, regularized, etc.) more | |
4894 | generally.") | |
4895 | ;; Any version of the GPL | |
4896 | (license (list license:gpl2+ license:gpl3+)))) | |
4897 | ||
c5f744a6 RW |
4898 | (define-public r-robust |
4899 | (package | |
4900 | (name "r-robust") | |
4901 | (version "0.4-18") | |
4902 | (source | |
4903 | (origin | |
4904 | (method url-fetch) | |
4905 | (uri (cran-uri "robust" version)) | |
4906 | (sha256 | |
4907 | (base32 | |
4908 | "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4")))) | |
4909 | (build-system r-build-system) | |
4910 | (propagated-inputs | |
4911 | `(("r-fit-models" ,r-fit-models) | |
4912 | ("r-lattice" ,r-lattice) | |
4913 | ("r-mass" ,r-mass) | |
4914 | ("r-robustbase" ,r-robustbase) | |
4915 | ("r-rrcov" ,r-rrcov))) | |
4916 | (native-inputs | |
4917 | `(("gfortran" ,gfortran))) | |
e9960d8c | 4918 | (home-page "https://cran.r-project.org/web/packages/robust") |
c5f744a6 RW |
4919 | (synopsis "Port of the S+ \"Robust Library\"") |
4920 | (description | |
4921 | "This package is a port of the S+ \"Robust Library\". It provides | |
4922 | methods for robust statistics, notably for robust regression and robust | |
4923 | multivariate analysis.") | |
4924 | (license license:gpl2))) | |
4925 | ||
5da4f84f RJPB |
4926 | (define-public r-trimcluster |
4927 | (package | |
4928 | (name "r-trimcluster") | |
77c027b9 | 4929 | (version "0.1-2.1") |
5da4f84f RJPB |
4930 | (source |
4931 | (origin | |
4932 | (method url-fetch) | |
4933 | (uri (cran-uri "trimcluster" version)) | |
4934 | (sha256 | |
4935 | (base32 | |
77c027b9 | 4936 | "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn")))) |
5da4f84f | 4937 | (build-system r-build-system) |
e9960d8c | 4938 | (home-page "https://cran.r-project.org/web/packages/trimcluster") |
5da4f84f RJPB |
4939 | (synopsis "Cluster analysis with trimming") |
4940 | (description | |
4941 | "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and | |
4942 | Matran (1997). This optimizes the k-means criterion under trimming a portion | |
4943 | of the points.") | |
97cb349d RW |
4944 | ;; Any GPL version |
4945 | (license (list license:gpl2+ license:gpl3+)))) | |
a409e8b5 RJPB |
4946 | |
4947 | (define-public r-fpc | |
4948 | (package | |
4949 | (name "r-fpc") | |
dc695341 | 4950 | (version "2.1-11.1") |
a409e8b5 RJPB |
4951 | (source |
4952 | (origin | |
4953 | (method url-fetch) | |
4954 | (uri (cran-uri "fpc" version)) | |
4955 | (sha256 | |
4956 | (base32 | |
dc695341 | 4957 | "1ari57hkgqsxh6khr6j52cfrzc0096cnn1q7ghxk2z4brdd4rznc")))) |
a409e8b5 RJPB |
4958 | (build-system r-build-system) |
4959 | (propagated-inputs | |
aeb64f3c RW |
4960 | `(("r-class" ,r-class) |
4961 | ("r-cluster" ,r-cluster) | |
4962 | ("r-diptest" ,r-diptest) | |
a409e8b5 RJPB |
4963 | ("r-flexmix" ,r-flexmix) |
4964 | ("r-kernlab" ,r-kernlab) | |
aeb64f3c | 4965 | ("r-mass" ,r-mass) |
a409e8b5 RJPB |
4966 | ("r-mclust" ,r-mclust) |
4967 | ("r-mvtnorm" ,r-mvtnorm) | |
4968 | ("r-prabclus" ,r-prabclus) | |
4969 | ("r-robustbase" ,r-robustbase) | |
4970 | ("r-trimcluster" ,r-trimcluster))) | |
e9960d8c | 4971 | (home-page "https://cran.r-project.org/web/packages/fpc") |
a409e8b5 RJPB |
4972 | (synopsis "Flexible procedures for clustering") |
4973 | (description | |
4974 | "This package provides various methods for clustering and cluster validation. | |
4975 | For example, it provides fixed point clustering, linear regression clustering, | |
4976 | clustering by merging Gaussian mixture components, as well as symmetric and | |
4977 | asymmetric discriminant projections for visualisation of the separation of | |
4978 | groupings.") | |
4979 | (license license:gpl2+))) | |
d4cebae2 RJPB |
4980 | |
4981 | (define-public r-vgam | |
4982 | (package | |
4983 | (name "r-vgam") | |
e51096b2 | 4984 | (version "1.1-1") |
d4cebae2 RJPB |
4985 | (source |
4986 | (origin | |
4987 | (method url-fetch) | |
4988 | (uri (cran-uri "VGAM" version)) | |
4989 | (sha256 | |
4990 | (base32 | |
e51096b2 | 4991 | "0lnsqx3q3k0c7sj8gj0n6shn2fyxwrh8xph8h1r1i23ybbb2n6fy")))) |
d4cebae2 RJPB |
4992 | (properties `((upstream-name . "VGAM"))) |
4993 | (build-system r-build-system) | |
4994 | (inputs | |
4995 | `(("gfortran" ,gfortran))) | |
4996 | (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM") | |
4997 | (synopsis "Vector generalized linear and additive models") | |
4998 | (description | |
4999 | "This package is an implementation of about 6 major classes of statistical | |
5000 | regression models. Currently only fixed-effects models are implemented, i.e., | |
5001 | no random-effects models. Many (150+) models and distributions are estimated | |
5002 | by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. | |
5003 | VGLMs can be loosely thought of as multivariate generalised linear models.") | |
5004 | (license license:gpl2+))) | |
7711f614 RJPB |
5005 | |
5006 | (define-public r-pbapply | |
5007 | (package | |
5008 | (name "r-pbapply") | |
b58220f5 | 5009 | (version "1.4-0") |
7711f614 RJPB |
5010 | (source |
5011 | (origin | |
5012 | (method url-fetch) | |
5013 | (uri (cran-uri "pbapply" version)) | |
5014 | (sha256 | |
5015 | (base32 | |
b58220f5 | 5016 | "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k")))) |
7711f614 RJPB |
5017 | (build-system r-build-system) |
5018 | (home-page "https://github.com/psolymos/pbapply") | |
5019 | (synopsis "Adding progress bar to apply functions") | |
5020 | (description | |
5021 | "This lightweight package that adds progress bar to vectorized R | |
5022 | functions apply. The implementation can easily be added to functions where | |
5023 | showing the progress is useful e.g. bootstrap.") | |
5024 | (license license:gpl2))) | |
e08ad766 | 5025 | |
0392f82f RJPB |
5026 | (define-public r-minqa |
5027 | (package | |
5028 | (name "r-minqa") | |
5029 | (version "1.2.4") | |
5030 | (source | |
5031 | (origin | |
5032 | (method url-fetch) | |
5033 | (uri (cran-uri "minqa" version)) | |
5034 | (sha256 | |
5035 | (base32 | |
5036 | "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg")))) | |
5037 | (build-system r-build-system) | |
5038 | (propagated-inputs | |
5039 | `(("r-rcpp" ,r-rcpp))) | |
5040 | (inputs | |
5041 | `(("gfortran" ,gfortran))) | |
5042 | (home-page "http://optimizer.r-forge.r-project.org") | |
5043 | (synopsis "Derivative-free optimization algorithms by quadratic approximation") | |
5044 | (description | |
5045 | "This package provides a derivative-free optimization by quadratic approximation | |
5046 | based on an interface to Fortran implementations by M. J. D. Powell.") | |
5047 | (license license:gpl2))) | |
21cfad44 RJPB |
5048 | |
5049 | (define-public r-rcppeigen | |
5050 | (package | |
5051 | (name "r-rcppeigen") | |
9b7df80b | 5052 | (version "0.3.3.5.0") |
21cfad44 RJPB |
5053 | (source |
5054 | (origin | |
5055 | (method url-fetch) | |
5056 | (uri (cran-uri "RcppEigen" version)) | |
5057 | (sha256 | |
5058 | (base32 | |
9b7df80b | 5059 | "01bz41c29591ybzqn4z88ss036ai3anh9figryvmfpqcfwbszip5")))) |
21cfad44 RJPB |
5060 | (properties `((upstream-name . "RcppEigen"))) |
5061 | (build-system r-build-system) | |
5062 | (propagated-inputs | |
aeb64f3c RW |
5063 | `(("r-rcpp" ,r-rcpp) |
5064 | ("r-matrix" ,r-matrix))) | |
21cfad44 RJPB |
5065 | (home-page "http://eigen.tuxfamily.org") |
5066 | (synopsis "Rcpp integration for the Eigen templated linear algebra library") | |
5067 | (description | |
5068 | "This package provides an integration of Eigen in R using a C++ template | |
5069 | library for linear algebra: matrices, vectors, numerical solvers and related algorithms. | |
5070 | It supports dense and sparse matrices on integer, floating point and complex numbers, | |
5071 | decompositions of such matrices, and solutions of linear systems.") | |
5072 | (license license:gpl2+))) | |
aa841000 RJPB |
5073 | |
5074 | (define-public r-modelmetrics | |
5075 | (package | |
5076 | (name "r-modelmetrics") | |
00281ea3 | 5077 | (version "1.2.2") |
aa841000 RJPB |
5078 | (source |
5079 | (origin | |
5080 | (method url-fetch) | |
5081 | (uri (cran-uri "ModelMetrics" version)) | |
5082 | (sha256 | |
5083 | (base32 | |
00281ea3 | 5084 | "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6")))) |
aa841000 RJPB |
5085 | (properties `((upstream-name . "ModelMetrics"))) |
5086 | (build-system r-build-system) | |
5087 | (propagated-inputs | |
f33a4748 RW |
5088 | `(("r-rcpp" ,r-rcpp) |
5089 | ("r-data-table" ,r-data-table))) | |
e9960d8c | 5090 | (home-page "https://cran.r-project.org/web/packages/ModelMetrics") |
aa841000 RJPB |
5091 | (synopsis "Rapid calculation of model metrics") |
5092 | (description | |
5093 | "Written in C++ using @code{Rcpp}, this package provides a collection of | |
5094 | metrics for evaluating models.") | |
5095 | (license license:gpl2+))) | |
545d0789 RJPB |
5096 | |
5097 | (define-public r-matrixmodels | |
5098 | (package | |
5099 | (name "r-matrixmodels") | |
5100 | (version "0.4-1") | |
5101 | (source | |
5102 | (origin | |
5103 | (method url-fetch) | |
5104 | (uri (cran-uri "MatrixModels" version)) | |
5105 | (sha256 | |
5106 | (base32 | |
5107 | "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy")))) | |
5108 | (properties `((upstream-name . "MatrixModels"))) | |
5109 | (build-system r-build-system) | |
aeb64f3c RW |
5110 | (propagated-inputs |
5111 | `(("r-matrix" ,r-matrix))) | |
545d0789 RJPB |
5112 | (home-page "https://cran.r-project.org/web/packages/MatrixModels") |
5113 | (synopsis "Modelling with sparse and dense matrices") | |
5114 | (description | |
5115 | "This package models with sparse and dense matrix matrices, | |
5116 | using modular prediction and response module classes.") | |
5117 | (license license:gpl2+))) | |
49dc1fa5 RJPB |
5118 | |
5119 | (define-public r-quantreg | |
5120 | (package | |
5121 | (name "r-quantreg") | |
aa72d7f7 | 5122 | (version "5.38") |
49dc1fa5 RJPB |
5123 | (source |
5124 | (origin | |
5125 | (method url-fetch) | |
5126 | (uri (cran-uri "quantreg" version)) | |
5127 | (sha256 | |
5128 | (base32 | |
aa72d7f7 | 5129 | "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1")))) |
49dc1fa5 RJPB |
5130 | (build-system r-build-system) |
5131 | (native-inputs | |
5132 | `(("gfortran" ,gfortran))) | |
5133 | (propagated-inputs | |
0d5bc938 RW |
5134 | `(("r-matrix" ,r-matrix) |
5135 | ("r-matrixmodels" ,r-matrixmodels) | |
49dc1fa5 | 5136 | ("r-sparsem" ,r-sparsem))) |
d062957a | 5137 | (home-page "https://www.r-project.org") |
49dc1fa5 RJPB |
5138 | (synopsis "Quantile regression") |
5139 | (description | |
5140 | "This package provides an estimation and inference methods for models | |
5141 | of conditional quantiles: linear and nonlinear parametric and non-parametric | |
5142 | models for conditional quantiles of a univariate response and several methods | |
5143 | for handling censored survival data. Portfolio selection methods based on | |
5144 | expected shortfall risk are also included.") | |
5145 | (license license:gpl2+))) | |
c549864d RJPB |
5146 | |
5147 | (define-public r-nloptr | |
5148 | (package | |
5149 | (name "r-nloptr") | |
6ab5670a | 5150 | (version "1.2.1") |
c549864d RJPB |
5151 | (source |
5152 | (origin | |
5153 | (method url-fetch) | |
5154 | (uri (cran-uri "nloptr" version)) | |
5155 | (sha256 | |
5156 | (base32 | |
6ab5670a | 5157 | "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz")))) |
c549864d RJPB |
5158 | (build-system r-build-system) |
5159 | (native-inputs | |
6ab5670a RW |
5160 | `(("r-knitr" ,r-knitr) ; for building vignettes |
5161 | ("pkg-config" ,pkg-config) | |
5162 | ("gfortran" ,gfortran))) | |
c549864d RJPB |
5163 | (inputs |
5164 | `(("nlopt" ,nlopt))) | |
e9960d8c | 5165 | (home-page "https://cran.r-project.org/web/packages/nloptr") |
c549864d RJPB |
5166 | (synopsis "R interface to NLopt") |
5167 | (description | |
5168 | "This package is interface to NLopt, a library for nonlinear | |
5169 | optimization. NLopt is a library for nonlinear optimization, providing a | |
5170 | common interface for a number of different free optimization routines | |
5171 | available online as well as original implementations of various other | |
5172 | algorithms.") | |
5173 | (license license:lgpl3))) | |
51fc7d8c RJPB |
5174 | |
5175 | (define-public r-lme4 | |
5176 | (package | |
5177 | (name "r-lme4") | |
7865c8c4 | 5178 | (version "1.1-19") |
51fc7d8c RJPB |
5179 | (source |
5180 | (origin | |
5181 | (method url-fetch) | |
5182 | (uri (cran-uri "lme4" version)) | |
5183 | (sha256 | |
5184 | (base32 | |
7865c8c4 | 5185 | "0j8xhkkcdv45ilab960s9jrcjk6jbzvd7w7myswv5fmalrpq52pf")))) |
51fc7d8c RJPB |
5186 | (build-system r-build-system) |
5187 | (native-inputs | |
5188 | `(("r-rcpp" ,r-rcpp) | |
5189 | ("r-rcppeigen" ,r-rcppeigen))) | |
5190 | (propagated-inputs | |
96071a6d RW |
5191 | `(("r-lattice" ,r-lattice) |
5192 | ("r-matrix" ,r-matrix) | |
5193 | ("r-minqa" ,r-minqa) | |
aeb64f3c RW |
5194 | ("r-nloptr" ,r-nloptr) |
5195 | ("r-mass" ,r-mass) | |
5196 | ("r-nlme" ,r-nlme))) | |
e9960d8c | 5197 | (home-page "https://cran.r-project.org/web/packages/lme4") |
51fc7d8c RJPB |
5198 | (synopsis "Linear mixed-effects models using eigen and S4") |
5199 | (description | |
5200 | "This package provides fit linear and generalized linear mixed-effects | |
5201 | models. The models and their components are represented using S4 classes and | |
5202 | methods. The core computational algorithms are implemented using the Eigen | |
5203 | C++ library for numerical linear algebra and RcppEigen glue.") | |
5204 | (license license:gpl2+))) | |
a3eb8c81 RJPB |
5205 | |
5206 | (define-public r-pbkrtest | |
5207 | (package | |
5208 | (name "r-pbkrtest") | |
da2260f9 | 5209 | (version "0.4-7") |
a3eb8c81 RJPB |
5210 | (source |
5211 | (origin | |
5212 | (method url-fetch) | |
5213 | (uri (cran-uri "pbkrtest" version)) | |
5214 | (sha256 | |
5215 | (base32 | |
da2260f9 | 5216 | "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw")))) |
a3eb8c81 RJPB |
5217 | (build-system r-build-system) |
5218 | (propagated-inputs | |
aeb64f3c RW |
5219 | `(("r-lme4" ,r-lme4) |
5220 | ("r-mass" ,r-mass) | |
5221 | ("r-matrix" ,r-matrix))) | |
a3eb8c81 RJPB |
5222 | (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/") |
5223 | (synopsis "Methods for linear mixed model comparison") | |
5224 | (description | |
5225 | "This package implements a parametric bootstrap test and a Kenward Roger | |
5226 | modification of F-tests for linear mixed effects models and a parametric | |
5227 | bootstrap test for generalized linear mixed models.") | |
5228 | (license license:gpl2+))) | |
ab2ec643 | 5229 | |
f1c7a242 RW |
5230 | (define-public r-cardata |
5231 | (package | |
5232 | (name "r-cardata") | |
16508df1 | 5233 | (version "3.0-2") |
f1c7a242 RW |
5234 | (source |
5235 | (origin | |
5236 | (method url-fetch) | |
5237 | (uri (cran-uri "carData" version)) | |
5238 | (sha256 | |
5239 | (base32 | |
16508df1 | 5240 | "152lfgaspgx6x2wzdb5p3zv6r87a0d2pg10h6fjmdr613kzlwp1v")))) |
f1c7a242 RW |
5241 | (properties `((upstream-name . "carData"))) |
5242 | (build-system r-build-system) | |
5243 | (home-page "https://r-forge.r-project.org/projects/car/") | |
5244 | (synopsis "Data Sets for the book Companion to Applied Regression") | |
5245 | (description | |
5246 | "This package provides datasets to accompany J. Fox and S. Weisberg, An R | |
5247 | Companion to Applied Regression, Third Edition, Sage.") | |
5248 | (license license:gpl2+))) | |
ab2ec643 RJPB |
5249 | |
5250 | (define-public r-car | |
5251 | (package | |
5252 | (name "r-car") | |
bfb994d8 | 5253 | (version "3.0-2") |
ab2ec643 RJPB |
5254 | (source |
5255 | (origin | |
5256 | (method url-fetch) | |
5257 | (uri (cran-uri "car" version)) | |
5258 | (sha256 | |
5259 | (base32 | |
bfb994d8 | 5260 | "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz")))) |
ab2ec643 RJPB |
5261 | (build-system r-build-system) |
5262 | (propagated-inputs | |
500224cb RW |
5263 | `(("r-abind" ,r-abind) |
5264 | ("r-cardata" ,r-cardata) | |
5265 | ("r-lme4" ,r-lme4) | |
5266 | ("r-maptools" ,r-maptools) | |
5267 | ("r-mass" ,r-mass) | |
aeb64f3c | 5268 | ("r-mgcv" ,r-mgcv) |
500224cb | 5269 | ("r-nlme" ,r-nlme) |
aeb64f3c RW |
5270 | ("r-nnet" ,r-nnet) |
5271 | ("r-pbkrtest" ,r-pbkrtest) | |
500224cb RW |
5272 | ("r-quantreg" ,r-quantreg) |
5273 | ("r-rio" ,r-rio))) | |
ab2ec643 RJPB |
5274 | (home-page "https://r-forge.r-project.org/projects/car/") |
5275 | (synopsis "Companion to applied regression") | |
5276 | (description | |
5277 | "This package provides functions and datasets from book Companion | |
5278 | to Applied regression, Second Edition, Sage, 2011.") | |
5279 | (license license:gpl2+))) | |
aa890f61 RJPB |
5280 | |
5281 | (define-public r-caret | |
5282 | (package | |
5283 | (name "r-caret") | |
2e4fc4ac | 5284 | (version "6.0-81") |
aa890f61 RJPB |
5285 | (source |
5286 | (origin | |
5287 | (method url-fetch) | |
5288 | (uri (cran-uri "caret" version)) | |
5289 | (sha256 | |
5290 | (base32 | |
2e4fc4ac | 5291 | "1fibrskjzq2f06b8gbrfp3263svfc5s5apsjwaqdg9qzs7sy7fpc")))) |
aa890f61 RJPB |
5292 | (build-system r-build-system) |
5293 | (propagated-inputs | |
d9c65e5a | 5294 | `(("r-foreach" ,r-foreach) |
aa890f61 | 5295 | ("r-ggplot2" ,r-ggplot2) |
3b74b7a2 | 5296 | ("r-lattice" ,r-lattice) |
aa890f61 | 5297 | ("r-modelmetrics" ,r-modelmetrics) |
3b74b7a2 | 5298 | ("r-nlme" ,r-nlme) |
aa890f61 | 5299 | ("r-plyr" ,r-plyr) |
d9c65e5a RW |
5300 | ("r-recipes" ,r-recipes) |
5301 | ("r-reshape2" ,r-reshape2) | |
5302 | ("r-withr" ,r-withr))) | |
aa890f61 RJPB |
5303 | (home-page "https://github.com/topepo/caret") |
5304 | (synopsis "Classification and regression training") | |
5305 | (description | |
5306 | "This package provides misc functions for training and plotting | |
5307 | classification and regression models.") | |
5308 | (license license:gpl2+))) | |
362ea0dc RJPB |
5309 | |
5310 | (define-public r-rcppprogress | |
5311 | (package | |
5312 | (name "r-rcppprogress") | |
d059a01e | 5313 | (version "0.4.1") |
362ea0dc RJPB |
5314 | (source |
5315 | (origin | |
5316 | (method url-fetch) | |
5317 | (uri (cran-uri "RcppProgress" version)) | |
5318 | (sha256 | |
5319 | (base32 | |
d059a01e | 5320 | "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi")))) |
362ea0dc RJPB |
5321 | (properties `((upstream-name . "RcppProgress"))) |
5322 | (build-system r-build-system) | |
5323 | (propagated-inputs | |
a3ae2fa5 RW |
5324 | `(("r-devtools" ,r-devtools) |
5325 | ("r-rcpp" ,r-rcpp))) | |
362ea0dc RJPB |
5326 | (home-page "https://github.com/kforner/rcpp_progress") |
5327 | (synopsis "Interruptible progress bar for C++ in R packages") | |
5328 | (description | |
5329 | "This package allows to display a progress bar in the R console for long running | |
5330 | computations taking place in C++ code, and support for interrupting those computations | |
5331 | even in multithreaded code, typically using OpenMP.") | |
5332 | (license license:gpl3+))) | |
fe68c8a9 RJPB |
5333 | |
5334 | (define-public r-mnormt | |
5335 | (package | |
5336 | (name "r-mnormt") | |
5337 | (version "1.5-5") | |
5338 | (source | |
5339 | (origin | |
5340 | (method url-fetch) | |
5341 | (uri (cran-uri "mnormt" version)) | |
5342 | (sha256 | |
5343 | (base32 | |
5344 | "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z")))) | |
5345 | (build-system r-build-system) | |
5346 | (native-inputs | |
5347 | `(("gfortran" ,gfortran))) | |
5348 | (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt") | |
5349 | (synopsis "Multivariate normal and \"t\" distributions") | |
5350 | (description | |
5351 | "This package provides functions for computing the density and the | |
5352 | distribution function of multivariate normal and \"t\" random variables, and | |
5353 | for generating random vectors sampled from these distributions. Probabilities | |
5354 | are computed via non-Monte Carlo methods.") | |
5355 | (license license:gpl2+))) | |
06085b5b RJPB |
5356 | |
5357 | (define-public r-numderiv | |
5358 | (package | |
5359 | (name "r-numderiv") | |
5360 | (version "2016.8-1") | |
5361 | (source | |
5362 | (origin | |
5363 | (method url-fetch) | |
5364 | (uri (cran-uri "numDeriv" version)) | |
5365 | (sha256 | |
5366 | (base32 | |
5367 | "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v")))) | |
5368 | (properties `((upstream-name . "numDeriv"))) | |
5369 | (build-system r-build-system) | |
5370 | (home-page "https://cran.r-project.org/web/packages/numDeriv") | |
5371 | (synopsis "Accurate numerical derivatives") | |
5372 | (description | |
5373 | "This package provides methods for calculating accurate numerical | |
5374 | first and second order derivatives.") | |
5375 | (license license:gpl2))) | |
5a200a24 RJPB |
5376 | |
5377 | (define-public r-sn | |
5378 | (package | |
5379 | (name "r-sn") | |
317f5a5a | 5380 | (version "1.5-3") |
5a200a24 RJPB |
5381 | (source |
5382 | (origin | |
5383 | (method url-fetch) | |
5384 | (uri (cran-uri "sn" version)) | |
5385 | (sha256 | |
5386 | (base32 | |
317f5a5a | 5387 | "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc")))) |
5a200a24 RJPB |
5388 | (build-system r-build-system) |
5389 | (propagated-inputs | |
5390 | `(("r-mnormt" ,r-mnormt) | |
5391 | ("r-numderiv" ,r-numderiv))) | |
5392 | (home-page "http://azzalini.stat.unipd.it/SN") | |
5393 | (synopsis "The skew-normal and skew-t distributions") | |
5394 | (description | |
5395 | "This packages provides functionalities to build and manipulate | |
5396 | probability distributions of the skew-normal family and some related | |
5397 | ones, notably the skew-t family, and provides related statistical | |
5398 | methods for data fitting and diagnostics, in the univariate and the | |
5399 | multivariate case.") | |
5400 | (license license:gpl2+))) | |
d1906e31 RJPB |
5401 | |
5402 | (define-public r-tclust | |
5403 | (package | |
5404 | (name "r-tclust") | |
14bb6f5f | 5405 | (version "1.4-1") |
d1906e31 RJPB |
5406 | (source |
5407 | (origin | |
5408 | (method url-fetch) | |
5409 | (uri (cran-uri "tclust" version)) | |
5410 | (sha256 | |
5411 | (base32 | |
14bb6f5f | 5412 | "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb")))) |
d1906e31 | 5413 | (build-system r-build-system) |
14bb6f5f | 5414 | ;; These are all suggested packages, not build dependencies. |
d1906e31 | 5415 | (propagated-inputs |
aeb64f3c RW |
5416 | `(("r-cluster" ,r-cluster) |
5417 | ("r-mclust" ,r-mclust) | |
d1906e31 RJPB |
5418 | ("r-mvtnorm" ,r-mvtnorm) |
5419 | ("r-sn" ,r-sn))) | |
e9960d8c | 5420 | (home-page "https://cran.r-project.org/web/packages/tclust") |
d1906e31 RJPB |
5421 | (synopsis "Robust trimmed clustering") |
5422 | (description | |
5423 | "This package implements different robust clustering | |
5424 | algorithms (@code{tclust}) based on trimming and including some graphical | |
5425 | diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") | |
5426 | (license license:gpl3))) | |
02eec38e RJPB |
5427 | |
5428 | (define-public r-ranger | |
5429 | (package | |
5430 | (name "r-ranger") | |
17abcd52 | 5431 | (version "0.11.2") |
02eec38e RJPB |
5432 | (source |
5433 | (origin | |
5434 | (method url-fetch) | |
5435 | (uri (cran-uri "ranger" version)) | |
5436 | (sha256 | |
5437 | (base32 | |
17abcd52 | 5438 | "1sxyzxmjc6lm8wcmq15j6sscnza7aay4mr3dyri2zngx6fa8mb0k")))) |
02eec38e RJPB |
5439 | (build-system r-build-system) |
5440 | (propagated-inputs | |
c628b841 RW |
5441 | `(("r-rcpp" ,r-rcpp) |
5442 | ("r-matrix" ,r-matrix) | |
5443 | ("r-rcppeigen" ,r-rcppeigen))) | |
02eec38e RJPB |
5444 | (home-page "https://github.com/imbs-hl/ranger") |
5445 | (synopsis "Fast implementation of random forests") | |
5446 | (description | |
5447 | "This package provides a fast implementation of Random Forests, | |
5448 | particularly suited for high dimensional data. Ensembles of classification, | |
5449 | regression, survival and probability prediction trees are supported. Data from | |
5450 | genome-wide association studies can be analyzed efficiently.") | |
5451 | (license license:gpl3))) | |
a5935d19 RJPB |
5452 | |
5453 | (define-public r-tsne | |
5454 | (package | |
5455 | (name "r-tsne") | |
5456 | (version "0.1-3") | |
5457 | (source | |
5458 | (origin | |
5459 | (method url-fetch) | |
5460 | (uri (cran-uri "tsne" version)) | |
5461 | (sha256 | |
5462 | (base32 | |
5463 | "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6")))) | |
5464 | (build-system r-build-system) | |
5465 | (home-page "https://github.com/jdonaldson/rtsne/") | |
5466 | (synopsis "t-Distributed Stochastic Neighbor Embedding for R") | |
5467 | (description | |
5468 | "This package provides a pure R implementation of the t-SNE algorithm.") | |
5469 | (license license:gpl2+))) | |
e2c4fe7c RW |
5470 | |
5471 | (define-public r-cairo | |
5472 | (package | |
5473 | (name "r-cairo") | |
5474 | (version "1.5-9") | |
5475 | (source | |
5476 | (origin | |
5477 | (method url-fetch) | |
5478 | (uri (cran-uri "Cairo" version)) | |
5479 | (sha256 | |
5480 | (base32 | |
5481 | "1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia")))) | |
5482 | (properties `((upstream-name . "Cairo"))) | |
5483 | (build-system r-build-system) | |
5484 | (inputs | |
5485 | `(("cairo" ,cairo) | |
5486 | ("libxt" ,libxt))) | |
5487 | (native-inputs | |
5488 | `(("pkg-config" ,pkg-config))) | |
5489 | (home-page "http://www.rforge.net/Cairo/") | |
5490 | (synopsis "R graphics device using Cairo graphics library") | |
5491 | (description | |
5492 | "This package provides a Cairo graphics device that can be use to | |
5493 | create high-quality vector (PDF, PostScript and SVG) and bitmap | |
5494 | output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 | |
5495 | and Win32). Since it uses the same back-end for all output, copying | |
5496 | across formats is WYSIWYG. Files are created without the dependence | |
5497 | on X11 or other external programs. This device supports alpha | |
5498 | channel (semi-transparent drawing) and resulting images can contain | |
5499 | transparent and semi-transparent regions. It is ideal for use in | |
5500 | server environments (file output) and as a replacement for other | |
5501 | devices that don't have Cairo's capabilities such as alpha support or | |
5502 | anti-aliasing. Backends are modular such that any subset of backends | |
5503 | is supported.") | |
5504 | (license license:gpl2))) | |
db0bb6f0 RW |
5505 | |
5506 | (define-public r-lubridate | |
5507 | (package | |
5508 | (name "r-lubridate") | |
9d448362 | 5509 | (version "1.7.4") |
db0bb6f0 RW |
5510 | (source |
5511 | (origin | |
5512 | (method url-fetch) | |
5513 | (uri (cran-uri "lubridate" version)) | |
5514 | (sha256 | |
5515 | (base32 | |
9d448362 | 5516 | "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i")))) |
db0bb6f0 RW |
5517 | (build-system r-build-system) |
5518 | (propagated-inputs | |
65a8cd66 RW |
5519 | `(("r-rcpp" ,r-rcpp) |
5520 | ("r-stringr" ,r-stringr))) | |
db0bb6f0 | 5521 | (home-page |
e9960d8c | 5522 | "https://cran.r-project.org/web/packages/lubridate") |
db0bb6f0 RW |
5523 | (synopsis "Make dealing with dates a little easier") |
5524 | (description | |
5525 | "This package provides functions to work with date-times and time-spans: | |
5526 | fast and user friendly parsing of date-time data, extraction and updating of | |
5527 | components of a date-time (years, months, days, hours, minutes, and seconds), | |
5528 | algebraic manipulation on date-time and time-span objects. The 'lubridate' | |
5529 | package has a consistent and memorable syntax that makes working with dates | |
5530 | easy and fun.") | |
5531 | (license license:gpl2))) | |
1dacc269 RW |
5532 | |
5533 | (define-public r-fdrtool | |
5534 | (package | |
5535 | (name "r-fdrtool") | |
5536 | (version "1.2.15") | |
5537 | (source | |
5538 | (origin | |
5539 | (method url-fetch) | |
5540 | (uri (cran-uri "fdrtool" version)) | |
5541 | (sha256 | |
5542 | (base32 | |
5543 | "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5")))) | |
5544 | (build-system r-build-system) | |
5545 | (home-page "http://strimmerlab.org/software/fdrtool/") | |
5546 | (synopsis "Estimation of false discovery rates and higher criticism") | |
5547 | (description | |
14e5f6b2 RW |
5548 | "This package provides tools to estimate tail area-based false discovery |
5549 | rates as well as local false discovery rates for a variety of null | |
5550 | models (p-values, z-scores, correlation coefficients, t-scores). The | |
5551 | proportion of null values and the parameters of the null distribution are | |
5552 | adaptively estimated from the data. In addition, the package contains | |
5553 | functions for non-parametric density estimation (Grenander estimator), for | |
5554 | monotone regression (isotonic regression and antitonic regression with | |
5555 | weights), for computing the @dfn{greatest convex minorant} (GCM) and the | |
5556 | @dfn{least concave majorant} (LCM), for the half-normal and correlation | |
5557 | distributions, and for computing empirical @dfn{higher criticism} (HC) scores | |
5558 | and the corresponding decision threshold.") | |
1dacc269 | 5559 | (license license:gpl3+))) |
4c77abc4 KM |
5560 | |
5561 | (define-public r-forcats | |
5562 | (package | |
5563 | (name "r-forcats") | |
8cc41c8f | 5564 | (version "0.3.0") |
4c77abc4 KM |
5565 | (source |
5566 | (origin | |
5567 | (method url-fetch) | |
5568 | (uri (cran-uri "forcats" version)) | |
5569 | (sha256 | |
5570 | (base32 | |
8cc41c8f | 5571 | "0mxn1hng43zdjh1v8shd80hrszrqahcpaqxs1s1sif0qxh84d0cm")))) |
4c77abc4 KM |
5572 | (build-system r-build-system) |
5573 | (propagated-inputs | |
5574 | `(("r-magrittr" ,r-magrittr) | |
8cc41c8f RW |
5575 | ("r-tibble" ,r-tibble) |
5576 | ("r-rlang" ,r-rlang))) | |
4c77abc4 KM |
5577 | (home-page "http://forcats.tidyverse.org") |
5578 | (synopsis "Tools for working with factors") | |
5579 | (description "This package provides helpers for reordering factor | |
5580 | levels (including moving specified levels to front, ordering by first | |
5581 | appearance, reversing, and randomly shuffling), and tools for modifying factor | |
5582 | levels (including collapsing rare levels into other, \"anonymizing\", and | |
5583 | manually \"recoding\").") | |
5584 | (license license:gpl3))) | |
7941d1ed RW |
5585 | |
5586 | (define-public r-tgstat | |
5587 | (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f") | |
5588 | (revision "1")) | |
5589 | (package | |
5590 | (name "r-tgstat") | |
5591 | (version (string-append "1.0.2-" revision "." (string-take changeset 7))) | |
5592 | (source | |
5593 | (origin | |
5594 | (method hg-fetch) | |
5595 | (uri (hg-reference | |
5596 | (url "https://bitbucket.org/tanaylab/tgstat") | |
5597 | (changeset changeset))) | |
76b27f42 | 5598 | (file-name (string-append name "-" version "-checkout")) |
7941d1ed RW |
5599 | (sha256 |
5600 | (base32 | |
5601 | "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn")))) | |
5602 | (build-system r-build-system) | |
5603 | (arguments | |
5604 | `(#:phases | |
5605 | (modify-phases %standard-phases | |
5606 | (add-after 'unpack 'fix-isnan | |
5607 | (lambda _ | |
5608 | (substitute* "src/tgstat.h" | |
5609 | (("#define isnan ::isnan") | |
5610 | "#define isnan std::isnan")) | |
5611 | #t))))) | |
5612 | (propagated-inputs | |
5613 | `(("r-rcpp" ,r-rcpp))) | |
5614 | (home-page "https://bitbucket.org/tanaylab/tgstat/") | |
5615 | (synopsis "Tanay's group statistical utilities") | |
5616 | (description | |
5617 | "The goal of tgstat is to provide fast and efficient statistical | |
5618 | tools.") | |
5619 | (license license:gpl2)))) | |
1f6f4c40 RW |
5620 | |
5621 | (define-public r-tgconfig | |
5622 | (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e") | |
5623 | (revision "1")) | |
5624 | (package | |
5625 | (name "r-tgconfig") | |
5626 | (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7))) | |
5627 | (source | |
5628 | (origin | |
5629 | (method hg-fetch) | |
5630 | (uri (hg-reference | |
5631 | (url "https://bitbucket.org/tanaylab/tgconfig") | |
5632 | (changeset changeset))) | |
4510f976 | 5633 | (file-name (string-append name "-" version "-checkout")) |
1f6f4c40 RW |
5634 | (sha256 |
5635 | (base32 | |
5636 | "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj")))) | |
5637 | (build-system r-build-system) | |
5638 | (propagated-inputs | |
5639 | `(("r-yaml" ,r-yaml))) | |
5640 | (home-page "https://bitbucket.org/tanaylab/tgconfig/") | |
5641 | (synopsis "Infrastructure for managing package parameters") | |
5642 | (description | |
5643 | "The goal of tgconfig is to provide infrastructure for managing package | |
5644 | parameters.") | |
5645 | (license license:gpl3)))) | |
e99f045c KM |
5646 | |
5647 | (define-public r-directlabels | |
5648 | (package | |
5649 | (name "r-directlabels") | |
beb0878f | 5650 | (version "2018.05.22") |
e99f045c KM |
5651 | (source |
5652 | (origin | |
5653 | (method url-fetch) | |
5654 | (uri (cran-uri "directlabels" version)) | |
5655 | (sha256 | |
5656 | (base32 | |
beb0878f | 5657 | "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv")))) |
e99f045c KM |
5658 | (build-system r-build-system) |
5659 | (propagated-inputs | |
5660 | `(("r-quadprog" ,r-quadprog))) | |
5661 | (home-page "http://directlabels.r-forge.r-project.org/") | |
5662 | (synopsis "Direct labels for multicolor plots") | |
5663 | (description | |
5664 | "This package provides an extensible framework for automatically placing | |
5665 | direct labels onto multicolor plots. Label positions are described using | |
5666 | positioning methods that can be re-used across several different plots. There | |
5667 | are heuristics for examining @code{trellis} and @code{ggplot} objects and | |
5668 | inferring an appropriate positioning method.") | |
5669 | (license license:gpl3))) | |
5f1bb222 RW |
5670 | |
5671 | (define-public r-catterplots | |
5672 | (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9") | |
5673 | (revision "2")) | |
5674 | (package | |
5675 | (name "r-catterplots") | |
5676 | (version (string-append "0-" revision "." (string-take commit 9))) | |
5677 | (source (origin | |
5678 | (method git-fetch) | |
5679 | (uri (git-reference | |
5680 | (url "https://github.com/Gibbsdavidl/CatterPlots.git") | |
5681 | (commit commit))) | |
5682 | (file-name (string-append name "-" version "-checkout")) | |
5683 | (sha256 | |
5684 | (base32 | |
5685 | "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg")))) | |
5686 | (build-system r-build-system) | |
5687 | (propagated-inputs | |
5688 | `(("r-png" ,r-png))) | |
5689 | (home-page "https://github.com/Gibbsdavidl/CatterPlots") | |
5690 | (synopsis "Scatter plots with cat shaped points") | |
5691 | (description "Did you ever wish you could make scatter plots with cat | |
5692 | shaped points? Now you can!") | |
5693 | (license license:asl2.0)))) | |
dbb35813 | 5694 | |
06c15ee5 OP |
5695 | (define-public r-colorout |
5696 | (package | |
5697 | (name "r-colorout") | |
5698 | (version "1.2-0") | |
5699 | (source | |
5700 | (origin | |
5701 | (method url-fetch) | |
5702 | (uri (string-append "https://github.com/jalvesaq/colorout/archive/" | |
5703 | "v" version ".tar.gz")) | |
5704 | (file-name (string-append name "-" version ".tar.gz")) | |
5705 | (sha256 | |
5706 | (base32 | |
5707 | "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v")))) | |
5708 | (build-system r-build-system) | |
5709 | (home-page "https://github.com/jalvesaq/colorout") | |
5710 | (synopsis "Colorize output in the R REPL") | |
5711 | (description "@code{colorout} is an R package that colorizes R output when | |
5712 | running in terminal emulator. | |
5713 | ||
5714 | R STDOUT is parsed and numbers, negative numbers, dates in the standard | |
5715 | format, strings, and R constants are identified and wrapped by special ANSI | |
5716 | scape codes that are interpreted by terminal emulators as commands to colorize | |
5717 | the output. R STDERR is also parsed to identify the expressions warning and | |
5718 | error and their translations to many languages. If these expressions are | |
5719 | found, the output is colorized accordingly; otherwise, it is colorized as | |
5720 | STDERROR (blue, by default). | |
5721 | ||
5722 | You can customize the colors according to your taste, guided by the color | |
5723 | table made by the command @code{show256Colors()}. You can also set the colors | |
5724 | to any arbitrary string. In this case, it is up to you to set valid values.") | |
5725 | (license license:gpl3+))) | |
5726 | ||
ec83abad EB |
5727 | (define-public r-txtplot |
5728 | (package | |
5729 | (name "r-txtplot") | |
5730 | (version "1.0-3") | |
5731 | (source | |
5732 | (origin | |
5733 | (method url-fetch) | |
5734 | (uri (cran-uri "txtplot" version)) | |
5735 | (sha256 | |
5736 | (base32 | |
5737 | "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h")))) | |
5738 | (build-system r-build-system) | |
5739 | (home-page "https://cran.r-project.org/web/packages/txtplot/") | |
5740 | (synopsis "Text-based plotting") | |
5741 | (description "This package provides functions to produce rudimentary ASCII | |
5742 | graphics directly in the terminal window. This package provides a basic | |
5743 | plotting function (and equivalents of curve, density, acf and barplot) as well | |
5744 | as a boxplot function.") | |
5745 | (license license:lgpl3+))) | |
5746 | ||
61f2587d RW |
5747 | (define-public python-rpy2 |
5748 | (package | |
5749 | (name "python-rpy2") | |
5750 | (version "2.9.4") | |
5751 | (source | |
5752 | (origin | |
5753 | (method url-fetch) | |
5754 | (uri (pypi-uri "rpy2" version)) | |
5755 | (sha256 | |
5756 | (base32 | |
5757 | "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy")))) | |
5758 | (build-system python-build-system) | |
5759 | (arguments | |
5760 | '(#:modules ((ice-9 ftw) | |
5761 | (srfi srfi-1) | |
5762 | (srfi srfi-26) | |
5763 | (guix build utils) | |
5764 | (guix build python-build-system)) | |
5765 | #:phases | |
5766 | (modify-phases %standard-phases | |
5767 | (replace 'check | |
5768 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
5769 | (let ((cwd (getcwd))) | |
5770 | (setenv "PYTHONPATH" | |
5771 | (string-append cwd "/build/" | |
5772 | (find (cut string-prefix? "lib" <>) | |
5773 | (scandir (string-append cwd "/build"))) | |
5774 | ":" | |
5775 | (getenv "PYTHONPATH")))) | |
5776 | (invoke "python" "-m" "rpy2.tests" "-v")))))) | |
5777 | (propagated-inputs | |
5778 | `(("python-six" ,python-six) | |
5779 | ("python-jinja2" ,python-jinja2) | |
5780 | ("python-pytz" ,python-pytz))) | |
5781 | (inputs | |
5782 | `(("readline" ,readline) | |
5783 | ("icu4c" ,icu4c) | |
5784 | ("pcre" ,pcre) | |
5785 | ("r-minimal" ,r-minimal) | |
5786 | ("r-survival" ,r-survival) | |
5787 | ("r-ggplot2" ,r-ggplot2) | |
5788 | ("r-rsqlite" ,r-rsqlite) | |
5789 | ("r-dplyr" ,r-dplyr) | |
5790 | ("r-dbplyr" ,r-dbplyr) | |
5791 | ("python-numpy" ,python-numpy))) | |
5792 | (native-inputs | |
5793 | `(("zlib" ,zlib))) | |
5794 | (home-page "https://rpy2.bitbucket.io/") | |
5795 | (synopsis "Python interface to the R language") | |
5796 | (description "rpy2 is a redesign and rewrite of rpy. It is providing a | |
5797 | low-level interface to R from Python, a proposed high-level interface, | |
5798 | including wrappers to graphical libraries, as well as R-like structures and | |
5799 | functions.") | |
5800 | ;; Any of these licenses can be picked for the R interface. The whole | |
5801 | ;; project is released under GPLv2+ according to the license declaration | |
5802 | ;; in "setup.py". | |
5803 | (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))) | |
5804 | ||
dbb35813 RW |
5805 | (define-public java-jdistlib |
5806 | (package | |
5807 | (name "java-jdistlib") | |
5808 | (version "0.4.5") | |
5809 | (source (origin | |
5810 | (method url-fetch) | |
5811 | (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-" | |
5812 | version "-src.jar")) | |
5813 | (sha256 | |
5814 | (base32 | |
5815 | "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11")))) | |
5816 | (build-system ant-build-system) | |
5817 | (arguments | |
5818 | `(#:jar-name "jdistlib.jar" | |
5819 | #:jdk ,icedtea-8 | |
5820 | #:tests? #f ; no dedicated test directory | |
5821 | #:phases | |
5822 | (modify-phases %standard-phases | |
5823 | (add-after 'unpack 'fix-broken-encoding | |
5824 | (lambda _ | |
5825 | (with-fluids ((%default-port-encoding "ISO-8859-1")) | |
5826 | (substitute* "src/jdistlib/Beta.java" | |
5827 | (("Scheff.+-Tukey") "Scheffe-Tukey"))) | |
5828 | #t))))) | |
5829 | (propagated-inputs | |
5830 | `(("java-jtransforms" ,java-jtransforms))) | |
5831 | (native-inputs | |
5832 | `(("java-junit" ,java-junit))) | |
5833 | (home-page "http://jdistlib.sourceforge.net/") | |
5834 | (synopsis "Java library of statistical distributions") | |
5835 | (description "JDistlib is the Java Statistical Distribution Library, a | |
5836 | Java package that provides routines for various statistical distributions.") | |
5837 | ;; The files that were translated from R code are under GPLv2+; some files | |
5838 | ;; are under the GPLv3, which is a mistake. The author confirmed in an | |
5839 | ;; email that this whole project should be under GPLv2+. | |
5840 | (license license:gpl2+))) | |
576e74ee RW |
5841 | |
5842 | (define-public emacs-ess | |
5843 | (package | |
5844 | (name "emacs-ess") | |
5845 | (version "17.11") | |
5846 | (source (origin | |
5847 | (method url-fetch) | |
5848 | (uri (string-append "https://github.com/emacs-ess/ESS/archive/v" | |
5849 | version ".tar.gz")) | |
5850 | (sha256 | |
5851 | (base32 | |
5852 | "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c")) | |
5853 | (file-name (string-append name "-" version ".tar.gz")) | |
5854 | (modules '((guix build utils))) | |
5855 | (snippet | |
5856 | '(begin | |
5857 | ;; Stop ESS from trying to bundle an external julia-mode.el. | |
5858 | (substitute* "lisp/Makefile" | |
5859 | (("^\tjulia-mode.elc\\\\\n") "") | |
5860 | (("^dist: all julia-mode.el") | |
5861 | "dist: all")) | |
5862 | ;; No need to build docs in so many formats. Also, skipping | |
5863 | ;; pdf lets us not pull in texlive. | |
5864 | (substitute* "doc/Makefile" | |
5865 | (("all : info text html pdf") | |
5866 | "all : info") | |
5867 | (("install: install-info install-other-docs") | |
5868 | "install: install-info")) | |
5869 | ;; Test fails upstream | |
5870 | (substitute* "test/ess-r-tests.el" | |
5871 | (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()") | |
5872 | "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed")) | |
5873 | #t)))) | |
5874 | (build-system gnu-build-system) | |
5875 | (arguments | |
5876 | (let ((base-directory "/share/emacs/site-lisp/guix.d/ess")) | |
5877 | `(#:make-flags (list (string-append "PREFIX=" %output) | |
5878 | (string-append "ETCDIR=" %output "/" | |
5879 | ,base-directory "/etc") | |
5880 | (string-append "LISPDIR=" %output "/" | |
5881 | ,base-directory)) | |
5882 | #:phases | |
5883 | (modify-phases %standard-phases | |
5884 | (delete 'configure) | |
5885 | (add-before 'build 'more-shebang-patching | |
5886 | (lambda* (#:key inputs #:allow-other-keys) | |
5887 | (substitute* "Makeconf" | |
5888 | (("SHELL = /bin/sh") | |
5889 | (string-append "SHELL = " (which "sh")))) | |
5890 | #t)) | |
5891 | (replace 'check | |
5892 | (lambda _ | |
5893 | (invoke "make" "test"))))))) | |
5894 | (inputs | |
5895 | `(("emacs" ,emacs-minimal) | |
5896 | ("r-minimal" ,r-minimal))) | |
5897 | (native-inputs | |
5898 | `(("perl" ,perl) | |
5899 | ("texinfo" ,texinfo))) | |
5900 | (propagated-inputs | |
5901 | `(("emacs-julia-mode" ,emacs-julia-mode))) | |
5902 | (home-page "https://ess.r-project.org/") | |
5903 | (synopsis "Emacs mode for statistical analysis programs") | |
5904 | (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU | |
5905 | Emacs. It is designed to support editing of scripts and interaction with | |
5906 | various statistical analysis programs such as R, Julia, and JAGS.") | |
5907 | (license license:gpl2+))) |