Commit | Line | Data |
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cb7e4867 | 1 | ;;; GNU Guix --- Functional package management for GNU |
d7786ce9 | 2 | ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> |
ed6094fc | 3 | ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com> |
f4cd2cea EF |
4 | ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> |
5 | ;;; Copyright © 2016 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> |
a1814e4a | 9 | ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> |
cb7e4867 RW |
10 | ;;; |
11 | ;;; This file is part of GNU Guix. | |
12 | ;;; | |
13 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
14 | ;;; under the terms of the GNU General Public License as published by | |
15 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
16 | ;;; your option) any later version. | |
17 | ;;; | |
18 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
19 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
20 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
21 | ;;; GNU General Public License for more details. | |
22 | ;;; | |
23 | ;;; You should have received a copy of the GNU General Public License | |
24 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
25 | ||
26 | (define-module (gnu packages statistics) | |
27 | #:use-module ((guix licenses) #:prefix license:) | |
28 | #:use-module (guix packages) | |
29 | #:use-module (guix download) | |
30 | #:use-module (guix utils) | |
31 | #:use-module (guix build-system gnu) | |
b12636e6 | 32 | #:use-module (guix build-system r) |
9bc08aa0 | 33 | #:use-module (guix build-system python) |
cb7e4867 RW |
34 | #:use-module (gnu packages) |
35 | #:use-module (gnu packages compression) | |
cefaa79c | 36 | #:use-module (gnu packages curl) |
cb7e4867 RW |
37 | #:use-module (gnu packages gcc) |
38 | #:use-module (gnu packages gtk) | |
0b65f1a0 JD |
39 | #:use-module (gnu packages gettext) |
40 | #:use-module (gnu packages glib) | |
77bdb276 | 41 | #:use-module (gnu packages haskell) |
cb7e4867 RW |
42 | #:use-module (gnu packages icu4c) |
43 | #:use-module (gnu packages image) | |
44 | #:use-module (gnu packages java) | |
2d21d44d | 45 | #:use-module (gnu packages machine-learning) |
cb7e4867 | 46 | #:use-module (gnu packages maths) |
07f911ba | 47 | #:use-module (gnu packages multiprecision) |
cb7e4867 RW |
48 | #:use-module (gnu packages pcre) |
49 | #:use-module (gnu packages perl) | |
50 | #:use-module (gnu packages pkg-config) | |
9bc08aa0 | 51 | #:use-module (gnu packages python) |
cb7e4867 | 52 | #:use-module (gnu packages readline) |
035711f1 | 53 | #:use-module (gnu packages ssh) |
cb7e4867 | 54 | #:use-module (gnu packages texinfo) |
035711f1 | 55 | #:use-module (gnu packages tls) |
ce0614dd | 56 | #:use-module (gnu packages base) |
6140747f | 57 | #:use-module (gnu packages web) |
67a167fd | 58 | #:use-module (gnu packages xml) |
9bc08aa0 RW |
59 | #:use-module (gnu packages xorg) |
60 | #:use-module (gnu packages zip) | |
61 | #:use-module (srfi srfi-1)) | |
cb7e4867 | 62 | |
0b65f1a0 JD |
63 | |
64 | (define-public pspp | |
65 | (package | |
66 | (name "pspp") | |
df2c7563 | 67 | (version "0.10.2") |
0b65f1a0 JD |
68 | (source |
69 | (origin | |
70 | (method url-fetch) | |
71 | (uri (string-append "mirror://gnu/pspp/pspp-" | |
72 | version ".tar.gz")) | |
73 | (sha256 | |
74 | (base32 | |
df2c7563 | 75 | "1afsq0a3iij64qacczvwhk81qg0q5rfqm055y5h9ls28d6paqz7p")))) |
0b65f1a0 JD |
76 | (build-system gnu-build-system) |
77 | (inputs | |
78 | `(("cairo" ,cairo) | |
b94a6ca0 | 79 | ("gettext" ,gettext-minimal) |
0b65f1a0 JD |
80 | ("gsl" ,gsl) |
81 | ("libxml2" ,libxml2) | |
82 | ("pango" ,pango) | |
83 | ("readline" ,readline) | |
84 | ("gtk" ,gtk+) | |
85 | ("gtksourceview" ,gtksourceview) | |
86 | ("zlib" ,zlib))) | |
87 | (native-inputs | |
88 | `(("glib" ,glib "bin") ;for glib-genmarshal | |
89 | ("perl" ,perl) | |
90 | ("pkg-config" ,pkg-config))) | |
91 | (home-page "http://www.gnu.org/software/pspp/") | |
92 | (synopsis "Statistical analysis") | |
93 | (description | |
94 | "GNU PSPP is a statistical analysis program. It can perform | |
95 | descriptive statistics, T-tests, linear regression and non-parametric tests. | |
96 | It features both a graphical interface as well as command-line input. PSPP | |
97 | is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data | |
98 | can be imported from spreadsheets, text files and database sources and it can | |
99 | be output in text, PostScript, PDF or HTML.") | |
100 | (license license:gpl3+))) | |
101 | ||
cb7e4867 RW |
102 | (define-public r |
103 | (package | |
104 | (name "r") | |
a1814e4a | 105 | (version "3.3.2") |
cb7e4867 RW |
106 | (source (origin |
107 | (method url-fetch) | |
108 | (uri (string-append "mirror://cran/src/base/R-" | |
109 | (version-prefix version 1) "/R-" | |
110 | version ".tar.gz")) | |
111 | (sha256 | |
112 | (base32 | |
a1814e4a | 113 | "0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j")))) |
cb7e4867 RW |
114 | (build-system gnu-build-system) |
115 | (arguments | |
ff2b1c17 RW |
116 | `(#:make-flags |
117 | (list (string-append "LDFLAGS=-Wl,-rpath=" | |
118 | (assoc-ref %outputs "out") | |
119 | "/lib/R/lib")) | |
120 | #:phases | |
f4f4ced8 | 121 | (modify-phases %standard-phases |
b5ce25cc RJ |
122 | (add-before 'configure 'patch-uname |
123 | (lambda* (#:key inputs #:allow-other-keys) | |
124 | (let ((uname-bin (string-append (assoc-ref inputs "coreutils") | |
125 | "/bin/uname"))) | |
126 | (substitute* "src/scripts/R.sh.in" | |
127 | (("uname") uname-bin))) | |
128 | #t)) | |
f4f4ced8 RW |
129 | (add-before |
130 | 'configure 'set-default-pager | |
131 | ;; Set default pager to "cat", because otherwise it is "false", | |
132 | ;; making "help()" print nothing at all. | |
133 | (lambda _ (setenv "PAGER" "cat") #t)) | |
e42eb908 | 134 | (add-before 'check 'set-timezone |
f4f4ced8 | 135 | ;; Some tests require the timezone to be set. |
e42eb908 RW |
136 | (lambda* (#:key inputs #:allow-other-keys) |
137 | (setenv "TZ" "UTC") | |
138 | (setenv "TZDIR" | |
139 | (string-append (assoc-ref inputs "tzdata") | |
140 | "/share/zoneinfo")) | |
141 | #t)) | |
af23b6e9 RW |
142 | (add-after 'build 'make-info |
143 | (lambda _ (zero? (system* "make" "info")))) | |
144 | (add-after 'build 'install-info | |
145 | (lambda _ (zero? (system* "make" "install-info"))))) | |
cb7e4867 | 146 | #:configure-flags |
eb2afd00 | 147 | '("--with-cairo" |
71e98ca5 | 148 | "--with-blas=-lopenblas" |
cb7e4867 RW |
149 | "--with-libpng" |
150 | "--with-jpeglib" | |
151 | "--with-libtiff" | |
152 | "--with-ICU" | |
153 | "--enable-R-shlib" | |
154 | "--enable-BLAS-shlib" | |
155 | "--with-system-zlib" | |
156 | "--with-system-bzlib" | |
157 | "--with-system-pcre" | |
158 | "--with-system-tre" | |
159 | "--with-system-xz"))) | |
5e9738b7 RW |
160 | ;; R has some support for Java. When the JDK is available at configure |
161 | ;; time environment variables pointing to the JDK will be recorded under | |
162 | ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R | |
163 | ;; CMD javareconf". "R CMD javareconf" appears to only be used to update | |
164 | ;; the recorded environment variables in $R_HOME/etc. Refer to | |
165 | ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support | |
166 | ;; for additional information. | |
167 | ||
168 | ;; As the JDK is a rather large input with only very limited effects on R, | |
169 | ;; we decided to drop it. | |
cb7e4867 RW |
170 | (native-inputs |
171 | `(("bzip2" ,bzip2) | |
172 | ("perl" ,perl) | |
173 | ("pkg-config" ,pkg-config) | |
cb7e4867 RW |
174 | ("texinfo" ,texinfo) ; for building HTML manuals |
175 | ("which" ,which) ; for tests/Examples/base-Ex.R | |
176 | ("xz" ,xz))) | |
177 | (inputs | |
05e9f30f RW |
178 | `(;; We need not only cairo here, but pango to ensure that tests for the |
179 | ;; "cairo" bitmapType plotting backend succeed. | |
180 | ("pango" ,pango) | |
b5ce25cc | 181 | ("coreutils" ,coreutils) |
e42eb908 RW |
182 | ("curl" ,curl) |
183 | ("tzdata" ,tzdata) | |
71e98ca5 | 184 | ("openblas" ,openblas) |
19afbea1 | 185 | ("gfortran" ,gfortran) |
cb7e4867 | 186 | ("icu4c" ,icu4c) |
cb7e4867 RW |
187 | ("libjpeg" ,libjpeg) |
188 | ("libpng" ,libpng) | |
189 | ("libtiff" ,libtiff) | |
190 | ("libxt" ,libxt) | |
191 | ("pcre" ,pcre) | |
192 | ("readline" ,readline) | |
193 | ("zlib" ,zlib))) | |
12a9f4af RW |
194 | (native-search-paths |
195 | (list (search-path-specification | |
196 | (variable "R_LIBS_SITE") | |
197 | (files (list "site-library/"))))) | |
cb7e4867 RW |
198 | (home-page "http://www.r-project.org/") |
199 | (synopsis "Environment for statistical computing and graphics") | |
200 | (description | |
201 | "R is a language and environment for statistical computing and graphics. | |
202 | It provides a variety of statistical techniques, such as linear and nonlinear | |
203 | modeling, classical statistical tests, time-series analysis, classification | |
204 | and clustering. It also provides robust support for producing | |
205 | publication-quality data plots. A large amount of 3rd-party packages are | |
206 | available, greatly increasing its breadth and scope.") | |
207 | (license license:gpl3+))) | |
b12636e6 | 208 | |
42066e6b BW |
209 | (define-public r-bit |
210 | (package | |
211 | (name "r-bit") | |
212 | (version "1.1-12") | |
213 | (source | |
214 | (origin | |
215 | (method url-fetch) | |
216 | (uri (cran-uri "bit" version)) | |
217 | (sha256 | |
218 | (base32 | |
219 | "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f")))) | |
220 | (build-system r-build-system) | |
221 | (home-page "http://ff.r-forge.r-project.org") | |
222 | (synopsis "Class for vectors of 1-bit booleans") | |
223 | (description | |
224 | "This package provides bitmapped vectors of booleans (no @code{NA}s), | |
225 | coercion from and to logicals, integers and integer subscripts, fast boolean | |
226 | operators and fast summary statistics. With @code{bit} class vectors of true | |
227 | binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") | |
228 | (license license:gpl2))) | |
229 | ||
ce3f92e7 BW |
230 | (define-public r-bit64 |
231 | (package | |
232 | (name "r-bit64") | |
233 | (version "0.9-5") | |
234 | (source | |
235 | (origin | |
236 | (method url-fetch) | |
237 | (uri (cran-uri "bit64" version)) | |
238 | (sha256 | |
239 | (base32 | |
240 | "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg")))) | |
241 | (build-system r-build-system) | |
242 | (propagated-inputs | |
243 | `(("r-bit" ,r-bit))) | |
244 | (home-page "http://ff.r-forge.r-project.org/") | |
245 | (synopsis "S3 class for vectors of 64 bit integers") | |
246 | (description | |
247 | "The bit64 package provides serializable S3 atomic 64 bit (signed) | |
248 | integers that can be used in vectors, matrices, arrays and @code{data.frames}. | |
249 | Methods are available for coercion from and to logicals, integers, doubles, | |
250 | characters and factors as well as many elementwise and summary functions. | |
251 | Many fast algorithmic operations such as @code{match} and @code{order} support | |
252 | interactive data exploration and manipulation and optionally leverage | |
253 | caching.") | |
254 | (license license:gpl2))) | |
255 | ||
b12636e6 RW |
256 | (define-public r-colorspace |
257 | (package | |
258 | (name "r-colorspace") | |
9e087a1f | 259 | (version "1.2-7") |
b12636e6 RW |
260 | (source |
261 | (origin | |
262 | (method url-fetch) | |
9cda3622 | 263 | (uri (cran-uri "colorspace" version)) |
b12636e6 | 264 | (sha256 |
9e087a1f | 265 | (base32 "0flw97iwwpkxy6si9cn982jhl61wb1rxi3r0nz2xxf0c3fzw18d5")))) |
b12636e6 RW |
266 | (build-system r-build-system) |
267 | (home-page "http://cran.r-project.org/web/packages/colorspace") | |
268 | (synopsis "Color space manipulation") | |
269 | (description | |
270 | "This package carries out a mapping between assorted color spaces | |
271 | including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar | |
272 | CIELAB. Qualitative, sequential, and diverging color palettes based on HCL | |
273 | colors are provided.") | |
274 | (license license:bsd-3))) | |
3587effb RW |
275 | |
276 | (define-public r-dichromat | |
277 | (package | |
278 | (name "r-dichromat") | |
279 | (version "2.0-0") | |
280 | (source | |
281 | (origin | |
282 | (method url-fetch) | |
9cda3622 | 283 | (uri (cran-uri "dichromat" version)) |
3587effb RW |
284 | (sha256 |
285 | (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i")))) | |
286 | (build-system r-build-system) | |
287 | (home-page "http://cran.r-project.org/web/packages/dichromat") | |
288 | (synopsis "Color schemes for dichromats") | |
289 | (description | |
290 | "Dichromat collapses red-green or green-blue distinctions to simulate the | |
291 | effects of different types of color-blindness.") | |
292 | (license license:gpl2+))) | |
177f38c7 RW |
293 | |
294 | (define-public r-digest | |
295 | (package | |
296 | (name "r-digest") | |
5aaa12df | 297 | (version "0.6.10") |
177f38c7 RW |
298 | (source |
299 | (origin | |
300 | (method url-fetch) | |
9cda3622 | 301 | (uri (cran-uri "digest" version)) |
177f38c7 | 302 | (sha256 |
5aaa12df | 303 | (base32 "07825781nl85gx3pqskc04ywgs0f874qj9z2nyrwz7h0aqks0l8c")))) |
177f38c7 | 304 | (build-system r-build-system) |
fe2087cc RW |
305 | ;; Vignettes require r-knitr, which requires r-digest, so we have to |
306 | ;; disable them and the tests. | |
307 | (arguments | |
308 | `(#:tests? #f | |
309 | #:configure-flags (list "--no-build-vignettes"))) | |
177f38c7 RW |
310 | (home-page "http://dirk.eddelbuettel.com/code/digest.html") |
311 | (synopsis "Create cryptographic hash digests of R objects") | |
312 | (description | |
313 | "This package contains an implementation of a function 'digest()' for the | |
314 | creation of hash digests of arbitrary R objects (using the md5, sha-1, | |
315 | sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison | |
316 | of R language objects, as well as a function 'hmac()' to create hash-based | |
317 | message authentication code. | |
318 | ||
319 | Please note that this package is not meant to be deployed for cryptographic | |
320 | purposes for which more comprehensive (and widely tested) libraries such as | |
321 | OpenSSL should be used.") | |
322 | (license license:gpl2+))) | |
112bb3c0 | 323 | |
52ad9cb6 RJ |
324 | (define-public r-estimability |
325 | (package | |
326 | (name "r-estimability") | |
327 | (version "1.1-1") | |
328 | (source (origin | |
329 | (method url-fetch) | |
330 | (uri (cran-uri "estimability" version)) | |
331 | (sha256 | |
332 | (base32 | |
333 | "049adh8i0ad0m0qln2ylqdxcs5v2q9zfignn2a50r5f93ip2ay6w")))) | |
334 | (build-system r-build-system) | |
335 | (home-page "http://cran.r-project.org/web/packages/estimability") | |
336 | (synopsis "Tools for assessing estimability of linear predictions") | |
337 | (description "Provides tools for determining estimability of linear | |
338 | functions of regression coefficients, and 'epredict' methods that handle | |
339 | non-estimable cases correctly.") | |
340 | (license license:gpl2+))) | |
341 | ||
112bb3c0 RW |
342 | (define-public r-gtable |
343 | (package | |
344 | (name "r-gtable") | |
345 | (version "0.1.2") | |
346 | (source | |
347 | (origin | |
348 | (method url-fetch) | |
9cda3622 | 349 | (uri (cran-uri "gtable" version)) |
112bb3c0 RW |
350 | (sha256 |
351 | (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh")))) | |
352 | (build-system r-build-system) | |
353 | (home-page "https://cran.r-project.org/web/packages/gtable") | |
354 | (synopsis "R library to arrange grobs in tables") | |
355 | (description | |
356 | "Gtable is a collection of tools to make it easier to work with | |
357 | \"tables\" of grobs.") | |
358 | (license license:gpl2+))) | |
b7eee9fc | 359 | |
0c77fd50 RW |
360 | (define-public r-pheatmap |
361 | (package | |
362 | (name "r-pheatmap") | |
363 | (version "1.0.8") | |
364 | (source | |
365 | (origin | |
366 | (method url-fetch) | |
367 | (uri (cran-uri "pheatmap" version)) | |
368 | (sha256 | |
369 | (base32 | |
370 | "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji")))) | |
371 | (build-system r-build-system) | |
372 | (propagated-inputs | |
373 | `(("r-gtable" ,r-gtable) | |
374 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
375 | ("r-scales" ,r-scales))) | |
376 | (home-page | |
377 | "http://cran.r-project.org/web/packages/pheatmap") | |
378 | (synopsis "Pretty heatmaps") | |
379 | (description | |
380 | "This package provides an implementation of heatmaps that offers more | |
381 | control over dimensions and appearance.") | |
382 | (license license:gpl2+))) | |
383 | ||
b7eee9fc RW |
384 | (define-public r-labeling |
385 | (package | |
386 | (name "r-labeling") | |
387 | (version "0.3") | |
388 | (source | |
389 | (origin | |
390 | (method url-fetch) | |
9cda3622 | 391 | (uri (cran-uri "labeling" version)) |
b7eee9fc RW |
392 | (sha256 |
393 | (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d")))) | |
394 | (build-system r-build-system) | |
395 | (home-page "http://cran.r-project.org/web/packages/labeling") | |
396 | (synopsis "Axis labeling algorithms") | |
397 | (description "The labeling package provides a range of axis labeling | |
398 | algorithms.") | |
399 | (license license:expat))) | |
d69c4b04 RW |
400 | |
401 | (define-public r-magrittr | |
402 | (package | |
403 | (name "r-magrittr") | |
404 | (version "1.5") | |
405 | (source | |
406 | (origin | |
407 | (method url-fetch) | |
9cda3622 | 408 | (uri (cran-uri "magrittr" version)) |
d69c4b04 RW |
409 | (sha256 |
410 | (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05")))) | |
411 | (build-system r-build-system) | |
412 | (home-page "http://cran.r-project.org/web/packages/magrittr/index.html") | |
413 | (synopsis "A forward-pipe operator for R") | |
414 | (description | |
415 | "Magrittr provides a mechanism for chaining commands with a new | |
416 | forward-pipe operator, %>%. This operator will forward a value, or the result | |
417 | of an expression, into the next function call/expression. There is flexible | |
418 | support for the type of right-hand side expressions. For more information, | |
419 | see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") | |
420 | (license license:expat))) | |
44373339 RW |
421 | |
422 | (define-public r-munsell | |
423 | (package | |
424 | (name "r-munsell") | |
a99bed8c | 425 | (version "0.4.3") |
44373339 RW |
426 | (source |
427 | (origin | |
428 | (method url-fetch) | |
9cda3622 | 429 | (uri (cran-uri "munsell" version)) |
44373339 | 430 | (sha256 |
a99bed8c | 431 | (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r")))) |
44373339 RW |
432 | (build-system r-build-system) |
433 | (propagated-inputs | |
434 | `(("r-colorspace" ,r-colorspace))) | |
435 | (home-page "http://cran.r-project.org/web/packages/munsell") | |
436 | (synopsis "Munsell colour system") | |
437 | (description | |
438 | "The Munsell package contains Functions for exploring and using the | |
439 | Munsell colour system.") | |
440 | (license license:expat))) | |
ea69e2f8 RW |
441 | |
442 | (define-public r-rcpp | |
443 | (package | |
444 | (name "r-rcpp") | |
cb27d6ba | 445 | (version "0.12.7") |
ea69e2f8 RW |
446 | (source |
447 | (origin | |
448 | (method url-fetch) | |
9cda3622 | 449 | (uri (cran-uri "Rcpp" version)) |
ea69e2f8 | 450 | (sha256 |
cb27d6ba | 451 | (base32 "1ipid4yfqp1k5c70f7bz7izzq63srmrcxhiqrnyilk2wgrvd7ypb")))) |
ea69e2f8 RW |
452 | (build-system r-build-system) |
453 | (home-page "http://www.rcpp.org") | |
454 | (synopsis "Seamless R and C++ Integration") | |
455 | (description | |
456 | "The Rcpp package provides R functions as well as C++ classes which offer | |
457 | a seamless integration of R and C++. Many R data types and objects can be | |
458 | mapped back and forth to C++ equivalents which facilitates both writing of new | |
459 | code as well as easier integration of third-party libraries. Documentation | |
460 | about Rcpp is provided by several vignettes included in this package, via the | |
461 | 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel | |
462 | and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see | |
463 | 'citation(\"Rcpp\")' for details on these last two.") | |
464 | (license license:gpl2+))) | |
7e10056b | 465 | |
092197a5 RW |
466 | (define-public r-matrix |
467 | (package | |
468 | (name "r-matrix") | |
03f72a1e | 469 | (version "1.2-7.1") |
092197a5 RW |
470 | (source |
471 | (origin | |
472 | (method url-fetch) | |
473 | (uri (cran-uri "Matrix" version)) | |
474 | (sha256 | |
475 | (base32 | |
03f72a1e | 476 | "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa")))) |
092197a5 RW |
477 | (properties `((upstream-name . "Matrix"))) |
478 | (build-system r-build-system) | |
479 | (propagated-inputs | |
480 | `(("r-lattice" ,r-lattice))) | |
481 | (home-page "http://Matrix.R-forge.R-project.org/") | |
482 | (synopsis "Sparse and dense matrix classes and methods") | |
483 | (description | |
484 | "This package provides classes and methods for dense and sparse matrices | |
485 | and operations on them using LAPACK and SuiteSparse.") | |
486 | (license license:gpl2+))) | |
487 | ||
08466208 BW |
488 | (define-public r-mgcv |
489 | (package | |
490 | (name "r-mgcv") | |
a751afb2 | 491 | (version "1.8-15") |
08466208 BW |
492 | (source |
493 | (origin | |
494 | (method url-fetch) | |
495 | (uri (cran-uri "mgcv" version)) | |
496 | (sha256 | |
497 | (base32 | |
a751afb2 | 498 | "05xzmsx51y92c0r0yihac8m9d3v1sqnn8ahcgm3q75j8z6zybsjs")))) |
08466208 BW |
499 | (build-system r-build-system) |
500 | (home-page "http://cran.r-project.org/web/packages/mgcv") | |
501 | (synopsis "Mixed generalised additive model computation") | |
502 | (description | |
503 | "GAMs, GAMMs and other generalized ridge regression with multiple smoothing | |
504 | parameter estimation by GCV, REML or UBRE/AIC. The library includes a | |
505 | @code{gam()} function, a wide variety of smoothers, JAGS support and | |
506 | distributions beyond the exponential family.") | |
507 | (license license:gpl2+))) | |
508 | ||
de682e6f BW |
509 | (define-public r-permute |
510 | (package | |
511 | (name "r-permute") | |
8b2f96e7 | 512 | (version "0.9-4") |
de682e6f BW |
513 | (source |
514 | (origin | |
515 | (method url-fetch) | |
516 | (uri (cran-uri "permute" version)) | |
517 | (sha256 | |
518 | (base32 | |
8b2f96e7 | 519 | "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5")))) |
de682e6f BW |
520 | (build-system r-build-system) |
521 | ;; Tests do not run correctly, but running them properly would entail a | |
522 | ;; circular dependency with vegan. | |
523 | (home-page "https://github.com/gavinsimpson/permute") | |
524 | (synopsis "Functions for Generating Restricted Permutations of Data") | |
525 | (description | |
526 | "This package provides a set of restricted permutation designs for freely | |
527 | exchangeable, line transects (time series), spatial grid designs and permutation | |
528 | of blocks (groups of samples). @code{permute} also allows split-plot designs, | |
529 | in which the whole-plots or split-plots or both can be freely exchangeable.") | |
530 | (license license:gpl2+))) | |
531 | ||
7e10056b RW |
532 | (define-public r-plyr |
533 | (package | |
534 | (name "r-plyr") | |
deb265a7 | 535 | (version "1.8.4") |
7e10056b RW |
536 | (source |
537 | (origin | |
538 | (method url-fetch) | |
9cda3622 | 539 | (uri (cran-uri "plyr" version)) |
7e10056b | 540 | (sha256 |
deb265a7 | 541 | (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0")))) |
7e10056b RW |
542 | (build-system r-build-system) |
543 | (native-inputs `(("r-rcpp" ,r-rcpp))) | |
544 | (home-page "http://had.co.nz/plyr") | |
545 | (synopsis "Tools for Splitting, Applying and Combining Data") | |
546 | (description | |
547 | "Plyr is a set of tools that solves a common set of problems: you need to | |
548 | break a big problem down into manageable pieces, operate on each piece and | |
549 | then put all the pieces back together. For example, you might want to fit a | |
550 | model to each spatial location or time point in your study, summarise data by | |
551 | panels or collapse high-dimensional arrays to simpler summary statistics.") | |
552 | (license license:expat))) | |
9a4d8968 RW |
553 | |
554 | (define-public r-proto | |
555 | (package | |
556 | (name "r-proto") | |
d13a4e25 | 557 | (version "1.0.0") |
9a4d8968 RW |
558 | (source |
559 | (origin | |
560 | (method url-fetch) | |
9cda3622 | 561 | (uri (cran-uri "proto" version)) |
9a4d8968 | 562 | (sha256 |
d13a4e25 | 563 | (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j")))) |
9a4d8968 | 564 | (build-system r-build-system) |
73ea83f5 | 565 | (home-page "https://github.com/hadley/proto") |
9a4d8968 RW |
566 | (synopsis "Prototype object-based programming") |
567 | (description | |
568 | "Proto is an object oriented system using object-based, also called | |
569 | prototype-based, rather than class-based object oriented ideas.") | |
570 | (license license:gpl2+))) | |
a45ba127 RW |
571 | |
572 | (define-public r-rcolorbrewer | |
573 | (package | |
574 | (name "r-rcolorbrewer") | |
575 | (version "1.1-2") | |
576 | (source | |
577 | (origin | |
578 | (method url-fetch) | |
9cda3622 | 579 | (uri (cran-uri "RColorBrewer" version)) |
a45ba127 RW |
580 | (sha256 |
581 | (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk")))) | |
582 | (build-system r-build-system) | |
583 | (home-page "http://cran.r-project.org/web/packages/RColorBrewer") | |
584 | (synopsis "ColorBrewer palettes") | |
585 | (description | |
586 | "This package provides color schemes for maps (and other graphics) | |
587 | designed by Cynthia Brewer as described at http://colorbrewer2.org") | |
588 | ;; Includes code licensed under bsd-4 | |
589 | (license license:asl2.0))) | |
4dca98dc | 590 | |
8e1bfc7e RW |
591 | (define-public r-sendmailr |
592 | (package | |
593 | (name "r-sendmailr") | |
594 | (version "1.2-1") | |
595 | (source | |
596 | (origin | |
597 | (method url-fetch) | |
598 | (uri (cran-uri "sendmailR" version)) | |
599 | (sha256 | |
600 | (base32 | |
601 | "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4")))) | |
602 | (properties `((upstream-name . "sendmailR"))) | |
603 | (build-system r-build-system) | |
604 | (propagated-inputs | |
605 | `(("r-base64enc" ,r-base64enc))) | |
606 | (home-page | |
607 | "http://cran.r-project.org/web/packages/sendmailR") | |
608 | (synopsis "Send email using R") | |
609 | (description | |
610 | "This package contains a simple SMTP client which provides a portable | |
611 | solution for sending email, including attachments, from within R.") | |
612 | (license license:gpl2+))) | |
613 | ||
4dca98dc RW |
614 | (define-public r-stringi |
615 | (package | |
616 | (name "r-stringi") | |
c2a9e991 | 617 | (version "1.1.2") |
4dca98dc RW |
618 | (source |
619 | (origin | |
620 | (method url-fetch) | |
9cda3622 | 621 | (uri (cran-uri "stringi" version)) |
4dca98dc RW |
622 | (sha256 |
623 | (base32 | |
c2a9e991 | 624 | "13i1p6j8mx31hsw2s4c2phm2llrrdakzixkm6i0axsxprri722z5")))) |
4dca98dc RW |
625 | (build-system r-build-system) |
626 | (inputs `(("icu4c" ,icu4c))) | |
627 | (native-inputs `(("pkg-config" ,pkg-config))) | |
628 | (home-page "http://stringi.rexamine.com/") | |
629 | (synopsis "Character string processing facilities") | |
630 | (description | |
631 | "This package allows for fast, correct, consistent, portable, as well as | |
632 | convenient character string/text processing in every locale and any native | |
633 | encoding. Owing to the use of the ICU library, the package provides R users | |
634 | with platform-independent functions known to Java, Perl, Python, PHP, and Ruby | |
635 | programmers. Among available features there are: pattern searching | |
636 | (e.g. via regular expressions), random string generation, string collation, | |
637 | transliteration, concatenation, date-time formatting and parsing, etc.") | |
638 | (license license:bsd-3))) | |
d5cd5c15 RW |
639 | |
640 | (define-public r-stringr | |
641 | (package | |
642 | (name "r-stringr") | |
bf1e9e45 | 643 | (version "1.1.0") |
d5cd5c15 RW |
644 | (source |
645 | (origin | |
646 | (method url-fetch) | |
9cda3622 | 647 | (uri (cran-uri "stringr" version)) |
d5cd5c15 | 648 | (sha256 |
bf1e9e45 | 649 | (base32 "0css5j4psl80br75chg6s1s3ipzf89f71bnbys34flp9yghg1cfc")))) |
d5cd5c15 RW |
650 | (build-system r-build-system) |
651 | (propagated-inputs | |
652 | `(("r-magrittr" ,r-magrittr) | |
653 | ("r-stringi" ,r-stringi))) | |
718a2bde | 654 | (home-page "https://github.com/hadley/stringr") |
d5cd5c15 RW |
655 | (synopsis "Simple, consistent wrappers for common string operations") |
656 | (description | |
657 | "Stringr is a consistent, simple and easy to use set of wrappers around | |
658 | the fantastic 'stringi' package. All function and argument names (and | |
659 | positions) are consistent, all functions deal with \"NA\"'s and zero length | |
660 | vectors in the same way, and the output from one function is easy to feed into | |
661 | the input of another.") | |
662 | (license license:gpl2+))) | |
9ca731ba RW |
663 | |
664 | (define-public r-reshape2 | |
665 | (package | |
666 | (name "r-reshape2") | |
2d9da70b | 667 | (version "1.4.2") |
9ca731ba RW |
668 | (source |
669 | (origin | |
670 | (method url-fetch) | |
9cda3622 | 671 | (uri (cran-uri "reshape2" version)) |
9ca731ba | 672 | (sha256 |
2d9da70b | 673 | (base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd")))) |
9ca731ba RW |
674 | (build-system r-build-system) |
675 | (propagated-inputs | |
676 | `(("r-plyr" ,r-plyr) | |
677 | ("r-rcpp" ,r-rcpp) | |
678 | ("r-stringr" ,r-stringr))) | |
679 | (home-page "https://github.com/hadley/reshape") | |
680 | (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package") | |
681 | (description | |
682 | "Reshape2 is an R library to flexibly restructure and aggregate data | |
683 | using just two functions: melt and dcast (or acast).") | |
684 | (license license:expat))) | |
a11ee478 RW |
685 | |
686 | (define-public r-scales | |
687 | (package | |
688 | (name "r-scales") | |
cf2e19a9 | 689 | (version "0.4.0") |
a11ee478 RW |
690 | (source |
691 | (origin | |
692 | (method url-fetch) | |
9cda3622 | 693 | (uri (cran-uri "scales" version)) |
a11ee478 | 694 | (sha256 |
cf2e19a9 | 695 | (base32 "19y6q4j8vpmc73dnn4ncp5wj44gri7m77ys3z2rn3crrcc9zc7l5")))) |
a11ee478 RW |
696 | (build-system r-build-system) |
697 | (propagated-inputs | |
698 | `(("r-dichromat" ,r-dichromat) | |
699 | ("r-labeling" ,r-labeling) | |
700 | ("r-munsell" ,r-munsell) | |
701 | ("r-plyr" ,r-plyr) | |
702 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
703 | ("r-rcpp" ,r-rcpp))) | |
704 | (home-page "https://github.com/hadley/scales") | |
705 | (synopsis "Scale functions for visualization") | |
706 | (description | |
707 | "This package provides graphical scales that map data to aesthetics, and | |
708 | provides methods for automatically determining breaks and labels for axes and | |
709 | legends.") | |
710 | (license license:expat))) | |
d11b808f RW |
711 | |
712 | (define-public r-ggplot2 | |
713 | (package | |
714 | (name "r-ggplot2") | |
b268e496 | 715 | (version "2.1.0") |
d11b808f RW |
716 | (source |
717 | (origin | |
718 | (method url-fetch) | |
9cda3622 | 719 | (uri (cran-uri "ggplot2" version)) |
d11b808f | 720 | (sha256 |
b268e496 | 721 | (base32 "0s9rvp0f736ji6p9xpxq54agxf95pjkql4sj7ag0hv2xhnp27hzj")))) |
d11b808f RW |
722 | (build-system r-build-system) |
723 | (propagated-inputs | |
724 | `(("r-digest" ,r-digest) | |
725 | ("r-gtable" ,r-gtable) | |
726 | ("r-plyr" ,r-plyr) | |
727 | ("r-proto" ,r-proto) | |
728 | ("r-reshape2" ,r-reshape2) | |
975cd29a BW |
729 | ("r-scales" ,r-scales) |
730 | ("r-svglite" ,r-svglite))) | |
d11b808f RW |
731 | (home-page "http://ggplot2.org") |
732 | (synopsis "An implementation of the grammar of graphics") | |
733 | (description | |
734 | "Ggplot2 is an implementation of the grammar of graphics in R. It | |
735 | combines the advantages of both base and lattice graphics: conditioning and | |
736 | shared axes are handled automatically, and you can still build up a plot step | |
737 | by step from multiple data sources. It also implements a sophisticated | |
738 | multidimensional conditioning system and a consistent interface to map data to | |
739 | aesthetic attributes.") | |
740 | (license license:gpl2+))) | |
ed6094fc | 741 | |
c5940b15 BW |
742 | (define-public r-gdtools |
743 | (package | |
744 | (name "r-gdtools") | |
054a9a78 | 745 | (version "0.1.1") |
c5940b15 BW |
746 | (source |
747 | (origin | |
748 | (method url-fetch) | |
749 | (uri (cran-uri "gdtools" version)) | |
750 | (sha256 | |
751 | (base32 | |
054a9a78 | 752 | "1l9d759x9s4ddz51sls8kcjps2i9kwfbc72dnagrdavh82h0al8n")))) |
c5940b15 BW |
753 | (build-system r-build-system) |
754 | (native-inputs | |
755 | `(("r-rcpp" ,r-rcpp) | |
756 | ("pkg-config" ,pkg-config))) | |
757 | (inputs | |
758 | `(("cairo" ,cairo))) | |
054a9a78 RW |
759 | (propagated-inputs |
760 | `(("r-withr" ,r-withr))) | |
c5940b15 BW |
761 | (home-page "http://cran.r-project.org/web/packages/gdtools") |
762 | (synopsis "Utilities for graphical rendering") | |
763 | (description | |
764 | "The @code{gdtools} package provides functionalities to get font metrics | |
765 | and to generate base64 encoded string from raster matrix.") | |
766 | (license license:gpl3))) | |
767 | ||
3aebedcc BW |
768 | (define-public r-svglite |
769 | (package | |
770 | (name "r-svglite") | |
771 | (version "1.1.0") | |
772 | (source | |
773 | (origin | |
774 | (method url-fetch) | |
775 | (uri (cran-uri "svglite" version)) | |
776 | (sha256 | |
777 | (base32 | |
778 | "11ryicjglfi6jvkk4jgg5kra42qbs5z2zid7jjhlslpjcljfwc70")))) | |
779 | (build-system r-build-system) | |
780 | (native-inputs `(("r-rcpp" ,r-rcpp))) | |
781 | (propagated-inputs | |
782 | `(("r-bh" ,r-bh) | |
783 | ("r-gdtools" ,r-gdtools))) | |
784 | (home-page "https://github.com/hadley/svglite") | |
785 | (synopsis "SVG graphics device") | |
786 | (description | |
787 | "@code{svglite} is a graphics device that produces clean | |
788 | @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or | |
789 | hand editing. Compared to the built-in @code{svg()}, @code{svglite} is | |
790 | considerably faster, produces smaller files, and leaves text as is.") | |
791 | (license license:gpl2+))) | |
792 | ||
ed6094fc VVP |
793 | (define-public r-assertthat |
794 | (package | |
795 | (name "r-assertthat") | |
796 | (version "0.1") | |
797 | (source (origin | |
798 | (method url-fetch) | |
9cda3622 | 799 | (uri (cran-uri "assertthat" version)) |
ed6094fc VVP |
800 | (sha256 |
801 | (base32 | |
802 | "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk")))) | |
803 | (build-system r-build-system) | |
804 | (home-page "https://github.com/hadley/assertthat") | |
805 | (synopsis "Easy pre and post assertions") | |
806 | (description | |
807 | "Assertthat is an extension to stopifnot() that makes it easy to declare | |
808 | the pre and post conditions that your code should satisfy, while also | |
809 | producing friendly error messages so that your users know what they've done | |
810 | wrong.") | |
811 | (license license:gpl3+))) | |
6af48134 VVP |
812 | |
813 | (define-public r-lazyeval | |
814 | (package | |
815 | (name "r-lazyeval") | |
6d6a917a | 816 | (version "0.2.0") |
6af48134 VVP |
817 | (source (origin |
818 | (method url-fetch) | |
9cda3622 | 819 | (uri (cran-uri "lazyeval" version)) |
6af48134 VVP |
820 | (sha256 |
821 | (base32 | |
6d6a917a | 822 | "1jwdz40nznlc44hpjli7h98gnpa4d98ifggmj7z88h84n9aqywqk")))) |
6af48134 VVP |
823 | (build-system r-build-system) |
824 | (home-page "https://github.com/hadley/lazyeval") | |
825 | (synopsis "Lazy (non-standard) evaluation in R") | |
826 | (description | |
827 | "This package provides the tools necessary to do non-standard | |
828 | evaluation (NSE) in R.") | |
829 | (license license:gpl3+))) | |
8ea6b30f VVP |
830 | |
831 | (define-public r-dbi | |
832 | (package | |
833 | (name "r-dbi") | |
5b67bd6e | 834 | (version "0.5-1") |
8ea6b30f VVP |
835 | (source (origin |
836 | (method url-fetch) | |
9cda3622 | 837 | (uri (cran-uri "DBI" version)) |
8ea6b30f VVP |
838 | (sha256 |
839 | (base32 | |
5b67bd6e | 840 | "1idwm9lkmz6ns6h0vvgml18mg0k7vjqiv9p5svrdcmx7r1rirpdi")))) |
8ea6b30f VVP |
841 | (build-system r-build-system) |
842 | (home-page "https://github.com/rstats-db/DBI") | |
843 | (synopsis "R database interface") | |
844 | (description | |
845 | "The DBI package provides a database interface (DBI) definition for | |
846 | communication between R and relational database management systems. All | |
847 | classes in this package are virtual and need to be extended by the various | |
848 | R/DBMS implementations.") | |
849 | (license license:lgpl2.0+))) | |
675c9f44 VVP |
850 | |
851 | (define-public r-bh | |
852 | (package | |
853 | (name "r-bh") | |
9a0ccf43 | 854 | (version "1.60.0-2") |
675c9f44 VVP |
855 | (source (origin |
856 | (method url-fetch) | |
857 | (uri (cran-uri "BH" version)) | |
858 | (sha256 | |
859 | (base32 | |
9a0ccf43 | 860 | "136497fng9bcvrf8favpj8inz96pxdwp1rrb2k00sxjxjbgawhg4")))) |
675c9f44 VVP |
861 | (build-system r-build-system) |
862 | (home-page "https://github.com/eddelbuettel/bh") | |
863 | (synopsis "R package providing subset of Boost headers") | |
864 | (description | |
865 | "This package aims to provide the most useful subset of Boost libraries | |
866 | for template use among CRAN packages.") | |
867 | (license license:boost1.0))) | |
256ccc92 VVP |
868 | |
869 | (define-public r-evaluate | |
870 | (package | |
871 | (name "r-evaluate") | |
e0a90931 | 872 | (version "0.10") |
256ccc92 VVP |
873 | (source (origin |
874 | (method url-fetch) | |
875 | (uri (cran-uri "evaluate" version)) | |
876 | (sha256 | |
877 | (base32 | |
e0a90931 | 878 | "0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1")))) |
256ccc92 VVP |
879 | (build-system r-build-system) |
880 | (propagated-inputs | |
881 | `(("r-stringr" ,r-stringr))) | |
882 | (home-page "https://github.com/hadley/evaluate") | |
883 | (synopsis "Parsing and evaluation tools for R") | |
884 | (description | |
885 | "This package provides tools that allow you to recreate the parsing, | |
886 | evaluation and display of R code, with enough information that you can | |
887 | accurately recreate what happens at the command line. The tools can easily be | |
888 | adapted for other output formats, such as HTML or LaTeX.") | |
889 | (license license:gpl3+))) | |
c5bf3abe VVP |
890 | |
891 | (define-public r-formatr | |
892 | (package | |
893 | (name "r-formatr") | |
df25b004 | 894 | (version "1.4") |
c5bf3abe VVP |
895 | (source (origin |
896 | (method url-fetch) | |
897 | (uri (cran-uri "formatR" version)) | |
898 | (sha256 | |
899 | (base32 | |
df25b004 | 900 | "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f")))) |
c5bf3abe VVP |
901 | (build-system r-build-system) |
902 | (home-page "http://yihui.name/formatR") | |
903 | (synopsis "Format R code automatically") | |
904 | (description | |
905 | "This package provides a function to format R source code. Spaces and | |
906 | indent will be added to the code automatically, and comments will be preserved | |
907 | under certain conditions, so that R code will be more human-readable and tidy. | |
908 | There is also a Shiny app as a user interface in this package.") | |
909 | (license license:gpl3+))) | |
ad3f005b VVP |
910 | |
911 | (define-public r-highr | |
912 | (package | |
913 | (name "r-highr") | |
d5130e63 | 914 | (version "0.6") |
ad3f005b VVP |
915 | (source (origin |
916 | (method url-fetch) | |
917 | (uri (cran-uri "highr" version)) | |
918 | (sha256 | |
919 | (base32 | |
d5130e63 | 920 | "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3")))) |
ad3f005b VVP |
921 | (build-system r-build-system) |
922 | (home-page "https://github.com/yihui/highr") | |
923 | (synopsis "Syntax highlighting for R source code") | |
924 | (description | |
925 | "This package provides syntax highlighting for R source code. Currently | |
926 | it supports LaTeX and HTML output. Source code of other languages is | |
927 | supported via Andre Simon's highlight package.") | |
928 | (license license:gpl3+))) | |
acbb40fa VVP |
929 | |
930 | (define-public r-mime | |
931 | (package | |
932 | (name "r-mime") | |
2d037a2d | 933 | (version "0.5") |
acbb40fa VVP |
934 | (source (origin |
935 | (method url-fetch) | |
936 | (uri (cran-uri "mime" version)) | |
937 | (sha256 | |
938 | (base32 | |
2d037a2d | 939 | "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw")))) |
acbb40fa VVP |
940 | (build-system r-build-system) |
941 | (home-page "https://github.com/yihui/mime") | |
942 | (synopsis "R package to map filenames to MIME types") | |
943 | (description | |
944 | "This package guesses the MIME type from a filename extension using the | |
945 | data derived from /etc/mime.types in UNIX-type systems.") | |
946 | (license license:gpl2))) | |
3f8ac353 VVP |
947 | |
948 | (define-public r-markdown | |
949 | (package | |
950 | (name "r-markdown") | |
951 | (version "0.7.7") | |
952 | (source (origin | |
953 | (method url-fetch) | |
954 | (uri (cran-uri "markdown" version)) | |
955 | (sha256 | |
956 | (base32 | |
957 | "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb")))) | |
958 | (build-system r-build-system) | |
959 | ;; Skip check phase because the tests require the r-knitr package to be | |
960 | ;; installed. This prevents installation failures. Knitr normally | |
961 | ;; shouldn't be available since r-markdown is a dependency of the r-knitr | |
962 | ;; package. | |
963 | (arguments `(#:tests? #f)) | |
964 | (propagated-inputs | |
965 | `(("r-mime" ,r-mime))) | |
966 | (home-page "https://github.com/rstudio/markdown") | |
967 | (synopsis "Markdown rendering for R") | |
968 | (description | |
969 | "This package provides R bindings to the Sundown Markdown rendering | |
970 | library (https://github.com/vmg/sundown). Markdown is a plain-text formatting | |
971 | syntax that can be converted to XHTML or other formats.") | |
972 | (license license:gpl2))) | |
ea3a8095 VVP |
973 | |
974 | (define-public r-yaml | |
975 | (package | |
976 | (name "r-yaml") | |
977 | (version "2.1.13") | |
978 | (source (origin | |
979 | (method url-fetch) | |
980 | (uri (cran-uri "yaml" version)) | |
981 | (sha256 | |
982 | (base32 | |
983 | "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6")))) | |
984 | (build-system r-build-system) | |
985 | (home-page "https://cran.r-project.org/web/packages/yaml/") | |
986 | (synopsis "Methods to convert R data to YAML and back") | |
987 | (description | |
988 | "This package implements the libyaml YAML 1.1 parser and | |
989 | emitter (http://pyyaml.org/wiki/LibYAML) for R.") | |
990 | (license license:bsd-3))) | |
213656b9 VVP |
991 | |
992 | (define-public r-knitr | |
993 | (package | |
994 | (name "r-knitr") | |
ad28491e | 995 | (version "1.14") |
213656b9 VVP |
996 | (source (origin |
997 | (method url-fetch) | |
998 | (uri (cran-uri "knitr" version)) | |
999 | (sha256 | |
1000 | (base32 | |
ad28491e | 1001 | "1v0s0knb294p7a2xkwy35bhg0w8p3qcgyphd748sj86hh8a30vds")))) |
213656b9 VVP |
1002 | (build-system r-build-system) |
1003 | (propagated-inputs | |
1004 | `(("r-evaluate" ,r-evaluate) | |
1005 | ("r-digest" ,r-digest) | |
1006 | ("r-formatr" ,r-formatr) | |
1007 | ("r-highr" ,r-highr) | |
1008 | ("r-markdown" ,r-markdown) | |
1009 | ("r-stringr" ,r-stringr) | |
1010 | ("r-yaml" ,r-yaml))) | |
1011 | (home-page "http://yihui.name/knitr/") | |
1012 | (synopsis "General-purpose package for dynamic report generation in R") | |
1013 | (description | |
1014 | "This package provides a general-purpose tool for dynamic report | |
1015 | generation in R using Literate Programming techniques.") | |
1016 | ;; The code is released under any version of the GPL. As it is used by | |
1017 | ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+ | |
1018 | ;; here. | |
1019 | (license license:gpl2+))) | |
4f0e8484 | 1020 | |
4ce3c287 RW |
1021 | (define-public r-knitrbootstrap |
1022 | (package | |
1023 | (name "r-knitrbootstrap") | |
1024 | (version "1.0.0") | |
1025 | (source | |
1026 | (origin | |
1027 | (method url-fetch) | |
1028 | (uri (cran-uri "knitrBootstrap" version)) | |
1029 | (sha256 | |
1030 | (base32 | |
1031 | "0pshn2slzqwpryklslsxwh1dmqcnwv6bwi7yfm6m342wjybpk0wl")))) | |
1032 | (properties `((upstream-name . "knitrBootstrap"))) | |
1033 | (build-system r-build-system) | |
1034 | (propagated-inputs | |
1035 | `(("r-knitr" ,r-knitr) | |
1036 | ("r-rmarkdown" ,r-rmarkdown))) | |
1037 | (home-page "https://github.com/jimhester/knitrBootstrap") | |
1038 | (synopsis "Knitr bootstrap framework") | |
1039 | (description | |
1040 | "This package provides a framework to create Bootstrap 3 HTML reports | |
1041 | from knitr Rmarkdown.") | |
1042 | (license license:expat))) | |
1043 | ||
4f0e8484 VVP |
1044 | (define-public r-microbenchmark |
1045 | (package | |
1046 | (name "r-microbenchmark") | |
8e4edf08 | 1047 | (version "1.4-2.1") |
4f0e8484 VVP |
1048 | (source (origin |
1049 | (method url-fetch) | |
1050 | (uri (cran-uri "microbenchmark" version)) | |
1051 | (sha256 | |
1052 | (base32 | |
8e4edf08 | 1053 | "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg")))) |
4f0e8484 VVP |
1054 | (build-system r-build-system) |
1055 | (propagated-inputs | |
1056 | `(("r-ggplot2" ,r-ggplot2))) | |
1057 | (home-page "https://cran.r-project.org/web/packages/microbenchmark/") | |
1058 | (synopsis "Accurate timing functions for R") | |
1059 | (description | |
1060 | "This package provides infrastructure to accurately measure and compare | |
1061 | the execution time of R expressions.") | |
1062 | (license license:bsd-2))) | |
1cf1cbb0 VVP |
1063 | |
1064 | (define-public r-codetools | |
1065 | (package | |
1066 | (name "r-codetools") | |
1067 | (version "0.2-14") | |
1068 | (source (origin | |
1069 | (method url-fetch) | |
1070 | (uri (cran-uri "codetools" version)) | |
1071 | (sha256 | |
1072 | (base32 | |
1073 | "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397")))) | |
1074 | (build-system r-build-system) | |
1075 | (home-page "https://cran.r-project.org/web/packages/codetools/index.html") | |
1076 | (synopsis "Code analysis tools for R") | |
1077 | (description "This package provides code analysis tools for R.") | |
1078 | (license license:gpl3+))) | |
0661b4db VVP |
1079 | |
1080 | (define-public r-pryr | |
1081 | (package | |
1082 | (name "r-pryr") | |
1083 | (version "0.1.2") | |
1084 | (source (origin | |
1085 | (method url-fetch) | |
1086 | (uri (cran-uri "pryr" version)) | |
1087 | (sha256 | |
1088 | (base32 | |
1089 | "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5")))) | |
1090 | (build-system r-build-system) | |
1091 | (propagated-inputs | |
1092 | `(("r-stringr" ,r-stringr) | |
1093 | ("r-codetools" ,r-codetools))) | |
1094 | (native-inputs | |
1095 | `(("r-rcpp" ,r-rcpp))) | |
1096 | (home-page "https://github.com/hadley/pryr") | |
1097 | (synopsis "Tools for computing on the R language") | |
1098 | (description | |
1099 | "This package provides useful tools to pry back the covers of R and | |
1100 | understand the language at a deeper level.") | |
1101 | (license license:gpl2))) | |
b668a95c VVP |
1102 | |
1103 | (define-public r-memoise | |
1104 | (package | |
1105 | (name "r-memoise") | |
618dbdd7 | 1106 | (version "1.0.0") |
b668a95c VVP |
1107 | (source (origin |
1108 | (method url-fetch) | |
1109 | (uri (cran-uri "memoise" version)) | |
1110 | (sha256 | |
1111 | (base32 | |
618dbdd7 | 1112 | "0sq2dhpvxy17v1baj256r0jnygdy3m5a8x4zh6vhv29957qnq6zx")))) |
b668a95c VVP |
1113 | (build-system r-build-system) |
1114 | (propagated-inputs | |
1115 | `(("r-digest" ,r-digest))) | |
1116 | (home-page "http://github.com/hadley/memoise") | |
1117 | (synopsis "Memoise functions for R") | |
1118 | (description | |
1119 | "This R package allows to cache the results of a function so that when | |
1120 | you call it again with the same arguments it returns the pre-computed value.") | |
1121 | (license license:expat))) | |
834f7ff3 VVP |
1122 | |
1123 | (define-public r-crayon | |
1124 | (package | |
1125 | (name "r-crayon") | |
344d5323 | 1126 | (version "1.3.2") |
834f7ff3 VVP |
1127 | (source (origin |
1128 | (method url-fetch) | |
1129 | (uri (cran-uri "crayon" version)) | |
1130 | (sha256 | |
1131 | (base32 | |
344d5323 | 1132 | "0s2yam18slph7xsw4pyc9f92gdyf609r5w92yax69zh57kb7asws")))) |
834f7ff3 VVP |
1133 | (build-system r-build-system) |
1134 | (propagated-inputs | |
1135 | `(("r-memoise" ,r-memoise))) | |
1136 | (home-page "https://github.com/gaborcsardi/crayon") | |
1137 | (synopsis "Colored terminal output for R") | |
1138 | (description | |
1139 | "Colored terminal output on terminals that support ANSI color and | |
1140 | highlight codes. It also works in Emacs ESS. ANSI color support is | |
1141 | automatically detected. Colors and highlighting can be combined and nested. | |
1142 | New styles can also be created easily. This package was inspired by the | |
1143 | \"chalk\" JavaScript project.") | |
1144 | (license license:expat))) | |
5b9789a6 | 1145 | |
35b2001a RW |
1146 | (define-public r-praise |
1147 | (package | |
1148 | (name "r-praise") | |
1149 | (version "1.0.0") | |
1150 | (source | |
1151 | (origin | |
1152 | (method url-fetch) | |
1153 | (uri (cran-uri "praise" version)) | |
1154 | (sha256 | |
1155 | (base32 | |
1156 | "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw")))) | |
1157 | (build-system r-build-system) | |
1158 | (home-page "https://github.com/gaborcsardi/praise") | |
1159 | (synopsis "Functions to praise users") | |
1160 | (description | |
1161 | "This package provides template functions to assist in building friendly | |
1162 | R packages that praise their users.") | |
1163 | (license license:expat))) | |
1164 | ||
5b9789a6 VVP |
1165 | (define-public r-testthat |
1166 | (package | |
1167 | (name "r-testthat") | |
383f6337 | 1168 | (version "1.0.2") |
5b9789a6 VVP |
1169 | (source (origin |
1170 | (method url-fetch) | |
1171 | (uri (cran-uri "testthat" version)) | |
1172 | (sha256 | |
1173 | (base32 | |
383f6337 | 1174 | "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf")))) |
5b9789a6 VVP |
1175 | (build-system r-build-system) |
1176 | (propagated-inputs | |
1177 | `(("r-digest" ,r-digest) | |
99eca2b1 RW |
1178 | ("r-crayon" ,r-crayon) |
1179 | ("r-magrittr" ,r-magrittr) | |
1180 | ("r-praise" ,r-praise) | |
1181 | ("r-r6" ,r-r6))) | |
5b9789a6 VVP |
1182 | (home-page "https://github.com/hadley/testthat") |
1183 | (synopsis "Unit testing for R") | |
1184 | (description | |
1185 | "This package provides a unit testing system for R designed to be fun, | |
1186 | flexible and easy to set up.") | |
1187 | (license license:expat))) | |
ffd4b478 VVP |
1188 | |
1189 | (define-public r-r6 | |
1190 | (package | |
1191 | (name "r-r6") | |
bff4dc63 | 1192 | (version "2.2.0") |
ffd4b478 VVP |
1193 | (source (origin |
1194 | (method url-fetch) | |
1195 | (uri (cran-uri "R6" version)) | |
1196 | (sha256 | |
1197 | (base32 | |
bff4dc63 | 1198 | "1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx")))) |
ffd4b478 | 1199 | (build-system r-build-system) |
ffd4b478 VVP |
1200 | (home-page "https://github.com/wch/R6/") |
1201 | (synopsis "Classes with reference semantics in R") | |
1202 | (description | |
1203 | "The R6 package allows the creation of classes with reference semantics, | |
1204 | similar to R's built-in reference classes. Compared to reference classes, R6 | |
1205 | classes are simpler and lighter-weight, and they are not built on S4 classes | |
1206 | so they do not require the methods package. These classes allow public and | |
1207 | private members, and they support inheritance, even when the classes are | |
1208 | defined in different packages.") | |
1209 | (license license:expat))) | |
2a3a8ae7 | 1210 | |
a589acfb RW |
1211 | (define-public r-tibble |
1212 | (package | |
1213 | (name "r-tibble") | |
1214 | (version "1.2") | |
1215 | (source | |
1216 | (origin | |
1217 | (method url-fetch) | |
1218 | (uri (cran-uri "tibble" version)) | |
1219 | (sha256 | |
1220 | (base32 | |
1221 | "011i352ylq9b4xfcj7h10h7qsqd9qkc1rzc0pr1gf8qjb788p2pd")))) | |
1222 | (build-system r-build-system) | |
1223 | (propagated-inputs | |
1224 | `(("r-assertthat" ,r-assertthat) | |
1225 | ("r-lazyeval" ,r-lazyeval) | |
1226 | ("r-rcpp" ,r-rcpp))) | |
1227 | (home-page "https://github.com/hadley/tibble") | |
1228 | (synopsis "Simple data frames") | |
1229 | (description | |
1230 | "This package provides a @code{tbl_df} class that offers better checking | |
1231 | and printing capabilities than traditional data frames.") | |
1232 | (license license:expat))) | |
1233 | ||
2a3a8ae7 VVP |
1234 | (define-public r-dplyr |
1235 | (package | |
1236 | (name "r-dplyr") | |
de1eebd7 | 1237 | (version "0.5.0") |
2a3a8ae7 VVP |
1238 | (source (origin |
1239 | (method url-fetch) | |
1240 | (uri (cran-uri "dplyr" version)) | |
1241 | (sha256 | |
1242 | (base32 | |
de1eebd7 | 1243 | "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk")))) |
2a3a8ae7 VVP |
1244 | (build-system r-build-system) |
1245 | (propagated-inputs | |
1246 | `(("r-assertthat" ,r-assertthat) | |
1247 | ("r-r6" ,r-r6) | |
1248 | ("r-magrittr" ,r-magrittr) | |
1249 | ("r-lazyeval" ,r-lazyeval) | |
de1eebd7 RW |
1250 | ("r-dbi" ,r-dbi) |
1251 | ("r-tibble" ,r-tibble))) | |
2a3a8ae7 VVP |
1252 | (native-inputs |
1253 | `(("r-rcpp" ,r-rcpp) | |
1254 | ("r-bh" ,r-bh))) | |
1255 | (home-page "https://github.com/hadley/dplyr") | |
1256 | (synopsis "Tools for working with data frames in R") | |
1257 | (description | |
1258 | "dplyr is the next iteration of plyr. It is focussed on tools for | |
1259 | working with data frames. It has three main goals: 1) identify the most | |
1260 | important data manipulation tools needed for data analysis and make them easy | |
1261 | to use in R; 2) provide fast performance for in-memory data by writing key | |
1262 | pieces of code in C++; 3) use the same code interface to work with data no | |
1263 | matter where it is stored, whether in a data frame, a data table or | |
1264 | database.") | |
1265 | (license license:expat))) | |
91312ebe | 1266 | |
b4d6f408 RW |
1267 | (define-public r-acepack |
1268 | (package | |
1269 | (name "r-acepack") | |
572e1a0c | 1270 | (version "1.4.1") |
b4d6f408 RW |
1271 | (source |
1272 | (origin | |
1273 | (method url-fetch) | |
1274 | (uri (cran-uri "acepack" version)) | |
1275 | (sha256 | |
1276 | (base32 | |
572e1a0c | 1277 | "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2")))) |
b4d6f408 RW |
1278 | (build-system r-build-system) |
1279 | (inputs | |
1280 | `(("gfortran" ,gfortran))) | |
1281 | (home-page "http://cran.r-project.org/web/packages/acepack") | |
1282 | (synopsis "Functions for regression transformations") | |
1283 | (description | |
1284 | "This package provides ACE and AVAS methods for choosing regression | |
1285 | transformations.") | |
1286 | (license license:expat))) | |
1287 | ||
0926b877 RW |
1288 | (define-public r-cluster |
1289 | (package | |
1290 | (name "r-cluster") | |
130410d9 | 1291 | (version "2.0.5") |
0926b877 RW |
1292 | (source |
1293 | (origin | |
1294 | (method url-fetch) | |
1295 | (uri (cran-uri "cluster" version)) | |
1296 | (sha256 | |
1297 | (base32 | |
130410d9 | 1298 | "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b")))) |
0926b877 RW |
1299 | (build-system r-build-system) |
1300 | (inputs | |
1301 | `(("gfortran" ,gfortran))) | |
1302 | (home-page "http://cran.r-project.org/web/packages/cluster") | |
1303 | (synopsis "Methods for data cluster analysis") | |
1304 | (description | |
1305 | "This package provides tools that are useful in finding groups in data. | |
1306 | It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding | |
1307 | Groups in Data\".") | |
1308 | (license license:gpl2+))) | |
1309 | ||
0837dd07 RW |
1310 | (define-public r-foreign |
1311 | (package | |
1312 | (name "r-foreign") | |
72263db7 | 1313 | (version "0.8-67") |
0837dd07 RW |
1314 | (source |
1315 | (origin | |
1316 | (method url-fetch) | |
1317 | (uri (cran-uri "foreign" version)) | |
1318 | (sha256 | |
1319 | (base32 | |
72263db7 | 1320 | "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd")))) |
0837dd07 RW |
1321 | (build-system r-build-system) |
1322 | (home-page "http://cran.r-project.org/web/packages/foreign") | |
1323 | (synopsis "Read data stored by other statistics software in R") | |
1324 | (description | |
1325 | "This package provides functions for reading and writing data stored by | |
1326 | some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and | |
1327 | for reading and writing some dBase files.") | |
1328 | (license license:gpl2+))) | |
1329 | ||
b1acb445 RW |
1330 | (define-public r-formula |
1331 | (package | |
1332 | (name "r-formula") | |
1333 | (version "1.2-1") | |
1334 | (source | |
1335 | (origin | |
1336 | (method url-fetch) | |
1337 | (uri (cran-uri "Formula" version)) | |
1338 | (sha256 | |
1339 | (base32 | |
1340 | "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax")))) | |
1341 | (properties `((upstream-name . "Formula"))) | |
1342 | (build-system r-build-system) | |
1343 | (home-page "http://cran.r-project.org/web/packages/Formula") | |
1344 | (synopsis "Extended model formulas") | |
1345 | (description | |
1346 | "This package provides a new class @code{Formula}, which extends the base | |
1347 | class @code{formula}. It supports extended formulas with multiple parts of | |
1348 | regressors on the right-hand side and/or multiple responses on the left-hand | |
1349 | side.") | |
1350 | (license (list license:gpl2+ license:gpl3+)))) | |
1351 | ||
97ee973d RW |
1352 | (define-public r-locfit |
1353 | (package | |
1354 | (name "r-locfit") | |
1355 | (version "1.5-9.1") | |
1356 | (source | |
1357 | (origin | |
1358 | (method url-fetch) | |
1359 | (uri (cran-uri "locfit" version)) | |
1360 | (sha256 | |
1361 | (base32 | |
1362 | "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m")))) | |
1363 | (build-system r-build-system) | |
1364 | (home-page "http://cran.r-project.org/web/packages/locfit") | |
1365 | (synopsis "Local regression, likelihood and density estimation") | |
1366 | (description | |
1367 | "This package provides functions used for local regression, likelihood | |
1368 | and density estimation.") | |
1369 | (license (list license:gpl2+ license:gpl3+)))) | |
1370 | ||
91312ebe VVP |
1371 | (define-public r-chron |
1372 | (package | |
1373 | (name "r-chron") | |
1374 | (version "2.3-47") | |
1375 | (source (origin | |
1376 | (method url-fetch) | |
1377 | (uri (cran-uri "chron" version)) | |
1378 | (sha256 | |
1379 | (base32 | |
1380 | "1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s")))) | |
1381 | (build-system r-build-system) | |
1382 | (home-page "http://cran.r-project.org/web/packages/chron") | |
1383 | (synopsis "Chronological R objects which can handle dates and times") | |
1384 | (description | |
1385 | "This package provides chronological R objects which can handle dates and | |
1386 | times.") | |
1387 | (license license:gpl2))) | |
0e4e03f8 | 1388 | |
62141c07 | 1389 | (define-public r-data-table |
0e4e03f8 | 1390 | (package |
62141c07 | 1391 | (name "r-data-table") |
0e4e03f8 VVP |
1392 | (version "1.9.6") |
1393 | (source (origin | |
1394 | (method url-fetch) | |
1395 | (uri (cran-uri "data.table" version)) | |
1396 | (sha256 | |
1397 | (base32 | |
1398 | "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g")))) | |
1399 | (build-system r-build-system) | |
1400 | (propagated-inputs | |
1401 | `(("r-chron" ,r-chron))) | |
1402 | (home-page "https://github.com/Rdatatable/data.table/wiki") | |
1403 | (synopsis "Enhanced version of data.frame R object") | |
1404 | (description | |
62141c07 RW |
1405 | "The R package @code{data.table} is an extension of @code{data.frame} |
1406 | providing functions for fast aggregation of large data (e.g. 100GB in RAM), | |
1407 | fast ordered joins, fast add/modify/delete of columns by group, column listing | |
1408 | and fast file reading.") | |
1409 | (license license:gpl3+))) | |
9bc08aa0 | 1410 | |
a73f4cd1 RW |
1411 | (define-public r-xtable |
1412 | (package | |
1413 | (name "r-xtable") | |
1414 | (version "1.8-2") | |
1415 | (source | |
1416 | (origin | |
1417 | (method url-fetch) | |
1418 | (uri (cran-uri "xtable" version)) | |
1419 | (sha256 | |
1420 | (base32 | |
1421 | "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn")))) | |
1422 | (build-system r-build-system) | |
1423 | (native-inputs | |
1424 | `(("r-knitr" ,r-knitr))) | |
1425 | (home-page "http://xtable.r-forge.r-project.org/") | |
1426 | (synopsis "Export R tables to LaTeX or HTML") | |
1427 | (description | |
1428 | "This package provides tools to export R data as LaTeX and HTML tables.") | |
1429 | (license license:gpl2+))) | |
1430 | ||
9bc08aa0 RW |
1431 | (define-public python-patsy |
1432 | (package | |
1433 | (name "python-patsy") | |
f4cd2cea | 1434 | (version "0.4.1") |
9bc08aa0 RW |
1435 | (source (origin |
1436 | (method url-fetch) | |
f4cd2cea | 1437 | (uri (pypi-uri "patsy" version ".zip")) |
9bc08aa0 RW |
1438 | (sha256 |
1439 | (base32 | |
f4cd2cea | 1440 | "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w")))) |
9bc08aa0 RW |
1441 | (build-system python-build-system) |
1442 | (arguments | |
1443 | `(#:phases | |
1444 | (modify-phases %standard-phases | |
b41a05ce | 1445 | (replace 'check (lambda _ (zero? (system* "nosetests" "-v"))))))) |
9bc08aa0 RW |
1446 | (propagated-inputs |
1447 | `(("python-numpy" ,python-numpy) | |
1448 | ("python-scipy" ,python-scipy) | |
1449 | ("python-six" ,python-six))) | |
1450 | (native-inputs | |
1451 | `(("python-nose" ,python-nose) | |
1452 | ("unzip" ,unzip))) | |
1453 | (home-page "https://github.com/pydata/patsy") | |
1454 | (synopsis "Describe statistical models and build design matrices") | |
1455 | (description | |
1456 | "Patsy is a Python package for describing statistical models and for | |
1457 | building design matrices.") | |
1458 | ;; The majority of the code is distributed under BSD-2. The module | |
1459 | ;; patsy.compat contains code derived from the Python standard library, | |
1460 | ;; and is covered by the PSFL. | |
5c31f4aa | 1461 | (license (list license:bsd-2 license:psfl)))) |
9bc08aa0 RW |
1462 | |
1463 | (define-public python2-patsy | |
5c31f4aa | 1464 | (package-with-python2 python-patsy)) |
37fdba7e RW |
1465 | |
1466 | (define-public python-statsmodels | |
1467 | (package | |
1468 | (name "python-statsmodels") | |
1469 | (version "0.6.1") | |
1470 | (source | |
1471 | (origin | |
1472 | (method url-fetch) | |
1473 | (uri (string-append "https://pypi.python.org/packages/source/" | |
1474 | "s/statsmodels/statsmodels-" version ".tar.gz")) | |
1475 | (sha256 | |
1476 | (base32 | |
8b52167e RW |
1477 | "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy")) |
1478 | (patches (search-patches "python-statsmodels-fix-tests.patch")))) | |
37fdba7e RW |
1479 | (build-system python-build-system) |
1480 | (arguments | |
1481 | `(#:phases | |
1482 | (modify-phases %standard-phases | |
1483 | ;; tests must be run after installation | |
1484 | (delete 'check) | |
1485 | (add-after 'unpack 'set-matplotlib-backend-to-agg | |
1486 | (lambda _ | |
1487 | ;; Set the matplotlib backend to Agg to avoid problems using the | |
1488 | ;; GTK backend without a display. | |
1489 | (substitute* (find-files "statsmodels/graphics/tests" "\\.py") | |
1490 | (("import matplotlib\\.pyplot as plt" line) | |
1491 | (string-append "import matplotlib;matplotlib.use('Agg');" | |
1492 | line))) | |
1493 | #t)) | |
1494 | (add-after 'install 'check | |
25b2c47d HG |
1495 | (lambda* (#:key inputs outputs #:allow-other-keys) |
1496 | ;; Make installed package available for running the tests | |
1497 | (add-installed-pythonpath inputs outputs) | |
1498 | (with-directory-excursion "/tmp" | |
1499 | (zero? (system* "nosetests" | |
1500 | "--stop" | |
1501 | "-v" "statsmodels")))))))) | |
37fdba7e RW |
1502 | (propagated-inputs |
1503 | `(("python-numpy" ,python-numpy) | |
1504 | ("python-scipy" ,python-scipy) | |
1505 | ("python-pandas" ,python-pandas) | |
1506 | ("python-patsy" ,python-patsy) | |
1507 | ("python-matplotlib" ,python-matplotlib))) | |
1508 | (native-inputs | |
1509 | `(("python-cython" ,python-cython) | |
1510 | ("python-nose" ,python-nose) | |
1511 | ("python-sphinx" ,python-sphinx))) | |
1512 | (home-page "http://statsmodels.sourceforge.net/") | |
1513 | (synopsis "Statistical modeling and econometrics in Python") | |
1514 | (description | |
1515 | "Statsmodels is a Python package that provides a complement to scipy for | |
1516 | statistical computations including descriptive statistics and estimation and | |
1517 | inference for statistical models.") | |
1518 | (license license:bsd-3))) | |
1519 | ||
1520 | (define-public python2-statsmodels | |
1521 | (let ((stats (package-with-python2 python-statsmodels))) | |
1522 | (package (inherit stats) | |
1523 | (propagated-inputs | |
8b52167e RW |
1524 | `(("python2-pytz" ,python2-pytz) |
1525 | ("python2-numpy" ,python2-numpy) | |
37fdba7e RW |
1526 | ("python2-scipy" ,python2-scipy) |
1527 | ("python2-pandas" ,python2-pandas) | |
1528 | ("python2-patsy" ,python2-patsy) | |
00e10c6e | 1529 | ("python2-matplotlib" ,python2-matplotlib)))))) |
67a167fd | 1530 | |
82047474 RJ |
1531 | (define-public r-coda |
1532 | (package | |
1533 | (name "r-coda") | |
1534 | (version "0.18-1") | |
1535 | (source (origin | |
1536 | (method url-fetch) | |
1537 | (uri (cran-uri "coda" version)) | |
1538 | (sha256 | |
1539 | (base32 | |
1540 | "03sc780734zj2kqcm8lkyvf76fql0jbfhkblpn8l58zmb6cqi958")))) | |
1541 | (build-system r-build-system) | |
1542 | (propagated-inputs | |
1543 | `(("r-lattice" ,r-lattice))) | |
1544 | (home-page "http://cran.r-project.org/web/packages/coda") | |
1545 | (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") | |
1546 | (description "This package provides functions for summarizing and plotting | |
1547 | the output from Markov Chain Monte Carlo (MCMC) simulations, as well as | |
1548 | diagnostic tests of convergence to the equilibrium distribution of the Markov | |
1549 | chain.") | |
1550 | (license license:gpl2+))) | |
1551 | ||
fdd0f7b2 RW |
1552 | (define-public r-ade4 |
1553 | (package | |
1554 | (name "r-ade4") | |
1555 | (version "1.7-4") | |
1556 | (source | |
1557 | (origin | |
1558 | (method url-fetch) | |
1559 | (uri (cran-uri "ade4" version)) | |
1560 | (sha256 | |
1561 | (base32 | |
1562 | "17sbicash7z4b63dlrbaf8xx2pbwh62vykzvhdjs43h8jkl881y7")))) | |
1563 | (build-system r-build-system) | |
1564 | (home-page "http://pbil.univ-lyon1.fr/ADE-4") | |
1565 | (synopsis "Multivariate data analysis and graphical display") | |
1566 | (description | |
1567 | "The ade4 package contains data analysis functions to analyze ecological | |
1568 | and environmental data in the framework of Euclidean exploratory methods.") | |
1569 | (license license:gpl2+))) | |
1570 | ||
67a167fd RW |
1571 | (define-public r-xml2 |
1572 | (package | |
1573 | (name "r-xml2") | |
e2ad0228 | 1574 | (version "1.0.0") |
67a167fd RW |
1575 | (source |
1576 | (origin | |
1577 | (method url-fetch) | |
1578 | (uri (cran-uri "xml2" version)) | |
1579 | (sha256 | |
1580 | (base32 | |
e2ad0228 | 1581 | "0f2alsrk3yykznbhnz4pcsg9mb72cv607vbapqx5kqfv39772kgr")))) |
67a167fd RW |
1582 | (build-system r-build-system) |
1583 | (inputs | |
1584 | `(("libxml2" ,libxml2))) | |
1585 | (propagated-inputs | |
1586 | `(("r-rcpp" ,r-rcpp) | |
1587 | ("r-bh" ,r-bh))) | |
1588 | (home-page "https://github.com/hadley/xml2") | |
1589 | (synopsis "Parse XML with R") | |
1590 | (description | |
1591 | "This package provides a simple, consistent interface to working with XML | |
1592 | files in R. It is built on top of the libxml2 C library.") | |
1593 | (license license:gpl2+))) | |
6140747f | 1594 | |
9003957e RW |
1595 | (define-public r-multitaper |
1596 | (package | |
1597 | (name "r-multitaper") | |
03306201 | 1598 | (version "1.0-12") |
9003957e RW |
1599 | (source |
1600 | (origin | |
1601 | (method url-fetch) | |
1602 | (uri (cran-uri "multitaper" version)) | |
1603 | (sha256 | |
1604 | (base32 | |
03306201 | 1605 | "011qpkwpjclfc24y2qqigmdnikqwdnanflfhihigh5b5k7qwgm5j")))) |
9003957e RW |
1606 | (build-system r-build-system) |
1607 | (native-inputs | |
1608 | `(("gfortran" ,gfortran))) | |
1609 | (home-page "http://github.com/wesleyburr/multitaper/") | |
1610 | (synopsis "Multitaper spectral analysis tools") | |
1611 | (description | |
1612 | "This package implements multitaper spectral estimation | |
1613 | techniques using prolate spheroidal sequences (Slepians) and sine | |
1614 | tapers for time series analysis. It includes an adaptive weighted | |
1615 | multitaper spectral estimate, a coherence estimate, Thomson's Harmonic | |
1616 | F-test, and complex demodulation. The Slepians sequences are | |
1617 | generated efficiently using a tridiagonal matrix solution, and | |
1618 | jackknifed confidence intervals are available for most estimates.") | |
1619 | (license license:gpl2+))) | |
1620 | ||
6140747f RW |
1621 | (define-public r-rversions |
1622 | (package | |
1623 | (name "r-rversions") | |
81147fe8 | 1624 | (version "1.0.3") |
6140747f RW |
1625 | (source (origin |
1626 | (method url-fetch) | |
1627 | (uri (cran-uri "rversions" version)) | |
1628 | (sha256 | |
1629 | (base32 | |
81147fe8 | 1630 | "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11")))) |
6140747f RW |
1631 | (build-system r-build-system) |
1632 | (propagated-inputs | |
1633 | `(("r-curl" ,r-curl) | |
1634 | ("r-xml2" ,r-xml2))) | |
1635 | (home-page "https://github.com/metacran/rversions") | |
1636 | (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") | |
1637 | (description | |
1638 | "This package provides functions to query the main R repository to find | |
1639 | the versions that @code{r-release} and @code{r-oldrel} refer to, and also all | |
1640 | previous R versions and their release dates.") | |
1641 | (license license:expat))) | |
1a77eccd RW |
1642 | |
1643 | (define-public r-whisker | |
1644 | (package | |
1645 | (name "r-whisker") | |
1646 | (version "0.3-2") | |
1647 | (source (origin | |
1648 | (method url-fetch) | |
1649 | (uri (cran-uri "whisker" version)) | |
1650 | (sha256 | |
1651 | (base32 | |
1652 | "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28")))) | |
1653 | (build-system r-build-system) | |
1654 | (home-page "http://github.com/edwindj/whisker") | |
1655 | (synopsis "Logicless mustache templating for R") | |
1656 | (description | |
1657 | "This package provides logicless templating, with a syntax that is not | |
1658 | limited to R.") | |
1659 | (license license:gpl3+))) | |
13d083af | 1660 | |
0d90462f RW |
1661 | (define-public r-backports |
1662 | (package | |
1663 | (name "r-backports") | |
41bc22a7 | 1664 | (version "1.0.4") |
0d90462f RW |
1665 | (source |
1666 | (origin | |
1667 | (method url-fetch) | |
1668 | (uri (cran-uri "backports" version)) | |
1669 | (sha256 | |
1670 | (base32 | |
41bc22a7 | 1671 | "0fssh5rnnvpp8wm0ml9gk765idwrgj07xyxpkhpidl9zwydxzif2")))) |
0d90462f RW |
1672 | (build-system r-build-system) |
1673 | (home-page "http://cran.r-project.org/web/packages/backports") | |
1674 | (synopsis "Reimplementations of functions introduced since R 3.0.0") | |
1675 | (description | |
1676 | "Provides implementations of functions which have been introduced in R | |
1677 | since version 3.0.0. The backports are conditionally exported which results | |
1678 | in R resolving the function names to the version shipped with R (if available) | |
1679 | and uses the implemented backports as fallback. This way package developers | |
1680 | can make use of the new functions without worrying about the minimum required | |
1681 | R version.") | |
1682 | (license license:gpl2+))) | |
1683 | ||
929d4aae RW |
1684 | (define-public r-checkmate |
1685 | (package | |
1686 | (name "r-checkmate") | |
fbe5161c | 1687 | (version "1.8.2") |
929d4aae RW |
1688 | (source |
1689 | (origin | |
1690 | (method url-fetch) | |
1691 | (uri (cran-uri "checkmate" version)) | |
1692 | (sha256 | |
1693 | (base32 | |
fbe5161c | 1694 | "1zqcggl9m7slvc0q6zyhssdypb7jzf3l9byl5vxh1qdwjiw2y64g")))) |
929d4aae RW |
1695 | (build-system r-build-system) |
1696 | (propagated-inputs | |
1697 | `(("r-backports" ,r-backports))) | |
1698 | (home-page "https://github.com/mllg/checkmate") | |
1699 | (synopsis "Fast and versatile argument checks") | |
1700 | (description | |
1701 | "This package provides tests and assertions to perform frequent argument | |
1702 | checks. A substantial part of the package was written in C to minimize any | |
1703 | worries about execution time overhead.") | |
1704 | (license license:bsd-3))) | |
1705 | ||
cd26ec3b RW |
1706 | (define-public r-bbmisc |
1707 | (package | |
1708 | (name "r-bbmisc") | |
1709 | (version "1.10") | |
1710 | (source | |
1711 | (origin | |
1712 | (method url-fetch) | |
1713 | (uri (cran-uri "BBmisc" version)) | |
1714 | (sha256 | |
1715 | (base32 | |
1716 | "0cw2mhw7qhdrx91zzd5iwyh7ch9fy4wxga8j63731q6sxr1airjl")))) | |
1717 | (properties `((upstream-name . "BBmisc"))) | |
1718 | (build-system r-build-system) | |
1719 | (propagated-inputs | |
1720 | `(("r-checkmate" ,r-checkmate))) | |
1721 | (home-page "https://github.com/berndbischl/BBmisc") | |
1722 | (synopsis "Miscellaneous functions for R package development") | |
1723 | (description | |
1724 | "This package provides miscellaneous helper functions for the development | |
1725 | of R packages.") | |
1726 | (license license:bsd-3))) | |
1727 | ||
dc4fb16d RW |
1728 | (define-public r-fail |
1729 | (package | |
1730 | (name "r-fail") | |
1731 | (version "1.3") | |
1732 | (source | |
1733 | (origin | |
1734 | (method url-fetch) | |
1735 | (uri (cran-uri "fail" version)) | |
1736 | (sha256 | |
1737 | (base32 | |
1738 | "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d")))) | |
1739 | (build-system r-build-system) | |
1740 | (propagated-inputs | |
1741 | `(("r-bbmisc" ,r-bbmisc) | |
1742 | ("r-checkmate" ,r-checkmate))) | |
1743 | (home-page "https://github.com/mllg/fail") | |
1744 | (synopsis "File abstraction interface layer (FAIL)") | |
1745 | (description | |
1746 | "This package provides a more comfortable interface to work with R data | |
1747 | or source files in a key-value fashion.") | |
1748 | (license license:bsd-3))) | |
1749 | ||
9e330278 RW |
1750 | (define-public r-batchjobs |
1751 | (package | |
1752 | (name "r-batchjobs") | |
1753 | (version "1.6") | |
1754 | (source | |
1755 | (origin | |
1756 | (method url-fetch) | |
1757 | (uri (cran-uri "BatchJobs" version)) | |
1758 | (sha256 | |
1759 | (base32 | |
1760 | "1kb99024jih5bycc226bl4jyvbbl1sg72q3m2wnlshl7s8p6vva0")))) | |
1761 | (properties `((upstream-name . "BatchJobs"))) | |
1762 | (build-system r-build-system) | |
1763 | (propagated-inputs | |
1764 | `(("r-bbmisc" ,r-bbmisc) | |
1765 | ("r-brew" ,r-brew) | |
1766 | ("r-checkmate" ,r-checkmate) | |
1767 | ("r-dbi" ,r-dbi) | |
1768 | ("r-digest" ,r-digest) | |
1769 | ("r-fail" ,r-fail) | |
1770 | ("r-rsqlite" ,r-rsqlite) | |
1771 | ("r-sendmailr" ,r-sendmailr) | |
1772 | ("r-stringr" ,r-stringr))) | |
1773 | (home-page "https://github.com/tudo-r/BatchJobs") | |
1774 | (synopsis "Batch computing with R") | |
1775 | (description | |
1776 | "This package provides @code{Map}, @code{Reduce} and @code{Filter} | |
1777 | variants to generate jobs on batch computing systems like PBS/Torque, LSF, | |
1778 | SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") | |
1779 | (license license:bsd-2))) | |
1780 | ||
13d083af RW |
1781 | (define-public r-brew |
1782 | (package | |
1783 | (name "r-brew") | |
1784 | (version "1.0-6") | |
1785 | (source (origin | |
1786 | (method url-fetch) | |
1787 | (uri (cran-uri "brew" version)) | |
1788 | (sha256 | |
1789 | (base32 | |
1790 | "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp")))) | |
1791 | (build-system r-build-system) | |
1792 | (home-page "http://cran.r-project.org/web/packages/brew") | |
1793 | (synopsis "Templating framework for report generation") | |
1794 | (description | |
1795 | "The brew package implements a templating framework for mixing text and R | |
1796 | code for report generation. The template syntax is similar to PHP, Ruby's erb | |
1797 | module, Java Server Pages, and Python's psp module.") | |
1798 | (license license:gpl2+))) | |
167c9882 RW |
1799 | |
1800 | (define-public r-roxygen2 | |
1801 | (package | |
1802 | (name "r-roxygen2") | |
904fa49d | 1803 | (version "5.0.1") |
167c9882 RW |
1804 | (source (origin |
1805 | (method url-fetch) | |
1806 | (uri (cran-uri "roxygen2" version)) | |
1807 | (sha256 | |
1808 | (base32 | |
904fa49d | 1809 | "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz")))) |
167c9882 RW |
1810 | (build-system r-build-system) |
1811 | (propagated-inputs | |
1812 | `(("r-brew" ,r-brew) | |
1813 | ("r-digest" ,r-digest) | |
1814 | ("r-rcpp" ,r-rcpp) | |
1815 | ("r-stringi" ,r-stringi) | |
1816 | ("r-stringr" ,r-stringr))) | |
1817 | (home-page "https://github.com/klutometis/roxygen") | |
1818 | (synopsis "In-source documentation system for R") | |
1819 | (description | |
1820 | "Roxygen2 is a Doxygen-like in-source documentation system for Rd, | |
1821 | collation, and NAMESPACE files.") | |
1822 | (license license:gpl2+))) | |
681e03c1 | 1823 | |
c26c0628 RW |
1824 | (define-public r-openssl |
1825 | (package | |
1826 | (name "r-openssl") | |
f8909816 | 1827 | (version "0.9.5") |
c26c0628 RW |
1828 | (source |
1829 | (origin | |
1830 | (method url-fetch) | |
1831 | (uri (cran-uri "openssl" version)) | |
1832 | (sha256 | |
1833 | (base32 | |
f8909816 | 1834 | "1lal8mmcwjhhln10mfi96ipv3d364k0wiviiln220wvhddcpr9pp")))) |
c26c0628 RW |
1835 | (build-system r-build-system) |
1836 | (inputs | |
1837 | `(("openssl" ,openssl))) | |
1838 | (home-page "https://github.com/jeroenooms/openssl") | |
1839 | (synopsis "Toolkit for encryption, signatures and certificates") | |
1840 | (description | |
1841 | "This package provides R bindings to OpenSSL libssl and libcrypto, plus | |
1842 | custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 | |
1843 | and P-521. Cryptographic signatures can either be created and verified | |
1844 | manually or via x509 certificates. AES block cipher is used in CBC mode for | |
1845 | symmetric encryption; RSA for asymmetric (public key) encryption. High-level | |
1846 | envelope functions combine RSA and AES for encrypting arbitrary sized data. | |
1847 | Other utilities include key generators, hash functions (md5, sha1, sha256, | |
1848 | etc), base64 encoder, a secure random number generator, and @code{bignum} math | |
1849 | methods for manually performing crypto calculations on large multibyte | |
1850 | integers.") | |
1851 | (license license:expat))) | |
1852 | ||
681e03c1 RW |
1853 | (define-public r-httr |
1854 | (package | |
1855 | (name "r-httr") | |
e58498b6 | 1856 | (version "1.2.1") |
681e03c1 RW |
1857 | (source (origin |
1858 | (method url-fetch) | |
1859 | (uri (cran-uri "httr" version)) | |
1860 | (sha256 | |
1861 | (base32 | |
e58498b6 | 1862 | "03kkjlhyvvi5znwaxfm6cmdsg3q7ivwsvkzgabhjdj2jxs80pfg7")))) |
681e03c1 RW |
1863 | (build-system r-build-system) |
1864 | (propagated-inputs | |
1865 | `(("r-curl" ,r-curl) | |
1866 | ("r-digest" ,r-digest) | |
1867 | ("r-jsonlite" ,r-jsonlite) | |
59bf9f4e | 1868 | ("r-openssl" ,r-openssl) |
681e03c1 RW |
1869 | ("r-mime" ,r-mime) |
1870 | ("r-r6" ,r-r6) | |
1871 | ("r-stringr" ,r-stringr))) | |
1872 | (home-page "https://github.com/hadley/httr") | |
1873 | (synopsis "Tools for working with URLs and HTTP") | |
1874 | (description | |
1875 | "The aim of httr is to provide a wrapper for RCurl customised to the | |
1876 | demands of modern web APIs. It provides useful tools for working with HTTP | |
1877 | organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration | |
1878 | functions make it easy to control additional request components.") | |
1879 | (license license:expat))) | |
035711f1 RW |
1880 | |
1881 | (define-public r-git2r | |
1882 | (package | |
1883 | (name "r-git2r") | |
3624ad71 | 1884 | (version "0.15.0") |
035711f1 RW |
1885 | (source (origin |
1886 | (method url-fetch) | |
1887 | (uri (cran-uri "git2r" version)) | |
1888 | (sha256 | |
1889 | (base32 | |
3624ad71 | 1890 | "1rpdf85wy9fp456ypvbhl3p9whkb7kgl0n7rkqxd2bhvyzkvjak8")))) |
035711f1 RW |
1891 | (build-system r-build-system) |
1892 | ;; This R package contains modified sources of libgit2. This modified | |
1893 | ;; version of libgit2 is built as the package is built. Hence libgit2 is | |
1894 | ;; not among the inputs of this package. | |
1895 | (inputs | |
1896 | `(("libssh2" ,libssh2) | |
1897 | ("openssl" ,openssl) | |
1898 | ("zlib" ,zlib))) | |
1899 | (home-page "https://github.com/ropensci/git2r") | |
1900 | (synopsis "Access Git repositories with R") | |
1901 | (description | |
1902 | "This package provides an R interface to the libgit2 library, which is a | |
1903 | pure C implementation of the Git core methods.") | |
1904 | ;; GPLv2 only with linking exception. | |
1905 | (license license:gpl2))) | |
81a4228b RW |
1906 | |
1907 | (define-public r-rstudioapi | |
1908 | (package | |
1909 | (name "r-rstudioapi") | |
e2cfac44 | 1910 | (version "0.6") |
81a4228b RW |
1911 | (source (origin |
1912 | (method url-fetch) | |
1913 | (uri (cran-uri "rstudioapi" version)) | |
1914 | (sha256 | |
1915 | (base32 | |
e2cfac44 | 1916 | "1zkvz72z6nw0xc8bhb21y5x1nk6avijs0w8n4vsbvw9sn76wc96s")))) |
81a4228b RW |
1917 | (build-system r-build-system) |
1918 | (home-page "http://cran.r-project.org/web/packages/rstudioapi") | |
1919 | (synopsis "Safely access the RStudio API") | |
1920 | (description | |
1921 | "This package provides functions to access the RStudio API and provide | |
1922 | informative error messages when it's not available.") | |
1923 | (license license:expat))) | |
d6e21589 RW |
1924 | |
1925 | (define-public r-devtools | |
1926 | (package | |
1927 | (name "r-devtools") | |
3bb9708a | 1928 | (version "1.12.0") |
d6e21589 RW |
1929 | (source (origin |
1930 | (method url-fetch) | |
1931 | (uri (cran-uri "devtools" version)) | |
1932 | (sha256 | |
1933 | (base32 | |
3bb9708a | 1934 | "16l18szmj482vf3dvl2fqwwa4zaqylmic1pk7dwh428cp0d86mzi")))) |
d6e21589 RW |
1935 | (build-system r-build-system) |
1936 | (propagated-inputs | |
1937 | `(("r-curl" ,r-curl) | |
1938 | ("r-digest" ,r-digest) | |
1939 | ("r-evaluate" ,r-evaluate) | |
1940 | ("r-git2r" ,r-git2r) | |
1941 | ("r-httr" ,r-httr) | |
1942 | ("r-jsonlite" ,r-jsonlite) | |
1943 | ("r-memoise" ,r-memoise) | |
1944 | ("r-roxygen2" ,r-roxygen2) | |
1945 | ("r-rstudioapi" ,r-rstudioapi) | |
1946 | ("r-rversions" ,r-rversions) | |
fa9f0e6c RJ |
1947 | ("r-whisker" ,r-whisker) |
1948 | ("r-withr" ,r-withr))) | |
d6e21589 RW |
1949 | (home-page "https://github.com/hadley/devtools") |
1950 | (synopsis "Tools to make developing R packages easier") | |
1951 | (description "The devtools package is a collection of package development | |
1952 | tools to simplify the devolpment of R packages.") | |
1953 | (license license:gpl2+))) | |
03af370f | 1954 | |
a080e50c RJ |
1955 | (define-public r-withr |
1956 | (package | |
1957 | (name "r-withr") | |
348bb8d6 | 1958 | (version "1.0.2") |
a080e50c RJ |
1959 | (source (origin |
1960 | (method url-fetch) | |
1961 | (uri (cran-uri "withr" version)) | |
1962 | (sha256 | |
1963 | (base32 | |
348bb8d6 | 1964 | "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493")))) |
a080e50c RJ |
1965 | (build-system r-build-system) |
1966 | (home-page "https://github.com/jimhester/withr") | |
1967 | (synopsis "Run code with temporarily modified global state") | |
1968 | (description | |
1969 | "This package provides a set of functions to run R code in an environment | |
1970 | in which global state has been temporarily modified. Many of these functions | |
1971 | were originally a part of the r-devtools package.") | |
1972 | (license license:gpl2+))) | |
1973 | ||
b90314b4 RW |
1974 | (define-public r-hms |
1975 | (package | |
1976 | (name "r-hms") | |
1977 | (version "0.2") | |
1978 | (source | |
1979 | (origin | |
1980 | (method url-fetch) | |
1981 | (uri (cran-uri "hms" version)) | |
1982 | (sha256 | |
1983 | (base32 | |
1984 | "0ln1dc26mkl5pc26vvyf01d35x75q6cjaj39cccxp67chbwbdlds")))) | |
1985 | (build-system r-build-system) | |
1986 | (home-page "https://github.com/rstats-db/hms") | |
1987 | (synopsis "Pretty time of day") | |
1988 | (description | |
1989 | "This package implements an S3 class for storing and formatting | |
1990 | time-of-day values, based on the @code{difftime} class.") | |
1991 | (license license:gpl3+))) | |
1992 | ||
03af370f RW |
1993 | (define-public r-readr |
1994 | (package | |
1995 | (name "r-readr") | |
8c6e2b84 | 1996 | (version "1.0.0") |
03af370f RW |
1997 | (source (origin |
1998 | (method url-fetch) | |
1999 | (uri (cran-uri "readr" version)) | |
2000 | (sha256 | |
2001 | (base32 | |
8c6e2b84 | 2002 | "0xji0dbal6xcxnsmjj678fw29n7wrj45wrd5ng99yhqqijcm9f6g")))) |
03af370f RW |
2003 | (build-system r-build-system) |
2004 | (propagated-inputs | |
2005 | `(("r-curl" ,r-curl) | |
2006 | ("r-rcpp" ,r-rcpp) | |
8c6e2b84 RW |
2007 | ("r-hms" ,r-hms) |
2008 | ("r-tibble" ,r-tibble) | |
2009 | ("r-r6" ,r-r6) | |
03af370f RW |
2010 | ("r-bh" ,r-bh))) |
2011 | (home-page "https://github.com/hadley/readr") | |
2012 | (synopsis "Read tabular data") | |
2013 | (description | |
2014 | "This package provides functions to read flat or tabular text files from | |
2015 | disk (or a connection).") | |
2016 | (license license:gpl2+))) | |
60a9d3d0 RW |
2017 | |
2018 | (define-public r-plotrix | |
2019 | (package | |
2020 | (name "r-plotrix") | |
bdfc2c95 | 2021 | (version "3.6-3") |
60a9d3d0 RW |
2022 | (source (origin |
2023 | (method url-fetch) | |
2024 | (uri (cran-uri "plotrix" version)) | |
2025 | (sha256 | |
2026 | (base32 | |
bdfc2c95 | 2027 | "0h97jra8zqssi9j4i0psa6c7ya49ya8jd2qc18lc61a4s2yn8w91")))) |
60a9d3d0 RW |
2028 | (build-system r-build-system) |
2029 | (home-page "http://cran.r-project.org/web/packages/plotrix") | |
2030 | (synopsis "Various plotting functions") | |
2031 | (description | |
2032 | "This package provides lots of plotting, various labeling, axis and color | |
2033 | scaling functions for R.") | |
2034 | (license license:gpl2+))) | |
2a40f763 RW |
2035 | |
2036 | (define-public r-gridbase | |
2037 | (package | |
2038 | (name "r-gridbase") | |
2039 | (version "0.4-7") | |
2040 | (source (origin | |
2041 | (method url-fetch) | |
2042 | (uri (cran-uri "gridBase" version)) | |
2043 | (sha256 | |
2044 | (base32 | |
2045 | "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy")))) | |
2046 | (build-system r-build-system) | |
2047 | (home-page "http://cran.r-project.org/web/packages/gridBase") | |
2048 | (synopsis "Integration of base and grid graphics") | |
2049 | (description | |
2050 | "This package provides an integration of base and grid graphics for R.") | |
2051 | (license license:gpl2+))) | |
ca3476cd RW |
2052 | |
2053 | (define-public r-lattice | |
2054 | (package | |
2055 | (name "r-lattice") | |
fce4dfd8 | 2056 | (version "0.20-34") |
ca3476cd RW |
2057 | (source (origin |
2058 | (method url-fetch) | |
2059 | (uri (cran-uri "lattice" version)) | |
2060 | (sha256 | |
2061 | (base32 | |
fce4dfd8 | 2062 | "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) |
ca3476cd RW |
2063 | (build-system r-build-system) |
2064 | (home-page "http://lattice.r-forge.r-project.org/") | |
2065 | (synopsis "High-level data visualization system") | |
2066 | (description | |
2067 | "The lattice package provides a powerful and elegant high-level data | |
2068 | visualization system inspired by Trellis graphics, with an emphasis on | |
2069 | multivariate data. Lattice is sufficient for typical graphics needs, and is | |
2070 | also flexible enough to handle most nonstandard requirements.") | |
2071 | (license license:gpl2+))) | |
e22d4ca4 | 2072 | |
b20abbcd RW |
2073 | (define-public r-latticeextra |
2074 | (package | |
2075 | (name "r-latticeextra") | |
2076 | (version "0.6-28") | |
2077 | (source | |
2078 | (origin | |
2079 | (method url-fetch) | |
2080 | (uri (cran-uri "latticeExtra" version)) | |
2081 | (sha256 | |
2082 | (base32 | |
2083 | "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq")))) | |
2084 | (properties `((upstream-name . "latticeExtra"))) | |
2085 | (build-system r-build-system) | |
2086 | (propagated-inputs | |
2087 | `(("r-lattice" ,r-lattice) | |
2088 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
2089 | (home-page "http://latticeextra.r-forge.r-project.org/") | |
2090 | (synopsis "Extra graphical utilities based on lattice") | |
2091 | (description | |
2092 | "Building on the infrastructure provided by the lattice package, this | |
2093 | package provides several new high-level graphics functions and methods, as | |
2094 | well as additional utilities such as panel and axis annotation functions.") | |
2095 | (license license:gpl2+))) | |
2096 | ||
e22d4ca4 RW |
2097 | (define-public r-rcpparmadillo |
2098 | (package | |
2099 | (name "r-rcpparmadillo") | |
062737a1 | 2100 | (version "0.7.500.0.0") |
e22d4ca4 RW |
2101 | (source (origin |
2102 | (method url-fetch) | |
2103 | (uri (cran-uri "RcppArmadillo" version)) | |
2104 | (sha256 | |
2105 | (base32 | |
062737a1 | 2106 | "06qb6877c5qd8lvnc4b27z8fwb5r5pyylkj0g6kj1rn868zkh5ps")) |
e22d4ca4 RW |
2107 | (modules '((guix build utils))) |
2108 | ;; Remove bundled armadillo sources | |
2109 | (snippet | |
2110 | '(begin | |
2111 | (delete-file-recursively "inst/include/armadillo_bits") | |
2112 | (delete-file "inst/include/armadillo"))))) | |
2113 | (properties `((upstream-name . "RcppArmadillo"))) | |
2114 | (build-system r-build-system) | |
2115 | (arguments | |
2116 | `(#:phases | |
2117 | (modify-phases %standard-phases | |
2118 | (add-after 'unpack 'link-against-armadillo | |
2119 | (lambda _ | |
2120 | (substitute* "src/Makevars" | |
2121 | (("PKG_LIBS=" prefix) | |
2122 | (string-append prefix "-larmadillo")))))))) | |
2123 | (propagated-inputs | |
2124 | `(("r-rcpp" ,r-rcpp) | |
2125 | ("armadillo" ,armadillo-for-rcpparmadillo))) | |
2126 | (home-page "https://github.com/RcppCore/RcppArmadillo") | |
2127 | (synopsis "Rcpp integration for the Armadillo linear algebra library") | |
2128 | (description | |
2129 | "Armadillo is a templated C++ linear algebra library that aims towards a | |
2130 | good balance between speed and ease of use. Integer, floating point and | |
2131 | complex numbers are supported, as well as a subset of trigonometric and | |
2132 | statistics functions. Various matrix decompositions are provided through | |
2133 | optional integration with LAPACK and ATLAS libraries. This package includes | |
2134 | the header files from the templated Armadillo library.") | |
2135 | ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp | |
2136 | ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or | |
2137 | ;; later, as is the rest of 'Rcpp'. | |
2138 | (license license:gpl2+))) | |
bb6d2dad RW |
2139 | |
2140 | (define-public r-bitops | |
2141 | (package | |
2142 | (name "r-bitops") | |
2143 | (version "1.0-6") | |
2144 | (source (origin | |
2145 | (method url-fetch) | |
2146 | (uri (cran-uri "bitops" version)) | |
2147 | (sha256 | |
2148 | (base32 | |
2149 | "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv")))) | |
2150 | (build-system r-build-system) | |
2151 | (home-page "http://cran.r-project.org/web/packages/bitops") | |
2152 | (synopsis "Bitwise operations") | |
2153 | (description | |
2154 | "This package provides functions for bitwise operations on integer | |
2155 | vectors.") | |
2156 | (license license:gpl2+))) | |
4c1f2705 RW |
2157 | |
2158 | (define-public r-catools | |
2159 | (package | |
2160 | (name "r-catools") | |
2161 | (version "1.17.1") | |
2162 | (source (origin | |
2163 | (method url-fetch) | |
2164 | (uri (cran-uri "caTools" version)) | |
2165 | (sha256 | |
2166 | (base32 | |
2167 | "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank")))) | |
2168 | (properties `((upstream-name . "caTools"))) | |
2169 | (build-system r-build-system) | |
2170 | (propagated-inputs | |
2171 | `(("r-bitops" ,r-bitops))) | |
2172 | (home-page "http://cran.r-project.org/web/packages/caTools") | |
2173 | (synopsis "Various tools including functions for moving window statistics") | |
2174 | (description | |
2175 | "This package contains several basic utility functions including: | |
2176 | moving (rolling, running) window statistic functions, read/write for GIF and | |
2177 | ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 | |
2178 | encoder/decoder, round-off-error-free sum and cumsum, etc.") | |
2179 | (license license:gpl3+))) | |
77bdb276 RW |
2180 | |
2181 | (define-public r-rmarkdown | |
2182 | (package | |
2183 | (name "r-rmarkdown") | |
8e1369f1 | 2184 | (version "1.1") |
77bdb276 RW |
2185 | (source |
2186 | (origin | |
2187 | (method url-fetch) | |
2188 | (uri (cran-uri "rmarkdown" version)) | |
2189 | (sha256 | |
2190 | (base32 | |
8e1369f1 | 2191 | "1czvkaz1ji3jyj6qrvbswisqs9d05ljqc4vjkfdrf6hygix7azd0")))) |
77bdb276 RW |
2192 | (properties `((upstream-name . "rmarkdown"))) |
2193 | (build-system r-build-system) | |
2194 | (propagated-inputs | |
2195 | `(("r-catools" ,r-catools) | |
8e1369f1 RW |
2196 | ("r-evaluate" ,r-evaluate) |
2197 | ("r-tibble" ,r-tibble) | |
77bdb276 | 2198 | ("r-htmltools" ,r-htmltools) |
87a7c55e RW |
2199 | ("r-jsonlite" ,r-jsonlite) |
2200 | ("r-base64enc" ,r-base64enc) | |
77bdb276 RW |
2201 | ("r-knitr" ,r-knitr) |
2202 | ("r-yaml" ,r-yaml) | |
2203 | ("ghc-pandoc" ,ghc-pandoc))) | |
2204 | (home-page "http://rmarkdown.rstudio.com") | |
2205 | (synopsis "Convert R Markdown documents into a variety of formats") | |
2206 | (description | |
2207 | "This package provides tools to convert R Markdown documents into a | |
2208 | variety of formats.") | |
2209 | (license license:gpl3+))) | |
b73751c8 RW |
2210 | |
2211 | (define-public r-gtable | |
2212 | (package | |
2213 | (name "r-gtable") | |
810e4195 | 2214 | (version "0.2.0") |
b73751c8 RW |
2215 | (source (origin |
2216 | (method url-fetch) | |
2217 | (uri (cran-uri "gtable" version)) | |
2218 | (sha256 | |
2219 | (base32 | |
810e4195 | 2220 | "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0")))) |
b73751c8 RW |
2221 | (properties `((upstream-name . "gtable"))) |
2222 | (build-system r-build-system) | |
2223 | (home-page "http://cran.r-project.org/web/packages/gtable") | |
2224 | (synopsis "Arrange grobs in tables") | |
2225 | (description | |
2226 | "This package provides tools to make it easier to work with tables of | |
2227 | grobs.") | |
2228 | (license license:gpl2+))) | |
9e47f30b RW |
2229 | |
2230 | (define-public r-gridextra | |
2231 | (package | |
2232 | (name "r-gridextra") | |
1647e10e | 2233 | (version "2.2.1") |
9e47f30b RW |
2234 | (source (origin |
2235 | (method url-fetch) | |
2236 | (uri (cran-uri "gridExtra" version)) | |
2237 | (sha256 | |
2238 | (base32 | |
1647e10e | 2239 | "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4")))) |
9e47f30b RW |
2240 | (properties `((upstream-name . "gridExtra"))) |
2241 | (build-system r-build-system) | |
2242 | (propagated-inputs | |
2243 | `(("r-gtable" ,r-gtable))) | |
2244 | (native-inputs | |
2245 | `(("r-knitr" ,r-knitr))) ;for building vignettes | |
2246 | (home-page "https://github.com/baptiste/gridextra") | |
2247 | (synopsis "Miscellaneous functions for \"Grid\" graphics") | |
2248 | (description | |
2249 | "This package provides a number of user-level functions to work with | |
2250 | @code{grid} graphics, notably to arrange multiple grid-based plots on a page, | |
2251 | and draw tables.") | |
2252 | (license license:gpl2+))) | |
2253 | ||
21e4d6a9 RW |
2254 | (define-public r-rsqlite |
2255 | (package | |
2256 | (name "r-rsqlite") | |
2257 | (version "1.0.0") | |
2258 | (source (origin | |
2259 | (method url-fetch) | |
2260 | (uri (cran-uri "RSQLite" version)) | |
2261 | (sha256 | |
2262 | (base32 | |
2263 | "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f")))) | |
2264 | (properties `((upstream-name . "RSQLite"))) | |
2265 | (build-system r-build-system) | |
2266 | (propagated-inputs | |
2267 | `(("r-dbi" ,r-dbi))) | |
2268 | (home-page "https://github.com/rstats-db/RSQLite") | |
2269 | (synopsis "SQLite interface for R") | |
2270 | (description | |
2271 | "This package embeds the SQLite database engine in R and provides an | |
2272 | interface compliant with the DBI package. The source for the SQLite | |
2273 | engine (version 3.8.6) is included.") | |
2274 | (license license:lgpl2.0+))) | |
2275 | ||
cefaa79c RW |
2276 | (define-public r-rcurl |
2277 | (package | |
2278 | (name "r-rcurl") | |
2279 | (version "1.95-0.1.2") | |
2280 | (source (origin | |
2281 | (method url-fetch) | |
2282 | (uri (string-append "http://www.bioconductor.org/packages/" | |
2283 | "release/extra/src/" | |
2284 | "contrib/RCurl_" version ".tar.gz")) | |
2285 | (sha256 | |
2286 | (base32 | |
2287 | "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc")))) | |
2288 | (properties `((upstream-name . "RCurl"))) | |
2289 | (build-system r-build-system) | |
2290 | (inputs | |
2291 | `(("libcurl" ,curl))) | |
2292 | (propagated-inputs | |
2293 | `(("r-bitops" ,r-bitops))) | |
2294 | (home-page "http://www.omegahat.org/RCurl") | |
2295 | (synopsis "General network client interface for R") | |
2296 | (description | |
2297 | "The package allows one to compose general HTTP requests and provides | |
2298 | convenient functions to fetch URIs, GET and POST forms, etc. and process the | |
2299 | results returned by the Web server. This provides a great deal of control | |
2300 | over the HTTP/FTP/... connection and the form of the request while providing a | |
2301 | higher-level interface than is available just using R socket connections. | |
2302 | Additionally, the underlying implementation is robust and extensive, | |
2303 | supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, | |
2304 | ldap, and also supports cookies, redirects, authentication, etc.") | |
2305 | (license license:bsd-3))) | |
2306 | ||
543ded36 RW |
2307 | (define-public r-xml |
2308 | (package | |
2309 | (name "r-xml") | |
1e4abc0f | 2310 | (version "3.98-1.4") |
543ded36 RW |
2311 | (source (origin |
2312 | (method url-fetch) | |
2313 | (uri (cran-uri "XML" version)) | |
2314 | (sha256 | |
2315 | (base32 | |
1e4abc0f | 2316 | "09hiy5a875v2fhsgrsfymrwccn9249wnnsr6ck2slrig65svq2lw")))) |
543ded36 RW |
2317 | (properties |
2318 | `((upstream-name . "XML"))) | |
2319 | (build-system r-build-system) | |
2320 | (inputs | |
2321 | `(("libxml2" ,libxml2))) | |
2322 | (propagated-inputs | |
2323 | `(("r-rcurl" ,r-rcurl))) | |
2324 | (home-page "http://www.omegahat.org/RSXML") | |
2325 | (synopsis "Tools for parsing and generating XML within R") | |
2326 | (description | |
2327 | "Many approaches for both reading and creating XML (and HTML) | |
2328 | documents (including DTDs), both local and accessible via HTTP or FTP. Also | |
2329 | offers access to an XPath \"interpreter\".") | |
2330 | (license license:bsd-2))) | |
2331 | ||
b74f64a9 RW |
2332 | (define-public r-xnomial |
2333 | (package | |
2334 | (name "r-xnomial") | |
2335 | (version "1.0.4") | |
2336 | (source | |
2337 | (origin (method url-fetch) | |
2338 | (uri (cran-uri "XNomial" version)) | |
2339 | (sha256 | |
2340 | (base32 | |
2341 | "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6")))) | |
2342 | (properties (quasiquote ((upstream-name . "XNomial")))) | |
2343 | (build-system r-build-system) | |
2344 | (home-page "http://cran.r-project.org/web/packages/XNomial") | |
2345 | (synopsis "Goodness-of-Fit test for multinomial data") | |
2346 | (description | |
2347 | "This package provides an exact Goodness-of-Fit test for | |
2348 | multinomial data with fixed probabilities. It can be used to | |
2349 | determine whether a set of counts fits a given expected ratio. To see | |
2350 | whether a set of observed counts fits an expectation, one can examine | |
2351 | all possible outcomes with @code{xmulti()} or a random sample of them | |
2352 | with @code{xmonte()} and find the probability of an observation | |
2353 | deviating from the expectation by at least as much as the observed. | |
2354 | As a measure of deviation from the expected, one can use the | |
2355 | log-likelihood ratio, the multinomial probability, or the classic | |
2356 | chi-square statistic. A histogram of the test statistic can also be | |
2357 | plotted and compared with the asymptotic curve.") | |
2358 | (license (list license:gpl2+ license:gpl3+)))) | |
2359 | ||
ca65d387 RW |
2360 | (define-public r-lambda-r |
2361 | (package | |
2362 | (name "r-lambda-r") | |
b9ab3b08 | 2363 | (version "1.1.9") |
ca65d387 RW |
2364 | (source (origin |
2365 | (method url-fetch) | |
2366 | (uri (cran-uri "lambda.r" version)) | |
2367 | (sha256 | |
2368 | (base32 | |
b9ab3b08 | 2369 | "1j6287iqvs3ill6r5g6ksf5809qp0l0nf20ib8266m1r09lc9j14")))) |
ca65d387 RW |
2370 | (properties `((upstream-name . "lambda.r"))) |
2371 | (build-system r-build-system) | |
2372 | (home-page "http://cran.r-project.org/web/packages/lambda.r") | |
2373 | (synopsis "Functional programming extension for R") | |
2374 | (description | |
2375 | "This package provides a language extension to efficiently write | |
2376 | functional programs in R. Syntax extensions include multi-part function | |
2377 | definitions, pattern matching, guard statements, built-in (optional) type | |
2378 | safety.") | |
2379 | (license license:lgpl3+))) | |
2380 | ||
b9ff33b5 RW |
2381 | (define-public r-futile-options |
2382 | (package | |
2383 | (name "r-futile-options") | |
2384 | (version "1.0.0") | |
2385 | (source (origin | |
2386 | (method url-fetch) | |
2387 | (uri (cran-uri "futile.options" version)) | |
2388 | (sha256 | |
2389 | (base32 | |
2390 | "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f")))) | |
2391 | (properties | |
2392 | `((upstream-name . "futile.options"))) | |
2393 | (build-system r-build-system) | |
2394 | (home-page "http://cran.r-project.org/web/packages/futile.options") | |
2395 | (synopsis "Options management framework") | |
2396 | (description | |
2397 | "The futile.options subsystem provides an easy user-defined options | |
2398 | management system that is properly scoped. This means that options created | |
2399 | via @code{futile.options} are fully self-contained and will not collide with | |
2400 | options defined in other packages.") | |
2401 | (license license:lgpl3+))) | |
2402 | ||
6b82f56c RW |
2403 | (define-public r-futile-logger |
2404 | (package | |
2405 | (name "r-futile-logger") | |
27f10d3d | 2406 | (version "1.4.3") |
6b82f56c RW |
2407 | (source (origin |
2408 | (method url-fetch) | |
2409 | (uri (cran-uri "futile.logger" version)) | |
2410 | (sha256 | |
2411 | (base32 | |
27f10d3d | 2412 | "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy")))) |
6b82f56c RW |
2413 | (properties `((upstream-name . "futile.logger"))) |
2414 | (build-system r-build-system) | |
2415 | (propagated-inputs | |
2416 | `(("r-futile-options" ,r-futile-options) | |
2417 | ("r-lambda-r" ,r-lambda-r))) | |
2418 | (home-page "http://cran.r-project.org/web/packages/futile.logger") | |
2419 | (synopsis "Logging utility for R") | |
2420 | (description | |
2421 | "This package provides a simple yet powerful logging utility. Based | |
2422 | loosely on log4j, futile.logger takes advantage of R idioms to make logging a | |
2423 | convenient and easy to use replacement for @code{cat} and @code{print} | |
2424 | statements.") | |
2425 | (license license:lgpl3+))) | |
2426 | ||
3e4c0c66 RW |
2427 | (define-public r-segmented |
2428 | (package | |
2429 | (name "r-segmented") | |
2430 | (version "0.5-1.4") | |
2431 | (source | |
2432 | (origin | |
2433 | (method url-fetch) | |
2434 | (uri (cran-uri "segmented" version)) | |
2435 | (sha256 | |
2436 | (base32 | |
2437 | "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i")))) | |
2438 | (build-system r-build-system) | |
2439 | (home-page "http://cran.r-project.org/web/packages/segmented") | |
2440 | (synopsis "Regression models with breakpoints estimation") | |
2441 | (description | |
2442 | "Given a regression model, segmented updates the model by adding one or | |
2443 | more segmented (i.e., piecewise-linear) relationships. Several variables with | |
2444 | multiple breakpoints are allowed.") | |
2445 | (license (list license:gpl2+ license:gpl3+)))) | |
2446 | ||
bc899123 RW |
2447 | (define-public r-snow |
2448 | (package | |
2449 | (name "r-snow") | |
cf738e96 | 2450 | (version "0.4-2") |
bc899123 RW |
2451 | (source (origin |
2452 | (method url-fetch) | |
2453 | (uri (cran-uri "snow" version)) | |
2454 | (sha256 | |
2455 | (base32 | |
cf738e96 | 2456 | "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf")))) |
bc899123 RW |
2457 | (build-system r-build-system) |
2458 | (home-page "http://cran.r-project.org/web/packages/snow") | |
2459 | (synopsis "Support for simple parallel computing in R") | |
2460 | (description | |
2461 | "The snow package provides support for simple parallel computing on a | |
2462 | network of workstations using R. A master R process calls @code{makeCluster} | |
2463 | to start a cluster of worker processes; the master process then uses functions | |
2464 | such as @code{clusterCall} and @code{clusterApply} to execute R code on the | |
2465 | worker processes and collect and return the results on the master.") | |
2466 | (license (list license:gpl2+ license:gpl3+)))) | |
2467 | ||
d706257b RW |
2468 | (define-public r-sparsem |
2469 | (package | |
2470 | (name "r-sparsem") | |
7931531a | 2471 | (version "1.72") |
d706257b RW |
2472 | (source (origin |
2473 | (method url-fetch) | |
2474 | (uri (cran-uri "SparseM" version)) | |
2475 | (sha256 | |
2476 | (base32 | |
7931531a | 2477 | "0zpb1swn9xjkb22sky10ixff7vqfiz9m36nkbc1qqbm9frcldnka")))) |
d706257b RW |
2478 | (properties |
2479 | `((upstream-name . "SparseM"))) | |
d7786ce9 RW |
2480 | (inputs |
2481 | `(("gfortran" ,gfortran))) | |
d706257b RW |
2482 | (build-system r-build-system) |
2483 | (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") | |
2484 | (synopsis "Sparse linear algebra") | |
2485 | (description | |
2486 | "This package provides some basic linear algebra functionality for sparse | |
2487 | matrices. It includes Cholesky decomposition and backsolving as well as | |
2488 | standard R subsetting and Kronecker products.") | |
2489 | (license license:gpl2+))) | |
2490 | ||
264df1a4 RW |
2491 | (define-public r-iterators |
2492 | (package | |
2493 | (name "r-iterators") | |
2494 | (version "1.0.8") | |
2495 | (source | |
2496 | (origin | |
2497 | (method url-fetch) | |
2498 | (uri (cran-uri "iterators" version)) | |
2499 | (sha256 | |
2500 | (base32 | |
2501 | "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf")))) | |
2502 | (build-system r-build-system) | |
2503 | (home-page "http://cran.r-project.org/web/packages/iterators") | |
2504 | (synopsis "Iterator construct for R") | |
2505 | (description | |
2506 | "This package provides support for iterators, which allow a programmer to | |
2507 | traverse through all the elements of a vector, list, or other collection of | |
2508 | data.") | |
2509 | (license license:asl2.0))) | |
2510 | ||
7a6f5f03 RW |
2511 | (define-public r-codetools |
2512 | (package | |
2513 | (name "r-codetools") | |
4f2ebc16 | 2514 | (version "0.2-15") |
7a6f5f03 RW |
2515 | (source |
2516 | (origin | |
2517 | (method url-fetch) | |
2518 | (uri (cran-uri "codetools" version)) | |
2519 | (sha256 | |
2520 | (base32 | |
4f2ebc16 | 2521 | "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) |
7a6f5f03 RW |
2522 | (build-system r-build-system) |
2523 | (home-page "http://cran.r-project.org/web/packages/codetools") | |
2524 | (synopsis "Code analysis tools for R") | |
2525 | (description "This package provides code analysis tools for R to check R | |
2526 | code for possible problems.") | |
2527 | (license (list license:gpl2+ license:gpl3+)))) | |
2528 | ||
b2cdb027 RW |
2529 | (define-public r-foreach |
2530 | (package | |
2531 | (name "r-foreach") | |
2532 | (version "1.4.3") | |
2533 | (source | |
2534 | (origin | |
2535 | (method url-fetch) | |
2536 | (uri (cran-uri "foreach" version)) | |
2537 | (sha256 | |
2538 | (base32 | |
2539 | "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y")))) | |
2540 | (build-system r-build-system) | |
2541 | (propagated-inputs | |
2542 | `(("r-codetools" ,r-codetools) | |
2543 | ("r-iterators" ,r-iterators))) | |
2544 | (home-page "http://cran.r-project.org/web/packages/foreach") | |
2545 | (synopsis "Foreach looping construct for R") | |
2546 | (description | |
2547 | "This package provides support for the @code{foreach} looping construct. | |
2548 | @code{foreach} is an idiom that allows for iterating over elements in a | |
2549 | collection, without the use of an explicit loop counter. This package in | |
2550 | particular is intended to be used for its return value, rather than for its | |
2551 | side effects. In that sense, it is similar to the standard @code{lapply} | |
2552 | function, but doesn't require the evaluation of a function. Using | |
2553 | @code{foreach} without side effects also facilitates executing the loop in | |
2554 | parallel.") | |
2555 | (license license:asl2.0))) | |
2556 | ||
71cafa04 RW |
2557 | (define-public r-doparallel |
2558 | (package | |
2559 | (name "r-doparallel") | |
2560 | (version "1.0.10") | |
2561 | (source | |
2562 | (origin | |
2563 | (method url-fetch) | |
2564 | (uri (cran-uri "doParallel" version)) | |
2565 | (sha256 | |
2566 | (base32 | |
2567 | "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh")))) | |
2568 | (properties `((upstream-name . "doParallel"))) | |
2569 | (build-system r-build-system) | |
2570 | (propagated-inputs | |
2571 | `(("r-foreach" ,r-foreach) | |
2572 | ("r-iterators" ,r-iterators))) | |
2573 | (home-page "http://cran.r-project.org/web/packages/doParallel") | |
2574 | (synopsis "Foreach parallel adaptor for the 'parallel' package") | |
2575 | (description | |
2576 | "This package provides a parallel backend for the @code{%dopar%} function | |
2577 | using the parallel package.") | |
2578 | (license license:gpl2+))) | |
2579 | ||
66cf0f05 RW |
2580 | (define-public r-domc |
2581 | (package | |
2582 | (name "r-domc") | |
2583 | (version "1.3.4") | |
2584 | (source | |
2585 | (origin | |
2586 | (method url-fetch) | |
2587 | (uri (cran-uri "doMC" version)) | |
2588 | (sha256 | |
2589 | (base32 | |
2590 | "0y47jl6g4f83r14pj8bafdzq1phj7bxy5dwyz3k43d2rr8phk8bn")))) | |
2591 | (properties `((upstream-name . "doMC"))) | |
2592 | (build-system r-build-system) | |
2593 | (propagated-inputs | |
2594 | `(("r-foreach" ,r-foreach) | |
2595 | ("r-iterators" ,r-iterators))) | |
2596 | (home-page "http://cran.r-project.org/web/packages/doMC") | |
2597 | (synopsis "Foreach parallel adaptor for the 'parallel' package") | |
2598 | (description | |
2599 | "This package provides a parallel backend for the @code{%dopar%} function | |
2600 | using the multicore functionality of the parallel package.") | |
2601 | (license license:gpl2+))) | |
2602 | ||
a8227e4a RW |
2603 | (define-public r-dt |
2604 | (package | |
2605 | (name "r-dt") | |
f791b689 | 2606 | (version "0.2") |
a8227e4a RW |
2607 | (source (origin |
2608 | (method url-fetch) | |
2609 | (uri (cran-uri "DT" version)) | |
2610 | (sha256 | |
2611 | (base32 | |
f791b689 | 2612 | "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1")))) |
a8227e4a RW |
2613 | (properties |
2614 | `((upstream-name . "DT"))) | |
2615 | (build-system r-build-system) | |
2616 | (propagated-inputs | |
2617 | `(("r-htmltools" ,r-htmltools) | |
2618 | ("r-htmlwidgets" ,r-htmlwidgets) | |
2619 | ("r-magrittr" ,r-magrittr))) | |
2620 | (home-page "http://rstudio.github.io/DT") | |
2621 | (synopsis "R wrapper of the DataTables JavaScript library") | |
2622 | (description | |
2623 | "This package allows for data objects in R to be rendered as HTML tables | |
2624 | using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). | |
2625 | The 'DataTables' library has been included in this R package.") | |
2626 | ;; The DT package as a whole is distributed under GPLv3. The DT package | |
2627 | ;; inludes other software components under different licenses: | |
2628 | ;; | |
2629 | ;; * Expat: jQuery, jquery.highlight.js, DataTables | |
2630 | ;; * ASL2.0: selectize.js | |
2631 | ;; * WTFPL: noUiSlider | |
2632 | (license (list license:gpl3 | |
2633 | license:expat | |
2634 | license:asl2.0 | |
2635 | (license:non-copyleft "http://www.wtfpl.net/txt/copying/"))))) | |
2636 | ||
a69a5935 RW |
2637 | (define-public r-base64enc |
2638 | (package | |
2639 | (name "r-base64enc") | |
2640 | (version "0.1-3") | |
2641 | (source (origin | |
2642 | (method url-fetch) | |
2643 | (uri (cran-uri "base64enc" version)) | |
2644 | (sha256 | |
2645 | (base32 | |
2646 | "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd")))) | |
2647 | (build-system r-build-system) | |
2648 | (home-page "http://www.rforge.net/base64enc") | |
2649 | (synopsis "Tools for Base64 encoding") | |
2650 | (description | |
2651 | "This package provides tools for handling Base64 encoding. It is more | |
2652 | flexible than the orphaned \"base64\" package.") | |
2653 | (license license:gpl2+))) | |
2654 | ||
dada39aa RW |
2655 | (define-public r-irlba |
2656 | (package | |
2657 | (name "r-irlba") | |
89242ea4 | 2658 | (version "2.1.2") |
dada39aa RW |
2659 | (source |
2660 | (origin | |
2661 | (method url-fetch) | |
2662 | (uri (cran-uri "irlba" version)) | |
2663 | (sha256 | |
2664 | (base32 | |
89242ea4 | 2665 | "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) |
dada39aa RW |
2666 | (build-system r-build-system) |
2667 | (home-page "http://cran.r-project.org/web/packages/irlba") | |
2668 | (synopsis "Methods for eigendecomposition of large matrices") | |
2669 | (description | |
2670 | "This package provides fast and memory efficient methods for truncated | |
2671 | singular and eigenvalue decompositions, as well as for principal component | |
2672 | analysis of large sparse or dense matrices.") | |
2673 | (license (list license:gpl2+ license:gpl3+)))) | |
2674 | ||
c7f04517 BW |
2675 | (define-public r-glmnet |
2676 | (package | |
2677 | (name "r-glmnet") | |
2678 | (version "2.0-5") | |
2679 | (source | |
2680 | (origin | |
2681 | (method url-fetch) | |
2682 | (uri (cran-uri "glmnet" version)) | |
2683 | (sha256 | |
2684 | (base32 | |
2685 | "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c")))) | |
2686 | (build-system r-build-system) | |
2687 | (inputs | |
2688 | `(("gfortran" ,gfortran))) | |
2689 | (propagated-inputs | |
2690 | `(("r-foreach" ,r-foreach))) | |
2691 | (home-page "http://www.jstatsoft.org/v33/i01") | |
2692 | (synopsis "Lasso and elastic-net regularized generalized linear models") | |
2693 | (description | |
2694 | "The glmnet package provides efficient procedures for fitting the entire | |
2695 | lasso or elastic-net regularization path for linear and Poisson regression, as | |
2696 | well as logistic, multinomial, Cox, multiple-response Gaussian and grouped | |
2697 | multinomial models. The algorithm uses cyclical coordinate descent in a | |
2698 | path-wise fashion.") | |
2699 | (license license:gpl2+))) | |
2700 | ||
3a6607f0 RW |
2701 | (define-public r-pkgmaker |
2702 | (package | |
2703 | (name "r-pkgmaker") | |
2704 | (version "0.22") | |
2705 | (source | |
2706 | (origin | |
2707 | (method url-fetch) | |
2708 | (uri (cran-uri "pkgmaker" version)) | |
2709 | (sha256 | |
2710 | (base32 | |
2711 | "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r")))) | |
2712 | (build-system r-build-system) | |
2713 | (propagated-inputs | |
2714 | `(("r-codetools" ,r-codetools) | |
2715 | ("r-digest" ,r-digest) | |
2716 | ("r-registry" ,r-registry) | |
2717 | ("r-stringr" ,r-stringr) | |
2718 | ("r-xtable" ,r-xtable))) | |
2719 | (home-page "https://renozao.github.io/pkgmaker") | |
2720 | (synopsis "Package development utilities") | |
2721 | (description | |
2722 | "This package provides some low-level utilities to use for R package | |
2723 | development. It currently provides managers for multiple package specific | |
2724 | options and registries, vignette, unit test and bibtex related utilities.") | |
2725 | (license license:gpl2+))) | |
2726 | ||
2d0f7d80 RW |
2727 | (define-public r-registry |
2728 | (package | |
2729 | (name "r-registry") | |
2730 | (version "0.3") | |
2731 | (source | |
2732 | (origin | |
2733 | (method url-fetch) | |
2734 | (uri (cran-uri "registry" version)) | |
2735 | (sha256 | |
2736 | (base32 | |
2737 | "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq")))) | |
2738 | (build-system r-build-system) | |
2739 | (home-page "http://cran.r-project.org/web/packages/registry") | |
2740 | (synopsis "Infrastructure for R package registries") | |
2741 | (description | |
2742 | "This package provides a generic infrastructure for creating and using R | |
2743 | package registries.") | |
2744 | (license license:gpl2+))) | |
2745 | ||
790034bd RW |
2746 | (define-public r-rngtools |
2747 | (package | |
2748 | (name "r-rngtools") | |
2749 | (version "1.2.4") | |
2750 | (source | |
2751 | (origin | |
2752 | (method url-fetch) | |
2753 | (uri (cran-uri "rngtools" version)) | |
2754 | (sha256 | |
2755 | (base32 | |
2756 | "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097")))) | |
2757 | (build-system r-build-system) | |
2758 | (propagated-inputs | |
2759 | `(("r-digest" ,r-digest) | |
2760 | ("r-pkgmaker" ,r-pkgmaker) | |
2761 | ("r-stringr" ,r-stringr))) | |
2762 | (home-page "https://renozao.github.io/rngtools") | |
2763 | (synopsis "Utility functions for working with random number generators") | |
2764 | (description | |
2765 | "This package contains a set of functions for working with Random Number | |
2766 | Generators (RNGs). In particular, it defines a generic S4 framework for | |
2767 | getting/setting the current RNG, or RNG data that are embedded into objects | |
2768 | for reproducibility. Notably, convenient default methods greatly facilitate | |
2769 | the way current RNG settings can be changed.") | |
2770 | (license license:gpl3+))) | |
2771 | ||
c72c1249 RW |
2772 | (define-public r-rtsne |
2773 | (package | |
2774 | (name "r-rtsne") | |
2775 | (version "0.11") | |
2776 | (source | |
2777 | (origin | |
2778 | (method url-fetch) | |
2779 | (uri (cran-uri "Rtsne" version)) | |
2780 | (sha256 | |
2781 | (base32 | |
2782 | "0zi4nxgpiv1gpdmcnqdhz5kymzp8m5xj02zpf290p1yyydl76bhy")))) | |
2783 | (properties `((upstream-name . "Rtsne"))) | |
2784 | (build-system r-build-system) | |
2785 | (propagated-inputs | |
2786 | `(("r-rcpp" ,r-rcpp))) | |
2787 | (home-page "https://github.com/jkrijthe/Rtsne") | |
2788 | (synopsis "T-distributed stochastic neighbor embedding") | |
2789 | (description | |
2790 | "This package provides an R wrapper around the fast T-distributed | |
2791 | Stochastic Neighbor Embedding using a Barnes-Hut implementation.") | |
2792 | ;; The declared license for this package is BSD-3, but it also includes | |
2793 | ;; code licensed under BSD-4. | |
2794 | (license (list license:bsd-3 license:bsd-4)))) | |
2795 | ||
c533589c RW |
2796 | (define-public r-e1071 |
2797 | (package | |
2798 | (name "r-e1071") | |
2799 | (version "1.6-7") | |
2800 | (source | |
2801 | (origin | |
2802 | (method url-fetch) | |
2803 | (uri (cran-uri "e1071" version)) | |
2804 | (sha256 | |
2805 | (base32 | |
2806 | "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h")))) | |
2807 | (build-system r-build-system) | |
2808 | (home-page "http://cran.r-project.org/web/packages/e1071") | |
2809 | (synopsis "Miscellaneous functions for probability theory") | |
2810 | (description | |
2811 | "This package provides functions for latent class analysis, short time | |
2812 | Fourier transform, fuzzy clustering, support vector machines, shortest path | |
2813 | computation, bagged clustering, naive Bayes classifier, and more.") | |
2814 | (license license:gpl2+))) | |
2815 | ||
c6105d69 RJ |
2816 | (define-public r-bigmemory-sri |
2817 | (package | |
2818 | (name "r-bigmemory-sri") | |
2819 | (version "0.1.3") | |
2820 | (source | |
2821 | (origin | |
2822 | (method url-fetch) | |
2823 | (uri (cran-uri "bigmemory.sri" version)) | |
2824 | (sha256 | |
2825 | (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m")))) | |
2826 | (properties | |
2827 | `((upstream-name . "bigmemory.sri"))) | |
2828 | (build-system r-build-system) | |
2829 | (home-page "http://cran.r-project.org/web/packages/bigmemory.sri") | |
2830 | (synopsis "Shared resource interface for the bigmemory package") | |
2831 | (description "This package provides a shared resource interface for the | |
2832 | bigmemory and synchronicity packages.") | |
2833 | ;; Users can choose either LGPLv3 or ASL2.0. | |
2834 | (license (list license:lgpl3 license:asl2.0)))) | |
4a838652 RJ |
2835 | |
2836 | (define-public r-synchronicity | |
2837 | (package | |
2838 | (name "r-synchronicity") | |
2839 | (version "1.1.9.1") | |
2840 | (source | |
2841 | (origin | |
2842 | (method url-fetch) | |
2843 | (uri (cran-uri "synchronicity" version)) | |
2844 | (sha256 | |
2845 | (base32 | |
2846 | "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c")))) | |
2847 | (build-system r-build-system) | |
2848 | (propagated-inputs | |
2849 | `(("r-bh" ,r-bh) | |
2850 | ("r-bigmemory-sri" ,r-bigmemory-sri) | |
2851 | ("r-rcpp" ,r-rcpp))) | |
2852 | (home-page "http://www.bigmemory.org") | |
2853 | (synopsis "Boost mutex functionality in R") | |
2854 | (description "This package provides support for synchronization | |
2855 | via mutexes and may eventually support interprocess communication and | |
2856 | message passing.") | |
2857 | ;; Users can choose either LGPLv3 or ASL2.0. | |
2858 | (license (list license:lgpl3 license:asl2.0)))) | |
59523c4c RJ |
2859 | |
2860 | (define-public r-bigmemory | |
2861 | (package | |
2862 | (name "r-bigmemory") | |
2863 | (version "4.5.19") | |
2864 | (source | |
2865 | (origin | |
2866 | (method url-fetch) | |
2867 | (uri (cran-uri "bigmemory" version)) | |
2868 | (sha256 | |
2869 | (base32 | |
2870 | "191gbzca557kpk7mdsg716vfyqpr7j5din6qb8hin4g1nkzzwmg6")))) | |
2871 | (build-system r-build-system) | |
2872 | (propagated-inputs | |
2873 | `(("r-bh" ,r-bh) | |
2874 | ("r-rcpp" ,r-rcpp) | |
2875 | ("r-bigmemory-sri" ,r-bigmemory-sri) | |
2876 | ("r-r-utils" ,r-r-utils))) | |
2877 | (home-page "http://www.bigmemory.org") | |
2878 | (synopsis "Manage large matrices with shared memory or memory-mapped files") | |
2879 | (description "This package provides methods to create, store, access, and | |
2880 | manipulate large matrices. Matrices are allocated to shared memory and may use | |
2881 | memory-mapped files.") | |
2882 | ;; Users can choose either LGPLv3 or ASL2.0. | |
2883 | (license (list license:lgpl3 license:asl2.0)))) | |
c6105d69 | 2884 | |
b783ff78 RW |
2885 | (define-public r-nmf |
2886 | (package | |
2887 | (name "r-nmf") | |
2888 | (version "0.20.6") | |
2889 | (source | |
2890 | (origin | |
2891 | (method url-fetch) | |
2892 | (uri (cran-uri "NMF" version)) | |
2893 | (sha256 | |
2894 | (base32 | |
2895 | "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z")))) | |
2896 | (properties `((upstream-name . "NMF"))) | |
2897 | (build-system r-build-system) | |
2898 | (propagated-inputs | |
2899 | `(("r-cluster" ,r-cluster) | |
8af47ef6 RJ |
2900 | ("r-bigmemory" ,r-bigmemory) |
2901 | ("r-synchronicity" ,r-synchronicity) | |
b783ff78 RW |
2902 | ("r-colorspace" ,r-colorspace) |
2903 | ("r-digest" ,r-digest) | |
2904 | ("r-doparallel" ,r-doparallel) | |
2905 | ("r-foreach" ,r-foreach) | |
2906 | ("r-ggplot2" ,r-ggplot2) | |
2907 | ("r-gridbase" ,r-gridbase) | |
2908 | ("r-pkgmaker" ,r-pkgmaker) | |
2909 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2910 | ("r-registry" ,r-registry) | |
2911 | ("r-reshape2" ,r-reshape2) | |
2912 | ("r-rngtools" ,r-rngtools) | |
2913 | ("r-stringr" ,r-stringr))) | |
2914 | (home-page "http://renozao.github.io/NMF") | |
2915 | (synopsis "Algorithms and framework for nonnegative matrix factorization") | |
2916 | (description | |
2917 | "This package provides a framework to perform Non-negative Matrix | |
2918 | Factorization (NMF). The package implements a set of already published | |
2919 | algorithms and seeding methods, and provides a framework to test, develop and | |
2920 | plug new or custom algorithms. Most of the built-in algorithms have been | |
2921 | optimized in C++, and the main interface function provides an easy way of | |
2922 | performing parallel computations on multicore machines.") | |
2923 | (license license:gpl2+))) | |
2924 | ||
07f911ba RW |
2925 | (define-public r-igraph |
2926 | (package | |
2927 | (name "r-igraph") | |
2928 | (version "1.0.1") | |
2929 | (source | |
2930 | (origin | |
2931 | (method url-fetch) | |
2932 | (uri (cran-uri "igraph" version)) | |
2933 | (sha256 | |
2934 | (base32 | |
2935 | "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w")))) | |
2936 | (build-system r-build-system) | |
2937 | (native-inputs | |
2938 | `(("gfortran" ,gfortran))) | |
2939 | (inputs | |
2940 | `(("gmp" ,gmp) | |
2941 | ("libxml2" ,libxml2))) | |
2942 | (propagated-inputs | |
2943 | `(("r-irlba" ,r-irlba) | |
2944 | ("r-magrittr" ,r-magrittr) | |
2945 | ("r-nmf" ,r-nmf))) | |
2946 | (home-page "http://igraph.org") | |
2947 | (synopsis "Network analysis and visualization") | |
2948 | (description | |
2949 | "This package provides routines for simple graphs and network analysis. | |
2950 | It can handle large graphs very well and provides functions for generating | |
2951 | random and regular graphs, graph visualization, centrality methods and much | |
2952 | more.") | |
2953 | (license license:gpl2+))) | |
2954 | ||
8bfe007c RW |
2955 | (define-public r-r-methodss3 |
2956 | (package | |
2957 | (name "r-r-methodss3") | |
887d45d4 | 2958 | (version "1.7.1") |
8bfe007c RW |
2959 | (source (origin |
2960 | (method url-fetch) | |
2961 | (uri (cran-uri "R.methodsS3" version)) | |
2962 | (sha256 | |
2963 | (base32 | |
887d45d4 | 2964 | "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24")))) |
8bfe007c RW |
2965 | (properties `((upstream-name . "R.methodsS3"))) |
2966 | (build-system r-build-system) | |
2967 | (home-page "http://cran.r-project.org/web/packages/R.methodsS3") | |
2968 | (synopsis "S3 methods simplified") | |
2969 | (description | |
2970 | "This package provides methods that simplify the setup of S3 generic | |
2971 | functions and S3 methods. Major effort has been made in making definition of | |
2972 | methods as simple as possible with a minimum of maintenance for package | |
2973 | developers. For example, generic functions are created automatically, if | |
2974 | missing, and naming conflict are automatically solved, if possible. The | |
2975 | method @code{setMethodS3()} is a good start for those who in the future may | |
2976 | want to migrate to S4.") | |
2977 | (license license:lgpl2.1+))) | |
2978 | ||
c8c75a8d RW |
2979 | (define-public r-r-oo |
2980 | (package | |
2981 | (name "r-r-oo") | |
f158b92c | 2982 | (version "1.21.0") |
c8c75a8d RW |
2983 | (source (origin |
2984 | (method url-fetch) | |
2985 | (uri (cran-uri "R.oo" version)) | |
2986 | (sha256 | |
2987 | (base32 | |
f158b92c | 2988 | "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34")))) |
c8c75a8d RW |
2989 | (properties `((upstream-name . "R.oo"))) |
2990 | (build-system r-build-system) | |
2991 | (propagated-inputs | |
2992 | `(("r-r-methodss3" ,r-r-methodss3))) | |
2993 | (home-page "https://github.com/HenrikBengtsson/R.oo") | |
2994 | (synopsis "R object-oriented programming with or without references") | |
2995 | (description | |
2996 | "This package provides methods and classes for object-oriented | |
2997 | programming in R with or without references. Large effort has been made on | |
2998 | making definition of methods as simple as possible with a minimum of | |
2999 | maintenance for package developers.") | |
3000 | (license license:lgpl2.1+))) | |
3001 | ||
9c94b53b RW |
3002 | (define-public r-r-utils |
3003 | (package | |
3004 | (name "r-r-utils") | |
fd54f65e | 3005 | (version "2.4.0") |
9c94b53b RW |
3006 | (source (origin |
3007 | (method url-fetch) | |
3008 | (uri (cran-uri "R.utils" version)) | |
3009 | (sha256 | |
3010 | (base32 | |
fd54f65e | 3011 | "0cn0wlmgwclmqak05825wrk9q894xa4qjqa7rn0i9p4ss7k6vifj")))) |
9c94b53b RW |
3012 | (properties `((upstream-name . "R.utils"))) |
3013 | (build-system r-build-system) | |
3014 | (propagated-inputs | |
3015 | `(("r-r-methodss3" ,r-r-methodss3) | |
3016 | ("r-r-oo" ,r-r-oo))) | |
3017 | (home-page "https://github.com/HenrikBengtsson/R.utils") | |
3018 | (synopsis "Various programming utilities") | |
3019 | (description | |
3020 | "This package provides utility functions useful when programming and | |
3021 | developing R packages.") | |
3022 | (license license:lgpl2.1+))) | |
3023 | ||
a63efbb4 RW |
3024 | (define-public r-r-cache |
3025 | (package | |
3026 | (name "r-r-cache") | |
3027 | (version "0.12.0") | |
3028 | (source (origin | |
3029 | (method url-fetch) | |
3030 | (uri (cran-uri "R.cache" version)) | |
3031 | (sha256 | |
3032 | (base32 | |
3033 | "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx")))) | |
3034 | (properties `((upstream-name . "R.cache"))) | |
3035 | (build-system r-build-system) | |
3036 | (propagated-inputs | |
3037 | `(("r-digest" ,r-digest) | |
3038 | ("r-r-methodss3" ,r-r-methodss3) | |
3039 | ("r-r-oo" ,r-r-oo) | |
3040 | ("r-r-utils" ,r-r-utils))) | |
3041 | (home-page "https://github.com/HenrikBengtsson/R.cache") | |
3042 | (synopsis "Light-weight caching of objects and results") | |
3043 | (description | |
3044 | "This package provides methods for caching or memoization of objects and | |
3045 | results. With this package, any R object can be cached in a key-value storage | |
3046 | where the key can be an arbitrary set of R objects. The cache memory is | |
3047 | persistent (on the file system).") | |
3048 | (license license:lgpl2.1+))) | |
3049 | ||
3703ffb4 RW |
3050 | (define-public r-r-rsp |
3051 | (package | |
3052 | (name "r-r-rsp") | |
b8f6a97e | 3053 | (version "0.30.0") |
3703ffb4 RW |
3054 | (source (origin |
3055 | (method url-fetch) | |
3056 | (uri (cran-uri "R.rsp" version)) | |
3057 | (sha256 | |
3058 | (base32 | |
b8f6a97e | 3059 | "1ssykygqkxzx9qblxhavxlf2z6r5bhk0s47yw1dllfiyc8zy7jv2")))) |
3703ffb4 RW |
3060 | (properties `((upstream-name . "R.rsp"))) |
3061 | (build-system r-build-system) | |
3062 | (propagated-inputs | |
3063 | `(("r-r-cache" ,r-r-cache) | |
3064 | ("r-r-methodss3" ,r-r-methodss3) | |
3065 | ("r-r-oo" ,r-r-oo) | |
3066 | ("r-r-utils" ,r-r-utils))) | |
3067 | (home-page "https://github.com/HenrikBengtsson/R.rsp") | |
3068 | (synopsis "Dynamic generation of scientific reports") | |
3069 | (description | |
3070 | "The RSP markup language provides a powerful markup for controlling the | |
3071 | content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr | |
3072 | documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary | |
3073 | to many other literate programming languages, with RSP it is straightforward | |
3074 | to loop over mixtures of code and text sections, e.g. in month-by-month | |
3075 | summaries. RSP has also several preprocessing directives for incorporating | |
3076 | static and dynamic contents of external files (local or online) among other | |
3077 | things. RSP is ideal for self-contained scientific reports and R package | |
3078 | vignettes.") | |
3079 | (license license:lgpl2.1+))) | |
3080 | ||
b5f13fdb RJ |
3081 | (define-public r-mvtnorm |
3082 | (package | |
3083 | (name "r-mvtnorm") | |
3084 | (version "1.0-5") | |
3085 | (source (origin | |
3086 | (method url-fetch) | |
3087 | (uri (cran-uri "mvtnorm" version)) | |
3088 | (sha256 | |
3089 | (base32 | |
3090 | "1pc1mi2h063gh4a40009xk5j6pf5bm4274i5kycln38dixsry3yh")))) | |
3091 | (build-system r-build-system) | |
3092 | (inputs | |
3093 | `(("gfortran" ,gfortran))) | |
3094 | (home-page "http://mvtnorm.R-forge.R-project.org") | |
3095 | (synopsis "Package for multivariate normal and t-distributions") | |
3096 | (description "This package can compute multivariate normal and | |
3097 | t-probabilities, quantiles, random deviates and densities.") | |
3098 | (license license:gpl2))) | |
3099 | ||
e05c37da RW |
3100 | (define-public r-matrixstats |
3101 | (package | |
3102 | (name "r-matrixstats") | |
a8e893b0 | 3103 | (version "0.51.0") |
e05c37da RW |
3104 | (source (origin |
3105 | (method url-fetch) | |
3106 | (uri (cran-uri "matrixStats" version)) | |
3107 | (sha256 | |
3108 | (base32 | |
a8e893b0 | 3109 | "0bsalx605kgb9nl7mfnq1qinkyd9s97p8plymsyfja1gmcnjrcpj")))) |
e05c37da RW |
3110 | (properties `((upstream-name . "matrixStats"))) |
3111 | (build-system r-build-system) | |
3112 | (native-inputs | |
3113 | `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes | |
3114 | (home-page "https://github.com/HenrikBengtsson/matrixStats") | |
3115 | (synopsis "Methods applying to vectors and matrix rows and columns") | |
3116 | (description | |
3117 | "This package provides methods operating on rows and columns of matrices, | |
3118 | e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are | |
3119 | also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and | |
3120 | @code{weightedMedians()}. All methods have been optimized for speed and | |
3121 | memory usage.") | |
3122 | (license license:artistic2.0))) | |
3123 | ||
a28d646b RW |
3124 | (define-public r-viridis |
3125 | (package | |
3126 | (name "r-viridis") | |
0fc42136 | 3127 | (version "0.3.4") |
a28d646b RW |
3128 | (source (origin |
3129 | (method url-fetch) | |
3130 | (uri (cran-uri "viridis" version)) | |
3131 | (sha256 | |
3132 | (base32 | |
0fc42136 | 3133 | "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j")))) |
a28d646b RW |
3134 | (build-system r-build-system) |
3135 | (propagated-inputs | |
3136 | `(("r-ggplot2" ,r-ggplot2) | |
3137 | ("r-gridextra" ,r-gridextra))) | |
3138 | (home-page "https://github.com/sjmgarnier/viridis") | |
3139 | (synopsis "Matplotlib default color map") | |
3140 | (description | |
3141 | "This package is a port of the new @url{matplotlib, | |
3142 | http://matplotlib.org/} color maps (@code{viridis}--the default--, | |
3143 | @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are | |
3144 | designed in such a way that they will analytically be perfectly | |
3145 | perceptually-uniform, both in regular form and also when converted to | |
3146 | black-and-white. They are also designed to be perceived by readers with the | |
3147 | most common form of color blindness.") | |
3148 | (license license:x11))) | |
3149 | ||
c6ab73e8 RW |
3150 | (define-public r-viridislite |
3151 | (package | |
3152 | (name "r-viridislite") | |
3153 | (version "0.1.3") | |
3154 | (source | |
3155 | (origin | |
3156 | (method url-fetch) | |
3157 | (uri (cran-uri "viridisLite" version)) | |
3158 | (sha256 | |
3159 | (base32 | |
3160 | "1b0fhj8i1m9jsz91gzag60k7vy7kk5xkdg31rc3h3spq96l66psp")))) | |
3161 | (properties `((upstream-name . "viridisLite"))) | |
3162 | (build-system r-build-system) | |
3163 | (home-page "https://github.com/sjmgarnier/viridisLite") | |
3164 | (synopsis "Default color maps from matplotlib") | |
3165 | (description | |
3166 | "This package is a port of the new @code{matplotlib} color maps ('viridis', | |
3167 | 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting | |
3168 | library for Python. These color maps are designed in such a way that they | |
3169 | will analytically be perfectly perceptually-uniform, both in regular form and | |
3170 | also when converted to black-and-white. They are also designed to be | |
3171 | perceived by readers with the most common form of color blindness. This is | |
3172 | the 'lite' version of the more complete @code{viridis} package.") | |
3173 | (license license:expat))) | |
3174 | ||
94b7e9b7 RW |
3175 | (define-public r-tidyr |
3176 | (package | |
3177 | (name "r-tidyr") | |
1b7f85f5 | 3178 | (version "0.6.0") |
94b7e9b7 RW |
3179 | (source |
3180 | (origin | |
3181 | (method url-fetch) | |
3182 | (uri (cran-uri "tidyr" version)) | |
3183 | (sha256 | |
3184 | (base32 | |
1b7f85f5 | 3185 | "1bpwbphgl43ym433b0nrshwhr7pprmj1wkpkamdzix1zvf9dcbc2")))) |
94b7e9b7 RW |
3186 | (build-system r-build-system) |
3187 | (propagated-inputs | |
3188 | `(("r-dplyr" ,r-dplyr) | |
3189 | ("r-lazyeval" ,r-lazyeval) | |
3190 | ("r-magrittr" ,r-magrittr) | |
3191 | ("r-rcpp" ,r-rcpp) | |
3192 | ("r-stringi" ,r-stringi))) | |
3193 | (home-page "https://github.com/hadley/tidyr") | |
3194 | (synopsis "Tidy data with `spread()` and `gather()` functions") | |
3195 | (description | |
3196 | "tidyr is a reframing of the reshape2 package designed to accompany the | |
3197 | tidy data framework, and to work hand-in-hand with magrittr and dplyr to build | |
3198 | a solid pipeline for data analysis. It is designed specifically for tidying | |
3199 | data, not the general reshaping that reshape2 does, or the general aggregation | |
3200 | that reshape did. In particular, built-in methods only work for data frames, | |
3201 | and tidyr provides no margins or aggregation.") | |
3202 | (license license:expat))) | |
3203 | ||
bae79538 RW |
3204 | (define-public r-hexbin |
3205 | (package | |
3206 | (name "r-hexbin") | |
3207 | (version "1.27.1") | |
3208 | (source | |
3209 | (origin | |
3210 | (method url-fetch) | |
3211 | (uri (cran-uri "hexbin" version)) | |
3212 | (sha256 | |
3213 | (base32 | |
3214 | "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh")))) | |
3215 | (build-system r-build-system) | |
3216 | (propagated-inputs | |
3217 | `(("r-lattice" ,r-lattice))) | |
3218 | (native-inputs | |
3219 | `(("gfortran" ,gfortran))) | |
3220 | (home-page "http://github.com/edzer/hexbin") | |
3221 | (synopsis "Hexagonal binning routines") | |
3222 | (description | |
3223 | "This package provides binning and plotting functions for hexagonal bins. | |
3224 | It uses and relies on grid graphics and formal (S4) classes and methods.") | |
3225 | (license license:gpl2+))) | |
a3c6445b RW |
3226 | |
3227 | (define-public r-purrr | |
3228 | (package | |
3229 | (name "r-purrr") | |
3230 | (version "0.2.2") | |
3231 | (source | |
3232 | (origin | |
3233 | (method url-fetch) | |
3234 | (uri (cran-uri "purrr" version)) | |
3235 | (sha256 | |
3236 | (base32 | |
3237 | "0lss8q733nv7s154wargm6vnxq55qygnxakib8xdj4jv0y86sxc3")))) | |
3238 | (build-system r-build-system) | |
3239 | (propagated-inputs | |
3240 | `(("r-bh" ,r-bh) | |
3241 | ("r-dplyr" ,r-dplyr) | |
3242 | ("r-lazyeval" ,r-lazyeval) | |
3243 | ("r-magrittr" ,r-magrittr) | |
3244 | ("r-rcpp" ,r-rcpp))) | |
3245 | (home-page "https://github.com/hadley/purrr") | |
3246 | (synopsis "Functional programming tools") | |
3247 | (description | |
3248 | "This package completes R's functional programming tools with missing | |
3249 | features present in other programming languages.") | |
3250 | (license license:gpl3+))) | |
bae79538 | 3251 | |
fbf6045e RW |
3252 | (define-public r-plotly |
3253 | (package | |
3254 | (name "r-plotly") | |
88cf917b | 3255 | (version "4.5.2") |
fbf6045e RW |
3256 | (source (origin |
3257 | (method url-fetch) | |
3258 | (uri (cran-uri "plotly" version)) | |
3259 | (sha256 | |
3260 | (base32 | |
88cf917b | 3261 | "08shs0qhy9js0fpj3d4rzfbwmw11ki3z5vg8jszfm6m69mfkgzw1")))) |
fbf6045e RW |
3262 | (build-system r-build-system) |
3263 | (propagated-inputs | |
3264 | `(("r-base64enc" ,r-base64enc) | |
3265 | ("r-digest" ,r-digest) | |
88cf917b | 3266 | ("r-dplyr" ,r-dplyr) |
fbf6045e | 3267 | ("r-ggplot2" ,r-ggplot2) |
2c81794e | 3268 | ("r-hexbin" ,r-hexbin) |
fbf6045e RW |
3269 | ("r-htmlwidgets" ,r-htmlwidgets) |
3270 | ("r-httr" ,r-httr) | |
3271 | ("r-jsonlite" ,r-jsonlite) | |
88cf917b | 3272 | ("r-lazyeval" ,r-lazyeval) |
fbf6045e | 3273 | ("r-magrittr" ,r-magrittr) |
88cf917b | 3274 | ("r-purrr" ,r-purrr) |
2c81794e | 3275 | ("r-scales" ,r-scales) |
88cf917b | 3276 | ("r-tibble" ,r-tibble) |
2c81794e | 3277 | ("r-tidyr" ,r-tidyr) |
88cf917b | 3278 | ("r-viridislite" ,r-viridislite))) |
fbf6045e RW |
3279 | (home-page "https://plot.ly/r") |
3280 | (synopsis "Create interactive web graphics") | |
3281 | (description | |
3282 | "This package enables the translation of ggplot2 graphs to an interactive | |
3283 | web-based version and/or the creation of custom web-based visualizations | |
3284 | directly from R. Once uploaded to a plotly account, plotly graphs (and the | |
3285 | data behind them) can be viewed and modified in a web browser.") | |
3286 | (license license:x11))) | |
3287 | ||
0947698c BW |
3288 | (define-public r-biased-urn |
3289 | (package | |
3290 | (name "r-biased-urn") | |
3291 | (version "1.07") | |
3292 | (source | |
3293 | (origin | |
3294 | (method url-fetch) | |
3295 | (uri (cran-uri "BiasedUrn" version)) | |
3296 | (sha256 | |
3297 | (base32 | |
3298 | "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) | |
3299 | (properties `((upstream-name . "BiasedUrn"))) | |
3300 | (build-system r-build-system) | |
3301 | (home-page "http://www.agner.org/random/") | |
3302 | (synopsis "Biased urn model distributions") | |
3303 | (description | |
3304 | "This package provides statistical models of biased sampling in the form | |
3305 | of univariate and multivariate noncentral hypergeometric distributions, | |
3306 | including Wallenius' noncentral hypergeometric distribution and Fisher's | |
3307 | noncentral hypergeometric distribution (also called extended hypergeometric | |
3308 | distribution).") | |
3309 | (license license:gpl3+))) | |
6499b70e | 3310 | |
58612fd2 RW |
3311 | (define-public r-rematch |
3312 | (package | |
3313 | (name "r-rematch") | |
3314 | (version "1.0.1") | |
3315 | (source | |
3316 | (origin | |
3317 | (method url-fetch) | |
3318 | (uri (cran-uri "rematch" version)) | |
3319 | (sha256 | |
3320 | (base32 | |
3321 | "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4")))) | |
3322 | (build-system r-build-system) | |
3323 | (home-page "https://github.com/MangoTheCat/rematch") | |
3324 | (synopsis "Match regular expressions with a nicer API") | |
3325 | (description | |
3326 | "This package provides a small wrapper on @code{regexpr} to extract the | |
3327 | matches and captured groups from the match of a regular expression to a | |
3328 | character vector.") | |
3329 | (license license:expat))) | |
3330 | ||
d427e03e RW |
3331 | (define-public r-cellranger |
3332 | (package | |
3333 | (name "r-cellranger") | |
3334 | (version "1.1.0") | |
3335 | (source | |
3336 | (origin | |
3337 | (method url-fetch) | |
3338 | (uri (cran-uri "cellranger" version)) | |
3339 | (sha256 | |
3340 | (base32 | |
3341 | "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x")))) | |
3342 | (build-system r-build-system) | |
3343 | (propagated-inputs | |
3344 | `(("r-rematch" ,r-rematch) | |
3345 | ("r-tibble" ,r-tibble))) | |
3346 | (home-page "https://github.com/rsheets/cellranger") | |
3347 | (synopsis "Translate spreadsheet cell ranges to rows and columns") | |
3348 | (description | |
3349 | "This package provides helper functions to work with spreadsheets and the | |
3350 | @code{A1:D10} style of cell range specification.") | |
3351 | (license license:expat))) | |
3352 | ||
9f5435d9 RW |
3353 | (define-public r-googlesheets |
3354 | (package | |
3355 | (name "r-googlesheets") | |
3356 | (version "0.2.1") | |
3357 | (source | |
3358 | (origin | |
3359 | (method url-fetch) | |
3360 | (uri (cran-uri "googlesheets" version)) | |
3361 | (sha256 | |
3362 | (base32 | |
3363 | "0ps13h1cv7fj5dh8s4nvwi64wnnyqdsadcaa4iizq1c5s615cwk3")))) | |
3364 | (build-system r-build-system) | |
3365 | (propagated-inputs | |
3366 | `(("r-cellranger" ,r-cellranger) | |
3367 | ("r-dplyr" ,r-dplyr) | |
3368 | ("r-httr" ,r-httr) | |
3369 | ("r-jsonlite" ,r-jsonlite) | |
3370 | ("r-purrr" ,r-purrr) | |
3371 | ("r-readr" ,r-readr) | |
3372 | ("r-stringr" ,r-stringr) | |
3373 | ("r-tidyr" ,r-tidyr) | |
3374 | ("r-xml2" ,r-xml2))) | |
3375 | (home-page "https://github.com/jennybc/googlesheets") | |
3376 | (synopsis "Manage Google spreadsheets from R") | |
3377 | (description "This package provides tools to interact with Google Sheets | |
3378 | from within R.") | |
3379 | (license license:expat))) | |
3380 | ||
e7d16ad1 RW |
3381 | (define-public r-spams |
3382 | (package | |
3383 | (name "r-spams") | |
3384 | (version "2.5-svn2014-07-04") | |
3385 | (source | |
3386 | (origin | |
3387 | (method url-fetch) | |
3388 | (uri (string-append "https://gforge.inria.fr/frs/download.php/33815/" | |
3389 | "spams-R-v" version ".tar.gz")) | |
3390 | (sha256 | |
3391 | (base32 | |
3392 | "1k459jg9a334slkw31w63l4d39xszjzsng7dv5j1mp78zifz7hvx")))) | |
3393 | (build-system r-build-system) | |
3394 | (arguments | |
3395 | `(#:phases | |
3396 | (modify-phases %standard-phases | |
3397 | (add-after 'unpack 'chdir | |
3398 | (lambda _ (chdir "spams") #t)) | |
3399 | ;; Since R 3.3.0 including R headers inside of an extern "C" block | |
3400 | ;; causes C headers to be included, which results in a lot of | |
3401 | ;; duplicate definitions. This can be avoided by defining | |
3402 | ;; NO_C_HEADERS before including the R headers. | |
3403 | (add-after 'chdir 'patch-use-of-R-headers | |
3404 | (lambda _ | |
3405 | (substitute* "src/spams.cpp" | |
3406 | (("#include <R.h>" line) | |
3407 | (string-append "#define NO_C_HEADERS\n" line))) | |
3408 | #t)) | |
3409 | ;; This looks like a syntax error. | |
3410 | (add-after 'chdir 'patch-isnan | |
3411 | (lambda _ | |
3412 | (substitute* '"src/spams/linalg/linalg.h" | |
3413 | (("if isnan\\(lambda\\) \\{") | |
3414 | "if (isnan(lambda)) {")) | |
3415 | #t))))) | |
3416 | (home-page "http://spams-devel.gforge.inria.fr") | |
3417 | (synopsis "Toolbox for solving sparse estimation problems") | |
3418 | (description "SPAMS (SPArse Modeling Software) is an optimization toolbox | |
3419 | for solving various sparse estimation problems. It includes tools for the | |
3420 | following problems: | |
3421 | ||
3422 | @enumerate | |
3423 | @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle | |
3424 | component analysis} (PCA), ...) | |
3425 | @item Solving sparse decomposition problems with LARS, coordinate descent, | |
3426 | OMP, SOMP, proximal methods | |
3427 | @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse | |
3428 | group lasso, tree-structured regularization, structured sparsity with | |
3429 | overlapping groups,...). | |
3430 | @end enumerate\n") | |
3431 | (license license:gpl3+))) | |
3432 | ||
2213730c RW |
3433 | (define-public r-rpart |
3434 | (package | |
3435 | (name "r-rpart") | |
3436 | (version "4.1-10") | |
3437 | (source | |
3438 | (origin | |
3439 | (method url-fetch) | |
3440 | (uri (cran-uri "rpart" version)) | |
3441 | (sha256 | |
3442 | (base32 | |
3443 | "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) | |
3444 | (build-system r-build-system) | |
3445 | (home-page "http://cran.r-project.org/web/packages/rpart") | |
3446 | (synopsis "Recursive partitioning and regression trees") | |
3447 | (description | |
3448 | "This package provides recursive partitioning functions for | |
3449 | classification, regression and survival trees.") | |
3450 | (license (list license:gpl2+ license:gpl3+)))) | |
3451 | ||
ebbd4d0b RW |
3452 | (define-public r-survival |
3453 | (package | |
3454 | (name "r-survival") | |
3455 | (version "2.40-1") | |
3456 | (source | |
3457 | (origin | |
3458 | (method url-fetch) | |
3459 | (uri (cran-uri "survival" version)) | |
3460 | (sha256 | |
3461 | (base32 | |
3462 | "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci")))) | |
3463 | (build-system r-build-system) | |
3464 | (home-page "https://github.com/therneau/survival") | |
3465 | (synopsis "Survival analysis") | |
3466 | (description | |
3467 | "This package contains the core survival analysis routines, including | |
3468 | definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) | |
3469 | curves, Cox models, and parametric accelerated failure time models.") | |
3470 | (license license:lgpl2.0+))) | |
3471 | ||
2d21d44d RW |
3472 | (define-public r-hmisc |
3473 | (package | |
3474 | (name "r-hmisc") | |
e7165916 | 3475 | (version "4.0-0") |
2d21d44d RW |
3476 | (source |
3477 | (origin | |
3478 | (method url-fetch) | |
3479 | (uri (cran-uri "Hmisc" version)) | |
3480 | (sha256 | |
3481 | (base32 | |
e7165916 | 3482 | "0azxmg9h9c456biydc0wpi9xhljmd37m8bv0zaadbvc93g7x0l4b")))) |
2d21d44d RW |
3483 | (properties `((upstream-name . "Hmisc"))) |
3484 | (build-system r-build-system) | |
3485 | (native-inputs | |
3486 | `(("gfortran" ,gfortran))) | |
3487 | (propagated-inputs | |
3488 | `(("r-acepack" ,r-acepack) | |
3489 | ("r-cluster" ,r-cluster) | |
3490 | ("r-data-table" ,r-data-table) | |
3491 | ("r-foreign" ,r-foreign) | |
3492 | ("r-formula" ,r-formula) | |
3493 | ("r-ggplot2" ,r-ggplot2) | |
3494 | ("r-gridextra" ,r-gridextra) | |
3495 | ("r-gtable" ,r-gtable) | |
3496 | ("r-lattice" ,r-lattice) | |
e7165916 RW |
3497 | ;; Hmisc needs survival >= 2.40.1, so it cannot use the survival |
3498 | ;; package that comes with R 3.3.1. | |
3499 | ("r-survival" ,r-survival) | |
2d21d44d | 3500 | ("r-latticeextra" ,r-latticeextra) |
e7165916 RW |
3501 | ("r-htmltable" ,r-htmltable) |
3502 | ("r-htmltools" ,r-htmltools) | |
3503 | ("r-viridis" ,r-viridis) | |
2d21d44d RW |
3504 | ("r-nnet" ,r-nnet) |
3505 | ("r-rpart" ,r-rpart))) | |
3506 | (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") | |
3507 | (synopsis "Miscellaneous data analysis and graphics functions") | |
3508 | (description | |
3509 | "This package contains many functions useful for data analysis, | |
3510 | high-level graphics, utility operations, functions for computing sample size | |
3511 | and power, importing and annotating datasets, imputing missing values, | |
3512 | advanced table making, variable clustering, character string manipulation, | |
3513 | conversion of R objects to LaTeX code, and recoding variables.") | |
3514 | (license license:gpl2+))) | |
3515 | ||
aa3b3910 RW |
3516 | (define-public r-runit |
3517 | (package | |
3518 | (name "r-runit") | |
3519 | (version "0.4.31") | |
3520 | (source | |
3521 | (origin | |
3522 | (method url-fetch) | |
3523 | (uri (cran-uri "RUnit" version)) | |
3524 | (sha256 | |
3525 | (base32 | |
3526 | "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx")))) | |
3527 | (properties `((upstream-name . "RUnit"))) | |
3528 | (build-system r-build-system) | |
3529 | (home-page "http://cran.r-project.org/web/packages/RUnit") | |
3530 | (synopsis "R unit test framework") | |
3531 | (description | |
3532 | "This package provides R functions implementing a standard unit testing | |
3533 | framework, with additional code inspection and report generation tools.") | |
3534 | (license license:gpl2+))) | |
3535 | ||
c9a66714 RW |
3536 | (define-public r-dynamictreecut |
3537 | (package | |
3538 | (name "r-dynamictreecut") | |
3539 | (version "1.63-1") | |
3540 | (source | |
3541 | (origin | |
3542 | (method url-fetch) | |
3543 | (uri (cran-uri "dynamicTreeCut" version)) | |
3544 | (sha256 | |
3545 | (base32 | |
3546 | "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3")))) | |
3547 | (properties `((upstream-name . "dynamicTreeCut"))) | |
3548 | (build-system r-build-system) | |
3549 | (home-page | |
3550 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/") | |
3551 | (synopsis "Detect clusters in hierarchical clustering dendrograms") | |
3552 | (description | |
3553 | "This package contains methods for the detection of clusters in | |
3554 | hierarchical clustering dendrograms.") | |
3555 | (license license:gpl2+))) | |
3556 | ||
c4708783 RW |
3557 | (define-public r-preprocesscore |
3558 | (package | |
3559 | (name "r-preprocesscore") | |
3560 | (version "1.36.0") | |
3561 | (source | |
3562 | (origin | |
3563 | (method url-fetch) | |
3564 | (uri (bioconductor-uri "preprocessCore" version)) | |
3565 | (sha256 | |
3566 | (base32 | |
3567 | "1n8y12q7145f385gm2k3c6y3vwvin7jlb47la4mnl7mar6pq9kmp")))) | |
3568 | (properties | |
3569 | `((upstream-name . "preprocessCore"))) | |
3570 | (build-system r-build-system) | |
3571 | (home-page "https://github.com/bmbolstad/preprocessCore") | |
3572 | (synopsis "Collection of pre-processing functions") | |
3573 | (description | |
3574 | "This package provides a library of core pre-processing and normalization | |
3575 | routines.") | |
3576 | (license license:lgpl2.0+))) | |
3577 | ||
1bd46f55 RW |
3578 | (define-public r-fastcluster |
3579 | (package | |
3580 | (name "r-fastcluster") | |
3581 | (version "1.1.20") | |
3582 | (source | |
3583 | (origin | |
3584 | (method url-fetch) | |
3585 | (uri (cran-uri "fastcluster" version)) | |
3586 | (sha256 | |
3587 | (base32 | |
3588 | "0rlbxhh894znf10x0xgkv9dzpibgq9jw5aqpgviccdnxc2c5hwid")))) | |
3589 | (build-system r-build-system) | |
3590 | (home-page "http://danifold.net/fastcluster.html") | |
3591 | (synopsis "Fast hierarchical clustering routines") | |
3592 | (description | |
3593 | "This package implements fast hierarchical, agglomerative clustering | |
3594 | routines. Part of the functionality is designed as drop-in replacement for | |
3595 | existing routines: @code{linkage()} in the SciPy package | |
3596 | @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package, | |
3597 | and the @code{flashClust} package. It provides the same functionality with | |
3598 | the benefit of a much faster implementation. Moreover, there are | |
3599 | memory-saving routines for clustering of vector data, which go beyond what the | |
3600 | existing packages provide.") | |
3601 | (license license:bsd-2))) | |
3602 | ||
6335bf1c RW |
3603 | (define-public r-sfsmisc |
3604 | (package | |
3605 | (name "r-sfsmisc") | |
3606 | (version "1.1-0") | |
3607 | (source | |
3608 | (origin | |
3609 | (method url-fetch) | |
3610 | (uri (cran-uri "sfsmisc" version)) | |
3611 | (sha256 | |
3612 | (base32 | |
3613 | "0580piv4n1nispl3pa8nfjjfnb8iwaqky2dzdy0aqnxrxgrhqhvz")))) | |
3614 | (build-system r-build-system) | |
3615 | (home-page "http://cran.r-project.org/web/packages/sfsmisc") | |
3616 | (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") | |
3617 | (description | |
3618 | "This package provides useful utilities from Seminar fuer Statistik ETH | |
3619 | Zurich, including many that are related to graphics.") | |
3620 | (license license:gpl2+))) | |
3621 | ||
1571f90e RW |
3622 | (define-public r-gtools |
3623 | (package | |
3624 | (name "r-gtools") | |
3625 | (version "3.5.0") | |
3626 | (source | |
3627 | (origin | |
3628 | (method url-fetch) | |
3629 | (uri (cran-uri "gtools" version)) | |
3630 | (sha256 | |
3631 | (base32 | |
3632 | "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6")))) | |
3633 | (build-system r-build-system) | |
3634 | (home-page "http://cran.r-project.org/web/packages/gtools") | |
3635 | (synopsis "Various R programming tools") | |
3636 | (description | |
3637 | "This package contains a collection of various functions to assist in R | |
3638 | programming, such as tools to assist in developing, updating, and maintaining | |
3639 | R and R packages, calculating the logit and inverse logit transformations, | |
3640 | tests for whether a value is missing, empty or contains only @code{NA} and | |
3641 | @code{NULL} values, and many more.") | |
3642 | (license license:gpl2))) | |
3643 | ||
6034cd90 RW |
3644 | (define-public r-gdata |
3645 | (package | |
3646 | (name "r-gdata") | |
3647 | (version "2.17.0") | |
3648 | (source | |
3649 | (origin | |
3650 | (method url-fetch) | |
3651 | (uri (cran-uri "gdata" version)) | |
3652 | (sha256 | |
3653 | (base32 | |
3654 | "0kiy3jbcszlpmarg311spdsfi5pn89wgy742dxsbzxk8907fr5w0")))) | |
3655 | (build-system r-build-system) | |
3656 | (inputs | |
3657 | `(("perl" ,perl))) | |
3658 | (propagated-inputs | |
3659 | `(("r-gtools" ,r-gtools))) | |
3660 | (home-page "http://cran.r-project.org/web/packages/gdata") | |
3661 | (synopsis "Various R programming tools for data manipulation") | |
3662 | (description | |
3663 | "This package provides various R programming tools for data manipulation, | |
3664 | including: | |
3665 | ||
3666 | @itemize | |
3667 | @item medical unit conversions | |
3668 | @item combining objects | |
3669 | @item character vector operations | |
3670 | @item factor manipulation | |
3671 | @item obtaining information about R objects | |
3672 | @item manipulating MS-Excel formatted files | |
3673 | @item generating fixed-width format files | |
3674 | @item extricating components of date and time objects | |
3675 | @item operations on columns of data frames | |
3676 | @item matrix operations | |
3677 | @item operations on vectors and data frames | |
3678 | @item value of last evaluated expression | |
3679 | @item wrapper for @code{sample} that ensures consistent behavior for | |
3680 | both scalar and vector arguments | |
3681 | @end itemize\n") | |
3682 | (license license:gpl2+))) | |
3683 | ||
0cfe0570 RW |
3684 | (define-public r-gplots |
3685 | (package | |
3686 | (name "r-gplots") | |
3687 | (version "3.0.1") | |
3688 | (source | |
3689 | (origin | |
3690 | (method url-fetch) | |
3691 | (uri (cran-uri "gplots" version)) | |
3692 | (sha256 | |
3693 | (base32 | |
3694 | "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l")))) | |
3695 | (build-system r-build-system) | |
3696 | (propagated-inputs | |
3697 | `(("r-catools" ,r-catools) | |
3698 | ("r-gdata" ,r-gdata) | |
3699 | ("r-gtools" ,r-gtools) | |
3700 | ("r-kernsmooth" ,r-kernsmooth))) | |
3701 | (home-page "http://cran.r-project.org/web/packages/gplots") | |
3702 | (synopsis "Various R programming tools for plotting data") | |
3703 | (description | |
3704 | "This package provides various R programming tools for plotting data, | |
3705 | including: | |
3706 | ||
3707 | @itemize | |
3708 | @item calculating and plotting locally smoothed summary function | |
3709 | @item enhanced versions of standard plots | |
3710 | @item manipulating colors | |
3711 | @item calculating and plotting two-dimensional data summaries | |
3712 | @item enhanced regression diagnostic plots | |
3713 | @item formula-enabled interface to @code{stats::lowess} function | |
3714 | @item displaying textual data in plots | |
3715 | @item baloon plots | |
3716 | @item plotting \"Venn\" diagrams | |
3717 | @item displaying Open-Office style plots | |
3718 | @item plotting multiple data on same region, with separate axes | |
3719 | @item plotting means and confidence intervals | |
3720 | @item spacing points in an x-y plot so they don't overlap | |
3721 | @end itemize\n") | |
3722 | (license license:gpl2+))) | |
3723 | ||
419a8a18 RW |
3724 | (define-public r-rocr |
3725 | (package | |
3726 | (name "r-rocr") | |
3727 | (version "1.0-7") | |
3728 | (source | |
3729 | (origin | |
3730 | (method url-fetch) | |
3731 | (uri (cran-uri "ROCR" version)) | |
3732 | (sha256 | |
3733 | (base32 | |
3734 | "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7")))) | |
3735 | (properties `((upstream-name . "ROCR"))) | |
3736 | (build-system r-build-system) | |
3737 | (propagated-inputs | |
3738 | `(("r-gplots" ,r-gplots))) | |
3739 | (home-page "http://rocr.bioinf.mpi-sb.mpg.de/") | |
3740 | (synopsis "Visualizing the performance of scoring classifiers") | |
3741 | (description | |
3742 | "ROCR is a flexible tool for creating cutoff-parameterized 2D performance | |
3743 | curves by freely combining two from over 25 performance measures (new | |
3744 | performance measures can be added using a standard interface). Curves from | |
3745 | different cross-validation or bootstrapping runs can be averaged by different | |
3746 | methods, and standard deviations, standard errors or box plots can be used to | |
3747 | visualize the variability across the runs. The parameterization can be | |
3748 | visualized by printing cutoff values at the corresponding curve positions, or | |
3749 | by coloring the curve according to cutoff. All components of a performance | |
3750 | plot can be quickly adjusted using a flexible parameter dispatching | |
3751 | mechanism.") | |
3752 | (license license:gpl2+))) | |
3753 | ||
557a4b8e RW |
3754 | (define-public r-kernsmooth |
3755 | (package | |
3756 | (name "r-kernsmooth") | |
3757 | (version "2.23-15") | |
3758 | (source | |
3759 | (origin | |
3760 | (method url-fetch) | |
3761 | (uri (cran-uri "KernSmooth" version)) | |
3762 | (sha256 | |
3763 | (base32 | |
3764 | "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) | |
3765 | (properties `((upstream-name . "KernSmooth"))) | |
3766 | (build-system r-build-system) | |
3767 | (inputs | |
3768 | `(("gfortran" ,gfortran))) | |
3769 | (home-page "http://cran.r-project.org/web/packages/KernSmooth") | |
3770 | (synopsis "Functions for kernel smoothing") | |
3771 | (description | |
3772 | "This package provides functions for kernel smoothing (and density | |
3773 | estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) | |
3774 | \"Kernel Smoothing\".") | |
3775 | ;; Unlimited use and distribution | |
3776 | (license (license:non-copyleft "file://LICENSE.note")))) | |
3777 | ||
031cf6b6 RJ |
3778 | (define-public r-zoo |
3779 | (package | |
3780 | (name "r-zoo") | |
3781 | (version "1.7-13") | |
3782 | (source (origin | |
3783 | (method url-fetch) | |
3784 | (uri (cran-uri "zoo" version)) | |
3785 | (sha256 | |
3786 | (base32 | |
3787 | "0m67bnrg7r1jxvs9p7rpa430szp5qfp65r056yb8bivpc16jd98c")))) | |
3788 | (build-system r-build-system) | |
3789 | (propagated-inputs | |
3790 | `(("r-lattice" ,r-lattice))) | |
3791 | (home-page "http://zoo.R-Forge.R-project.org/") | |
3792 | (synopsis "S3 infrastructure for regular and irregular time series") | |
3793 | (description "This package contains an S3 class with methods for totally | |
3794 | ordered indexed observations. It is particularly aimed at irregular time | |
3795 | series of numeric vectors/matrices and factors.") | |
3796 | (license license:gpl2+))) | |
3797 | ||
6499b70e RW |
3798 | (define-public r-ztable |
3799 | (package | |
3800 | (name "r-ztable") | |
3801 | (version "0.1.5") | |
3802 | (source (origin | |
3803 | (method url-fetch) | |
3804 | (uri (cran-uri "ztable" version)) | |
3805 | (sha256 | |
3806 | (base32 | |
3807 | "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r")))) | |
3808 | (build-system r-build-system) | |
3809 | (home-page "http://cran.r-project.org/web/packages/ztable") | |
3810 | (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") | |
3811 | (description | |
3812 | "This package provides functions to make zebra-striped tables (tables | |
3813 | with alternating row colors) in LaTeX and HTML formats easily from | |
3814 | @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova}, | |
3815 | @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and | |
3816 | @code{cbind.mytable} objects.") | |
3817 | (license license:gpl2+))) |