Commit | Line | Data |
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cb7e4867 | 1 | ;;; GNU Guix --- Functional package management for GNU |
26a281ef | 2 | ;;; Copyright © 2015, 2016, 2017 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> |
37337699 | 9 | ;;; Copyright © 2016, 2017 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") | |
4621acfd RW |
119 | "/lib/R/lib") |
120 | ;; This affects the embedded timestamp of only the core packages. | |
121 | "PKG_BUILT_STAMP=1970-01-01") | |
ff2b1c17 | 122 | #:phases |
f4f4ced8 | 123 | (modify-phases %standard-phases |
b5ce25cc RJ |
124 | (add-before 'configure 'patch-uname |
125 | (lambda* (#:key inputs #:allow-other-keys) | |
126 | (let ((uname-bin (string-append (assoc-ref inputs "coreutils") | |
127 | "/bin/uname"))) | |
128 | (substitute* "src/scripts/R.sh.in" | |
129 | (("uname") uname-bin))) | |
130 | #t)) | |
4621acfd RW |
131 | (add-after 'unpack 'build-recommended-packages-reproducibly |
132 | (lambda _ | |
133 | (substitute* "src/library/Recommended/Makefile.in" | |
745c687b RW |
134 | (("INSTALL_OPTS =(.*)" line rest ) |
135 | (string-append "INSTALL_OPTS = --built-timestamp=1970-01-01" | |
136 | rest))) | |
beaa026a RW |
137 | ;; Ensure that gzipped files are reproducible |
138 | (substitute* '("src/library/grDevices/Makefile.in" | |
139 | "doc/manual/Makefile.in") | |
140 | (("R_GZIPCMD\\)" line) | |
141 | (string-append line " -n"))) | |
142 | ;; This library is installed using "install_package_description", | |
143 | ;; so we need to pass the "builtStamp" argument. | |
144 | (substitute* "src/library/tools/Makefile.in" | |
145 | (("(install_package_description\\(.*\"')\\)\"" line prefix) | |
146 | (string-append prefix ", builtStamp='1970-01-01')\""))) | |
4621acfd RW |
147 | #t)) |
148 | (add-before 'configure 'set-default-pager | |
f4f4ced8 RW |
149 | ;; Set default pager to "cat", because otherwise it is "false", |
150 | ;; making "help()" print nothing at all. | |
151 | (lambda _ (setenv "PAGER" "cat") #t)) | |
e42eb908 | 152 | (add-before 'check 'set-timezone |
f4f4ced8 | 153 | ;; Some tests require the timezone to be set. |
e42eb908 RW |
154 | (lambda* (#:key inputs #:allow-other-keys) |
155 | (setenv "TZ" "UTC") | |
156 | (setenv "TZDIR" | |
157 | (string-append (assoc-ref inputs "tzdata") | |
158 | "/share/zoneinfo")) | |
159 | #t)) | |
af23b6e9 RW |
160 | (add-after 'build 'make-info |
161 | (lambda _ (zero? (system* "make" "info")))) | |
162 | (add-after 'build 'install-info | |
163 | (lambda _ (zero? (system* "make" "install-info"))))) | |
cb7e4867 | 164 | #:configure-flags |
eb2afd00 | 165 | '("--with-cairo" |
71e98ca5 | 166 | "--with-blas=-lopenblas" |
cb7e4867 RW |
167 | "--with-libpng" |
168 | "--with-jpeglib" | |
169 | "--with-libtiff" | |
170 | "--with-ICU" | |
171 | "--enable-R-shlib" | |
172 | "--enable-BLAS-shlib" | |
173 | "--with-system-zlib" | |
174 | "--with-system-bzlib" | |
175 | "--with-system-pcre" | |
176 | "--with-system-tre" | |
177 | "--with-system-xz"))) | |
5e9738b7 RW |
178 | ;; R has some support for Java. When the JDK is available at configure |
179 | ;; time environment variables pointing to the JDK will be recorded under | |
180 | ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R | |
181 | ;; CMD javareconf". "R CMD javareconf" appears to only be used to update | |
182 | ;; the recorded environment variables in $R_HOME/etc. Refer to | |
183 | ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support | |
184 | ;; for additional information. | |
185 | ||
186 | ;; As the JDK is a rather large input with only very limited effects on R, | |
187 | ;; we decided to drop it. | |
cb7e4867 RW |
188 | (native-inputs |
189 | `(("bzip2" ,bzip2) | |
190 | ("perl" ,perl) | |
191 | ("pkg-config" ,pkg-config) | |
cb7e4867 RW |
192 | ("texinfo" ,texinfo) ; for building HTML manuals |
193 | ("which" ,which) ; for tests/Examples/base-Ex.R | |
194 | ("xz" ,xz))) | |
195 | (inputs | |
05e9f30f RW |
196 | `(;; We need not only cairo here, but pango to ensure that tests for the |
197 | ;; "cairo" bitmapType plotting backend succeed. | |
198 | ("pango" ,pango) | |
b5ce25cc | 199 | ("coreutils" ,coreutils) |
e42eb908 RW |
200 | ("curl" ,curl) |
201 | ("tzdata" ,tzdata) | |
71e98ca5 | 202 | ("openblas" ,openblas) |
19afbea1 | 203 | ("gfortran" ,gfortran) |
cb7e4867 | 204 | ("icu4c" ,icu4c) |
cb7e4867 RW |
205 | ("libjpeg" ,libjpeg) |
206 | ("libpng" ,libpng) | |
207 | ("libtiff" ,libtiff) | |
208 | ("libxt" ,libxt) | |
209 | ("pcre" ,pcre) | |
210 | ("readline" ,readline) | |
211 | ("zlib" ,zlib))) | |
12a9f4af RW |
212 | (native-search-paths |
213 | (list (search-path-specification | |
214 | (variable "R_LIBS_SITE") | |
215 | (files (list "site-library/"))))) | |
cb7e4867 RW |
216 | (home-page "http://www.r-project.org/") |
217 | (synopsis "Environment for statistical computing and graphics") | |
218 | (description | |
219 | "R is a language and environment for statistical computing and graphics. | |
220 | It provides a variety of statistical techniques, such as linear and nonlinear | |
221 | modeling, classical statistical tests, time-series analysis, classification | |
222 | and clustering. It also provides robust support for producing | |
223 | publication-quality data plots. A large amount of 3rd-party packages are | |
224 | available, greatly increasing its breadth and scope.") | |
225 | (license license:gpl3+))) | |
b12636e6 | 226 | |
42066e6b BW |
227 | (define-public r-bit |
228 | (package | |
229 | (name "r-bit") | |
230 | (version "1.1-12") | |
231 | (source | |
232 | (origin | |
233 | (method url-fetch) | |
234 | (uri (cran-uri "bit" version)) | |
235 | (sha256 | |
236 | (base32 | |
237 | "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f")))) | |
238 | (build-system r-build-system) | |
239 | (home-page "http://ff.r-forge.r-project.org") | |
240 | (synopsis "Class for vectors of 1-bit booleans") | |
241 | (description | |
242 | "This package provides bitmapped vectors of booleans (no @code{NA}s), | |
243 | coercion from and to logicals, integers and integer subscripts, fast boolean | |
244 | operators and fast summary statistics. With @code{bit} class vectors of true | |
245 | binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") | |
246 | (license license:gpl2))) | |
247 | ||
ce3f92e7 BW |
248 | (define-public r-bit64 |
249 | (package | |
250 | (name "r-bit64") | |
251 | (version "0.9-5") | |
252 | (source | |
253 | (origin | |
254 | (method url-fetch) | |
255 | (uri (cran-uri "bit64" version)) | |
256 | (sha256 | |
257 | (base32 | |
258 | "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg")))) | |
259 | (build-system r-build-system) | |
260 | (propagated-inputs | |
261 | `(("r-bit" ,r-bit))) | |
262 | (home-page "http://ff.r-forge.r-project.org/") | |
263 | (synopsis "S3 class for vectors of 64 bit integers") | |
264 | (description | |
265 | "The bit64 package provides serializable S3 atomic 64 bit (signed) | |
266 | integers that can be used in vectors, matrices, arrays and @code{data.frames}. | |
267 | Methods are available for coercion from and to logicals, integers, doubles, | |
268 | characters and factors as well as many elementwise and summary functions. | |
269 | Many fast algorithmic operations such as @code{match} and @code{order} support | |
270 | interactive data exploration and manipulation and optionally leverage | |
271 | caching.") | |
272 | (license license:gpl2))) | |
273 | ||
b12636e6 RW |
274 | (define-public r-colorspace |
275 | (package | |
276 | (name "r-colorspace") | |
94a6f20b | 277 | (version "1.3-2") |
b12636e6 RW |
278 | (source |
279 | (origin | |
280 | (method url-fetch) | |
9cda3622 | 281 | (uri (cran-uri "colorspace" version)) |
b12636e6 | 282 | (sha256 |
94a6f20b | 283 | (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx")))) |
b12636e6 RW |
284 | (build-system r-build-system) |
285 | (home-page "http://cran.r-project.org/web/packages/colorspace") | |
286 | (synopsis "Color space manipulation") | |
287 | (description | |
288 | "This package carries out a mapping between assorted color spaces | |
289 | including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar | |
290 | CIELAB. Qualitative, sequential, and diverging color palettes based on HCL | |
291 | colors are provided.") | |
292 | (license license:bsd-3))) | |
3587effb RW |
293 | |
294 | (define-public r-dichromat | |
295 | (package | |
296 | (name "r-dichromat") | |
297 | (version "2.0-0") | |
298 | (source | |
299 | (origin | |
300 | (method url-fetch) | |
9cda3622 | 301 | (uri (cran-uri "dichromat" version)) |
3587effb RW |
302 | (sha256 |
303 | (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i")))) | |
304 | (build-system r-build-system) | |
305 | (home-page "http://cran.r-project.org/web/packages/dichromat") | |
306 | (synopsis "Color schemes for dichromats") | |
307 | (description | |
308 | "Dichromat collapses red-green or green-blue distinctions to simulate the | |
309 | effects of different types of color-blindness.") | |
310 | (license license:gpl2+))) | |
177f38c7 RW |
311 | |
312 | (define-public r-digest | |
313 | (package | |
314 | (name "r-digest") | |
5aaa12df | 315 | (version "0.6.10") |
177f38c7 RW |
316 | (source |
317 | (origin | |
318 | (method url-fetch) | |
9cda3622 | 319 | (uri (cran-uri "digest" version)) |
177f38c7 | 320 | (sha256 |
5aaa12df | 321 | (base32 "07825781nl85gx3pqskc04ywgs0f874qj9z2nyrwz7h0aqks0l8c")))) |
177f38c7 | 322 | (build-system r-build-system) |
fe2087cc RW |
323 | ;; Vignettes require r-knitr, which requires r-digest, so we have to |
324 | ;; disable them and the tests. | |
325 | (arguments | |
326 | `(#:tests? #f | |
327 | #:configure-flags (list "--no-build-vignettes"))) | |
177f38c7 RW |
328 | (home-page "http://dirk.eddelbuettel.com/code/digest.html") |
329 | (synopsis "Create cryptographic hash digests of R objects") | |
330 | (description | |
331 | "This package contains an implementation of a function 'digest()' for the | |
332 | creation of hash digests of arbitrary R objects (using the md5, sha-1, | |
333 | sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison | |
334 | of R language objects, as well as a function 'hmac()' to create hash-based | |
335 | message authentication code. | |
336 | ||
337 | Please note that this package is not meant to be deployed for cryptographic | |
338 | purposes for which more comprehensive (and widely tested) libraries such as | |
339 | OpenSSL should be used.") | |
340 | (license license:gpl2+))) | |
112bb3c0 | 341 | |
52ad9cb6 RJ |
342 | (define-public r-estimability |
343 | (package | |
344 | (name "r-estimability") | |
58b93ad5 | 345 | (version "1.2") |
52ad9cb6 RJ |
346 | (source (origin |
347 | (method url-fetch) | |
348 | (uri (cran-uri "estimability" version)) | |
349 | (sha256 | |
350 | (base32 | |
58b93ad5 | 351 | "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h")))) |
52ad9cb6 RJ |
352 | (build-system r-build-system) |
353 | (home-page "http://cran.r-project.org/web/packages/estimability") | |
354 | (synopsis "Tools for assessing estimability of linear predictions") | |
355 | (description "Provides tools for determining estimability of linear | |
356 | functions of regression coefficients, and 'epredict' methods that handle | |
357 | non-estimable cases correctly.") | |
358 | (license license:gpl2+))) | |
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") | |
eebac90a | 445 | (version "0.12.8") |
ea69e2f8 RW |
446 | (source |
447 | (origin | |
448 | (method url-fetch) | |
9cda3622 | 449 | (uri (cran-uri "Rcpp" version)) |
ea69e2f8 | 450 | (sha256 |
eebac90a | 451 | (base32 "0is1vql1q82g7yakad4skx707ip0fx3rgdwv9a8mi8259gly2qji")))) |
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") | |
8a8fc31c | 491 | (version "1.8-16") |
08466208 BW |
492 | (source |
493 | (origin | |
494 | (method url-fetch) | |
495 | (uri (cran-uri "mgcv" version)) | |
496 | (sha256 | |
497 | (base32 | |
8a8fc31c | 498 | "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj")))) |
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") | |
b94b03b7 | 689 | (version "0.4.1") |
a11ee478 RW |
690 | (source |
691 | (origin | |
692 | (method url-fetch) | |
9cda3622 | 693 | (uri (cran-uri "scales" version)) |
a11ee478 | 694 | (sha256 |
b94b03b7 | 695 | (base32 "1lqccfmqdwrw0cjyqvw2zvgpk2jvnqrfb303l1raqyyf3zxqhav4")))) |
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") | |
da13738e | 715 | (version "2.2.1") |
d11b808f RW |
716 | (source |
717 | (origin | |
718 | (method url-fetch) | |
9cda3622 | 719 | (uri (cran-uri "ggplot2" version)) |
d11b808f | 720 | (sha256 |
da13738e | 721 | (base32 "0543782ddv2hp6s0l702mnxfg8n7a6qlbm8bm55x22hnqgz8kg2z")))) |
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) | |
ab01f1cd RW |
727 | ("r-lazyeval" ,r-lazyeval) |
728 | ("r-tibble" ,r-tibble) | |
d11b808f | 729 | ("r-reshape2" ,r-reshape2) |
e4b6c565 BW |
730 | ("r-scales" ,r-scales) |
731 | ("r-svglite" ,r-svglite))) ; Needed for 'ggsave' | |
d11b808f RW |
732 | (home-page "http://ggplot2.org") |
733 | (synopsis "An implementation of the grammar of graphics") | |
734 | (description | |
735 | "Ggplot2 is an implementation of the grammar of graphics in R. It | |
736 | combines the advantages of both base and lattice graphics: conditioning and | |
737 | shared axes are handled automatically, and you can still build up a plot step | |
738 | by step from multiple data sources. It also implements a sophisticated | |
739 | multidimensional conditioning system and a consistent interface to map data to | |
740 | aesthetic attributes.") | |
741 | (license license:gpl2+))) | |
ed6094fc | 742 | |
c5940b15 BW |
743 | (define-public r-gdtools |
744 | (package | |
745 | (name "r-gdtools") | |
48a87bbe | 746 | (version "0.1.3") |
c5940b15 BW |
747 | (source |
748 | (origin | |
749 | (method url-fetch) | |
750 | (uri (cran-uri "gdtools" version)) | |
751 | (sha256 | |
752 | (base32 | |
48a87bbe | 753 | "1prh814lw3qkgnf0760cvpic1k68jhlkpcxlksv8chjkvsrnnf09")))) |
c5940b15 BW |
754 | (build-system r-build-system) |
755 | (native-inputs | |
756 | `(("r-rcpp" ,r-rcpp) | |
757 | ("pkg-config" ,pkg-config))) | |
758 | (inputs | |
759 | `(("cairo" ,cairo))) | |
054a9a78 RW |
760 | (propagated-inputs |
761 | `(("r-withr" ,r-withr))) | |
c5940b15 BW |
762 | (home-page "http://cran.r-project.org/web/packages/gdtools") |
763 | (synopsis "Utilities for graphical rendering") | |
764 | (description | |
765 | "The @code{gdtools} package provides functionalities to get font metrics | |
766 | and to generate base64 encoded string from raster matrix.") | |
767 | (license license:gpl3))) | |
768 | ||
3aebedcc BW |
769 | (define-public r-svglite |
770 | (package | |
771 | (name "r-svglite") | |
dd4ae295 | 772 | (version "1.2.0") |
3aebedcc BW |
773 | (source |
774 | (origin | |
775 | (method url-fetch) | |
776 | (uri (cran-uri "svglite" version)) | |
777 | (sha256 | |
778 | (base32 | |
dd4ae295 | 779 | "1s1gvmlmmna5y4jsn9h6438pg5b86fl4nwfvkgm6n4h6ljfgqyx3")))) |
3aebedcc BW |
780 | (build-system r-build-system) |
781 | (native-inputs `(("r-rcpp" ,r-rcpp))) | |
782 | (propagated-inputs | |
783 | `(("r-bh" ,r-bh) | |
784 | ("r-gdtools" ,r-gdtools))) | |
785 | (home-page "https://github.com/hadley/svglite") | |
786 | (synopsis "SVG graphics device") | |
787 | (description | |
788 | "@code{svglite} is a graphics device that produces clean | |
789 | @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or | |
790 | hand editing. Compared to the built-in @code{svg()}, @code{svglite} is | |
791 | considerably faster, produces smaller files, and leaves text as is.") | |
792 | (license license:gpl2+))) | |
793 | ||
ed6094fc VVP |
794 | (define-public r-assertthat |
795 | (package | |
796 | (name "r-assertthat") | |
797 | (version "0.1") | |
798 | (source (origin | |
799 | (method url-fetch) | |
9cda3622 | 800 | (uri (cran-uri "assertthat" version)) |
ed6094fc VVP |
801 | (sha256 |
802 | (base32 | |
803 | "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk")))) | |
804 | (build-system r-build-system) | |
805 | (home-page "https://github.com/hadley/assertthat") | |
806 | (synopsis "Easy pre and post assertions") | |
807 | (description | |
808 | "Assertthat is an extension to stopifnot() that makes it easy to declare | |
809 | the pre and post conditions that your code should satisfy, while also | |
810 | producing friendly error messages so that your users know what they've done | |
811 | wrong.") | |
812 | (license license:gpl3+))) | |
6af48134 VVP |
813 | |
814 | (define-public r-lazyeval | |
815 | (package | |
816 | (name "r-lazyeval") | |
6d6a917a | 817 | (version "0.2.0") |
6af48134 VVP |
818 | (source (origin |
819 | (method url-fetch) | |
9cda3622 | 820 | (uri (cran-uri "lazyeval" version)) |
6af48134 VVP |
821 | (sha256 |
822 | (base32 | |
6d6a917a | 823 | "1jwdz40nznlc44hpjli7h98gnpa4d98ifggmj7z88h84n9aqywqk")))) |
6af48134 VVP |
824 | (build-system r-build-system) |
825 | (home-page "https://github.com/hadley/lazyeval") | |
826 | (synopsis "Lazy (non-standard) evaluation in R") | |
827 | (description | |
828 | "This package provides the tools necessary to do non-standard | |
829 | evaluation (NSE) in R.") | |
830 | (license license:gpl3+))) | |
8ea6b30f VVP |
831 | |
832 | (define-public r-dbi | |
833 | (package | |
834 | (name "r-dbi") | |
5b67bd6e | 835 | (version "0.5-1") |
8ea6b30f VVP |
836 | (source (origin |
837 | (method url-fetch) | |
9cda3622 | 838 | (uri (cran-uri "DBI" version)) |
8ea6b30f VVP |
839 | (sha256 |
840 | (base32 | |
5b67bd6e | 841 | "1idwm9lkmz6ns6h0vvgml18mg0k7vjqiv9p5svrdcmx7r1rirpdi")))) |
8ea6b30f VVP |
842 | (build-system r-build-system) |
843 | (home-page "https://github.com/rstats-db/DBI") | |
844 | (synopsis "R database interface") | |
845 | (description | |
846 | "The DBI package provides a database interface (DBI) definition for | |
847 | communication between R and relational database management systems. All | |
848 | classes in this package are virtual and need to be extended by the various | |
849 | R/DBMS implementations.") | |
850 | (license license:lgpl2.0+))) | |
675c9f44 VVP |
851 | |
852 | (define-public r-bh | |
853 | (package | |
854 | (name "r-bh") | |
fd7810d3 | 855 | (version "1.62.0-1") |
675c9f44 VVP |
856 | (source (origin |
857 | (method url-fetch) | |
858 | (uri (cran-uri "BH" version)) | |
859 | (sha256 | |
860 | (base32 | |
fd7810d3 | 861 | "01vfdpfznd4ynqql33z238xr262mvy3i80lyi8l3a3p3hi0a262p")))) |
675c9f44 VVP |
862 | (build-system r-build-system) |
863 | (home-page "https://github.com/eddelbuettel/bh") | |
864 | (synopsis "R package providing subset of Boost headers") | |
865 | (description | |
866 | "This package aims to provide the most useful subset of Boost libraries | |
867 | for template use among CRAN packages.") | |
868 | (license license:boost1.0))) | |
256ccc92 VVP |
869 | |
870 | (define-public r-evaluate | |
871 | (package | |
872 | (name "r-evaluate") | |
e0a90931 | 873 | (version "0.10") |
256ccc92 VVP |
874 | (source (origin |
875 | (method url-fetch) | |
876 | (uri (cran-uri "evaluate" version)) | |
877 | (sha256 | |
878 | (base32 | |
e0a90931 | 879 | "0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1")))) |
256ccc92 VVP |
880 | (build-system r-build-system) |
881 | (propagated-inputs | |
882 | `(("r-stringr" ,r-stringr))) | |
883 | (home-page "https://github.com/hadley/evaluate") | |
884 | (synopsis "Parsing and evaluation tools for R") | |
885 | (description | |
886 | "This package provides tools that allow you to recreate the parsing, | |
887 | evaluation and display of R code, with enough information that you can | |
888 | accurately recreate what happens at the command line. The tools can easily be | |
889 | adapted for other output formats, such as HTML or LaTeX.") | |
890 | (license license:gpl3+))) | |
c5bf3abe VVP |
891 | |
892 | (define-public r-formatr | |
893 | (package | |
894 | (name "r-formatr") | |
df25b004 | 895 | (version "1.4") |
c5bf3abe VVP |
896 | (source (origin |
897 | (method url-fetch) | |
898 | (uri (cran-uri "formatR" version)) | |
899 | (sha256 | |
900 | (base32 | |
df25b004 | 901 | "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f")))) |
c5bf3abe VVP |
902 | (build-system r-build-system) |
903 | (home-page "http://yihui.name/formatR") | |
904 | (synopsis "Format R code automatically") | |
905 | (description | |
906 | "This package provides a function to format R source code. Spaces and | |
907 | indent will be added to the code automatically, and comments will be preserved | |
908 | under certain conditions, so that R code will be more human-readable and tidy. | |
909 | There is also a Shiny app as a user interface in this package.") | |
910 | (license license:gpl3+))) | |
ad3f005b VVP |
911 | |
912 | (define-public r-highr | |
913 | (package | |
914 | (name "r-highr") | |
d5130e63 | 915 | (version "0.6") |
ad3f005b VVP |
916 | (source (origin |
917 | (method url-fetch) | |
918 | (uri (cran-uri "highr" version)) | |
919 | (sha256 | |
920 | (base32 | |
d5130e63 | 921 | "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3")))) |
ad3f005b VVP |
922 | (build-system r-build-system) |
923 | (home-page "https://github.com/yihui/highr") | |
924 | (synopsis "Syntax highlighting for R source code") | |
925 | (description | |
926 | "This package provides syntax highlighting for R source code. Currently | |
927 | it supports LaTeX and HTML output. Source code of other languages is | |
928 | supported via Andre Simon's highlight package.") | |
929 | (license license:gpl3+))) | |
acbb40fa VVP |
930 | |
931 | (define-public r-mime | |
932 | (package | |
933 | (name "r-mime") | |
2d037a2d | 934 | (version "0.5") |
acbb40fa VVP |
935 | (source (origin |
936 | (method url-fetch) | |
937 | (uri (cran-uri "mime" version)) | |
938 | (sha256 | |
939 | (base32 | |
2d037a2d | 940 | "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw")))) |
acbb40fa VVP |
941 | (build-system r-build-system) |
942 | (home-page "https://github.com/yihui/mime") | |
943 | (synopsis "R package to map filenames to MIME types") | |
944 | (description | |
945 | "This package guesses the MIME type from a filename extension using the | |
946 | data derived from /etc/mime.types in UNIX-type systems.") | |
947 | (license license:gpl2))) | |
3f8ac353 VVP |
948 | |
949 | (define-public r-markdown | |
950 | (package | |
951 | (name "r-markdown") | |
952 | (version "0.7.7") | |
953 | (source (origin | |
954 | (method url-fetch) | |
955 | (uri (cran-uri "markdown" version)) | |
956 | (sha256 | |
957 | (base32 | |
958 | "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb")))) | |
959 | (build-system r-build-system) | |
960 | ;; Skip check phase because the tests require the r-knitr package to be | |
961 | ;; installed. This prevents installation failures. Knitr normally | |
962 | ;; shouldn't be available since r-markdown is a dependency of the r-knitr | |
963 | ;; package. | |
964 | (arguments `(#:tests? #f)) | |
965 | (propagated-inputs | |
966 | `(("r-mime" ,r-mime))) | |
967 | (home-page "https://github.com/rstudio/markdown") | |
968 | (synopsis "Markdown rendering for R") | |
969 | (description | |
970 | "This package provides R bindings to the Sundown Markdown rendering | |
971 | library (https://github.com/vmg/sundown). Markdown is a plain-text formatting | |
972 | syntax that can be converted to XHTML or other formats.") | |
973 | (license license:gpl2))) | |
ea3a8095 VVP |
974 | |
975 | (define-public r-yaml | |
976 | (package | |
977 | (name "r-yaml") | |
9cdf10f1 | 978 | (version "2.1.14") |
ea3a8095 VVP |
979 | (source (origin |
980 | (method url-fetch) | |
981 | (uri (cran-uri "yaml" version)) | |
982 | (sha256 | |
983 | (base32 | |
9cdf10f1 | 984 | "0x88xicrf7vwp77xgan27mnpdljhpkn0pz5kphnwqi3ddy25k9a1")))) |
ea3a8095 VVP |
985 | (build-system r-build-system) |
986 | (home-page "https://cran.r-project.org/web/packages/yaml/") | |
987 | (synopsis "Methods to convert R data to YAML and back") | |
988 | (description | |
989 | "This package implements the libyaml YAML 1.1 parser and | |
990 | emitter (http://pyyaml.org/wiki/LibYAML) for R.") | |
991 | (license license:bsd-3))) | |
213656b9 VVP |
992 | |
993 | (define-public r-knitr | |
994 | (package | |
995 | (name "r-knitr") | |
eaec5506 | 996 | (version "1.15.1") |
213656b9 VVP |
997 | (source (origin |
998 | (method url-fetch) | |
999 | (uri (cran-uri "knitr" version)) | |
1000 | (sha256 | |
1001 | (base32 | |
eaec5506 | 1002 | "1pbxd3k7kv5sa1a5gxm0zc2bhjxdgx2nfch9xap5k85djmgsfqc1")))) |
213656b9 VVP |
1003 | (build-system r-build-system) |
1004 | (propagated-inputs | |
1005 | `(("r-evaluate" ,r-evaluate) | |
1006 | ("r-digest" ,r-digest) | |
213656b9 VVP |
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 | 1063 | |
0661b4db VVP |
1064 | (define-public r-pryr |
1065 | (package | |
1066 | (name "r-pryr") | |
1067 | (version "0.1.2") | |
1068 | (source (origin | |
1069 | (method url-fetch) | |
1070 | (uri (cran-uri "pryr" version)) | |
1071 | (sha256 | |
1072 | (base32 | |
1073 | "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5")))) | |
1074 | (build-system r-build-system) | |
1075 | (propagated-inputs | |
1076 | `(("r-stringr" ,r-stringr) | |
1077 | ("r-codetools" ,r-codetools))) | |
1078 | (native-inputs | |
1079 | `(("r-rcpp" ,r-rcpp))) | |
1080 | (home-page "https://github.com/hadley/pryr") | |
1081 | (synopsis "Tools for computing on the R language") | |
1082 | (description | |
1083 | "This package provides useful tools to pry back the covers of R and | |
1084 | understand the language at a deeper level.") | |
1085 | (license license:gpl2))) | |
b668a95c VVP |
1086 | |
1087 | (define-public r-memoise | |
1088 | (package | |
1089 | (name "r-memoise") | |
618dbdd7 | 1090 | (version "1.0.0") |
b668a95c VVP |
1091 | (source (origin |
1092 | (method url-fetch) | |
1093 | (uri (cran-uri "memoise" version)) | |
1094 | (sha256 | |
1095 | (base32 | |
618dbdd7 | 1096 | "0sq2dhpvxy17v1baj256r0jnygdy3m5a8x4zh6vhv29957qnq6zx")))) |
b668a95c VVP |
1097 | (build-system r-build-system) |
1098 | (propagated-inputs | |
1099 | `(("r-digest" ,r-digest))) | |
1100 | (home-page "http://github.com/hadley/memoise") | |
1101 | (synopsis "Memoise functions for R") | |
1102 | (description | |
1103 | "This R package allows to cache the results of a function so that when | |
1104 | you call it again with the same arguments it returns the pre-computed value.") | |
1105 | (license license:expat))) | |
834f7ff3 VVP |
1106 | |
1107 | (define-public r-crayon | |
1108 | (package | |
1109 | (name "r-crayon") | |
344d5323 | 1110 | (version "1.3.2") |
834f7ff3 VVP |
1111 | (source (origin |
1112 | (method url-fetch) | |
1113 | (uri (cran-uri "crayon" version)) | |
1114 | (sha256 | |
1115 | (base32 | |
344d5323 | 1116 | "0s2yam18slph7xsw4pyc9f92gdyf609r5w92yax69zh57kb7asws")))) |
834f7ff3 VVP |
1117 | (build-system r-build-system) |
1118 | (propagated-inputs | |
1119 | `(("r-memoise" ,r-memoise))) | |
1120 | (home-page "https://github.com/gaborcsardi/crayon") | |
1121 | (synopsis "Colored terminal output for R") | |
1122 | (description | |
1123 | "Colored terminal output on terminals that support ANSI color and | |
1124 | highlight codes. It also works in Emacs ESS. ANSI color support is | |
1125 | automatically detected. Colors and highlighting can be combined and nested. | |
1126 | New styles can also be created easily. This package was inspired by the | |
1127 | \"chalk\" JavaScript project.") | |
1128 | (license license:expat))) | |
5b9789a6 | 1129 | |
35b2001a RW |
1130 | (define-public r-praise |
1131 | (package | |
1132 | (name "r-praise") | |
1133 | (version "1.0.0") | |
1134 | (source | |
1135 | (origin | |
1136 | (method url-fetch) | |
1137 | (uri (cran-uri "praise" version)) | |
1138 | (sha256 | |
1139 | (base32 | |
1140 | "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw")))) | |
1141 | (build-system r-build-system) | |
1142 | (home-page "https://github.com/gaborcsardi/praise") | |
1143 | (synopsis "Functions to praise users") | |
1144 | (description | |
1145 | "This package provides template functions to assist in building friendly | |
1146 | R packages that praise their users.") | |
1147 | (license license:expat))) | |
1148 | ||
5b9789a6 VVP |
1149 | (define-public r-testthat |
1150 | (package | |
1151 | (name "r-testthat") | |
383f6337 | 1152 | (version "1.0.2") |
5b9789a6 VVP |
1153 | (source (origin |
1154 | (method url-fetch) | |
1155 | (uri (cran-uri "testthat" version)) | |
1156 | (sha256 | |
1157 | (base32 | |
383f6337 | 1158 | "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf")))) |
5b9789a6 VVP |
1159 | (build-system r-build-system) |
1160 | (propagated-inputs | |
1161 | `(("r-digest" ,r-digest) | |
99eca2b1 RW |
1162 | ("r-crayon" ,r-crayon) |
1163 | ("r-magrittr" ,r-magrittr) | |
1164 | ("r-praise" ,r-praise) | |
1165 | ("r-r6" ,r-r6))) | |
5b9789a6 VVP |
1166 | (home-page "https://github.com/hadley/testthat") |
1167 | (synopsis "Unit testing for R") | |
1168 | (description | |
1169 | "This package provides a unit testing system for R designed to be fun, | |
1170 | flexible and easy to set up.") | |
1171 | (license license:expat))) | |
ffd4b478 VVP |
1172 | |
1173 | (define-public r-r6 | |
1174 | (package | |
1175 | (name "r-r6") | |
bff4dc63 | 1176 | (version "2.2.0") |
ffd4b478 VVP |
1177 | (source (origin |
1178 | (method url-fetch) | |
1179 | (uri (cran-uri "R6" version)) | |
1180 | (sha256 | |
1181 | (base32 | |
bff4dc63 | 1182 | "1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx")))) |
ffd4b478 | 1183 | (build-system r-build-system) |
ffd4b478 VVP |
1184 | (home-page "https://github.com/wch/R6/") |
1185 | (synopsis "Classes with reference semantics in R") | |
1186 | (description | |
1187 | "The R6 package allows the creation of classes with reference semantics, | |
1188 | similar to R's built-in reference classes. Compared to reference classes, R6 | |
1189 | classes are simpler and lighter-weight, and they are not built on S4 classes | |
1190 | so they do not require the methods package. These classes allow public and | |
1191 | private members, and they support inheritance, even when the classes are | |
1192 | defined in different packages.") | |
1193 | (license license:expat))) | |
2a3a8ae7 | 1194 | |
a589acfb RW |
1195 | (define-public r-tibble |
1196 | (package | |
1197 | (name "r-tibble") | |
1198 | (version "1.2") | |
1199 | (source | |
1200 | (origin | |
1201 | (method url-fetch) | |
1202 | (uri (cran-uri "tibble" version)) | |
1203 | (sha256 | |
1204 | (base32 | |
1205 | "011i352ylq9b4xfcj7h10h7qsqd9qkc1rzc0pr1gf8qjb788p2pd")))) | |
1206 | (build-system r-build-system) | |
1207 | (propagated-inputs | |
1208 | `(("r-assertthat" ,r-assertthat) | |
1209 | ("r-lazyeval" ,r-lazyeval) | |
1210 | ("r-rcpp" ,r-rcpp))) | |
1211 | (home-page "https://github.com/hadley/tibble") | |
1212 | (synopsis "Simple data frames") | |
1213 | (description | |
1214 | "This package provides a @code{tbl_df} class that offers better checking | |
1215 | and printing capabilities than traditional data frames.") | |
1216 | (license license:expat))) | |
1217 | ||
2a3a8ae7 VVP |
1218 | (define-public r-dplyr |
1219 | (package | |
1220 | (name "r-dplyr") | |
de1eebd7 | 1221 | (version "0.5.0") |
2a3a8ae7 VVP |
1222 | (source (origin |
1223 | (method url-fetch) | |
1224 | (uri (cran-uri "dplyr" version)) | |
1225 | (sha256 | |
1226 | (base32 | |
de1eebd7 | 1227 | "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk")))) |
2a3a8ae7 VVP |
1228 | (build-system r-build-system) |
1229 | (propagated-inputs | |
1230 | `(("r-assertthat" ,r-assertthat) | |
1231 | ("r-r6" ,r-r6) | |
1232 | ("r-magrittr" ,r-magrittr) | |
1233 | ("r-lazyeval" ,r-lazyeval) | |
de1eebd7 RW |
1234 | ("r-dbi" ,r-dbi) |
1235 | ("r-tibble" ,r-tibble))) | |
2a3a8ae7 VVP |
1236 | (native-inputs |
1237 | `(("r-rcpp" ,r-rcpp) | |
1238 | ("r-bh" ,r-bh))) | |
1239 | (home-page "https://github.com/hadley/dplyr") | |
1240 | (synopsis "Tools for working with data frames in R") | |
1241 | (description | |
1242 | "dplyr is the next iteration of plyr. It is focussed on tools for | |
1243 | working with data frames. It has three main goals: 1) identify the most | |
1244 | important data manipulation tools needed for data analysis and make them easy | |
1245 | to use in R; 2) provide fast performance for in-memory data by writing key | |
1246 | pieces of code in C++; 3) use the same code interface to work with data no | |
1247 | matter where it is stored, whether in a data frame, a data table or | |
1248 | database.") | |
1249 | (license license:expat))) | |
91312ebe | 1250 | |
b4d6f408 RW |
1251 | (define-public r-acepack |
1252 | (package | |
1253 | (name "r-acepack") | |
572e1a0c | 1254 | (version "1.4.1") |
b4d6f408 RW |
1255 | (source |
1256 | (origin | |
1257 | (method url-fetch) | |
1258 | (uri (cran-uri "acepack" version)) | |
1259 | (sha256 | |
1260 | (base32 | |
572e1a0c | 1261 | "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2")))) |
b4d6f408 RW |
1262 | (build-system r-build-system) |
1263 | (inputs | |
1264 | `(("gfortran" ,gfortran))) | |
1265 | (home-page "http://cran.r-project.org/web/packages/acepack") | |
1266 | (synopsis "Functions for regression transformations") | |
1267 | (description | |
1268 | "This package provides ACE and AVAS methods for choosing regression | |
1269 | transformations.") | |
1270 | (license license:expat))) | |
1271 | ||
0926b877 RW |
1272 | (define-public r-cluster |
1273 | (package | |
1274 | (name "r-cluster") | |
130410d9 | 1275 | (version "2.0.5") |
0926b877 RW |
1276 | (source |
1277 | (origin | |
1278 | (method url-fetch) | |
1279 | (uri (cran-uri "cluster" version)) | |
1280 | (sha256 | |
1281 | (base32 | |
130410d9 | 1282 | "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b")))) |
0926b877 RW |
1283 | (build-system r-build-system) |
1284 | (inputs | |
1285 | `(("gfortran" ,gfortran))) | |
1286 | (home-page "http://cran.r-project.org/web/packages/cluster") | |
1287 | (synopsis "Methods for data cluster analysis") | |
1288 | (description | |
1289 | "This package provides tools that are useful in finding groups in data. | |
1290 | It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding | |
1291 | Groups in Data\".") | |
1292 | (license license:gpl2+))) | |
1293 | ||
0837dd07 RW |
1294 | (define-public r-foreign |
1295 | (package | |
1296 | (name "r-foreign") | |
72263db7 | 1297 | (version "0.8-67") |
0837dd07 RW |
1298 | (source |
1299 | (origin | |
1300 | (method url-fetch) | |
1301 | (uri (cran-uri "foreign" version)) | |
1302 | (sha256 | |
1303 | (base32 | |
72263db7 | 1304 | "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd")))) |
0837dd07 RW |
1305 | (build-system r-build-system) |
1306 | (home-page "http://cran.r-project.org/web/packages/foreign") | |
1307 | (synopsis "Read data stored by other statistics software in R") | |
1308 | (description | |
1309 | "This package provides functions for reading and writing data stored by | |
1310 | some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and | |
1311 | for reading and writing some dBase files.") | |
1312 | (license license:gpl2+))) | |
1313 | ||
b1acb445 RW |
1314 | (define-public r-formula |
1315 | (package | |
1316 | (name "r-formula") | |
1317 | (version "1.2-1") | |
1318 | (source | |
1319 | (origin | |
1320 | (method url-fetch) | |
1321 | (uri (cran-uri "Formula" version)) | |
1322 | (sha256 | |
1323 | (base32 | |
1324 | "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax")))) | |
1325 | (properties `((upstream-name . "Formula"))) | |
1326 | (build-system r-build-system) | |
1327 | (home-page "http://cran.r-project.org/web/packages/Formula") | |
1328 | (synopsis "Extended model formulas") | |
1329 | (description | |
1330 | "This package provides a new class @code{Formula}, which extends the base | |
1331 | class @code{formula}. It supports extended formulas with multiple parts of | |
1332 | regressors on the right-hand side and/or multiple responses on the left-hand | |
1333 | side.") | |
1334 | (license (list license:gpl2+ license:gpl3+)))) | |
1335 | ||
97ee973d RW |
1336 | (define-public r-locfit |
1337 | (package | |
1338 | (name "r-locfit") | |
1339 | (version "1.5-9.1") | |
1340 | (source | |
1341 | (origin | |
1342 | (method url-fetch) | |
1343 | (uri (cran-uri "locfit" version)) | |
1344 | (sha256 | |
1345 | (base32 | |
1346 | "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m")))) | |
1347 | (build-system r-build-system) | |
1348 | (home-page "http://cran.r-project.org/web/packages/locfit") | |
1349 | (synopsis "Local regression, likelihood and density estimation") | |
1350 | (description | |
1351 | "This package provides functions used for local regression, likelihood | |
1352 | and density estimation.") | |
1353 | (license (list license:gpl2+ license:gpl3+)))) | |
1354 | ||
91312ebe VVP |
1355 | (define-public r-chron |
1356 | (package | |
1357 | (name "r-chron") | |
3607afbe | 1358 | (version "2.3-48") |
91312ebe VVP |
1359 | (source (origin |
1360 | (method url-fetch) | |
1361 | (uri (cran-uri "chron" version)) | |
1362 | (sha256 | |
1363 | (base32 | |
3607afbe | 1364 | "1q1d0p2wq19w3mpfqnrg8nmspxqmhv4ap52r393s6y3abl36ccac")))) |
91312ebe VVP |
1365 | (build-system r-build-system) |
1366 | (home-page "http://cran.r-project.org/web/packages/chron") | |
1367 | (synopsis "Chronological R objects which can handle dates and times") | |
1368 | (description | |
1369 | "This package provides chronological R objects which can handle dates and | |
1370 | times.") | |
1371 | (license license:gpl2))) | |
0e4e03f8 | 1372 | |
62141c07 | 1373 | (define-public r-data-table |
0e4e03f8 | 1374 | (package |
62141c07 | 1375 | (name "r-data-table") |
76ce7c37 | 1376 | (version "1.10.0") |
0e4e03f8 VVP |
1377 | (source (origin |
1378 | (method url-fetch) | |
1379 | (uri (cran-uri "data.table" version)) | |
1380 | (sha256 | |
1381 | (base32 | |
76ce7c37 | 1382 | "1168arn4wjd1jj7kgr4sb8xd52hr8p8iqp85g5jwp3mkz4p76qfg")))) |
0e4e03f8 | 1383 | (build-system r-build-system) |
0e4e03f8 VVP |
1384 | (home-page "https://github.com/Rdatatable/data.table/wiki") |
1385 | (synopsis "Enhanced version of data.frame R object") | |
1386 | (description | |
62141c07 RW |
1387 | "The R package @code{data.table} is an extension of @code{data.frame} |
1388 | providing functions for fast aggregation of large data (e.g. 100GB in RAM), | |
1389 | fast ordered joins, fast add/modify/delete of columns by group, column listing | |
1390 | and fast file reading.") | |
1391 | (license license:gpl3+))) | |
9bc08aa0 | 1392 | |
a73f4cd1 RW |
1393 | (define-public r-xtable |
1394 | (package | |
1395 | (name "r-xtable") | |
1396 | (version "1.8-2") | |
1397 | (source | |
1398 | (origin | |
1399 | (method url-fetch) | |
1400 | (uri (cran-uri "xtable" version)) | |
1401 | (sha256 | |
1402 | (base32 | |
1403 | "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn")))) | |
1404 | (build-system r-build-system) | |
1405 | (native-inputs | |
1406 | `(("r-knitr" ,r-knitr))) | |
1407 | (home-page "http://xtable.r-forge.r-project.org/") | |
1408 | (synopsis "Export R tables to LaTeX or HTML") | |
1409 | (description | |
1410 | "This package provides tools to export R data as LaTeX and HTML tables.") | |
1411 | (license license:gpl2+))) | |
1412 | ||
9bc08aa0 RW |
1413 | (define-public python-patsy |
1414 | (package | |
1415 | (name "python-patsy") | |
f4cd2cea | 1416 | (version "0.4.1") |
9bc08aa0 RW |
1417 | (source (origin |
1418 | (method url-fetch) | |
f4cd2cea | 1419 | (uri (pypi-uri "patsy" version ".zip")) |
9bc08aa0 RW |
1420 | (sha256 |
1421 | (base32 | |
f4cd2cea | 1422 | "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w")))) |
9bc08aa0 RW |
1423 | (build-system python-build-system) |
1424 | (arguments | |
1425 | `(#:phases | |
1426 | (modify-phases %standard-phases | |
b41a05ce | 1427 | (replace 'check (lambda _ (zero? (system* "nosetests" "-v"))))))) |
9bc08aa0 RW |
1428 | (propagated-inputs |
1429 | `(("python-numpy" ,python-numpy) | |
1430 | ("python-scipy" ,python-scipy) | |
1431 | ("python-six" ,python-six))) | |
1432 | (native-inputs | |
1433 | `(("python-nose" ,python-nose) | |
1434 | ("unzip" ,unzip))) | |
1435 | (home-page "https://github.com/pydata/patsy") | |
1436 | (synopsis "Describe statistical models and build design matrices") | |
1437 | (description | |
1438 | "Patsy is a Python package for describing statistical models and for | |
1439 | building design matrices.") | |
1440 | ;; The majority of the code is distributed under BSD-2. The module | |
1441 | ;; patsy.compat contains code derived from the Python standard library, | |
1442 | ;; and is covered by the PSFL. | |
5c31f4aa | 1443 | (license (list license:bsd-2 license:psfl)))) |
9bc08aa0 RW |
1444 | |
1445 | (define-public python2-patsy | |
5c31f4aa | 1446 | (package-with-python2 python-patsy)) |
37fdba7e RW |
1447 | |
1448 | (define-public python-statsmodels | |
1449 | (package | |
1450 | (name "python-statsmodels") | |
6cb74776 | 1451 | (version "0.8.0") |
37fdba7e RW |
1452 | (source |
1453 | (origin | |
1454 | (method url-fetch) | |
6cb74776 | 1455 | (uri (pypi-uri "statsmodels" version)) |
37fdba7e RW |
1456 | (sha256 |
1457 | (base32 | |
6cb74776 | 1458 | "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6")) |
8b52167e | 1459 | (patches (search-patches "python-statsmodels-fix-tests.patch")))) |
37fdba7e RW |
1460 | (build-system python-build-system) |
1461 | (arguments | |
1462 | `(#:phases | |
1463 | (modify-phases %standard-phases | |
1464 | ;; tests must be run after installation | |
1465 | (delete 'check) | |
1466 | (add-after 'unpack 'set-matplotlib-backend-to-agg | |
1467 | (lambda _ | |
1468 | ;; Set the matplotlib backend to Agg to avoid problems using the | |
1469 | ;; GTK backend without a display. | |
6cb74776 MB |
1470 | (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py") |
1471 | '("statsmodels/tsa/vector_ar/tests/test_var.py" | |
1472 | "statsmodels/duration/tests/test_survfunc.py")) | |
37fdba7e RW |
1473 | (("import matplotlib\\.pyplot as plt" line) |
1474 | (string-append "import matplotlib;matplotlib.use('Agg');" | |
1475 | line))) | |
1476 | #t)) | |
1477 | (add-after 'install 'check | |
25b2c47d HG |
1478 | (lambda* (#:key inputs outputs #:allow-other-keys) |
1479 | ;; Make installed package available for running the tests | |
1480 | (add-installed-pythonpath inputs outputs) | |
1481 | (with-directory-excursion "/tmp" | |
1482 | (zero? (system* "nosetests" | |
1483 | "--stop" | |
1484 | "-v" "statsmodels")))))))) | |
37fdba7e RW |
1485 | (propagated-inputs |
1486 | `(("python-numpy" ,python-numpy) | |
1487 | ("python-scipy" ,python-scipy) | |
1488 | ("python-pandas" ,python-pandas) | |
1489 | ("python-patsy" ,python-patsy) | |
1490 | ("python-matplotlib" ,python-matplotlib))) | |
1491 | (native-inputs | |
1492 | `(("python-cython" ,python-cython) | |
1493 | ("python-nose" ,python-nose) | |
1494 | ("python-sphinx" ,python-sphinx))) | |
1495 | (home-page "http://statsmodels.sourceforge.net/") | |
1496 | (synopsis "Statistical modeling and econometrics in Python") | |
1497 | (description | |
1498 | "Statsmodels is a Python package that provides a complement to scipy for | |
1499 | statistical computations including descriptive statistics and estimation and | |
1500 | inference for statistical models.") | |
1501 | (license license:bsd-3))) | |
1502 | ||
1503 | (define-public python2-statsmodels | |
1504 | (let ((stats (package-with-python2 python-statsmodels))) | |
1505 | (package (inherit stats) | |
1506 | (propagated-inputs | |
8b52167e RW |
1507 | `(("python2-pytz" ,python2-pytz) |
1508 | ("python2-numpy" ,python2-numpy) | |
37fdba7e RW |
1509 | ("python2-scipy" ,python2-scipy) |
1510 | ("python2-pandas" ,python2-pandas) | |
1511 | ("python2-patsy" ,python2-patsy) | |
00e10c6e | 1512 | ("python2-matplotlib" ,python2-matplotlib)))))) |
67a167fd | 1513 | |
82047474 RJ |
1514 | (define-public r-coda |
1515 | (package | |
1516 | (name "r-coda") | |
62350c07 | 1517 | (version "0.19-1") |
82047474 RJ |
1518 | (source (origin |
1519 | (method url-fetch) | |
1520 | (uri (cran-uri "coda" version)) | |
1521 | (sha256 | |
1522 | (base32 | |
62350c07 | 1523 | "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl")))) |
82047474 | 1524 | (build-system r-build-system) |
82047474 RJ |
1525 | (home-page "http://cran.r-project.org/web/packages/coda") |
1526 | (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") | |
1527 | (description "This package provides functions for summarizing and plotting | |
1528 | the output from Markov Chain Monte Carlo (MCMC) simulations, as well as | |
1529 | diagnostic tests of convergence to the equilibrium distribution of the Markov | |
1530 | chain.") | |
1531 | (license license:gpl2+))) | |
1532 | ||
fdd0f7b2 RW |
1533 | (define-public r-ade4 |
1534 | (package | |
1535 | (name "r-ade4") | |
abb6f054 | 1536 | (version "1.7-5") |
fdd0f7b2 RW |
1537 | (source |
1538 | (origin | |
1539 | (method url-fetch) | |
1540 | (uri (cran-uri "ade4" version)) | |
1541 | (sha256 | |
1542 | (base32 | |
abb6f054 | 1543 | "0aaqbnydm5fb37nrvqj4bx6hxax7255j426cwh2lh88nyvznbq37")))) |
fdd0f7b2 RW |
1544 | (build-system r-build-system) |
1545 | (home-page "http://pbil.univ-lyon1.fr/ADE-4") | |
1546 | (synopsis "Multivariate data analysis and graphical display") | |
1547 | (description | |
1548 | "The ade4 package contains data analysis functions to analyze ecological | |
1549 | and environmental data in the framework of Euclidean exploratory methods.") | |
1550 | (license license:gpl2+))) | |
1551 | ||
67a167fd RW |
1552 | (define-public r-xml2 |
1553 | (package | |
1554 | (name "r-xml2") | |
e2ad0228 | 1555 | (version "1.0.0") |
67a167fd RW |
1556 | (source |
1557 | (origin | |
1558 | (method url-fetch) | |
1559 | (uri (cran-uri "xml2" version)) | |
1560 | (sha256 | |
1561 | (base32 | |
e2ad0228 | 1562 | "0f2alsrk3yykznbhnz4pcsg9mb72cv607vbapqx5kqfv39772kgr")))) |
67a167fd RW |
1563 | (build-system r-build-system) |
1564 | (inputs | |
1565 | `(("libxml2" ,libxml2))) | |
1566 | (propagated-inputs | |
1567 | `(("r-rcpp" ,r-rcpp) | |
1568 | ("r-bh" ,r-bh))) | |
1569 | (home-page "https://github.com/hadley/xml2") | |
1570 | (synopsis "Parse XML with R") | |
1571 | (description | |
1572 | "This package provides a simple, consistent interface to working with XML | |
1573 | files in R. It is built on top of the libxml2 C library.") | |
1574 | (license license:gpl2+))) | |
6140747f | 1575 | |
9003957e RW |
1576 | (define-public r-multitaper |
1577 | (package | |
1578 | (name "r-multitaper") | |
03306201 | 1579 | (version "1.0-12") |
9003957e RW |
1580 | (source |
1581 | (origin | |
1582 | (method url-fetch) | |
1583 | (uri (cran-uri "multitaper" version)) | |
1584 | (sha256 | |
1585 | (base32 | |
03306201 | 1586 | "011qpkwpjclfc24y2qqigmdnikqwdnanflfhihigh5b5k7qwgm5j")))) |
9003957e RW |
1587 | (build-system r-build-system) |
1588 | (native-inputs | |
1589 | `(("gfortran" ,gfortran))) | |
1590 | (home-page "http://github.com/wesleyburr/multitaper/") | |
1591 | (synopsis "Multitaper spectral analysis tools") | |
1592 | (description | |
1593 | "This package implements multitaper spectral estimation | |
1594 | techniques using prolate spheroidal sequences (Slepians) and sine | |
1595 | tapers for time series analysis. It includes an adaptive weighted | |
1596 | multitaper spectral estimate, a coherence estimate, Thomson's Harmonic | |
1597 | F-test, and complex demodulation. The Slepians sequences are | |
1598 | generated efficiently using a tridiagonal matrix solution, and | |
1599 | jackknifed confidence intervals are available for most estimates.") | |
1600 | (license license:gpl2+))) | |
1601 | ||
6140747f RW |
1602 | (define-public r-rversions |
1603 | (package | |
1604 | (name "r-rversions") | |
81147fe8 | 1605 | (version "1.0.3") |
6140747f RW |
1606 | (source (origin |
1607 | (method url-fetch) | |
1608 | (uri (cran-uri "rversions" version)) | |
1609 | (sha256 | |
1610 | (base32 | |
81147fe8 | 1611 | "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11")))) |
6140747f RW |
1612 | (build-system r-build-system) |
1613 | (propagated-inputs | |
1614 | `(("r-curl" ,r-curl) | |
1615 | ("r-xml2" ,r-xml2))) | |
1616 | (home-page "https://github.com/metacran/rversions") | |
1617 | (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") | |
1618 | (description | |
1619 | "This package provides functions to query the main R repository to find | |
1620 | the versions that @code{r-release} and @code{r-oldrel} refer to, and also all | |
1621 | previous R versions and their release dates.") | |
1622 | (license license:expat))) | |
1a77eccd RW |
1623 | |
1624 | (define-public r-whisker | |
1625 | (package | |
1626 | (name "r-whisker") | |
1627 | (version "0.3-2") | |
1628 | (source (origin | |
1629 | (method url-fetch) | |
1630 | (uri (cran-uri "whisker" version)) | |
1631 | (sha256 | |
1632 | (base32 | |
1633 | "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28")))) | |
1634 | (build-system r-build-system) | |
1635 | (home-page "http://github.com/edwindj/whisker") | |
1636 | (synopsis "Logicless mustache templating for R") | |
1637 | (description | |
1638 | "This package provides logicless templating, with a syntax that is not | |
1639 | limited to R.") | |
1640 | (license license:gpl3+))) | |
13d083af | 1641 | |
0d90462f RW |
1642 | (define-public r-backports |
1643 | (package | |
1644 | (name "r-backports") | |
41bc22a7 | 1645 | (version "1.0.4") |
0d90462f RW |
1646 | (source |
1647 | (origin | |
1648 | (method url-fetch) | |
1649 | (uri (cran-uri "backports" version)) | |
1650 | (sha256 | |
1651 | (base32 | |
41bc22a7 | 1652 | "0fssh5rnnvpp8wm0ml9gk765idwrgj07xyxpkhpidl9zwydxzif2")))) |
0d90462f RW |
1653 | (build-system r-build-system) |
1654 | (home-page "http://cran.r-project.org/web/packages/backports") | |
1655 | (synopsis "Reimplementations of functions introduced since R 3.0.0") | |
1656 | (description | |
1657 | "Provides implementations of functions which have been introduced in R | |
1658 | since version 3.0.0. The backports are conditionally exported which results | |
1659 | in R resolving the function names to the version shipped with R (if available) | |
1660 | and uses the implemented backports as fallback. This way package developers | |
1661 | can make use of the new functions without worrying about the minimum required | |
1662 | R version.") | |
1663 | (license license:gpl2+))) | |
1664 | ||
929d4aae RW |
1665 | (define-public r-checkmate |
1666 | (package | |
1667 | (name "r-checkmate") | |
fbe5161c | 1668 | (version "1.8.2") |
929d4aae RW |
1669 | (source |
1670 | (origin | |
1671 | (method url-fetch) | |
1672 | (uri (cran-uri "checkmate" version)) | |
1673 | (sha256 | |
1674 | (base32 | |
fbe5161c | 1675 | "1zqcggl9m7slvc0q6zyhssdypb7jzf3l9byl5vxh1qdwjiw2y64g")))) |
929d4aae RW |
1676 | (build-system r-build-system) |
1677 | (propagated-inputs | |
1678 | `(("r-backports" ,r-backports))) | |
1679 | (home-page "https://github.com/mllg/checkmate") | |
1680 | (synopsis "Fast and versatile argument checks") | |
1681 | (description | |
1682 | "This package provides tests and assertions to perform frequent argument | |
1683 | checks. A substantial part of the package was written in C to minimize any | |
1684 | worries about execution time overhead.") | |
1685 | (license license:bsd-3))) | |
1686 | ||
cd26ec3b RW |
1687 | (define-public r-bbmisc |
1688 | (package | |
1689 | (name "r-bbmisc") | |
1690 | (version "1.10") | |
1691 | (source | |
1692 | (origin | |
1693 | (method url-fetch) | |
1694 | (uri (cran-uri "BBmisc" version)) | |
1695 | (sha256 | |
1696 | (base32 | |
1697 | "0cw2mhw7qhdrx91zzd5iwyh7ch9fy4wxga8j63731q6sxr1airjl")))) | |
1698 | (properties `((upstream-name . "BBmisc"))) | |
1699 | (build-system r-build-system) | |
1700 | (propagated-inputs | |
1701 | `(("r-checkmate" ,r-checkmate))) | |
1702 | (home-page "https://github.com/berndbischl/BBmisc") | |
1703 | (synopsis "Miscellaneous functions for R package development") | |
1704 | (description | |
1705 | "This package provides miscellaneous helper functions for the development | |
1706 | of R packages.") | |
1707 | (license license:bsd-3))) | |
1708 | ||
dc4fb16d RW |
1709 | (define-public r-fail |
1710 | (package | |
1711 | (name "r-fail") | |
1712 | (version "1.3") | |
1713 | (source | |
1714 | (origin | |
1715 | (method url-fetch) | |
1716 | (uri (cran-uri "fail" version)) | |
1717 | (sha256 | |
1718 | (base32 | |
1719 | "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d")))) | |
1720 | (build-system r-build-system) | |
1721 | (propagated-inputs | |
1722 | `(("r-bbmisc" ,r-bbmisc) | |
1723 | ("r-checkmate" ,r-checkmate))) | |
1724 | (home-page "https://github.com/mllg/fail") | |
1725 | (synopsis "File abstraction interface layer (FAIL)") | |
1726 | (description | |
1727 | "This package provides a more comfortable interface to work with R data | |
1728 | or source files in a key-value fashion.") | |
1729 | (license license:bsd-3))) | |
1730 | ||
9e330278 RW |
1731 | (define-public r-batchjobs |
1732 | (package | |
1733 | (name "r-batchjobs") | |
1734 | (version "1.6") | |
1735 | (source | |
1736 | (origin | |
1737 | (method url-fetch) | |
1738 | (uri (cran-uri "BatchJobs" version)) | |
1739 | (sha256 | |
1740 | (base32 | |
1741 | "1kb99024jih5bycc226bl4jyvbbl1sg72q3m2wnlshl7s8p6vva0")))) | |
1742 | (properties `((upstream-name . "BatchJobs"))) | |
1743 | (build-system r-build-system) | |
1744 | (propagated-inputs | |
1745 | `(("r-bbmisc" ,r-bbmisc) | |
1746 | ("r-brew" ,r-brew) | |
1747 | ("r-checkmate" ,r-checkmate) | |
1748 | ("r-dbi" ,r-dbi) | |
1749 | ("r-digest" ,r-digest) | |
1750 | ("r-fail" ,r-fail) | |
1751 | ("r-rsqlite" ,r-rsqlite) | |
1752 | ("r-sendmailr" ,r-sendmailr) | |
1753 | ("r-stringr" ,r-stringr))) | |
1754 | (home-page "https://github.com/tudo-r/BatchJobs") | |
1755 | (synopsis "Batch computing with R") | |
1756 | (description | |
1757 | "This package provides @code{Map}, @code{Reduce} and @code{Filter} | |
1758 | variants to generate jobs on batch computing systems like PBS/Torque, LSF, | |
1759 | SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") | |
1760 | (license license:bsd-2))) | |
1761 | ||
13d083af RW |
1762 | (define-public r-brew |
1763 | (package | |
1764 | (name "r-brew") | |
1765 | (version "1.0-6") | |
1766 | (source (origin | |
1767 | (method url-fetch) | |
1768 | (uri (cran-uri "brew" version)) | |
1769 | (sha256 | |
1770 | (base32 | |
1771 | "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp")))) | |
1772 | (build-system r-build-system) | |
1773 | (home-page "http://cran.r-project.org/web/packages/brew") | |
1774 | (synopsis "Templating framework for report generation") | |
1775 | (description | |
1776 | "The brew package implements a templating framework for mixing text and R | |
1777 | code for report generation. The template syntax is similar to PHP, Ruby's erb | |
1778 | module, Java Server Pages, and Python's psp module.") | |
1779 | (license license:gpl2+))) | |
167c9882 RW |
1780 | |
1781 | (define-public r-roxygen2 | |
1782 | (package | |
1783 | (name "r-roxygen2") | |
904fa49d | 1784 | (version "5.0.1") |
167c9882 RW |
1785 | (source (origin |
1786 | (method url-fetch) | |
1787 | (uri (cran-uri "roxygen2" version)) | |
1788 | (sha256 | |
1789 | (base32 | |
904fa49d | 1790 | "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz")))) |
167c9882 RW |
1791 | (build-system r-build-system) |
1792 | (propagated-inputs | |
1793 | `(("r-brew" ,r-brew) | |
1794 | ("r-digest" ,r-digest) | |
1795 | ("r-rcpp" ,r-rcpp) | |
1796 | ("r-stringi" ,r-stringi) | |
1797 | ("r-stringr" ,r-stringr))) | |
1798 | (home-page "https://github.com/klutometis/roxygen") | |
1799 | (synopsis "In-source documentation system for R") | |
1800 | (description | |
1801 | "Roxygen2 is a Doxygen-like in-source documentation system for Rd, | |
1802 | collation, and NAMESPACE files.") | |
1803 | (license license:gpl2+))) | |
681e03c1 | 1804 | |
c26c0628 RW |
1805 | (define-public r-openssl |
1806 | (package | |
1807 | (name "r-openssl") | |
437d064d | 1808 | (version "0.9.6") |
c26c0628 RW |
1809 | (source |
1810 | (origin | |
1811 | (method url-fetch) | |
1812 | (uri (cran-uri "openssl" version)) | |
1813 | (sha256 | |
1814 | (base32 | |
437d064d | 1815 | "0ffwllii8xl6sa2v66134g0fwaw1y3zn3mvaa4nrc120vv5d3mkd")))) |
c26c0628 RW |
1816 | (build-system r-build-system) |
1817 | (inputs | |
1818 | `(("openssl" ,openssl))) | |
1819 | (home-page "https://github.com/jeroenooms/openssl") | |
1820 | (synopsis "Toolkit for encryption, signatures and certificates") | |
1821 | (description | |
1822 | "This package provides R bindings to OpenSSL libssl and libcrypto, plus | |
1823 | custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 | |
1824 | and P-521. Cryptographic signatures can either be created and verified | |
1825 | manually or via x509 certificates. AES block cipher is used in CBC mode for | |
1826 | symmetric encryption; RSA for asymmetric (public key) encryption. High-level | |
1827 | envelope functions combine RSA and AES for encrypting arbitrary sized data. | |
1828 | Other utilities include key generators, hash functions (md5, sha1, sha256, | |
1829 | etc), base64 encoder, a secure random number generator, and @code{bignum} math | |
1830 | methods for manually performing crypto calculations on large multibyte | |
1831 | integers.") | |
1832 | (license license:expat))) | |
1833 | ||
681e03c1 RW |
1834 | (define-public r-httr |
1835 | (package | |
1836 | (name "r-httr") | |
e58498b6 | 1837 | (version "1.2.1") |
681e03c1 RW |
1838 | (source (origin |
1839 | (method url-fetch) | |
1840 | (uri (cran-uri "httr" version)) | |
1841 | (sha256 | |
1842 | (base32 | |
e58498b6 | 1843 | "03kkjlhyvvi5znwaxfm6cmdsg3q7ivwsvkzgabhjdj2jxs80pfg7")))) |
681e03c1 RW |
1844 | (build-system r-build-system) |
1845 | (propagated-inputs | |
1846 | `(("r-curl" ,r-curl) | |
1847 | ("r-digest" ,r-digest) | |
1848 | ("r-jsonlite" ,r-jsonlite) | |
59bf9f4e | 1849 | ("r-openssl" ,r-openssl) |
681e03c1 RW |
1850 | ("r-mime" ,r-mime) |
1851 | ("r-r6" ,r-r6) | |
1852 | ("r-stringr" ,r-stringr))) | |
1853 | (home-page "https://github.com/hadley/httr") | |
1854 | (synopsis "Tools for working with URLs and HTTP") | |
1855 | (description | |
1856 | "The aim of httr is to provide a wrapper for RCurl customised to the | |
1857 | demands of modern web APIs. It provides useful tools for working with HTTP | |
1858 | organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration | |
1859 | functions make it easy to control additional request components.") | |
1860 | (license license:expat))) | |
035711f1 RW |
1861 | |
1862 | (define-public r-git2r | |
1863 | (package | |
1864 | (name "r-git2r") | |
0c74399d | 1865 | (version "0.18.0") |
035711f1 RW |
1866 | (source (origin |
1867 | (method url-fetch) | |
1868 | (uri (cran-uri "git2r" version)) | |
1869 | (sha256 | |
1870 | (base32 | |
0c74399d | 1871 | "0bgzdsdi9n6l8pchivs6a2g4ksa56qs8hygpyv2c0ndqmx4jxcwi")))) |
035711f1 RW |
1872 | (build-system r-build-system) |
1873 | ;; This R package contains modified sources of libgit2. This modified | |
1874 | ;; version of libgit2 is built as the package is built. Hence libgit2 is | |
1875 | ;; not among the inputs of this package. | |
1876 | (inputs | |
1877 | `(("libssh2" ,libssh2) | |
1878 | ("openssl" ,openssl) | |
1879 | ("zlib" ,zlib))) | |
1880 | (home-page "https://github.com/ropensci/git2r") | |
1881 | (synopsis "Access Git repositories with R") | |
1882 | (description | |
1883 | "This package provides an R interface to the libgit2 library, which is a | |
1884 | pure C implementation of the Git core methods.") | |
1885 | ;; GPLv2 only with linking exception. | |
1886 | (license license:gpl2))) | |
81a4228b RW |
1887 | |
1888 | (define-public r-rstudioapi | |
1889 | (package | |
1890 | (name "r-rstudioapi") | |
e2cfac44 | 1891 | (version "0.6") |
81a4228b RW |
1892 | (source (origin |
1893 | (method url-fetch) | |
1894 | (uri (cran-uri "rstudioapi" version)) | |
1895 | (sha256 | |
1896 | (base32 | |
e2cfac44 | 1897 | "1zkvz72z6nw0xc8bhb21y5x1nk6avijs0w8n4vsbvw9sn76wc96s")))) |
81a4228b RW |
1898 | (build-system r-build-system) |
1899 | (home-page "http://cran.r-project.org/web/packages/rstudioapi") | |
1900 | (synopsis "Safely access the RStudio API") | |
1901 | (description | |
1902 | "This package provides functions to access the RStudio API and provide | |
1903 | informative error messages when it's not available.") | |
1904 | (license license:expat))) | |
d6e21589 RW |
1905 | |
1906 | (define-public r-devtools | |
1907 | (package | |
1908 | (name "r-devtools") | |
3bb9708a | 1909 | (version "1.12.0") |
d6e21589 RW |
1910 | (source (origin |
1911 | (method url-fetch) | |
1912 | (uri (cran-uri "devtools" version)) | |
1913 | (sha256 | |
1914 | (base32 | |
3bb9708a | 1915 | "16l18szmj482vf3dvl2fqwwa4zaqylmic1pk7dwh428cp0d86mzi")))) |
d6e21589 RW |
1916 | (build-system r-build-system) |
1917 | (propagated-inputs | |
1918 | `(("r-curl" ,r-curl) | |
1919 | ("r-digest" ,r-digest) | |
1920 | ("r-evaluate" ,r-evaluate) | |
1921 | ("r-git2r" ,r-git2r) | |
1922 | ("r-httr" ,r-httr) | |
1923 | ("r-jsonlite" ,r-jsonlite) | |
1924 | ("r-memoise" ,r-memoise) | |
1925 | ("r-roxygen2" ,r-roxygen2) | |
1926 | ("r-rstudioapi" ,r-rstudioapi) | |
1927 | ("r-rversions" ,r-rversions) | |
fa9f0e6c RJ |
1928 | ("r-whisker" ,r-whisker) |
1929 | ("r-withr" ,r-withr))) | |
d6e21589 RW |
1930 | (home-page "https://github.com/hadley/devtools") |
1931 | (synopsis "Tools to make developing R packages easier") | |
1932 | (description "The devtools package is a collection of package development | |
1933 | tools to simplify the devolpment of R packages.") | |
1934 | (license license:gpl2+))) | |
03af370f | 1935 | |
a080e50c RJ |
1936 | (define-public r-withr |
1937 | (package | |
1938 | (name "r-withr") | |
348bb8d6 | 1939 | (version "1.0.2") |
a080e50c RJ |
1940 | (source (origin |
1941 | (method url-fetch) | |
1942 | (uri (cran-uri "withr" version)) | |
1943 | (sha256 | |
1944 | (base32 | |
348bb8d6 | 1945 | "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493")))) |
a080e50c RJ |
1946 | (build-system r-build-system) |
1947 | (home-page "https://github.com/jimhester/withr") | |
1948 | (synopsis "Run code with temporarily modified global state") | |
1949 | (description | |
1950 | "This package provides a set of functions to run R code in an environment | |
1951 | in which global state has been temporarily modified. Many of these functions | |
1952 | were originally a part of the r-devtools package.") | |
1953 | (license license:gpl2+))) | |
1954 | ||
b90314b4 RW |
1955 | (define-public r-hms |
1956 | (package | |
1957 | (name "r-hms") | |
2a1c1b80 | 1958 | (version "0.3") |
b90314b4 RW |
1959 | (source |
1960 | (origin | |
1961 | (method url-fetch) | |
1962 | (uri (cran-uri "hms" version)) | |
1963 | (sha256 | |
1964 | (base32 | |
2a1c1b80 | 1965 | "127znf522r5mn3k6frhdd7pqh063bs3l85gn9h7cx50hpjf2as4k")))) |
b90314b4 RW |
1966 | (build-system r-build-system) |
1967 | (home-page "https://github.com/rstats-db/hms") | |
1968 | (synopsis "Pretty time of day") | |
1969 | (description | |
1970 | "This package implements an S3 class for storing and formatting | |
1971 | time-of-day values, based on the @code{difftime} class.") | |
1972 | (license license:gpl3+))) | |
1973 | ||
03af370f RW |
1974 | (define-public r-readr |
1975 | (package | |
1976 | (name "r-readr") | |
8c6e2b84 | 1977 | (version "1.0.0") |
03af370f RW |
1978 | (source (origin |
1979 | (method url-fetch) | |
1980 | (uri (cran-uri "readr" version)) | |
1981 | (sha256 | |
1982 | (base32 | |
8c6e2b84 | 1983 | "0xji0dbal6xcxnsmjj678fw29n7wrj45wrd5ng99yhqqijcm9f6g")))) |
03af370f RW |
1984 | (build-system r-build-system) |
1985 | (propagated-inputs | |
1986 | `(("r-curl" ,r-curl) | |
1987 | ("r-rcpp" ,r-rcpp) | |
8c6e2b84 RW |
1988 | ("r-hms" ,r-hms) |
1989 | ("r-tibble" ,r-tibble) | |
1990 | ("r-r6" ,r-r6) | |
03af370f RW |
1991 | ("r-bh" ,r-bh))) |
1992 | (home-page "https://github.com/hadley/readr") | |
1993 | (synopsis "Read tabular data") | |
1994 | (description | |
1995 | "This package provides functions to read flat or tabular text files from | |
1996 | disk (or a connection).") | |
1997 | (license license:gpl2+))) | |
60a9d3d0 RW |
1998 | |
1999 | (define-public r-plotrix | |
2000 | (package | |
2001 | (name "r-plotrix") | |
7b030c9f | 2002 | (version "3.6-4") |
60a9d3d0 RW |
2003 | (source (origin |
2004 | (method url-fetch) | |
2005 | (uri (cran-uri "plotrix" version)) | |
2006 | (sha256 | |
2007 | (base32 | |
7b030c9f | 2008 | "1wxzjnzvkl3aga51ad2xhv4s7v46kvnp4z0nz4cb9cn10057sfw8")))) |
60a9d3d0 RW |
2009 | (build-system r-build-system) |
2010 | (home-page "http://cran.r-project.org/web/packages/plotrix") | |
2011 | (synopsis "Various plotting functions") | |
2012 | (description | |
2013 | "This package provides lots of plotting, various labeling, axis and color | |
2014 | scaling functions for R.") | |
2015 | (license license:gpl2+))) | |
2a40f763 RW |
2016 | |
2017 | (define-public r-gridbase | |
2018 | (package | |
2019 | (name "r-gridbase") | |
2020 | (version "0.4-7") | |
2021 | (source (origin | |
2022 | (method url-fetch) | |
2023 | (uri (cran-uri "gridBase" version)) | |
2024 | (sha256 | |
2025 | (base32 | |
2026 | "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy")))) | |
2027 | (build-system r-build-system) | |
2028 | (home-page "http://cran.r-project.org/web/packages/gridBase") | |
2029 | (synopsis "Integration of base and grid graphics") | |
2030 | (description | |
2031 | "This package provides an integration of base and grid graphics for R.") | |
2032 | (license license:gpl2+))) | |
ca3476cd RW |
2033 | |
2034 | (define-public r-lattice | |
2035 | (package | |
2036 | (name "r-lattice") | |
fce4dfd8 | 2037 | (version "0.20-34") |
ca3476cd RW |
2038 | (source (origin |
2039 | (method url-fetch) | |
2040 | (uri (cran-uri "lattice" version)) | |
2041 | (sha256 | |
2042 | (base32 | |
fce4dfd8 | 2043 | "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) |
ca3476cd RW |
2044 | (build-system r-build-system) |
2045 | (home-page "http://lattice.r-forge.r-project.org/") | |
2046 | (synopsis "High-level data visualization system") | |
2047 | (description | |
2048 | "The lattice package provides a powerful and elegant high-level data | |
2049 | visualization system inspired by Trellis graphics, with an emphasis on | |
2050 | multivariate data. Lattice is sufficient for typical graphics needs, and is | |
2051 | also flexible enough to handle most nonstandard requirements.") | |
2052 | (license license:gpl2+))) | |
e22d4ca4 | 2053 | |
b20abbcd RW |
2054 | (define-public r-latticeextra |
2055 | (package | |
2056 | (name "r-latticeextra") | |
2057 | (version "0.6-28") | |
2058 | (source | |
2059 | (origin | |
2060 | (method url-fetch) | |
2061 | (uri (cran-uri "latticeExtra" version)) | |
2062 | (sha256 | |
2063 | (base32 | |
2064 | "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq")))) | |
2065 | (properties `((upstream-name . "latticeExtra"))) | |
2066 | (build-system r-build-system) | |
2067 | (propagated-inputs | |
2068 | `(("r-lattice" ,r-lattice) | |
2069 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
2070 | (home-page "http://latticeextra.r-forge.r-project.org/") | |
2071 | (synopsis "Extra graphical utilities based on lattice") | |
2072 | (description | |
2073 | "Building on the infrastructure provided by the lattice package, this | |
2074 | package provides several new high-level graphics functions and methods, as | |
2075 | well as additional utilities such as panel and axis annotation functions.") | |
2076 | (license license:gpl2+))) | |
2077 | ||
e22d4ca4 RW |
2078 | (define-public r-rcpparmadillo |
2079 | (package | |
2080 | (name "r-rcpparmadillo") | |
a8e45b32 | 2081 | (version "0.7.600.1.0") |
e22d4ca4 RW |
2082 | (source (origin |
2083 | (method url-fetch) | |
2084 | (uri (cran-uri "RcppArmadillo" version)) | |
2085 | (sha256 | |
2086 | (base32 | |
a8e45b32 | 2087 | "0k1wniip184j0ckcg9kcjy2q4mcfj5jpd1nkk4l0ab75ad8znywv")) |
e22d4ca4 RW |
2088 | (modules '((guix build utils))) |
2089 | ;; Remove bundled armadillo sources | |
2090 | (snippet | |
2091 | '(begin | |
2092 | (delete-file-recursively "inst/include/armadillo_bits") | |
2093 | (delete-file "inst/include/armadillo"))))) | |
2094 | (properties `((upstream-name . "RcppArmadillo"))) | |
2095 | (build-system r-build-system) | |
2096 | (arguments | |
2097 | `(#:phases | |
2098 | (modify-phases %standard-phases | |
2099 | (add-after 'unpack 'link-against-armadillo | |
2100 | (lambda _ | |
2101 | (substitute* "src/Makevars" | |
2102 | (("PKG_LIBS=" prefix) | |
2103 | (string-append prefix "-larmadillo")))))))) | |
2104 | (propagated-inputs | |
2105 | `(("r-rcpp" ,r-rcpp) | |
2106 | ("armadillo" ,armadillo-for-rcpparmadillo))) | |
2107 | (home-page "https://github.com/RcppCore/RcppArmadillo") | |
2108 | (synopsis "Rcpp integration for the Armadillo linear algebra library") | |
2109 | (description | |
2110 | "Armadillo is a templated C++ linear algebra library that aims towards a | |
2111 | good balance between speed and ease of use. Integer, floating point and | |
2112 | complex numbers are supported, as well as a subset of trigonometric and | |
2113 | statistics functions. Various matrix decompositions are provided through | |
2114 | optional integration with LAPACK and ATLAS libraries. This package includes | |
2115 | the header files from the templated Armadillo library.") | |
2116 | ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp | |
2117 | ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or | |
2118 | ;; later, as is the rest of 'Rcpp'. | |
2119 | (license license:gpl2+))) | |
bb6d2dad RW |
2120 | |
2121 | (define-public r-bitops | |
2122 | (package | |
2123 | (name "r-bitops") | |
2124 | (version "1.0-6") | |
2125 | (source (origin | |
2126 | (method url-fetch) | |
2127 | (uri (cran-uri "bitops" version)) | |
2128 | (sha256 | |
2129 | (base32 | |
2130 | "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv")))) | |
2131 | (build-system r-build-system) | |
2132 | (home-page "http://cran.r-project.org/web/packages/bitops") | |
2133 | (synopsis "Bitwise operations") | |
2134 | (description | |
2135 | "This package provides functions for bitwise operations on integer | |
2136 | vectors.") | |
2137 | (license license:gpl2+))) | |
4c1f2705 RW |
2138 | |
2139 | (define-public r-catools | |
2140 | (package | |
2141 | (name "r-catools") | |
2142 | (version "1.17.1") | |
2143 | (source (origin | |
2144 | (method url-fetch) | |
2145 | (uri (cran-uri "caTools" version)) | |
2146 | (sha256 | |
2147 | (base32 | |
2148 | "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank")))) | |
2149 | (properties `((upstream-name . "caTools"))) | |
2150 | (build-system r-build-system) | |
2151 | (propagated-inputs | |
2152 | `(("r-bitops" ,r-bitops))) | |
2153 | (home-page "http://cran.r-project.org/web/packages/caTools") | |
2154 | (synopsis "Various tools including functions for moving window statistics") | |
2155 | (description | |
2156 | "This package contains several basic utility functions including: | |
2157 | moving (rolling, running) window statistic functions, read/write for GIF and | |
2158 | ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 | |
2159 | encoder/decoder, round-off-error-free sum and cumsum, etc.") | |
2160 | (license license:gpl3+))) | |
77bdb276 | 2161 | |
046e27e3 RW |
2162 | (define-public r-rprojroot |
2163 | (package | |
2164 | (name "r-rprojroot") | |
2165 | (version "1.1") | |
2166 | (source | |
2167 | (origin | |
2168 | (method url-fetch) | |
2169 | (uri (cran-uri "rprojroot" version)) | |
2170 | (sha256 | |
2171 | (base32 | |
2172 | "04ywfpar4d2hyi4rh4fbixrbzd665gpa2jhx67g8857cr70pp0nh")))) | |
2173 | (build-system r-build-system) | |
2174 | (propagated-inputs | |
2175 | `(("r-backports" ,r-backports))) | |
2176 | (home-page "https://github.com/krlmlr/rprojroot") | |
2177 | (synopsis "Finding files in project subdirectories") | |
2178 | (description | |
2179 | "This package helps accessing files relative to a project root. It | |
2180 | provides helpers for robust, reliable and flexible paths to files below a | |
2181 | project root. The root of a project is defined as a directory that matches a | |
2182 | certain criterion, e.g., it contains a certain regular file.") | |
2183 | (license license:gpl3))) | |
2184 | ||
77bdb276 RW |
2185 | (define-public r-rmarkdown |
2186 | (package | |
2187 | (name "r-rmarkdown") | |
ca380feb | 2188 | (version "1.3") |
77bdb276 RW |
2189 | (source |
2190 | (origin | |
2191 | (method url-fetch) | |
2192 | (uri (cran-uri "rmarkdown" version)) | |
2193 | (sha256 | |
2194 | (base32 | |
ca380feb | 2195 | "1vvxyf3zhyxx6k697lia299456hryp8nh3zr0fc27f3107a8mcjf")))) |
77bdb276 RW |
2196 | (properties `((upstream-name . "rmarkdown"))) |
2197 | (build-system r-build-system) | |
2198 | (propagated-inputs | |
2199 | `(("r-catools" ,r-catools) | |
8e1369f1 | 2200 | ("r-evaluate" ,r-evaluate) |
77bdb276 | 2201 | ("r-htmltools" ,r-htmltools) |
87a7c55e RW |
2202 | ("r-jsonlite" ,r-jsonlite) |
2203 | ("r-base64enc" ,r-base64enc) | |
77bdb276 | 2204 | ("r-knitr" ,r-knitr) |
ca380feb | 2205 | ("r-rprojroot" ,r-rprojroot) |
77bdb276 RW |
2206 | ("r-yaml" ,r-yaml) |
2207 | ("ghc-pandoc" ,ghc-pandoc))) | |
2208 | (home-page "http://rmarkdown.rstudio.com") | |
2209 | (synopsis "Convert R Markdown documents into a variety of formats") | |
2210 | (description | |
2211 | "This package provides tools to convert R Markdown documents into a | |
2212 | variety of formats.") | |
2213 | (license license:gpl3+))) | |
b73751c8 RW |
2214 | |
2215 | (define-public r-gtable | |
2216 | (package | |
2217 | (name "r-gtable") | |
810e4195 | 2218 | (version "0.2.0") |
b73751c8 RW |
2219 | (source (origin |
2220 | (method url-fetch) | |
2221 | (uri (cran-uri "gtable" version)) | |
2222 | (sha256 | |
2223 | (base32 | |
810e4195 | 2224 | "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0")))) |
b73751c8 RW |
2225 | (properties `((upstream-name . "gtable"))) |
2226 | (build-system r-build-system) | |
9c53993f TGR |
2227 | (home-page "https://cran.r-project.org/web/packages/gtable") |
2228 | (synopsis "R library to arrange grobs in tables") | |
b73751c8 | 2229 | (description |
9c53993f TGR |
2230 | "Gtable is a collection of tools to make it easier to work with |
2231 | \"tables\" of grobs.") | |
b73751c8 | 2232 | (license license:gpl2+))) |
9e47f30b RW |
2233 | |
2234 | (define-public r-gridextra | |
2235 | (package | |
2236 | (name "r-gridextra") | |
1647e10e | 2237 | (version "2.2.1") |
9e47f30b RW |
2238 | (source (origin |
2239 | (method url-fetch) | |
2240 | (uri (cran-uri "gridExtra" version)) | |
2241 | (sha256 | |
2242 | (base32 | |
1647e10e | 2243 | "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4")))) |
9e47f30b RW |
2244 | (properties `((upstream-name . "gridExtra"))) |
2245 | (build-system r-build-system) | |
2246 | (propagated-inputs | |
2247 | `(("r-gtable" ,r-gtable))) | |
2248 | (native-inputs | |
2249 | `(("r-knitr" ,r-knitr))) ;for building vignettes | |
2250 | (home-page "https://github.com/baptiste/gridextra") | |
2251 | (synopsis "Miscellaneous functions for \"Grid\" graphics") | |
2252 | (description | |
2253 | "This package provides a number of user-level functions to work with | |
2254 | @code{grid} graphics, notably to arrange multiple grid-based plots on a page, | |
2255 | and draw tables.") | |
2256 | (license license:gpl2+))) | |
2257 | ||
28c041af RW |
2258 | (define-public r-plogr |
2259 | (package | |
2260 | (name "r-plogr") | |
2261 | (version "0.1-1") | |
2262 | (source | |
2263 | (origin | |
2264 | (method url-fetch) | |
2265 | (uri (cran-uri "plogr" version)) | |
2266 | (sha256 | |
2267 | (base32 | |
2268 | "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) | |
2269 | (build-system r-build-system) | |
2270 | (home-page "https://github.com/krlmlr/plogr") | |
2271 | (synopsis "R bindings for the plog C++ logging library") | |
2272 | (description | |
2273 | "This package provides the header files for a stripped-down version of | |
2274 | the plog header-only C++ logging library, and a method to log to R's standard | |
2275 | error stream.") | |
2276 | (license license:expat))) | |
2277 | ||
21e4d6a9 RW |
2278 | (define-public r-rsqlite |
2279 | (package | |
2280 | (name "r-rsqlite") | |
35bb2ff8 | 2281 | (version "1.1-1") |
21e4d6a9 RW |
2282 | (source (origin |
2283 | (method url-fetch) | |
2284 | (uri (cran-uri "RSQLite" version)) | |
2285 | (sha256 | |
2286 | (base32 | |
35bb2ff8 | 2287 | "11vnzds5gidgakdmsbdn0bvnsz064ym1savwb7l6gc1bjn7xa2k4")))) |
21e4d6a9 RW |
2288 | (properties `((upstream-name . "RSQLite"))) |
2289 | (build-system r-build-system) | |
2290 | (propagated-inputs | |
35bb2ff8 RW |
2291 | `(("r-dbi" ,r-dbi) |
2292 | ("r-bh" ,r-bh) | |
2293 | ("r-memoise" ,r-memoise) | |
2294 | ("r-plogr" ,r-plogr) | |
2295 | ("r-rcpp" ,r-rcpp))) | |
21e4d6a9 RW |
2296 | (home-page "https://github.com/rstats-db/RSQLite") |
2297 | (synopsis "SQLite interface for R") | |
2298 | (description | |
2299 | "This package embeds the SQLite database engine in R and provides an | |
2300 | interface compliant with the DBI package. The source for the SQLite | |
2301 | engine (version 3.8.6) is included.") | |
2302 | (license license:lgpl2.0+))) | |
2303 | ||
cefaa79c RW |
2304 | (define-public r-rcurl |
2305 | (package | |
2306 | (name "r-rcurl") | |
2307 | (version "1.95-0.1.2") | |
2308 | (source (origin | |
2309 | (method url-fetch) | |
2310 | (uri (string-append "http://www.bioconductor.org/packages/" | |
2311 | "release/extra/src/" | |
2312 | "contrib/RCurl_" version ".tar.gz")) | |
2313 | (sha256 | |
2314 | (base32 | |
2315 | "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc")))) | |
2316 | (properties `((upstream-name . "RCurl"))) | |
2317 | (build-system r-build-system) | |
2318 | (inputs | |
2319 | `(("libcurl" ,curl))) | |
2320 | (propagated-inputs | |
2321 | `(("r-bitops" ,r-bitops))) | |
2322 | (home-page "http://www.omegahat.org/RCurl") | |
2323 | (synopsis "General network client interface for R") | |
2324 | (description | |
2325 | "The package allows one to compose general HTTP requests and provides | |
2326 | convenient functions to fetch URIs, GET and POST forms, etc. and process the | |
2327 | results returned by the Web server. This provides a great deal of control | |
2328 | over the HTTP/FTP/... connection and the form of the request while providing a | |
2329 | higher-level interface than is available just using R socket connections. | |
2330 | Additionally, the underlying implementation is robust and extensive, | |
2331 | supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, | |
2332 | ldap, and also supports cookies, redirects, authentication, etc.") | |
2333 | (license license:bsd-3))) | |
2334 | ||
543ded36 RW |
2335 | (define-public r-xml |
2336 | (package | |
2337 | (name "r-xml") | |
db1b38af | 2338 | (version "3.98-1.5") |
543ded36 RW |
2339 | (source (origin |
2340 | (method url-fetch) | |
2341 | (uri (cran-uri "XML" version)) | |
2342 | (sha256 | |
2343 | (base32 | |
db1b38af | 2344 | "0dcdj7ryn8lm7wmv4hqhh9jxa5k97l6ad8xyvb932yfkwj1g1byy")))) |
543ded36 RW |
2345 | (properties |
2346 | `((upstream-name . "XML"))) | |
2347 | (build-system r-build-system) | |
2348 | (inputs | |
2349 | `(("libxml2" ,libxml2))) | |
543ded36 RW |
2350 | (home-page "http://www.omegahat.org/RSXML") |
2351 | (synopsis "Tools for parsing and generating XML within R") | |
2352 | (description | |
2353 | "Many approaches for both reading and creating XML (and HTML) | |
2354 | documents (including DTDs), both local and accessible via HTTP or FTP. Also | |
2355 | offers access to an XPath \"interpreter\".") | |
2356 | (license license:bsd-2))) | |
2357 | ||
b74f64a9 RW |
2358 | (define-public r-xnomial |
2359 | (package | |
2360 | (name "r-xnomial") | |
2361 | (version "1.0.4") | |
2362 | (source | |
2363 | (origin (method url-fetch) | |
2364 | (uri (cran-uri "XNomial" version)) | |
2365 | (sha256 | |
2366 | (base32 | |
2367 | "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6")))) | |
2368 | (properties (quasiquote ((upstream-name . "XNomial")))) | |
2369 | (build-system r-build-system) | |
2370 | (home-page "http://cran.r-project.org/web/packages/XNomial") | |
2371 | (synopsis "Goodness-of-Fit test for multinomial data") | |
2372 | (description | |
2373 | "This package provides an exact Goodness-of-Fit test for | |
2374 | multinomial data with fixed probabilities. It can be used to | |
2375 | determine whether a set of counts fits a given expected ratio. To see | |
2376 | whether a set of observed counts fits an expectation, one can examine | |
2377 | all possible outcomes with @code{xmulti()} or a random sample of them | |
2378 | with @code{xmonte()} and find the probability of an observation | |
2379 | deviating from the expectation by at least as much as the observed. | |
2380 | As a measure of deviation from the expected, one can use the | |
2381 | log-likelihood ratio, the multinomial probability, or the classic | |
2382 | chi-square statistic. A histogram of the test statistic can also be | |
2383 | plotted and compared with the asymptotic curve.") | |
2384 | (license (list license:gpl2+ license:gpl3+)))) | |
2385 | ||
ca65d387 RW |
2386 | (define-public r-lambda-r |
2387 | (package | |
2388 | (name "r-lambda-r") | |
b9ab3b08 | 2389 | (version "1.1.9") |
ca65d387 RW |
2390 | (source (origin |
2391 | (method url-fetch) | |
2392 | (uri (cran-uri "lambda.r" version)) | |
2393 | (sha256 | |
2394 | (base32 | |
b9ab3b08 | 2395 | "1j6287iqvs3ill6r5g6ksf5809qp0l0nf20ib8266m1r09lc9j14")))) |
ca65d387 RW |
2396 | (properties `((upstream-name . "lambda.r"))) |
2397 | (build-system r-build-system) | |
2398 | (home-page "http://cran.r-project.org/web/packages/lambda.r") | |
2399 | (synopsis "Functional programming extension for R") | |
2400 | (description | |
2401 | "This package provides a language extension to efficiently write | |
2402 | functional programs in R. Syntax extensions include multi-part function | |
2403 | definitions, pattern matching, guard statements, built-in (optional) type | |
2404 | safety.") | |
2405 | (license license:lgpl3+))) | |
2406 | ||
b9ff33b5 RW |
2407 | (define-public r-futile-options |
2408 | (package | |
2409 | (name "r-futile-options") | |
2410 | (version "1.0.0") | |
2411 | (source (origin | |
2412 | (method url-fetch) | |
2413 | (uri (cran-uri "futile.options" version)) | |
2414 | (sha256 | |
2415 | (base32 | |
2416 | "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f")))) | |
2417 | (properties | |
2418 | `((upstream-name . "futile.options"))) | |
2419 | (build-system r-build-system) | |
2420 | (home-page "http://cran.r-project.org/web/packages/futile.options") | |
2421 | (synopsis "Options management framework") | |
2422 | (description | |
2423 | "The futile.options subsystem provides an easy user-defined options | |
2424 | management system that is properly scoped. This means that options created | |
2425 | via @code{futile.options} are fully self-contained and will not collide with | |
2426 | options defined in other packages.") | |
2427 | (license license:lgpl3+))) | |
2428 | ||
6b82f56c RW |
2429 | (define-public r-futile-logger |
2430 | (package | |
2431 | (name "r-futile-logger") | |
27f10d3d | 2432 | (version "1.4.3") |
6b82f56c RW |
2433 | (source (origin |
2434 | (method url-fetch) | |
2435 | (uri (cran-uri "futile.logger" version)) | |
2436 | (sha256 | |
2437 | (base32 | |
27f10d3d | 2438 | "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy")))) |
6b82f56c RW |
2439 | (properties `((upstream-name . "futile.logger"))) |
2440 | (build-system r-build-system) | |
2441 | (propagated-inputs | |
2442 | `(("r-futile-options" ,r-futile-options) | |
2443 | ("r-lambda-r" ,r-lambda-r))) | |
2444 | (home-page "http://cran.r-project.org/web/packages/futile.logger") | |
2445 | (synopsis "Logging utility for R") | |
2446 | (description | |
2447 | "This package provides a simple yet powerful logging utility. Based | |
2448 | loosely on log4j, futile.logger takes advantage of R idioms to make logging a | |
2449 | convenient and easy to use replacement for @code{cat} and @code{print} | |
2450 | statements.") | |
2451 | (license license:lgpl3+))) | |
2452 | ||
3e4c0c66 RW |
2453 | (define-public r-segmented |
2454 | (package | |
2455 | (name "r-segmented") | |
2456 | (version "0.5-1.4") | |
2457 | (source | |
2458 | (origin | |
2459 | (method url-fetch) | |
2460 | (uri (cran-uri "segmented" version)) | |
2461 | (sha256 | |
2462 | (base32 | |
2463 | "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i")))) | |
2464 | (build-system r-build-system) | |
2465 | (home-page "http://cran.r-project.org/web/packages/segmented") | |
2466 | (synopsis "Regression models with breakpoints estimation") | |
2467 | (description | |
2468 | "Given a regression model, segmented updates the model by adding one or | |
2469 | more segmented (i.e., piecewise-linear) relationships. Several variables with | |
2470 | multiple breakpoints are allowed.") | |
2471 | (license (list license:gpl2+ license:gpl3+)))) | |
2472 | ||
bc899123 RW |
2473 | (define-public r-snow |
2474 | (package | |
2475 | (name "r-snow") | |
cf738e96 | 2476 | (version "0.4-2") |
bc899123 RW |
2477 | (source (origin |
2478 | (method url-fetch) | |
2479 | (uri (cran-uri "snow" version)) | |
2480 | (sha256 | |
2481 | (base32 | |
cf738e96 | 2482 | "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf")))) |
bc899123 RW |
2483 | (build-system r-build-system) |
2484 | (home-page "http://cran.r-project.org/web/packages/snow") | |
2485 | (synopsis "Support for simple parallel computing in R") | |
2486 | (description | |
2487 | "The snow package provides support for simple parallel computing on a | |
2488 | network of workstations using R. A master R process calls @code{makeCluster} | |
2489 | to start a cluster of worker processes; the master process then uses functions | |
2490 | such as @code{clusterCall} and @code{clusterApply} to execute R code on the | |
2491 | worker processes and collect and return the results on the master.") | |
2492 | (license (list license:gpl2+ license:gpl3+)))) | |
2493 | ||
d706257b RW |
2494 | (define-public r-sparsem |
2495 | (package | |
2496 | (name "r-sparsem") | |
773a5011 | 2497 | (version "1.74") |
d706257b RW |
2498 | (source (origin |
2499 | (method url-fetch) | |
2500 | (uri (cran-uri "SparseM" version)) | |
2501 | (sha256 | |
2502 | (base32 | |
773a5011 | 2503 | "1fpfhld887y5lyb8jydprmv5krqm1fk6n53z942b4g4z1v4g04j7")))) |
d706257b RW |
2504 | (properties |
2505 | `((upstream-name . "SparseM"))) | |
d7786ce9 RW |
2506 | (inputs |
2507 | `(("gfortran" ,gfortran))) | |
d706257b RW |
2508 | (build-system r-build-system) |
2509 | (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") | |
2510 | (synopsis "Sparse linear algebra") | |
2511 | (description | |
2512 | "This package provides some basic linear algebra functionality for sparse | |
2513 | matrices. It includes Cholesky decomposition and backsolving as well as | |
2514 | standard R subsetting and Kronecker products.") | |
2515 | (license license:gpl2+))) | |
2516 | ||
264df1a4 RW |
2517 | (define-public r-iterators |
2518 | (package | |
2519 | (name "r-iterators") | |
2520 | (version "1.0.8") | |
2521 | (source | |
2522 | (origin | |
2523 | (method url-fetch) | |
2524 | (uri (cran-uri "iterators" version)) | |
2525 | (sha256 | |
2526 | (base32 | |
2527 | "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf")))) | |
2528 | (build-system r-build-system) | |
2529 | (home-page "http://cran.r-project.org/web/packages/iterators") | |
2530 | (synopsis "Iterator construct for R") | |
2531 | (description | |
2532 | "This package provides support for iterators, which allow a programmer to | |
2533 | traverse through all the elements of a vector, list, or other collection of | |
2534 | data.") | |
2535 | (license license:asl2.0))) | |
2536 | ||
7a6f5f03 RW |
2537 | (define-public r-codetools |
2538 | (package | |
2539 | (name "r-codetools") | |
4f2ebc16 | 2540 | (version "0.2-15") |
7a6f5f03 RW |
2541 | (source |
2542 | (origin | |
2543 | (method url-fetch) | |
2544 | (uri (cran-uri "codetools" version)) | |
2545 | (sha256 | |
2546 | (base32 | |
4f2ebc16 | 2547 | "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) |
7a6f5f03 | 2548 | (build-system r-build-system) |
fe08b1a7 | 2549 | (home-page "https://cran.r-project.org/web/packages/codetools") |
7a6f5f03 RW |
2550 | (synopsis "Code analysis tools for R") |
2551 | (description "This package provides code analysis tools for R to check R | |
2552 | code for possible problems.") | |
2553 | (license (list license:gpl2+ license:gpl3+)))) | |
2554 | ||
b2cdb027 RW |
2555 | (define-public r-foreach |
2556 | (package | |
2557 | (name "r-foreach") | |
2558 | (version "1.4.3") | |
2559 | (source | |
2560 | (origin | |
2561 | (method url-fetch) | |
2562 | (uri (cran-uri "foreach" version)) | |
2563 | (sha256 | |
2564 | (base32 | |
2565 | "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y")))) | |
2566 | (build-system r-build-system) | |
2567 | (propagated-inputs | |
2568 | `(("r-codetools" ,r-codetools) | |
2569 | ("r-iterators" ,r-iterators))) | |
2570 | (home-page "http://cran.r-project.org/web/packages/foreach") | |
2571 | (synopsis "Foreach looping construct for R") | |
2572 | (description | |
2573 | "This package provides support for the @code{foreach} looping construct. | |
2574 | @code{foreach} is an idiom that allows for iterating over elements in a | |
2575 | collection, without the use of an explicit loop counter. This package in | |
2576 | particular is intended to be used for its return value, rather than for its | |
2577 | side effects. In that sense, it is similar to the standard @code{lapply} | |
2578 | function, but doesn't require the evaluation of a function. Using | |
2579 | @code{foreach} without side effects also facilitates executing the loop in | |
2580 | parallel.") | |
2581 | (license license:asl2.0))) | |
2582 | ||
71cafa04 RW |
2583 | (define-public r-doparallel |
2584 | (package | |
2585 | (name "r-doparallel") | |
2586 | (version "1.0.10") | |
2587 | (source | |
2588 | (origin | |
2589 | (method url-fetch) | |
2590 | (uri (cran-uri "doParallel" version)) | |
2591 | (sha256 | |
2592 | (base32 | |
2593 | "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh")))) | |
2594 | (properties `((upstream-name . "doParallel"))) | |
2595 | (build-system r-build-system) | |
2596 | (propagated-inputs | |
2597 | `(("r-foreach" ,r-foreach) | |
2598 | ("r-iterators" ,r-iterators))) | |
2599 | (home-page "http://cran.r-project.org/web/packages/doParallel") | |
2600 | (synopsis "Foreach parallel adaptor for the 'parallel' package") | |
2601 | (description | |
2602 | "This package provides a parallel backend for the @code{%dopar%} function | |
2603 | using the parallel package.") | |
2604 | (license license:gpl2+))) | |
2605 | ||
66cf0f05 RW |
2606 | (define-public r-domc |
2607 | (package | |
2608 | (name "r-domc") | |
2609 | (version "1.3.4") | |
2610 | (source | |
2611 | (origin | |
2612 | (method url-fetch) | |
2613 | (uri (cran-uri "doMC" version)) | |
2614 | (sha256 | |
2615 | (base32 | |
2616 | "0y47jl6g4f83r14pj8bafdzq1phj7bxy5dwyz3k43d2rr8phk8bn")))) | |
2617 | (properties `((upstream-name . "doMC"))) | |
2618 | (build-system r-build-system) | |
2619 | (propagated-inputs | |
2620 | `(("r-foreach" ,r-foreach) | |
2621 | ("r-iterators" ,r-iterators))) | |
2622 | (home-page "http://cran.r-project.org/web/packages/doMC") | |
2623 | (synopsis "Foreach parallel adaptor for the 'parallel' package") | |
2624 | (description | |
2625 | "This package provides a parallel backend for the @code{%dopar%} function | |
2626 | using the multicore functionality of the parallel package.") | |
2627 | (license license:gpl2+))) | |
2628 | ||
a8227e4a RW |
2629 | (define-public r-dt |
2630 | (package | |
2631 | (name "r-dt") | |
f791b689 | 2632 | (version "0.2") |
a8227e4a RW |
2633 | (source (origin |
2634 | (method url-fetch) | |
2635 | (uri (cran-uri "DT" version)) | |
2636 | (sha256 | |
2637 | (base32 | |
f791b689 | 2638 | "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1")))) |
a8227e4a RW |
2639 | (properties |
2640 | `((upstream-name . "DT"))) | |
2641 | (build-system r-build-system) | |
2642 | (propagated-inputs | |
2643 | `(("r-htmltools" ,r-htmltools) | |
2644 | ("r-htmlwidgets" ,r-htmlwidgets) | |
2645 | ("r-magrittr" ,r-magrittr))) | |
2646 | (home-page "http://rstudio.github.io/DT") | |
2647 | (synopsis "R wrapper of the DataTables JavaScript library") | |
2648 | (description | |
2649 | "This package allows for data objects in R to be rendered as HTML tables | |
2650 | using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). | |
2651 | The 'DataTables' library has been included in this R package.") | |
2652 | ;; The DT package as a whole is distributed under GPLv3. The DT package | |
2653 | ;; inludes other software components under different licenses: | |
2654 | ;; | |
2655 | ;; * Expat: jQuery, jquery.highlight.js, DataTables | |
2656 | ;; * ASL2.0: selectize.js | |
2657 | ;; * WTFPL: noUiSlider | |
2658 | (license (list license:gpl3 | |
2659 | license:expat | |
2660 | license:asl2.0 | |
2661 | (license:non-copyleft "http://www.wtfpl.net/txt/copying/"))))) | |
2662 | ||
a69a5935 RW |
2663 | (define-public r-base64enc |
2664 | (package | |
2665 | (name "r-base64enc") | |
2666 | (version "0.1-3") | |
2667 | (source (origin | |
2668 | (method url-fetch) | |
2669 | (uri (cran-uri "base64enc" version)) | |
2670 | (sha256 | |
2671 | (base32 | |
2672 | "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd")))) | |
2673 | (build-system r-build-system) | |
2674 | (home-page "http://www.rforge.net/base64enc") | |
2675 | (synopsis "Tools for Base64 encoding") | |
2676 | (description | |
2677 | "This package provides tools for handling Base64 encoding. It is more | |
2678 | flexible than the orphaned \"base64\" package.") | |
2679 | (license license:gpl2+))) | |
2680 | ||
dada39aa RW |
2681 | (define-public r-irlba |
2682 | (package | |
2683 | (name "r-irlba") | |
89242ea4 | 2684 | (version "2.1.2") |
dada39aa RW |
2685 | (source |
2686 | (origin | |
2687 | (method url-fetch) | |
2688 | (uri (cran-uri "irlba" version)) | |
2689 | (sha256 | |
2690 | (base32 | |
89242ea4 | 2691 | "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) |
dada39aa RW |
2692 | (build-system r-build-system) |
2693 | (home-page "http://cran.r-project.org/web/packages/irlba") | |
2694 | (synopsis "Methods for eigendecomposition of large matrices") | |
2695 | (description | |
2696 | "This package provides fast and memory efficient methods for truncated | |
2697 | singular and eigenvalue decompositions, as well as for principal component | |
2698 | analysis of large sparse or dense matrices.") | |
2699 | (license (list license:gpl2+ license:gpl3+)))) | |
2700 | ||
c7f04517 BW |
2701 | (define-public r-glmnet |
2702 | (package | |
2703 | (name "r-glmnet") | |
2704 | (version "2.0-5") | |
2705 | (source | |
2706 | (origin | |
2707 | (method url-fetch) | |
2708 | (uri (cran-uri "glmnet" version)) | |
2709 | (sha256 | |
2710 | (base32 | |
2711 | "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c")))) | |
2712 | (build-system r-build-system) | |
2713 | (inputs | |
2714 | `(("gfortran" ,gfortran))) | |
2715 | (propagated-inputs | |
2716 | `(("r-foreach" ,r-foreach))) | |
2717 | (home-page "http://www.jstatsoft.org/v33/i01") | |
2718 | (synopsis "Lasso and elastic-net regularized generalized linear models") | |
2719 | (description | |
2720 | "The glmnet package provides efficient procedures for fitting the entire | |
2721 | lasso or elastic-net regularization path for linear and Poisson regression, as | |
2722 | well as logistic, multinomial, Cox, multiple-response Gaussian and grouped | |
2723 | multinomial models. The algorithm uses cyclical coordinate descent in a | |
2724 | path-wise fashion.") | |
2725 | (license license:gpl2+))) | |
2726 | ||
3a6607f0 RW |
2727 | (define-public r-pkgmaker |
2728 | (package | |
2729 | (name "r-pkgmaker") | |
2730 | (version "0.22") | |
2731 | (source | |
2732 | (origin | |
2733 | (method url-fetch) | |
2734 | (uri (cran-uri "pkgmaker" version)) | |
2735 | (sha256 | |
2736 | (base32 | |
2737 | "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r")))) | |
2738 | (build-system r-build-system) | |
2739 | (propagated-inputs | |
2740 | `(("r-codetools" ,r-codetools) | |
2741 | ("r-digest" ,r-digest) | |
2742 | ("r-registry" ,r-registry) | |
2743 | ("r-stringr" ,r-stringr) | |
2744 | ("r-xtable" ,r-xtable))) | |
2745 | (home-page "https://renozao.github.io/pkgmaker") | |
2746 | (synopsis "Package development utilities") | |
2747 | (description | |
2748 | "This package provides some low-level utilities to use for R package | |
2749 | development. It currently provides managers for multiple package specific | |
2750 | options and registries, vignette, unit test and bibtex related utilities.") | |
2751 | (license license:gpl2+))) | |
2752 | ||
2d0f7d80 RW |
2753 | (define-public r-registry |
2754 | (package | |
2755 | (name "r-registry") | |
2756 | (version "0.3") | |
2757 | (source | |
2758 | (origin | |
2759 | (method url-fetch) | |
2760 | (uri (cran-uri "registry" version)) | |
2761 | (sha256 | |
2762 | (base32 | |
2763 | "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq")))) | |
2764 | (build-system r-build-system) | |
2765 | (home-page "http://cran.r-project.org/web/packages/registry") | |
2766 | (synopsis "Infrastructure for R package registries") | |
2767 | (description | |
2768 | "This package provides a generic infrastructure for creating and using R | |
2769 | package registries.") | |
2770 | (license license:gpl2+))) | |
2771 | ||
790034bd RW |
2772 | (define-public r-rngtools |
2773 | (package | |
2774 | (name "r-rngtools") | |
2775 | (version "1.2.4") | |
2776 | (source | |
2777 | (origin | |
2778 | (method url-fetch) | |
2779 | (uri (cran-uri "rngtools" version)) | |
2780 | (sha256 | |
2781 | (base32 | |
2782 | "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097")))) | |
2783 | (build-system r-build-system) | |
2784 | (propagated-inputs | |
2785 | `(("r-digest" ,r-digest) | |
2786 | ("r-pkgmaker" ,r-pkgmaker) | |
2787 | ("r-stringr" ,r-stringr))) | |
2788 | (home-page "https://renozao.github.io/rngtools") | |
2789 | (synopsis "Utility functions for working with random number generators") | |
2790 | (description | |
2791 | "This package contains a set of functions for working with Random Number | |
2792 | Generators (RNGs). In particular, it defines a generic S4 framework for | |
2793 | getting/setting the current RNG, or RNG data that are embedded into objects | |
2794 | for reproducibility. Notably, convenient default methods greatly facilitate | |
2795 | the way current RNG settings can be changed.") | |
2796 | (license license:gpl3+))) | |
2797 | ||
c72c1249 RW |
2798 | (define-public r-rtsne |
2799 | (package | |
2800 | (name "r-rtsne") | |
2801 | (version "0.11") | |
2802 | (source | |
2803 | (origin | |
2804 | (method url-fetch) | |
2805 | (uri (cran-uri "Rtsne" version)) | |
2806 | (sha256 | |
2807 | (base32 | |
2808 | "0zi4nxgpiv1gpdmcnqdhz5kymzp8m5xj02zpf290p1yyydl76bhy")))) | |
2809 | (properties `((upstream-name . "Rtsne"))) | |
2810 | (build-system r-build-system) | |
2811 | (propagated-inputs | |
2812 | `(("r-rcpp" ,r-rcpp))) | |
2813 | (home-page "https://github.com/jkrijthe/Rtsne") | |
2814 | (synopsis "T-distributed stochastic neighbor embedding") | |
2815 | (description | |
2816 | "This package provides an R wrapper around the fast T-distributed | |
2817 | Stochastic Neighbor Embedding using a Barnes-Hut implementation.") | |
2818 | ;; The declared license for this package is BSD-3, but it also includes | |
2819 | ;; code licensed under BSD-4. | |
2820 | (license (list license:bsd-3 license:bsd-4)))) | |
2821 | ||
c533589c RW |
2822 | (define-public r-e1071 |
2823 | (package | |
2824 | (name "r-e1071") | |
2825 | (version "1.6-7") | |
2826 | (source | |
2827 | (origin | |
2828 | (method url-fetch) | |
2829 | (uri (cran-uri "e1071" version)) | |
2830 | (sha256 | |
2831 | (base32 | |
2832 | "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h")))) | |
2833 | (build-system r-build-system) | |
2834 | (home-page "http://cran.r-project.org/web/packages/e1071") | |
2835 | (synopsis "Miscellaneous functions for probability theory") | |
2836 | (description | |
2837 | "This package provides functions for latent class analysis, short time | |
2838 | Fourier transform, fuzzy clustering, support vector machines, shortest path | |
2839 | computation, bagged clustering, naive Bayes classifier, and more.") | |
2840 | (license license:gpl2+))) | |
2841 | ||
c6105d69 RJ |
2842 | (define-public r-bigmemory-sri |
2843 | (package | |
2844 | (name "r-bigmemory-sri") | |
2845 | (version "0.1.3") | |
2846 | (source | |
2847 | (origin | |
2848 | (method url-fetch) | |
2849 | (uri (cran-uri "bigmemory.sri" version)) | |
2850 | (sha256 | |
2851 | (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m")))) | |
2852 | (properties | |
2853 | `((upstream-name . "bigmemory.sri"))) | |
2854 | (build-system r-build-system) | |
2855 | (home-page "http://cran.r-project.org/web/packages/bigmemory.sri") | |
2856 | (synopsis "Shared resource interface for the bigmemory package") | |
2857 | (description "This package provides a shared resource interface for the | |
2858 | bigmemory and synchronicity packages.") | |
2859 | ;; Users can choose either LGPLv3 or ASL2.0. | |
2860 | (license (list license:lgpl3 license:asl2.0)))) | |
4a838652 RJ |
2861 | |
2862 | (define-public r-synchronicity | |
2863 | (package | |
2864 | (name "r-synchronicity") | |
2865 | (version "1.1.9.1") | |
2866 | (source | |
2867 | (origin | |
2868 | (method url-fetch) | |
2869 | (uri (cran-uri "synchronicity" version)) | |
2870 | (sha256 | |
2871 | (base32 | |
2872 | "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c")))) | |
2873 | (build-system r-build-system) | |
2874 | (propagated-inputs | |
2875 | `(("r-bh" ,r-bh) | |
2876 | ("r-bigmemory-sri" ,r-bigmemory-sri) | |
2877 | ("r-rcpp" ,r-rcpp))) | |
2878 | (home-page "http://www.bigmemory.org") | |
2879 | (synopsis "Boost mutex functionality in R") | |
2880 | (description "This package provides support for synchronization | |
2881 | via mutexes and may eventually support interprocess communication and | |
2882 | message passing.") | |
2883 | ;; Users can choose either LGPLv3 or ASL2.0. | |
2884 | (license (list license:lgpl3 license:asl2.0)))) | |
59523c4c RJ |
2885 | |
2886 | (define-public r-bigmemory | |
2887 | (package | |
2888 | (name "r-bigmemory") | |
2889 | (version "4.5.19") | |
2890 | (source | |
2891 | (origin | |
2892 | (method url-fetch) | |
2893 | (uri (cran-uri "bigmemory" version)) | |
2894 | (sha256 | |
2895 | (base32 | |
2896 | "191gbzca557kpk7mdsg716vfyqpr7j5din6qb8hin4g1nkzzwmg6")))) | |
2897 | (build-system r-build-system) | |
2898 | (propagated-inputs | |
2899 | `(("r-bh" ,r-bh) | |
2900 | ("r-rcpp" ,r-rcpp) | |
2901 | ("r-bigmemory-sri" ,r-bigmemory-sri) | |
2902 | ("r-r-utils" ,r-r-utils))) | |
2903 | (home-page "http://www.bigmemory.org") | |
2904 | (synopsis "Manage large matrices with shared memory or memory-mapped files") | |
2905 | (description "This package provides methods to create, store, access, and | |
2906 | manipulate large matrices. Matrices are allocated to shared memory and may use | |
2907 | memory-mapped files.") | |
2908 | ;; Users can choose either LGPLv3 or ASL2.0. | |
2909 | (license (list license:lgpl3 license:asl2.0)))) | |
c6105d69 | 2910 | |
b783ff78 RW |
2911 | (define-public r-nmf |
2912 | (package | |
2913 | (name "r-nmf") | |
2914 | (version "0.20.6") | |
2915 | (source | |
2916 | (origin | |
2917 | (method url-fetch) | |
2918 | (uri (cran-uri "NMF" version)) | |
2919 | (sha256 | |
2920 | (base32 | |
2921 | "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z")))) | |
2922 | (properties `((upstream-name . "NMF"))) | |
2923 | (build-system r-build-system) | |
2924 | (propagated-inputs | |
2925 | `(("r-cluster" ,r-cluster) | |
8af47ef6 RJ |
2926 | ("r-bigmemory" ,r-bigmemory) |
2927 | ("r-synchronicity" ,r-synchronicity) | |
b783ff78 RW |
2928 | ("r-colorspace" ,r-colorspace) |
2929 | ("r-digest" ,r-digest) | |
2930 | ("r-doparallel" ,r-doparallel) | |
2931 | ("r-foreach" ,r-foreach) | |
2932 | ("r-ggplot2" ,r-ggplot2) | |
2933 | ("r-gridbase" ,r-gridbase) | |
2934 | ("r-pkgmaker" ,r-pkgmaker) | |
2935 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
2936 | ("r-registry" ,r-registry) | |
2937 | ("r-reshape2" ,r-reshape2) | |
2938 | ("r-rngtools" ,r-rngtools) | |
2939 | ("r-stringr" ,r-stringr))) | |
2940 | (home-page "http://renozao.github.io/NMF") | |
2941 | (synopsis "Algorithms and framework for nonnegative matrix factorization") | |
2942 | (description | |
2943 | "This package provides a framework to perform Non-negative Matrix | |
2944 | Factorization (NMF). The package implements a set of already published | |
2945 | algorithms and seeding methods, and provides a framework to test, develop and | |
2946 | plug new or custom algorithms. Most of the built-in algorithms have been | |
2947 | optimized in C++, and the main interface function provides an easy way of | |
2948 | performing parallel computations on multicore machines.") | |
2949 | (license license:gpl2+))) | |
2950 | ||
07f911ba RW |
2951 | (define-public r-igraph |
2952 | (package | |
2953 | (name "r-igraph") | |
2954 | (version "1.0.1") | |
2955 | (source | |
2956 | (origin | |
2957 | (method url-fetch) | |
2958 | (uri (cran-uri "igraph" version)) | |
2959 | (sha256 | |
2960 | (base32 | |
2961 | "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w")))) | |
2962 | (build-system r-build-system) | |
2963 | (native-inputs | |
2964 | `(("gfortran" ,gfortran))) | |
2965 | (inputs | |
2966 | `(("gmp" ,gmp) | |
2967 | ("libxml2" ,libxml2))) | |
2968 | (propagated-inputs | |
2969 | `(("r-irlba" ,r-irlba) | |
2970 | ("r-magrittr" ,r-magrittr) | |
2971 | ("r-nmf" ,r-nmf))) | |
2972 | (home-page "http://igraph.org") | |
2973 | (synopsis "Network analysis and visualization") | |
2974 | (description | |
2975 | "This package provides routines for simple graphs and network analysis. | |
2976 | It can handle large graphs very well and provides functions for generating | |
2977 | random and regular graphs, graph visualization, centrality methods and much | |
2978 | more.") | |
2979 | (license license:gpl2+))) | |
2980 | ||
8bfe007c RW |
2981 | (define-public r-r-methodss3 |
2982 | (package | |
2983 | (name "r-r-methodss3") | |
887d45d4 | 2984 | (version "1.7.1") |
8bfe007c RW |
2985 | (source (origin |
2986 | (method url-fetch) | |
2987 | (uri (cran-uri "R.methodsS3" version)) | |
2988 | (sha256 | |
2989 | (base32 | |
887d45d4 | 2990 | "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24")))) |
8bfe007c RW |
2991 | (properties `((upstream-name . "R.methodsS3"))) |
2992 | (build-system r-build-system) | |
2993 | (home-page "http://cran.r-project.org/web/packages/R.methodsS3") | |
2994 | (synopsis "S3 methods simplified") | |
2995 | (description | |
2996 | "This package provides methods that simplify the setup of S3 generic | |
2997 | functions and S3 methods. Major effort has been made in making definition of | |
2998 | methods as simple as possible with a minimum of maintenance for package | |
2999 | developers. For example, generic functions are created automatically, if | |
3000 | missing, and naming conflict are automatically solved, if possible. The | |
3001 | method @code{setMethodS3()} is a good start for those who in the future may | |
3002 | want to migrate to S4.") | |
3003 | (license license:lgpl2.1+))) | |
3004 | ||
c8c75a8d RW |
3005 | (define-public r-r-oo |
3006 | (package | |
3007 | (name "r-r-oo") | |
f158b92c | 3008 | (version "1.21.0") |
c8c75a8d RW |
3009 | (source (origin |
3010 | (method url-fetch) | |
3011 | (uri (cran-uri "R.oo" version)) | |
3012 | (sha256 | |
3013 | (base32 | |
f158b92c | 3014 | "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34")))) |
c8c75a8d RW |
3015 | (properties `((upstream-name . "R.oo"))) |
3016 | (build-system r-build-system) | |
3017 | (propagated-inputs | |
3018 | `(("r-r-methodss3" ,r-r-methodss3))) | |
3019 | (home-page "https://github.com/HenrikBengtsson/R.oo") | |
3020 | (synopsis "R object-oriented programming with or without references") | |
3021 | (description | |
3022 | "This package provides methods and classes for object-oriented | |
3023 | programming in R with or without references. Large effort has been made on | |
3024 | making definition of methods as simple as possible with a minimum of | |
3025 | maintenance for package developers.") | |
3026 | (license license:lgpl2.1+))) | |
3027 | ||
9c94b53b RW |
3028 | (define-public r-r-utils |
3029 | (package | |
3030 | (name "r-r-utils") | |
1a44753b | 3031 | (version "2.5.0") |
9c94b53b RW |
3032 | (source (origin |
3033 | (method url-fetch) | |
3034 | (uri (cran-uri "R.utils" version)) | |
3035 | (sha256 | |
3036 | (base32 | |
1a44753b | 3037 | "17q3w5dlly5xl2srrzsmf9s7vs5d576vqbcs6sr2p5x4qvqa1q8s")))) |
9c94b53b RW |
3038 | (properties `((upstream-name . "R.utils"))) |
3039 | (build-system r-build-system) | |
3040 | (propagated-inputs | |
3041 | `(("r-r-methodss3" ,r-r-methodss3) | |
3042 | ("r-r-oo" ,r-r-oo))) | |
3043 | (home-page "https://github.com/HenrikBengtsson/R.utils") | |
3044 | (synopsis "Various programming utilities") | |
3045 | (description | |
3046 | "This package provides utility functions useful when programming and | |
3047 | developing R packages.") | |
3048 | (license license:lgpl2.1+))) | |
3049 | ||
a63efbb4 RW |
3050 | (define-public r-r-cache |
3051 | (package | |
3052 | (name "r-r-cache") | |
3053 | (version "0.12.0") | |
3054 | (source (origin | |
3055 | (method url-fetch) | |
3056 | (uri (cran-uri "R.cache" version)) | |
3057 | (sha256 | |
3058 | (base32 | |
3059 | "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx")))) | |
3060 | (properties `((upstream-name . "R.cache"))) | |
3061 | (build-system r-build-system) | |
3062 | (propagated-inputs | |
3063 | `(("r-digest" ,r-digest) | |
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.cache") | |
3068 | (synopsis "Light-weight caching of objects and results") | |
3069 | (description | |
3070 | "This package provides methods for caching or memoization of objects and | |
3071 | results. With this package, any R object can be cached in a key-value storage | |
3072 | where the key can be an arbitrary set of R objects. The cache memory is | |
3073 | persistent (on the file system).") | |
3074 | (license license:lgpl2.1+))) | |
3075 | ||
3703ffb4 RW |
3076 | (define-public r-r-rsp |
3077 | (package | |
3078 | (name "r-r-rsp") | |
54aa6eb6 | 3079 | (version "0.40.0") |
3703ffb4 RW |
3080 | (source (origin |
3081 | (method url-fetch) | |
3082 | (uri (cran-uri "R.rsp" version)) | |
3083 | (sha256 | |
3084 | (base32 | |
54aa6eb6 | 3085 | "1hz5fnxz30m3cc7x7ha1swx4pn8c2244z6ka6v9m3l5lpdgc1367")))) |
3703ffb4 RW |
3086 | (properties `((upstream-name . "R.rsp"))) |
3087 | (build-system r-build-system) | |
3088 | (propagated-inputs | |
3089 | `(("r-r-cache" ,r-r-cache) | |
3090 | ("r-r-methodss3" ,r-r-methodss3) | |
3091 | ("r-r-oo" ,r-r-oo) | |
3092 | ("r-r-utils" ,r-r-utils))) | |
3093 | (home-page "https://github.com/HenrikBengtsson/R.rsp") | |
3094 | (synopsis "Dynamic generation of scientific reports") | |
3095 | (description | |
3096 | "The RSP markup language provides a powerful markup for controlling the | |
3097 | content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr | |
3098 | documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary | |
3099 | to many other literate programming languages, with RSP it is straightforward | |
3100 | to loop over mixtures of code and text sections, e.g. in month-by-month | |
3101 | summaries. RSP has also several preprocessing directives for incorporating | |
3102 | static and dynamic contents of external files (local or online) among other | |
3103 | things. RSP is ideal for self-contained scientific reports and R package | |
3104 | vignettes.") | |
3105 | (license license:lgpl2.1+))) | |
3106 | ||
b5f13fdb RJ |
3107 | (define-public r-mvtnorm |
3108 | (package | |
3109 | (name "r-mvtnorm") | |
3110 | (version "1.0-5") | |
3111 | (source (origin | |
3112 | (method url-fetch) | |
3113 | (uri (cran-uri "mvtnorm" version)) | |
3114 | (sha256 | |
3115 | (base32 | |
3116 | "1pc1mi2h063gh4a40009xk5j6pf5bm4274i5kycln38dixsry3yh")))) | |
3117 | (build-system r-build-system) | |
3118 | (inputs | |
3119 | `(("gfortran" ,gfortran))) | |
3120 | (home-page "http://mvtnorm.R-forge.R-project.org") | |
3121 | (synopsis "Package for multivariate normal and t-distributions") | |
3122 | (description "This package can compute multivariate normal and | |
3123 | t-probabilities, quantiles, random deviates and densities.") | |
3124 | (license license:gpl2))) | |
3125 | ||
e05c37da RW |
3126 | (define-public r-matrixstats |
3127 | (package | |
3128 | (name "r-matrixstats") | |
a8e893b0 | 3129 | (version "0.51.0") |
e05c37da RW |
3130 | (source (origin |
3131 | (method url-fetch) | |
3132 | (uri (cran-uri "matrixStats" version)) | |
3133 | (sha256 | |
3134 | (base32 | |
a8e893b0 | 3135 | "0bsalx605kgb9nl7mfnq1qinkyd9s97p8plymsyfja1gmcnjrcpj")))) |
e05c37da RW |
3136 | (properties `((upstream-name . "matrixStats"))) |
3137 | (build-system r-build-system) | |
3138 | (native-inputs | |
3139 | `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes | |
3140 | (home-page "https://github.com/HenrikBengtsson/matrixStats") | |
3141 | (synopsis "Methods applying to vectors and matrix rows and columns") | |
3142 | (description | |
3143 | "This package provides methods operating on rows and columns of matrices, | |
3144 | e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are | |
3145 | also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and | |
3146 | @code{weightedMedians()}. All methods have been optimized for speed and | |
3147 | memory usage.") | |
3148 | (license license:artistic2.0))) | |
3149 | ||
a28d646b RW |
3150 | (define-public r-viridis |
3151 | (package | |
3152 | (name "r-viridis") | |
0fc42136 | 3153 | (version "0.3.4") |
a28d646b RW |
3154 | (source (origin |
3155 | (method url-fetch) | |
3156 | (uri (cran-uri "viridis" version)) | |
3157 | (sha256 | |
3158 | (base32 | |
0fc42136 | 3159 | "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j")))) |
a28d646b RW |
3160 | (build-system r-build-system) |
3161 | (propagated-inputs | |
3162 | `(("r-ggplot2" ,r-ggplot2) | |
3163 | ("r-gridextra" ,r-gridextra))) | |
3164 | (home-page "https://github.com/sjmgarnier/viridis") | |
3165 | (synopsis "Matplotlib default color map") | |
3166 | (description | |
3167 | "This package is a port of the new @url{matplotlib, | |
3168 | http://matplotlib.org/} color maps (@code{viridis}--the default--, | |
3169 | @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are | |
3170 | designed in such a way that they will analytically be perfectly | |
3171 | perceptually-uniform, both in regular form and also when converted to | |
3172 | black-and-white. They are also designed to be perceived by readers with the | |
3173 | most common form of color blindness.") | |
3174 | (license license:x11))) | |
3175 | ||
c6ab73e8 RW |
3176 | (define-public r-viridislite |
3177 | (package | |
3178 | (name "r-viridislite") | |
3179 | (version "0.1.3") | |
3180 | (source | |
3181 | (origin | |
3182 | (method url-fetch) | |
3183 | (uri (cran-uri "viridisLite" version)) | |
3184 | (sha256 | |
3185 | (base32 | |
3186 | "1b0fhj8i1m9jsz91gzag60k7vy7kk5xkdg31rc3h3spq96l66psp")))) | |
3187 | (properties `((upstream-name . "viridisLite"))) | |
3188 | (build-system r-build-system) | |
3189 | (home-page "https://github.com/sjmgarnier/viridisLite") | |
3190 | (synopsis "Default color maps from matplotlib") | |
3191 | (description | |
3192 | "This package is a port of the new @code{matplotlib} color maps ('viridis', | |
3193 | 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting | |
3194 | library for Python. These color maps are designed in such a way that they | |
3195 | will analytically be perfectly perceptually-uniform, both in regular form and | |
3196 | also when converted to black-and-white. They are also designed to be | |
3197 | perceived by readers with the most common form of color blindness. This is | |
3198 | the 'lite' version of the more complete @code{viridis} package.") | |
3199 | (license license:expat))) | |
3200 | ||
94b7e9b7 RW |
3201 | (define-public r-tidyr |
3202 | (package | |
3203 | (name "r-tidyr") | |
1b7f85f5 | 3204 | (version "0.6.0") |
94b7e9b7 RW |
3205 | (source |
3206 | (origin | |
3207 | (method url-fetch) | |
3208 | (uri (cran-uri "tidyr" version)) | |
3209 | (sha256 | |
3210 | (base32 | |
1b7f85f5 | 3211 | "1bpwbphgl43ym433b0nrshwhr7pprmj1wkpkamdzix1zvf9dcbc2")))) |
94b7e9b7 RW |
3212 | (build-system r-build-system) |
3213 | (propagated-inputs | |
3214 | `(("r-dplyr" ,r-dplyr) | |
3215 | ("r-lazyeval" ,r-lazyeval) | |
3216 | ("r-magrittr" ,r-magrittr) | |
3217 | ("r-rcpp" ,r-rcpp) | |
3218 | ("r-stringi" ,r-stringi))) | |
3219 | (home-page "https://github.com/hadley/tidyr") | |
3220 | (synopsis "Tidy data with `spread()` and `gather()` functions") | |
3221 | (description | |
3222 | "tidyr is a reframing of the reshape2 package designed to accompany the | |
3223 | tidy data framework, and to work hand-in-hand with magrittr and dplyr to build | |
3224 | a solid pipeline for data analysis. It is designed specifically for tidying | |
3225 | data, not the general reshaping that reshape2 does, or the general aggregation | |
3226 | that reshape did. In particular, built-in methods only work for data frames, | |
3227 | and tidyr provides no margins or aggregation.") | |
3228 | (license license:expat))) | |
3229 | ||
bae79538 RW |
3230 | (define-public r-hexbin |
3231 | (package | |
3232 | (name "r-hexbin") | |
3233 | (version "1.27.1") | |
3234 | (source | |
3235 | (origin | |
3236 | (method url-fetch) | |
3237 | (uri (cran-uri "hexbin" version)) | |
3238 | (sha256 | |
3239 | (base32 | |
3240 | "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh")))) | |
3241 | (build-system r-build-system) | |
3242 | (propagated-inputs | |
3243 | `(("r-lattice" ,r-lattice))) | |
3244 | (native-inputs | |
3245 | `(("gfortran" ,gfortran))) | |
3246 | (home-page "http://github.com/edzer/hexbin") | |
3247 | (synopsis "Hexagonal binning routines") | |
3248 | (description | |
3249 | "This package provides binning and plotting functions for hexagonal bins. | |
3250 | It uses and relies on grid graphics and formal (S4) classes and methods.") | |
3251 | (license license:gpl2+))) | |
a3c6445b RW |
3252 | |
3253 | (define-public r-purrr | |
3254 | (package | |
3255 | (name "r-purrr") | |
3256 | (version "0.2.2") | |
3257 | (source | |
3258 | (origin | |
3259 | (method url-fetch) | |
3260 | (uri (cran-uri "purrr" version)) | |
3261 | (sha256 | |
3262 | (base32 | |
3263 | "0lss8q733nv7s154wargm6vnxq55qygnxakib8xdj4jv0y86sxc3")))) | |
3264 | (build-system r-build-system) | |
3265 | (propagated-inputs | |
3266 | `(("r-bh" ,r-bh) | |
3267 | ("r-dplyr" ,r-dplyr) | |
3268 | ("r-lazyeval" ,r-lazyeval) | |
3269 | ("r-magrittr" ,r-magrittr) | |
3270 | ("r-rcpp" ,r-rcpp))) | |
3271 | (home-page "https://github.com/hadley/purrr") | |
3272 | (synopsis "Functional programming tools") | |
3273 | (description | |
3274 | "This package completes R's functional programming tools with missing | |
3275 | features present in other programming languages.") | |
3276 | (license license:gpl3+))) | |
bae79538 | 3277 | |
fbf6045e RW |
3278 | (define-public r-plotly |
3279 | (package | |
3280 | (name "r-plotly") | |
3a181dc4 | 3281 | (version "4.5.6") |
fbf6045e RW |
3282 | (source (origin |
3283 | (method url-fetch) | |
3284 | (uri (cran-uri "plotly" version)) | |
3285 | (sha256 | |
3286 | (base32 | |
3a181dc4 | 3287 | "09yw977yxlcxv57kni3q899zrxyxa6pznr06cylr9lqkyr7llfhx")))) |
fbf6045e RW |
3288 | (build-system r-build-system) |
3289 | (propagated-inputs | |
3290 | `(("r-base64enc" ,r-base64enc) | |
3291 | ("r-digest" ,r-digest) | |
88cf917b | 3292 | ("r-dplyr" ,r-dplyr) |
fbf6045e | 3293 | ("r-ggplot2" ,r-ggplot2) |
2c81794e | 3294 | ("r-hexbin" ,r-hexbin) |
fbf6045e RW |
3295 | ("r-htmlwidgets" ,r-htmlwidgets) |
3296 | ("r-httr" ,r-httr) | |
3297 | ("r-jsonlite" ,r-jsonlite) | |
88cf917b | 3298 | ("r-lazyeval" ,r-lazyeval) |
fbf6045e | 3299 | ("r-magrittr" ,r-magrittr) |
88cf917b | 3300 | ("r-purrr" ,r-purrr) |
2c81794e | 3301 | ("r-scales" ,r-scales) |
88cf917b | 3302 | ("r-tibble" ,r-tibble) |
2c81794e | 3303 | ("r-tidyr" ,r-tidyr) |
88cf917b | 3304 | ("r-viridislite" ,r-viridislite))) |
fbf6045e RW |
3305 | (home-page "https://plot.ly/r") |
3306 | (synopsis "Create interactive web graphics") | |
3307 | (description | |
3308 | "This package enables the translation of ggplot2 graphs to an interactive | |
3309 | web-based version and/or the creation of custom web-based visualizations | |
3310 | directly from R. Once uploaded to a plotly account, plotly graphs (and the | |
3311 | data behind them) can be viewed and modified in a web browser.") | |
3312 | (license license:x11))) | |
3313 | ||
0947698c BW |
3314 | (define-public r-biased-urn |
3315 | (package | |
3316 | (name "r-biased-urn") | |
3317 | (version "1.07") | |
3318 | (source | |
3319 | (origin | |
3320 | (method url-fetch) | |
3321 | (uri (cran-uri "BiasedUrn" version)) | |
3322 | (sha256 | |
3323 | (base32 | |
3324 | "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) | |
3325 | (properties `((upstream-name . "BiasedUrn"))) | |
3326 | (build-system r-build-system) | |
3327 | (home-page "http://www.agner.org/random/") | |
3328 | (synopsis "Biased urn model distributions") | |
3329 | (description | |
3330 | "This package provides statistical models of biased sampling in the form | |
3331 | of univariate and multivariate noncentral hypergeometric distributions, | |
3332 | including Wallenius' noncentral hypergeometric distribution and Fisher's | |
3333 | noncentral hypergeometric distribution (also called extended hypergeometric | |
3334 | distribution).") | |
3335 | (license license:gpl3+))) | |
6499b70e | 3336 | |
58612fd2 RW |
3337 | (define-public r-rematch |
3338 | (package | |
3339 | (name "r-rematch") | |
3340 | (version "1.0.1") | |
3341 | (source | |
3342 | (origin | |
3343 | (method url-fetch) | |
3344 | (uri (cran-uri "rematch" version)) | |
3345 | (sha256 | |
3346 | (base32 | |
3347 | "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4")))) | |
3348 | (build-system r-build-system) | |
3349 | (home-page "https://github.com/MangoTheCat/rematch") | |
3350 | (synopsis "Match regular expressions with a nicer API") | |
3351 | (description | |
3352 | "This package provides a small wrapper on @code{regexpr} to extract the | |
3353 | matches and captured groups from the match of a regular expression to a | |
3354 | character vector.") | |
3355 | (license license:expat))) | |
3356 | ||
d427e03e RW |
3357 | (define-public r-cellranger |
3358 | (package | |
3359 | (name "r-cellranger") | |
3360 | (version "1.1.0") | |
3361 | (source | |
3362 | (origin | |
3363 | (method url-fetch) | |
3364 | (uri (cran-uri "cellranger" version)) | |
3365 | (sha256 | |
3366 | (base32 | |
3367 | "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x")))) | |
3368 | (build-system r-build-system) | |
3369 | (propagated-inputs | |
3370 | `(("r-rematch" ,r-rematch) | |
3371 | ("r-tibble" ,r-tibble))) | |
3372 | (home-page "https://github.com/rsheets/cellranger") | |
3373 | (synopsis "Translate spreadsheet cell ranges to rows and columns") | |
3374 | (description | |
3375 | "This package provides helper functions to work with spreadsheets and the | |
3376 | @code{A1:D10} style of cell range specification.") | |
3377 | (license license:expat))) | |
3378 | ||
9f5435d9 RW |
3379 | (define-public r-googlesheets |
3380 | (package | |
3381 | (name "r-googlesheets") | |
3382 | (version "0.2.1") | |
3383 | (source | |
3384 | (origin | |
3385 | (method url-fetch) | |
3386 | (uri (cran-uri "googlesheets" version)) | |
3387 | (sha256 | |
3388 | (base32 | |
3389 | "0ps13h1cv7fj5dh8s4nvwi64wnnyqdsadcaa4iizq1c5s615cwk3")))) | |
3390 | (build-system r-build-system) | |
3391 | (propagated-inputs | |
3392 | `(("r-cellranger" ,r-cellranger) | |
3393 | ("r-dplyr" ,r-dplyr) | |
3394 | ("r-httr" ,r-httr) | |
3395 | ("r-jsonlite" ,r-jsonlite) | |
3396 | ("r-purrr" ,r-purrr) | |
3397 | ("r-readr" ,r-readr) | |
3398 | ("r-stringr" ,r-stringr) | |
3399 | ("r-tidyr" ,r-tidyr) | |
3400 | ("r-xml2" ,r-xml2))) | |
3401 | (home-page "https://github.com/jennybc/googlesheets") | |
3402 | (synopsis "Manage Google spreadsheets from R") | |
3403 | (description "This package provides tools to interact with Google Sheets | |
3404 | from within R.") | |
3405 | (license license:expat))) | |
3406 | ||
e7d16ad1 RW |
3407 | (define-public r-spams |
3408 | (package | |
3409 | (name "r-spams") | |
3410 | (version "2.5-svn2014-07-04") | |
3411 | (source | |
3412 | (origin | |
3413 | (method url-fetch) | |
3414 | (uri (string-append "https://gforge.inria.fr/frs/download.php/33815/" | |
3415 | "spams-R-v" version ".tar.gz")) | |
3416 | (sha256 | |
3417 | (base32 | |
3418 | "1k459jg9a334slkw31w63l4d39xszjzsng7dv5j1mp78zifz7hvx")))) | |
3419 | (build-system r-build-system) | |
3420 | (arguments | |
3421 | `(#:phases | |
3422 | (modify-phases %standard-phases | |
3423 | (add-after 'unpack 'chdir | |
3424 | (lambda _ (chdir "spams") #t)) | |
3425 | ;; Since R 3.3.0 including R headers inside of an extern "C" block | |
3426 | ;; causes C headers to be included, which results in a lot of | |
3427 | ;; duplicate definitions. This can be avoided by defining | |
3428 | ;; NO_C_HEADERS before including the R headers. | |
3429 | (add-after 'chdir 'patch-use-of-R-headers | |
3430 | (lambda _ | |
3431 | (substitute* "src/spams.cpp" | |
3432 | (("#include <R.h>" line) | |
3433 | (string-append "#define NO_C_HEADERS\n" line))) | |
3434 | #t)) | |
3435 | ;; This looks like a syntax error. | |
3436 | (add-after 'chdir 'patch-isnan | |
3437 | (lambda _ | |
3438 | (substitute* '"src/spams/linalg/linalg.h" | |
3439 | (("if isnan\\(lambda\\) \\{") | |
3440 | "if (isnan(lambda)) {")) | |
3441 | #t))))) | |
3442 | (home-page "http://spams-devel.gforge.inria.fr") | |
3443 | (synopsis "Toolbox for solving sparse estimation problems") | |
3444 | (description "SPAMS (SPArse Modeling Software) is an optimization toolbox | |
3445 | for solving various sparse estimation problems. It includes tools for the | |
3446 | following problems: | |
3447 | ||
3448 | @enumerate | |
3449 | @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle | |
3450 | component analysis} (PCA), ...) | |
3451 | @item Solving sparse decomposition problems with LARS, coordinate descent, | |
3452 | OMP, SOMP, proximal methods | |
3453 | @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse | |
3454 | group lasso, tree-structured regularization, structured sparsity with | |
3455 | overlapping groups,...). | |
3456 | @end enumerate\n") | |
3457 | (license license:gpl3+))) | |
3458 | ||
2213730c RW |
3459 | (define-public r-rpart |
3460 | (package | |
3461 | (name "r-rpart") | |
3462 | (version "4.1-10") | |
3463 | (source | |
3464 | (origin | |
3465 | (method url-fetch) | |
3466 | (uri (cran-uri "rpart" version)) | |
3467 | (sha256 | |
3468 | (base32 | |
3469 | "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) | |
3470 | (build-system r-build-system) | |
3471 | (home-page "http://cran.r-project.org/web/packages/rpart") | |
3472 | (synopsis "Recursive partitioning and regression trees") | |
3473 | (description | |
3474 | "This package provides recursive partitioning functions for | |
3475 | classification, regression and survival trees.") | |
3476 | (license (list license:gpl2+ license:gpl3+)))) | |
3477 | ||
ebbd4d0b RW |
3478 | (define-public r-survival |
3479 | (package | |
3480 | (name "r-survival") | |
3481 | (version "2.40-1") | |
3482 | (source | |
3483 | (origin | |
3484 | (method url-fetch) | |
3485 | (uri (cran-uri "survival" version)) | |
3486 | (sha256 | |
3487 | (base32 | |
3488 | "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci")))) | |
3489 | (build-system r-build-system) | |
3490 | (home-page "https://github.com/therneau/survival") | |
3491 | (synopsis "Survival analysis") | |
3492 | (description | |
3493 | "This package contains the core survival analysis routines, including | |
3494 | definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) | |
3495 | curves, Cox models, and parametric accelerated failure time models.") | |
3496 | (license license:lgpl2.0+))) | |
3497 | ||
0811f0f9 RW |
3498 | (define-public r-base64 |
3499 | (package | |
3500 | (name "r-base64") | |
3501 | (version "2.0") | |
3502 | (source | |
3503 | (origin | |
3504 | (method url-fetch) | |
3505 | (uri (cran-uri "base64" version)) | |
3506 | (sha256 | |
3507 | (base32 | |
3508 | "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf")))) | |
3509 | (build-system r-build-system) | |
3510 | (propagated-inputs | |
3511 | `(("r-openssl" ,r-openssl))) | |
3512 | (home-page "http://cran.r-project.org/web/packages/base64") | |
3513 | (synopsis "Base64 encoder and decoder") | |
3514 | (description | |
3515 | "This package is a compatibility wrapper to replace the orphaned package | |
3516 | by Romain Francois. New applications should use the openssl or base64enc | |
3517 | package instead.") | |
3518 | (license license:expat))) | |
3519 | ||
2d21d44d RW |
3520 | (define-public r-hmisc |
3521 | (package | |
3522 | (name "r-hmisc") | |
807db78f | 3523 | (version "4.0-2") |
2d21d44d RW |
3524 | (source |
3525 | (origin | |
3526 | (method url-fetch) | |
3527 | (uri (cran-uri "Hmisc" version)) | |
3528 | (sha256 | |
3529 | (base32 | |
807db78f | 3530 | "1lg9k0kj803wsm3h0a991q9l2lrgsqryzfv2z79b88kjbfapqpqr")))) |
2d21d44d RW |
3531 | (properties `((upstream-name . "Hmisc"))) |
3532 | (build-system r-build-system) | |
3533 | (native-inputs | |
3534 | `(("gfortran" ,gfortran))) | |
3535 | (propagated-inputs | |
3536 | `(("r-acepack" ,r-acepack) | |
ab607061 | 3537 | ("r-base64" ,r-base64) |
807db78f | 3538 | ("r-base64enc" ,r-base64enc) |
2d21d44d | 3539 | ("r-data-table" ,r-data-table) |
2d21d44d RW |
3540 | ("r-formula" ,r-formula) |
3541 | ("r-ggplot2" ,r-ggplot2) | |
3542 | ("r-gridextra" ,r-gridextra) | |
3543 | ("r-gtable" ,r-gtable) | |
e7165916 | 3544 | ;; Hmisc needs survival >= 2.40.1, so it cannot use the survival |
ab607061 | 3545 | ;; package that comes with R 3.3.2. |
e7165916 | 3546 | ("r-survival" ,r-survival) |
2d21d44d | 3547 | ("r-latticeextra" ,r-latticeextra) |
e7165916 RW |
3548 | ("r-htmltable" ,r-htmltable) |
3549 | ("r-htmltools" ,r-htmltools) | |
ab607061 | 3550 | ("r-viridis" ,r-viridis))) |
2d21d44d RW |
3551 | (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") |
3552 | (synopsis "Miscellaneous data analysis and graphics functions") | |
3553 | (description | |
3554 | "This package contains many functions useful for data analysis, | |
3555 | high-level graphics, utility operations, functions for computing sample size | |
3556 | and power, importing and annotating datasets, imputing missing values, | |
3557 | advanced table making, variable clustering, character string manipulation, | |
3558 | conversion of R objects to LaTeX code, and recoding variables.") | |
3559 | (license license:gpl2+))) | |
3560 | ||
aa3b3910 RW |
3561 | (define-public r-runit |
3562 | (package | |
3563 | (name "r-runit") | |
3564 | (version "0.4.31") | |
3565 | (source | |
3566 | (origin | |
3567 | (method url-fetch) | |
3568 | (uri (cran-uri "RUnit" version)) | |
3569 | (sha256 | |
3570 | (base32 | |
3571 | "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx")))) | |
3572 | (properties `((upstream-name . "RUnit"))) | |
3573 | (build-system r-build-system) | |
3574 | (home-page "http://cran.r-project.org/web/packages/RUnit") | |
3575 | (synopsis "R unit test framework") | |
3576 | (description | |
3577 | "This package provides R functions implementing a standard unit testing | |
3578 | framework, with additional code inspection and report generation tools.") | |
3579 | (license license:gpl2+))) | |
3580 | ||
c9a66714 RW |
3581 | (define-public r-dynamictreecut |
3582 | (package | |
3583 | (name "r-dynamictreecut") | |
3584 | (version "1.63-1") | |
3585 | (source | |
3586 | (origin | |
3587 | (method url-fetch) | |
3588 | (uri (cran-uri "dynamicTreeCut" version)) | |
3589 | (sha256 | |
3590 | (base32 | |
3591 | "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3")))) | |
3592 | (properties `((upstream-name . "dynamicTreeCut"))) | |
3593 | (build-system r-build-system) | |
3594 | (home-page | |
3595 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/") | |
3596 | (synopsis "Detect clusters in hierarchical clustering dendrograms") | |
3597 | (description | |
3598 | "This package contains methods for the detection of clusters in | |
3599 | hierarchical clustering dendrograms.") | |
3600 | (license license:gpl2+))) | |
3601 | ||
c4708783 RW |
3602 | (define-public r-preprocesscore |
3603 | (package | |
3604 | (name "r-preprocesscore") | |
3605 | (version "1.36.0") | |
3606 | (source | |
3607 | (origin | |
3608 | (method url-fetch) | |
3609 | (uri (bioconductor-uri "preprocessCore" version)) | |
3610 | (sha256 | |
3611 | (base32 | |
3612 | "1n8y12q7145f385gm2k3c6y3vwvin7jlb47la4mnl7mar6pq9kmp")))) | |
3613 | (properties | |
3614 | `((upstream-name . "preprocessCore"))) | |
3615 | (build-system r-build-system) | |
3616 | (home-page "https://github.com/bmbolstad/preprocessCore") | |
3617 | (synopsis "Collection of pre-processing functions") | |
3618 | (description | |
3619 | "This package provides a library of core pre-processing and normalization | |
3620 | routines.") | |
3621 | (license license:lgpl2.0+))) | |
3622 | ||
1bd46f55 RW |
3623 | (define-public r-fastcluster |
3624 | (package | |
3625 | (name "r-fastcluster") | |
53941eb7 | 3626 | (version "1.1.22") |
1bd46f55 RW |
3627 | (source |
3628 | (origin | |
3629 | (method url-fetch) | |
3630 | (uri (cran-uri "fastcluster" version)) | |
3631 | (sha256 | |
3632 | (base32 | |
53941eb7 | 3633 | "006k9isra5biyavqwci61avladw19mhp6kmkjj3777rl1r4r8b9z")))) |
1bd46f55 RW |
3634 | (build-system r-build-system) |
3635 | (home-page "http://danifold.net/fastcluster.html") | |
3636 | (synopsis "Fast hierarchical clustering routines") | |
3637 | (description | |
3638 | "This package implements fast hierarchical, agglomerative clustering | |
3639 | routines. Part of the functionality is designed as drop-in replacement for | |
3640 | existing routines: @code{linkage()} in the SciPy package | |
3641 | @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package, | |
3642 | and the @code{flashClust} package. It provides the same functionality with | |
3643 | the benefit of a much faster implementation. Moreover, there are | |
3644 | memory-saving routines for clustering of vector data, which go beyond what the | |
3645 | existing packages provide.") | |
3646 | (license license:bsd-2))) | |
3647 | ||
6335bf1c RW |
3648 | (define-public r-sfsmisc |
3649 | (package | |
3650 | (name "r-sfsmisc") | |
3651 | (version "1.1-0") | |
3652 | (source | |
3653 | (origin | |
3654 | (method url-fetch) | |
3655 | (uri (cran-uri "sfsmisc" version)) | |
3656 | (sha256 | |
3657 | (base32 | |
3658 | "0580piv4n1nispl3pa8nfjjfnb8iwaqky2dzdy0aqnxrxgrhqhvz")))) | |
3659 | (build-system r-build-system) | |
3660 | (home-page "http://cran.r-project.org/web/packages/sfsmisc") | |
3661 | (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") | |
3662 | (description | |
3663 | "This package provides useful utilities from Seminar fuer Statistik ETH | |
3664 | Zurich, including many that are related to graphics.") | |
3665 | (license license:gpl2+))) | |
3666 | ||
1571f90e RW |
3667 | (define-public r-gtools |
3668 | (package | |
3669 | (name "r-gtools") | |
3670 | (version "3.5.0") | |
3671 | (source | |
3672 | (origin | |
3673 | (method url-fetch) | |
3674 | (uri (cran-uri "gtools" version)) | |
3675 | (sha256 | |
3676 | (base32 | |
3677 | "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6")))) | |
3678 | (build-system r-build-system) | |
3679 | (home-page "http://cran.r-project.org/web/packages/gtools") | |
3680 | (synopsis "Various R programming tools") | |
3681 | (description | |
3682 | "This package contains a collection of various functions to assist in R | |
3683 | programming, such as tools to assist in developing, updating, and maintaining | |
3684 | R and R packages, calculating the logit and inverse logit transformations, | |
3685 | tests for whether a value is missing, empty or contains only @code{NA} and | |
3686 | @code{NULL} values, and many more.") | |
3687 | (license license:gpl2))) | |
3688 | ||
6034cd90 RW |
3689 | (define-public r-gdata |
3690 | (package | |
3691 | (name "r-gdata") | |
3692 | (version "2.17.0") | |
3693 | (source | |
3694 | (origin | |
3695 | (method url-fetch) | |
3696 | (uri (cran-uri "gdata" version)) | |
3697 | (sha256 | |
3698 | (base32 | |
3699 | "0kiy3jbcszlpmarg311spdsfi5pn89wgy742dxsbzxk8907fr5w0")))) | |
3700 | (build-system r-build-system) | |
3701 | (inputs | |
3702 | `(("perl" ,perl))) | |
3703 | (propagated-inputs | |
3704 | `(("r-gtools" ,r-gtools))) | |
3705 | (home-page "http://cran.r-project.org/web/packages/gdata") | |
3706 | (synopsis "Various R programming tools for data manipulation") | |
3707 | (description | |
3708 | "This package provides various R programming tools for data manipulation, | |
3709 | including: | |
3710 | ||
3711 | @itemize | |
3712 | @item medical unit conversions | |
3713 | @item combining objects | |
3714 | @item character vector operations | |
3715 | @item factor manipulation | |
3716 | @item obtaining information about R objects | |
3717 | @item manipulating MS-Excel formatted files | |
3718 | @item generating fixed-width format files | |
3719 | @item extricating components of date and time objects | |
3720 | @item operations on columns of data frames | |
3721 | @item matrix operations | |
3722 | @item operations on vectors and data frames | |
3723 | @item value of last evaluated expression | |
3724 | @item wrapper for @code{sample} that ensures consistent behavior for | |
3725 | both scalar and vector arguments | |
3726 | @end itemize\n") | |
3727 | (license license:gpl2+))) | |
3728 | ||
0cfe0570 RW |
3729 | (define-public r-gplots |
3730 | (package | |
3731 | (name "r-gplots") | |
3732 | (version "3.0.1") | |
3733 | (source | |
3734 | (origin | |
3735 | (method url-fetch) | |
3736 | (uri (cran-uri "gplots" version)) | |
3737 | (sha256 | |
3738 | (base32 | |
3739 | "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l")))) | |
3740 | (build-system r-build-system) | |
3741 | (propagated-inputs | |
3742 | `(("r-catools" ,r-catools) | |
3743 | ("r-gdata" ,r-gdata) | |
3744 | ("r-gtools" ,r-gtools) | |
3745 | ("r-kernsmooth" ,r-kernsmooth))) | |
3746 | (home-page "http://cran.r-project.org/web/packages/gplots") | |
3747 | (synopsis "Various R programming tools for plotting data") | |
3748 | (description | |
3749 | "This package provides various R programming tools for plotting data, | |
3750 | including: | |
3751 | ||
3752 | @itemize | |
3753 | @item calculating and plotting locally smoothed summary function | |
3754 | @item enhanced versions of standard plots | |
3755 | @item manipulating colors | |
3756 | @item calculating and plotting two-dimensional data summaries | |
3757 | @item enhanced regression diagnostic plots | |
3758 | @item formula-enabled interface to @code{stats::lowess} function | |
3759 | @item displaying textual data in plots | |
3760 | @item baloon plots | |
3761 | @item plotting \"Venn\" diagrams | |
3762 | @item displaying Open-Office style plots | |
3763 | @item plotting multiple data on same region, with separate axes | |
3764 | @item plotting means and confidence intervals | |
3765 | @item spacing points in an x-y plot so they don't overlap | |
3766 | @end itemize\n") | |
3767 | (license license:gpl2+))) | |
3768 | ||
419a8a18 RW |
3769 | (define-public r-rocr |
3770 | (package | |
3771 | (name "r-rocr") | |
3772 | (version "1.0-7") | |
3773 | (source | |
3774 | (origin | |
3775 | (method url-fetch) | |
3776 | (uri (cran-uri "ROCR" version)) | |
3777 | (sha256 | |
3778 | (base32 | |
3779 | "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7")))) | |
3780 | (properties `((upstream-name . "ROCR"))) | |
3781 | (build-system r-build-system) | |
3782 | (propagated-inputs | |
3783 | `(("r-gplots" ,r-gplots))) | |
3784 | (home-page "http://rocr.bioinf.mpi-sb.mpg.de/") | |
3785 | (synopsis "Visualizing the performance of scoring classifiers") | |
3786 | (description | |
3787 | "ROCR is a flexible tool for creating cutoff-parameterized 2D performance | |
3788 | curves by freely combining two from over 25 performance measures (new | |
3789 | performance measures can be added using a standard interface). Curves from | |
3790 | different cross-validation or bootstrapping runs can be averaged by different | |
3791 | methods, and standard deviations, standard errors or box plots can be used to | |
3792 | visualize the variability across the runs. The parameterization can be | |
3793 | visualized by printing cutoff values at the corresponding curve positions, or | |
3794 | by coloring the curve according to cutoff. All components of a performance | |
3795 | plot can be quickly adjusted using a flexible parameter dispatching | |
3796 | mechanism.") | |
3797 | (license license:gpl2+))) | |
3798 | ||
557a4b8e RW |
3799 | (define-public r-kernsmooth |
3800 | (package | |
3801 | (name "r-kernsmooth") | |
3802 | (version "2.23-15") | |
3803 | (source | |
3804 | (origin | |
3805 | (method url-fetch) | |
3806 | (uri (cran-uri "KernSmooth" version)) | |
3807 | (sha256 | |
3808 | (base32 | |
3809 | "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) | |
3810 | (properties `((upstream-name . "KernSmooth"))) | |
3811 | (build-system r-build-system) | |
3812 | (inputs | |
3813 | `(("gfortran" ,gfortran))) | |
3814 | (home-page "http://cran.r-project.org/web/packages/KernSmooth") | |
3815 | (synopsis "Functions for kernel smoothing") | |
3816 | (description | |
3817 | "This package provides functions for kernel smoothing (and density | |
3818 | estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) | |
3819 | \"Kernel Smoothing\".") | |
3820 | ;; Unlimited use and distribution | |
3821 | (license (license:non-copyleft "file://LICENSE.note")))) | |
3822 | ||
031cf6b6 RJ |
3823 | (define-public r-zoo |
3824 | (package | |
3825 | (name "r-zoo") | |
c729d3dc | 3826 | (version "1.7-14") |
031cf6b6 RJ |
3827 | (source (origin |
3828 | (method url-fetch) | |
3829 | (uri (cran-uri "zoo" version)) | |
3830 | (sha256 | |
3831 | (base32 | |
c729d3dc | 3832 | "167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28")))) |
031cf6b6 | 3833 | (build-system r-build-system) |
031cf6b6 RJ |
3834 | (home-page "http://zoo.R-Forge.R-project.org/") |
3835 | (synopsis "S3 infrastructure for regular and irregular time series") | |
3836 | (description "This package contains an S3 class with methods for totally | |
3837 | ordered indexed observations. It is particularly aimed at irregular time | |
3838 | series of numeric vectors/matrices and factors.") | |
3839 | (license license:gpl2+))) | |
3840 | ||
6499b70e RW |
3841 | (define-public r-ztable |
3842 | (package | |
3843 | (name "r-ztable") | |
3844 | (version "0.1.5") | |
3845 | (source (origin | |
3846 | (method url-fetch) | |
3847 | (uri (cran-uri "ztable" version)) | |
3848 | (sha256 | |
3849 | (base32 | |
3850 | "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r")))) | |
3851 | (build-system r-build-system) | |
3852 | (home-page "http://cran.r-project.org/web/packages/ztable") | |
3853 | (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") | |
3854 | (description | |
3855 | "This package provides functions to make zebra-striped tables (tables | |
3856 | with alternating row colors) in LaTeX and HTML formats easily from | |
3857 | @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova}, | |
3858 | @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and | |
3859 | @code{cbind.mytable} objects.") | |
3860 | (license license:gpl2+))) | |
06958135 RJPB |
3861 | |
3862 | (define-public r-vipor | |
3863 | (package | |
3864 | (name "r-vipor") | |
3865 | (version "0.4.4") | |
3866 | (source (origin | |
3867 | (method url-fetch) | |
3868 | (uri (cran-uri "vipor" version)) | |
3869 | (sha256 | |
3870 | (base32 | |
3871 | "0p1z9a3fazl78pj8a1i2n62v8hrs8cinq82j9wpawhmfkn3dggss")))) | |
3872 | (build-system r-build-system) | |
3873 | (home-page "http://cran.r-project.org/web/packages/vipor") | |
3874 | (synopsis "Plot categorical data using noise and density estimates") | |
3875 | (description | |
3876 | "This package provides tools to generate a violin point plot, a | |
3877 | combination of a violin/histogram plot and a scatter plot by offsetting points | |
3878 | within a category based on their density using quasirandom noise.") | |
3879 | (license license:gpl2+))) | |
6ba27985 RJPB |
3880 | |
3881 | (define-public r-beeswarm | |
3882 | (package | |
3883 | (name "r-beeswarm") | |
3884 | (version "0.2.3") | |
3885 | (source (origin | |
3886 | (method url-fetch) | |
3887 | (uri (cran-uri "beeswarm" version)) | |
3888 | (sha256 | |
3889 | (base32 | |
3890 | "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581")))) | |
3891 | (build-system r-build-system) | |
3892 | (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/") | |
3893 | (synopsis "Implementation of bee swarm plots") | |
3894 | (description | |
3895 | "This package provides an implementation of bee swarm plots. The bee | |
3896 | swarm plot is a one-dimensional scatter plot like stripchart, but with | |
3897 | closely-packed, non-overlapping points.") | |
3898 | (license license:artistic2.0))) | |
649d0c48 RJPB |
3899 | |
3900 | (define-public r-sourcetools | |
3901 | (package | |
3902 | (name "r-sourcetools") | |
3903 | (version "0.1.5") | |
3904 | (source | |
3905 | (origin | |
3906 | (method url-fetch) | |
3907 | (uri (cran-uri "sourcetools" version)) | |
3908 | (sha256 | |
3909 | (base32 | |
3910 | "0jx6kslygfqaic3cmjwag3dy98q1a2dw20cz7z8agsknmmbk6dy2")))) | |
3911 | (build-system r-build-system) | |
3912 | (home-page "http://cran.r-project.org/web/packages/sourcetools") | |
3913 | (synopsis "Tools for reading, tokenizing and parsing R code") | |
3914 | (description | |
3915 | "The sourcetools package provides both an R and C++ interface for the | |
3916 | tokenization of R code, and helpers for interacting with the tokenized | |
3917 | representation of R code.") | |
3918 | (license license:expat))) | |
29430416 RJPB |
3919 | |
3920 | (define-public r-ggbeeswarm | |
3921 | (package | |
3922 | (name "r-ggbeeswarm") | |
3923 | (version "0.5.3") | |
3924 | (source (origin | |
3925 | (method url-fetch) | |
3926 | (uri (cran-uri "ggbeeswarm" version)) | |
3927 | (sha256 | |
3928 | (base32 | |
3929 | "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd")))) | |
3930 | (build-system r-build-system) | |
3931 | (propagated-inputs | |
3932 | `(("r-beeswarm" ,r-beeswarm) | |
3933 | ("r-ggplot2" ,r-ggplot2) | |
3934 | ("r-vipor" ,r-vipor))) | |
3935 | (home-page "https://github.com/eclarke/ggbeeswarm") | |
3936 | (synopsis "Categorical scatter (violin point) plots") | |
3937 | (description | |
3938 | "This package provides two methods of plotting categorical scatter plots | |
3939 | such that the arrangement of points within a category reflects the density of | |
3940 | data at that region, and avoids over-plotting.") | |
3941 | (license license:gpl2+))) | |
2fd261a3 | 3942 | |
ac1f1e4e RJ |
3943 | (define-public r-ggthemes |
3944 | (package | |
3945 | (name "r-ggthemes") | |
3946 | (version "3.3.0") | |
3947 | (source (origin | |
3948 | (method url-fetch) | |
3949 | (uri (cran-uri "ggthemes" version)) | |
3950 | (sha256 | |
3951 | (base32 | |
3952 | "1qdxg2siwsiq32fmgcxn4vihgxad9v8q0aqigl7a94c26bwxs7y2")))) | |
3953 | (build-system r-build-system) | |
3954 | (propagated-inputs | |
3955 | `(("r-assertthat" ,r-assertthat) | |
3956 | ("r-colorspace" ,r-colorspace) | |
3957 | ("r-ggplot2" ,r-ggplot2) | |
3958 | ("r-scales" ,r-scales))) | |
3959 | (home-page "https://cran.rstudio.com/web/packages/ggthemes") | |
3960 | (synopsis "Extra themes, scales and geoms for @code{ggplot2}") | |
3961 | (description "This package provides extra themes and scales for | |
3962 | @code{ggplot2} that replicate the look of plots by Edward Tufte and | |
3963 | Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The | |
3964 | Wall Street Journal, among others. This package also provides | |
3965 | @code{geoms} for Tufte's box plot and range frame.") | |
3966 | (license license:gpl2))) | |
3967 | ||
2fd261a3 RJPB |
3968 | (define-public r-statmod |
3969 | (package | |
3970 | (name "r-statmod") | |
3971 | (version "1.4.27") | |
3972 | (source (origin | |
3973 | (method url-fetch) | |
3974 | (uri (cran-uri "statmod" version)) | |
3975 | (sha256 | |
3976 | (base32 | |
3977 | "14yilq9d3z20hig4rs8bjqyydw3dfx90mhmzvw9w8p16h0s595sn")))) | |
3978 | (build-system r-build-system) | |
3979 | (home-page "http://cran.r-project.org/web/packages/statmod") | |
3980 | (native-inputs | |
3981 | `(("gfortran" ,gfortran))) | |
3982 | (synopsis "Statistical modeling") | |
3983 | (description | |
3984 | "This package provides a collection of algorithms and functions to aid | |
3985 | statistical modeling. It includes growth curve comparisons, limiting dilution | |
3986 | analysis (aka ELDA), mixed linear models, heteroscedastic regression, | |
3987 | inverse-Gaussian probability calculations, Gauss quadrature and a secure | |
3988 | convergence algorithm for nonlinear models. It also includes advanced | |
3989 | generalized linear model functions that implement secure convergence, | |
3990 | dispersion modeling and Tweedie power-law families.") | |
3991 | ;; Statmod is distributed under either license | |
3992 | (license (list license:gpl2 license:gpl3)))) | |
5f764dd7 | 3993 | |
c6dced88 RJPB |
3994 | (define-public r-rann |
3995 | (package | |
3996 | (name "r-rann") | |
3997 | (version "2.5") | |
3998 | (source (origin | |
3999 | (method url-fetch) | |
4000 | (uri (cran-uri "RANN" version)) | |
4001 | (sha256 | |
4002 | (base32 | |
4003 | "007cgqg9bybg2zlljbv5m6cmlm3r6i251018rpgjcn0xnm9sjsj7")))) | |
4004 | (properties | |
4005 | `((upstream-name . "RANN"))) | |
4006 | (build-system r-build-system) | |
4007 | (home-page "https://github.com/jefferis/RANN") | |
4008 | (synopsis "Fast nearest neighbour search") | |
4009 | (description | |
4010 | "This package finds the k nearest neighbours for every point in a given | |
4011 | dataset in O(N log N) time using Arya and Mount's ANN library. Provides | |
4012 | approximate, exact searches, fixed radius searches, bd and kb trees.") | |
4013 | (license license:gpl3+))) | |
4014 | ||
5f764dd7 RW |
4015 | (define-public r-fivethirtyeight |
4016 | (package | |
4017 | (name "r-fivethirtyeight") | |
4018 | (version "0.1.0") | |
4019 | (source | |
4020 | (origin | |
4021 | (method url-fetch) | |
4022 | (uri (string-append "https://mran.microsoft.com/src/contrib/" | |
4023 | "fivethirtyeight_" version ".tar.gz")) | |
4024 | (sha256 | |
4025 | (base32 | |
4026 | "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl")))) | |
4027 | (build-system r-build-system) | |
4028 | (propagated-inputs | |
4029 | `(("r-knitr" ,r-knitr) | |
4030 | ("r-rmarkdown" ,r-rmarkdown) | |
4031 | ("r-dplyr" ,r-dplyr) | |
4032 | ("r-readr" ,r-readr) | |
4033 | ("r-ggplot2" ,r-ggplot2) | |
4034 | ("r-magrittr" ,r-magrittr) | |
4035 | ("r-stringr" ,r-stringr))) | |
4036 | (home-page "https://mran.microsoft.com/package/fivethirtyeight/") | |
4037 | (synopsis "Data and code behind the stories at FiveThirtyEight") | |
4038 | (description "This R package provides access to the code and data sets | |
4039 | published by the statistics blog FiveThirtyEight.") | |
4040 | (license license:expat))) | |
26a281ef RW |
4041 | |
4042 | (define-public r-compquadform | |
4043 | (package | |
4044 | (name "r-compquadform") | |
4045 | (version "1.4.2") | |
4046 | (source | |
4047 | (origin | |
4048 | (method url-fetch) | |
4049 | (uri (cran-uri "CompQuadForm" version)) | |
4050 | (sha256 | |
4051 | (base32 | |
4052 | "0bsgbdblxpv57mbwnf51xyiydp2bqyxkg4zzwqki85cv5xqlrq1n")))) | |
4053 | (properties `((upstream-name . "CompQuadForm"))) | |
4054 | (build-system r-build-system) | |
4055 | (home-page "http://cran.r-project.org/web/packages/CompQuadForm") | |
4056 | (synopsis "Distribution function of quadratic forms in normal variables") | |
4057 | (description | |
4058 | "This package provides functions to compute the distribution function of | |
4059 | quadratic forms in normal variables using Imhof's method, Davies's algorithm, | |
4060 | Farebrother's algorithm or Liu et al.'s algorithm.") | |
4061 | (license license:gpl2+))) | |
c6017f72 RJPB |
4062 | |
4063 | (define-public r-cowplot | |
4064 | (package | |
4065 | (name "r-cowplot") | |
4066 | (version "0.7.0") | |
4067 | (source | |
4068 | (origin | |
4069 | (method url-fetch) | |
4070 | (uri (cran-uri "cowplot" version)) | |
4071 | (sha256 | |
4072 | (base32 | |
4073 | "03iimcsh1pk7iqzjdlfcj43b8khijdk4hg00j4jdllv19xsfb0hx")))) | |
4074 | (build-system r-build-system) | |
4075 | (propagated-inputs | |
4076 | `(("r-ggplot2" ,r-ggplot2) | |
4077 | ("r-gtable" ,r-gtable) | |
4078 | ("r-plyr" ,r-plyr))) | |
4079 | (home-page "https://github.com/wilkelab/cowplot") | |
4080 | (synopsis "Streamlined plot theme and plot annotations for ggplot2") | |
4081 | (description | |
4082 | "This package provides some helpful extensions and modifications to the | |
4083 | ggplot2 package to combine multiple ggplot2 plots into one and label them with | |
4084 | letters, as is often required for scientific publications.") | |
4085 | (license license:gpl2))) | |
efba686c RJPB |
4086 | |
4087 | (define-public r-mixtools | |
4088 | (package | |
4089 | (name "r-mixtools") | |
4090 | (version "1.0.4") | |
4091 | (source | |
4092 | (origin | |
4093 | (method url-fetch) | |
4094 | (uri (cran-uri "mixtools" version)) | |
4095 | (sha256 | |
4096 | (base32 | |
4097 | "133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32")))) | |
4098 | (build-system r-build-system) | |
4099 | (propagated-inputs | |
4100 | `(("r-segmented" ,r-segmented))) | |
4101 | (home-page "http://cran.r-project.org/web/packages/mixtools") | |
4102 | (synopsis "Tools for analyzing finite mixture models") | |
4103 | (description | |
4104 | "This package provides a collection of R functions for analyzing finite | |
4105 | mixture models.") | |
4106 | (license license:gpl2+))) | |
793f2edb RJPB |
4107 | |
4108 | (define-public r-lars | |
4109 | (package | |
4110 | (name "r-lars") | |
4111 | (version "1.2") | |
4112 | (source | |
4113 | (origin | |
4114 | (method url-fetch) | |
4115 | (uri (cran-uri "lars" version)) | |
4116 | (sha256 | |
4117 | (base32 | |
4118 | "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34")))) | |
4119 | (build-system r-build-system) | |
4120 | (inputs | |
4121 | `(("gfortran" ,gfortran))) | |
4122 | (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS") | |
4123 | (synopsis "Least angle regression software") | |
4124 | (description | |
4125 | "Least Angle Regression (\"LAR\") is a model selection algorithm; a | |
4126 | useful and less greedy version of traditional forward selection methods. A | |
4127 | simple modification of the LAR algorithm implements Tibshirani's Lasso; the | |
4128 | Lasso modification of LARS calculates the entire Lasso path of coefficients | |
4129 | for a given problem at the cost of a single least squares fit. Another LARS | |
4130 | modification efficiently implements epsilon Forward Stagewise linear | |
4131 | regression.") | |
4132 | (license license:gpl2))) | |
e431eb67 RJPB |
4133 | |
4134 | (define-public r-fastica | |
4135 | (package | |
4136 | (name "r-fastica") | |
4137 | (version "1.2-0") | |
4138 | (source | |
4139 | (origin | |
4140 | (method url-fetch) | |
4141 | (uri (cran-uri "fastICA" version)) | |
4142 | (sha256 | |
4143 | (base32 | |
4144 | "0ykk78fsk5da2g16i4wji85bvji7nayjvkfp07hyaxq9d15jmf0r")))) | |
4145 | (properties `((upstream-name . "fastICA"))) | |
4146 | (build-system r-build-system) | |
4147 | (home-page "http://cran.r-project.org/web/packages/fastICA") | |
4148 | (synopsis "FastICA algorithms to perform ICA and projection pursuit") | |
4149 | (description | |
4150 | "This package provides an implementation of the FastICA algorithm to | |
4151 | perform @dfn{independent component analysis} (ICA) and projection pursuit.") | |
4152 | ;; Any GPL version. | |
4153 | (license license:gpl3+))) | |
37337699 RJPB |
4154 | |
4155 | (define-public r-randomforest | |
4156 | (package | |
4157 | (name "r-randomforest") | |
4158 | (version "4.6-12") | |
4159 | (source | |
4160 | (origin | |
4161 | (method url-fetch) | |
4162 | (uri (cran-uri "randomForest" version)) | |
4163 | (sha256 | |
4164 | (base32 | |
4165 | "1i43idaihhl6nwqw42v9dqpl6f8z3ykcn2in32lh2755i27jylbf")))) | |
4166 | (properties `((upstream-name . "randomForest"))) | |
4167 | (build-system r-build-system) | |
4168 | (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/") | |
4169 | (native-inputs | |
4170 | `(("gfortran" ,gfortran))) | |
4171 | (synopsis "Breiman and Cutler's random forests for classification and regression") | |
4172 | (description | |
4173 | "This package provides the Breiman and Cutler's random forests algorithm, based on a | |
4174 | forest of trees using random inputs, for classification and regression.") | |
4175 | (license license:gpl2+))) |