Commit | Line | Data |
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056468dc | 1 | ;;; GNU Guix --- Functional package management for GNU |
0f5ae473 | 2 | ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> |
46130b7b | 3 | ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> |
c80fb90f | 4 | ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> |
682768de | 5 | ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> |
97b44f5e | 6 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
53cc59a1 | 7 | ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> |
109b2f7c | 8 | ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com> |
c56739df | 9 | ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net> |
96e22362 | 10 | ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com> |
d2a507ef | 11 | ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> |
1cde7467 | 12 | ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> |
c994418b | 13 | ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> |
b55697fb | 14 | ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com> |
60a166c6 | 15 | ;;; Copyright © 2018 Leo Famulari <leo@famulari.name> |
d9bec9a8 | 16 | ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> |
dcc7fad0 | 17 | ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> |
4b3ff362 | 18 | ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org> |
100f5602 | 19 | ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> |
16fddf17 | 20 | ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> |
056468dc RW |
21 | ;;; |
22 | ;;; This file is part of GNU Guix. | |
23 | ;;; | |
24 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
25 | ;;; under the terms of the GNU General Public License as published by | |
26 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
27 | ;;; your option) any later version. | |
28 | ;;; | |
29 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
30 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
31 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
32 | ;;; GNU General Public License for more details. | |
33 | ;;; | |
34 | ;;; You should have received a copy of the GNU General Public License | |
35 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
36 | ||
37 | (define-module (gnu packages cran) | |
38 | #:use-module ((guix licenses) #:prefix license:) | |
39 | #:use-module (guix packages) | |
40 | #:use-module (guix download) | |
92ce1883 | 41 | #:use-module (guix git-download) |
056468dc | 42 | #:use-module (guix utils) |
c69d27db | 43 | #:use-module (guix build-system r) |
44b0c5b5 | 44 | #:use-module (gnu packages algebra) |
ff939ef4 | 45 | #:use-module (gnu packages base) |
f33cb7ab | 46 | #:use-module (gnu packages bioinformatics) |
7002c44f | 47 | #:use-module (gnu packages c) |
546fc4aa | 48 | #:use-module (gnu packages compression) |
92ce1883 | 49 | #:use-module (gnu packages curl) |
d9bec9a8 | 50 | #:use-module (gnu packages databases) |
f338e480 | 51 | #:use-module (gnu packages fontutils) |
062b6dbd | 52 | #:use-module (gnu packages gcc) |
d884e407 | 53 | #:use-module (gnu packages geo) |
d0eb09a1 | 54 | #:use-module (gnu packages ghostscript) |
f338e480 | 55 | #:use-module (gnu packages gl) |
01af264d | 56 | #:use-module (gnu packages gnome) |
3d62d98e | 57 | #:use-module (gnu packages graph) |
01af264d | 58 | #:use-module (gnu packages gtk) |
dddbc90c | 59 | #:use-module (gnu packages haskell-xyz) |
3f6e6e98 | 60 | #:use-module (gnu packages icu4c) |
f338e480 | 61 | #:use-module (gnu packages image) |
dab3e92c | 62 | #:use-module (gnu packages imagemagick) |
3f6e6e98 | 63 | #:use-module (gnu packages java) |
92ce1883 | 64 | #:use-module (gnu packages javascript) |
ba42da24 | 65 | #:use-module (gnu packages lisp-xyz) |
f97ce815 | 66 | #:use-module (gnu packages machine-learning) |
521e0703 | 67 | #:use-module (gnu packages maths) |
94989d4b | 68 | #:use-module (gnu packages mpi) |
1ab51604 | 69 | #:use-module (gnu packages multiprecision) |
f313baf0 | 70 | #:use-module (gnu packages networking) |
3f6e6e98 | 71 | #:use-module (gnu packages pcre) |
e0268ff2 | 72 | #:use-module (gnu packages perl) |
e33498b8 | 73 | #:use-module (gnu packages pkg-config) |
9f56ceec | 74 | #:use-module (gnu packages python) |
984a8aa6 | 75 | #:use-module (gnu packages python-xyz) |
e0268ff2 | 76 | #:use-module (gnu packages statistics) |
f9d9c831 | 77 | #:use-module (gnu packages tcl) |
9944399a | 78 | #:use-module (gnu packages tls) |
f338e480 RW |
79 | #:use-module (gnu packages web) |
80 | #:use-module (gnu packages xorg)) | |
056468dc | 81 | |
88e4ed55 RW |
82 | (define-public r-clipr |
83 | (package | |
84 | (name "r-clipr") | |
710ecc9c | 85 | (version "0.7.0") |
88e4ed55 RW |
86 | (source |
87 | (origin | |
88 | (method url-fetch) | |
89 | (uri (cran-uri "clipr" version)) | |
90 | (sha256 | |
91 | (base32 | |
710ecc9c | 92 | "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903")))) |
88e4ed55 RW |
93 | (build-system r-build-system) |
94 | (home-page "https://github.com/mdlincoln/clipr") | |
95 | (synopsis "Read and write from the system clipboard") | |
96 | (description | |
97 | "This package provides simple utility functions to read from and write to | |
98 | the system clipboards.") | |
99 | (license license:gpl3))) | |
100 | ||
46130b7b RW |
101 | (define-public r-scales |
102 | (package | |
103 | (name "r-scales") | |
54a8cb96 | 104 | (version "1.1.0") |
46130b7b RW |
105 | (source |
106 | (origin | |
107 | (method url-fetch) | |
108 | (uri (cran-uri "scales" version)) | |
109 | (sha256 | |
54a8cb96 | 110 | (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y")))) |
46130b7b RW |
111 | (build-system r-build-system) |
112 | (propagated-inputs | |
54a8cb96 RW |
113 | `(("r-farver" ,r-farver) |
114 | ("r-labeling" ,r-labeling) | |
115 | ("r-lifecycle" ,r-lifecycle) | |
46130b7b RW |
116 | ("r-munsell" ,r-munsell) |
117 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
46130b7b RW |
118 | ("r-r6" ,r-r6) |
119 | ("r-viridislite" ,r-viridislite))) | |
120 | (home-page "https://github.com/hadley/scales") | |
121 | (synopsis "Scale functions for visualization") | |
122 | (description | |
123 | "This package provides graphical scales that map data to aesthetics, and | |
124 | provides methods for automatically determining breaks and labels for axes and | |
125 | legends.") | |
126 | (license license:expat))) | |
127 | ||
5b720c15 RW |
128 | (define-public r-pheatmap |
129 | (package | |
130 | (name "r-pheatmap") | |
131 | (version "1.0.12") | |
132 | (source | |
133 | (origin | |
134 | (method url-fetch) | |
135 | (uri (cran-uri "pheatmap" version)) | |
136 | (sha256 | |
137 | (base32 | |
138 | "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) | |
139 | (build-system r-build-system) | |
140 | (propagated-inputs | |
141 | `(("r-gtable" ,r-gtable) | |
142 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
143 | ("r-scales" ,r-scales))) | |
144 | (home-page "https://cran.r-project.org/web/packages/pheatmap") | |
145 | (synopsis "Pretty heatmaps") | |
146 | (description | |
147 | "This package provides an implementation of heatmaps that offers more | |
148 | control over dimensions and appearance.") | |
149 | (license license:gpl2+))) | |
150 | ||
3f22a115 RW |
151 | (define-public r-ellipsis |
152 | (package | |
153 | (name "r-ellipsis") | |
f3575adf | 154 | (version "0.3.0") |
3f22a115 RW |
155 | (source |
156 | (origin | |
157 | (method url-fetch) | |
158 | (uri (cran-uri "ellipsis" version)) | |
159 | (sha256 | |
160 | (base32 | |
f3575adf | 161 | "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b")))) |
3f22a115 | 162 | (build-system r-build-system) |
a4bc73b2 RW |
163 | (propagated-inputs |
164 | `(("r-rlang" ,r-rlang))) | |
3f22a115 RW |
165 | (home-page "https://github.com/hadley/ellipsis") |
166 | (synopsis "Tools for working with additional arguments") | |
167 | (description | |
168 | "In S3 generics, it's useful to take @code{...} so that methods can have | |
169 | additional arguments. But this flexibility comes at a cost: misspelled | |
170 | arguments will be silently ignored. The @code{ellipsis} package is an | |
171 | experiment that allows a generic to warn if any arguments passed in @code{...} | |
172 | are not used.") | |
173 | (license license:gpl3))) | |
174 | ||
0b2883e1 RW |
175 | (define-public r-grr |
176 | (package | |
177 | (name "r-grr") | |
178 | (version "0.9.5") | |
179 | (source | |
180 | (origin | |
181 | (method url-fetch) | |
182 | (uri (cran-uri "grr" version)) | |
183 | (sha256 | |
184 | (base32 | |
185 | "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9")))) | |
186 | (build-system r-build-system) | |
187 | (home-page "https://cran.r-project.org/web/packages/grr") | |
188 | (synopsis "Alternative implementations of base R functions") | |
189 | (description | |
190 | "This package provides alternative implementations of some base R | |
191 | functions, including @code{sort}, @code{order}, and @code{match}. The | |
192 | functions are simplified but can be faster or have other advantages.") | |
193 | (license license:gpl3))) | |
194 | ||
cf51d895 RW |
195 | (define-public r-matrix-utils |
196 | (package | |
197 | (name "r-matrix-utils") | |
198 | (version "0.9.7") | |
199 | (source | |
200 | (origin | |
201 | (method url-fetch) | |
202 | (uri (cran-uri "Matrix.utils" version)) | |
203 | (sha256 | |
204 | (base32 | |
205 | "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va")))) | |
206 | (properties `((upstream-name . "Matrix.utils"))) | |
207 | (build-system r-build-system) | |
208 | (propagated-inputs | |
209 | `(("r-grr" ,r-grr) | |
210 | ("r-matrix" ,r-matrix))) | |
211 | (home-page "https://github.com/cvarrichio/Matrix.utils") | |
212 | (synopsis | |
213 | "Data.frame-Like Operations on Sparse and Dense Matrix Objects") | |
214 | (description | |
215 | "This package implements data manipulation methods such as @code{cast}, | |
216 | @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like | |
217 | objects.") | |
218 | (license license:gpl3))) | |
219 | ||
2b106a8d RW |
220 | (define-public r-sys |
221 | (package | |
222 | (name "r-sys") | |
d9a382ec | 223 | (version "3.3") |
2b106a8d RW |
224 | (source |
225 | (origin | |
226 | (method url-fetch) | |
227 | (uri (cran-uri "sys" version)) | |
228 | (sha256 | |
229 | (base32 | |
d9a382ec | 230 | "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6")))) |
2b106a8d RW |
231 | (build-system r-build-system) |
232 | (home-page "https://github.com/jeroen/sys") | |
233 | (synopsis "Powerful and reliable tools for running system commands in R") | |
234 | (description | |
235 | "This package provides drop-in replacements for the base @code{system2()} | |
236 | function with fine control and consistent behavior across platforms. It | |
237 | supports clean interruption, timeout, background tasks, and streaming STDIN / | |
238 | STDOUT / STDERR over binary or text connections. The package also provides | |
239 | functions for evaluating expressions inside a temporary fork. Such | |
240 | evaluations have no side effects on the main R process, and support reliable | |
241 | interrupts and timeouts. This provides the basis for a sandboxing | |
242 | mechanism.") | |
243 | (license license:expat))) | |
244 | ||
9d3a4672 RW |
245 | (define-public r-askpass |
246 | (package | |
247 | (name "r-askpass") | |
248 | (version "1.1") | |
249 | (source | |
250 | (origin | |
251 | (method url-fetch) | |
252 | (uri (cran-uri "askpass" version)) | |
253 | (sha256 | |
254 | (base32 | |
255 | "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) | |
256 | (build-system r-build-system) | |
257 | (propagated-inputs `(("r-sys" ,r-sys))) | |
258 | (home-page "https://github.com/jeroen/askpass") | |
259 | (synopsis "Safe password entry for R") | |
260 | (description | |
261 | "This package provides cross-platform utilities for prompting the user | |
262 | for credentials or a passphrase, for example to authenticate with a server or | |
263 | read a protected key.") | |
264 | (license license:expat))) | |
265 | ||
c80fb90f RW |
266 | (define-public r-vegan |
267 | (package | |
268 | (name "r-vegan") | |
0ce4b23d | 269 | (version "2.5-6") |
c80fb90f RW |
270 | (source |
271 | (origin | |
272 | (method url-fetch) | |
273 | (uri (cran-uri "vegan" version)) | |
274 | (sha256 | |
275 | (base32 | |
0ce4b23d | 276 | "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k")))) |
c80fb90f RW |
277 | (build-system r-build-system) |
278 | (native-inputs | |
279 | `(("gfortran" ,gfortran))) | |
280 | (propagated-inputs | |
281 | `(("r-cluster" ,r-cluster) | |
282 | ("r-knitr" ,r-knitr) ; needed for vignettes | |
283 | ("r-lattice" ,r-lattice) | |
284 | ("r-mass" ,r-mass) | |
285 | ("r-mgcv" ,r-mgcv) | |
286 | ("r-permute" ,r-permute))) | |
287 | (home-page "https://cran.r-project.org/web/packages/vegan") | |
288 | (synopsis "Functions for community ecology") | |
289 | (description | |
290 | "The vegan package provides tools for descriptive community ecology. It | |
291 | has most basic functions of diversity analysis, community ordination and | |
292 | dissimilarity analysis. Most of its multivariate tools can be used for other | |
293 | data types as well.") | |
294 | (license license:gpl2+))) | |
295 | ||
786d3de2 CR |
296 | (define-public r-tidyverse |
297 | (package | |
298 | (name "r-tidyverse") | |
10faf810 | 299 | (version "1.3.0") |
786d3de2 CR |
300 | (source |
301 | (origin | |
302 | (method url-fetch) | |
303 | (uri (cran-uri "tidyverse" version)) | |
304 | (sha256 | |
305 | (base32 | |
10faf810 | 306 | "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd")))) |
786d3de2 CR |
307 | (build-system r-build-system) |
308 | (propagated-inputs | |
309 | `(("r-broom" ,r-broom) | |
310 | ("r-cli" ,r-cli) | |
311 | ("r-crayon" ,r-crayon) | |
312 | ("r-dbplyr" ,r-dbplyr) | |
313 | ("r-dplyr" ,r-dplyr) | |
314 | ("r-forcats" ,r-forcats) | |
315 | ("r-ggplot2" ,r-ggplot2) | |
316 | ("r-haven" ,r-haven) | |
317 | ("r-hms" ,r-hms) | |
318 | ("r-httr" ,r-httr) | |
319 | ("r-jsonlite" ,r-jsonlite) | |
320 | ("r-lubridate" ,r-lubridate) | |
321 | ("r-magrittr" ,r-magrittr) | |
322 | ("r-modelr" ,r-modelr) | |
10faf810 | 323 | ("r-pillar" ,r-pillar) |
786d3de2 CR |
324 | ("r-purrr" ,r-purrr) |
325 | ("r-readr" ,r-readr) | |
326 | ("r-readxl" ,r-readxl) | |
327 | ("r-reprex" ,r-reprex) | |
328 | ("r-rlang" ,r-rlang) | |
329 | ("r-rstudioapi" ,r-rstudioapi) | |
330 | ("r-rvest" ,r-rvest) | |
331 | ("r-stringr" ,r-stringr) | |
332 | ("r-tibble" ,r-tibble) | |
333 | ("r-tidyr" ,r-tidyr) | |
334 | ("r-xml2" ,r-xml2))) | |
335 | (home-page "https://tidyverse.tidyverse.org") | |
336 | (synopsis "Install and load packages from the \"Tidyverse\"") | |
337 | (description | |
338 | "The @code{tidyverse} is a set of packages that work in harmony because | |
339 | they share common data representations and API design. This package is | |
340 | designed to make it easy to install and load multiple tidyverse packages in a | |
341 | single step.") | |
342 | (license license:gpl3))) | |
343 | ||
8a1ef6ac CR |
344 | (define-public r-rvest |
345 | (package | |
346 | (name "r-rvest") | |
92c00040 | 347 | (version "0.3.5") |
8a1ef6ac CR |
348 | (source |
349 | (origin | |
350 | (method url-fetch) | |
351 | (uri (cran-uri "rvest" version)) | |
352 | (sha256 | |
92c00040 | 353 | (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf")))) |
8a1ef6ac CR |
354 | (build-system r-build-system) |
355 | (propagated-inputs | |
356 | `(("r-httr" ,r-httr) | |
357 | ("r-magrittr" ,r-magrittr) | |
358 | ("r-selectr" ,r-selectr) | |
359 | ("r-xml2" ,r-xml2))) | |
360 | (home-page "https://github.com/hadley/rvest") | |
361 | (synopsis "Simple web scraping for R") | |
362 | (description | |
363 | "@code{r-rvest} helps you scrape information from web pages. It is | |
364 | designed to work with @code{magrittr} to make it easy to express common web | |
365 | scraping tasks, inspired by libraries like @code{BeautifulSoup}.") | |
366 | (license license:gpl3))) | |
367 | ||
81a9d4a4 CR |
368 | (define-public r-selectr |
369 | (package | |
370 | (name "r-selectr") | |
33ac1901 | 371 | (version "0.4-2") |
81a9d4a4 CR |
372 | (source |
373 | (origin | |
374 | (method url-fetch) | |
375 | (uri (cran-uri "selectr" version)) | |
376 | (sha256 | |
33ac1901 | 377 | (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m")))) |
81a9d4a4 | 378 | (build-system r-build-system) |
41e8bd77 RW |
379 | (propagated-inputs |
380 | `(("r-stringr" ,r-stringr) | |
381 | ("r-r6" ,r-r6))) | |
81a9d4a4 CR |
382 | (home-page "https://sjp.co.nz/projects/selectr/") |
383 | (synopsis "Translate CSS selectors to XPath expressions") | |
384 | (description | |
385 | "@code{r-selectr} translates a CSS3 selector into an equivalent XPath | |
386 | expression. This allows you to use CSS selectors when working with the XML | |
387 | package as it can only evaluate XPath expressions. Also provided are | |
388 | convenience functions useful for using CSS selectors on XML nodes. This | |
389 | package is a port of the Python package @code{cssselect}.") | |
390 | (license license:bsd-3))) | |
391 | ||
948740b0 CR |
392 | (define-public r-reprex |
393 | (package | |
394 | (name "r-reprex") | |
bd9f1479 | 395 | (version "0.3.0") |
948740b0 CR |
396 | (source |
397 | (origin | |
398 | (method url-fetch) | |
399 | (uri (cran-uri "reprex" version)) | |
400 | (sha256 | |
401 | (base32 | |
bd9f1479 | 402 | "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10")))) |
948740b0 CR |
403 | (build-system r-build-system) |
404 | (propagated-inputs | |
405 | `(("r-callr" ,r-callr) | |
e3c1e93e | 406 | ("r-clipr" ,r-clipr) |
1c9906c2 | 407 | ("r-fs" ,r-fs) |
e3c1e93e | 408 | ("r-rlang" ,r-rlang) |
948740b0 | 409 | ("r-rmarkdown" ,r-rmarkdown) |
e3c1e93e RW |
410 | ("r-whisker" ,r-whisker) |
411 | ("r-withr" ,r-withr))) | |
948740b0 CR |
412 | (home-page "https://github.com/tidyverse/reprex") |
413 | (synopsis "Prepare reproducible R code examples for sharing") | |
414 | (description | |
415 | "This package provides a convenience wrapper that uses the | |
416 | @code{rmarkdown} package to render small snippets of code to target formats | |
417 | that include both code and output. The goal is to encourage the sharing of | |
418 | small, reproducible, and runnable examples on code-oriented websites or email. | |
419 | @code{reprex} also extracts clean, runnable R code from various common formats, | |
420 | such as copy/paste from an R session.") | |
421 | (license license:expat))) | |
422 | ||
10487c30 CR |
423 | (define-public r-callr |
424 | (package | |
425 | (name "r-callr") | |
5e97576b | 426 | (version "3.4.0") |
10487c30 CR |
427 | (source |
428 | (origin | |
429 | (method url-fetch) | |
430 | (uri (cran-uri "callr" version)) | |
431 | (sha256 | |
432 | (base32 | |
5e97576b | 433 | "1hvxw2glizq8g0qnxakcxh8jc5scn0hp1x8i70fdpqwwbgx49slr")))) |
10487c30 CR |
434 | (build-system r-build-system) |
435 | (propagated-inputs | |
527c6055 | 436 | `(("r-r6" ,r-r6) |
6034a62a | 437 | ("r-processx" ,r-processx))) |
10487c30 CR |
438 | (home-page "https://github.com/r-lib/callr#readme") |
439 | (synopsis "Call R from R") | |
440 | (description | |
441 | "It is sometimes useful to perform a computation in a separate R process, | |
b3fed5ed | 442 | without affecting the current R process at all. This package does exactly |
10487c30 CR |
443 | that.") |
444 | (license license:expat))) | |
445 | ||
d7637e5e CR |
446 | (define-public r-readxl |
447 | (package | |
448 | (name "r-readxl") | |
50d063b5 | 449 | (version "1.3.1") |
d7637e5e CR |
450 | (source |
451 | (origin | |
452 | (method url-fetch) | |
453 | (uri (cran-uri "readxl" version)) | |
454 | (sha256 | |
455 | (base32 | |
50d063b5 | 456 | "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14")))) |
d7637e5e CR |
457 | (build-system r-build-system) |
458 | (propagated-inputs | |
459 | `(("r-cellranger" ,r-cellranger) | |
b140569e | 460 | ("r-progress" ,r-progress) |
d7637e5e CR |
461 | ("r-rcpp" ,r-rcpp) |
462 | ("r-tibble" ,r-tibble))) | |
463 | (home-page "https://readxl.tidyverse.org") | |
464 | (synopsis "Read Excel files") | |
465 | (description | |
466 | "This package lets you import Excel files into R. It supports | |
467 | @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via | |
468 | the embedded @code{RapidXML} C++ library.") | |
469 | ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and | |
470 | ;; 'rapidxml' which is Boost. | |
471 | (license (list license:gpl3 license:bsd-2 license:boost1.0)))) | |
472 | ||
9a91c925 CR |
473 | (define-public r-modelr |
474 | (package | |
475 | (name "r-modelr") | |
7ef25083 | 476 | (version "0.1.5") |
9a91c925 CR |
477 | (source |
478 | (origin | |
479 | (method url-fetch) | |
480 | (uri (cran-uri "modelr" version)) | |
481 | (sha256 | |
482 | (base32 | |
7ef25083 | 483 | "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5")))) |
9a91c925 CR |
484 | (build-system r-build-system) |
485 | (propagated-inputs | |
486 | `(("r-broom" ,r-broom) | |
487 | ("r-dplyr" ,r-dplyr) | |
9a91c925 CR |
488 | ("r-magrittr" ,r-magrittr) |
489 | ("r-purrr" ,r-purrr) | |
7ef25083 | 490 | ("r-rlang" ,r-rlang) |
9a91c925 CR |
491 | ("r-tibble" ,r-tibble) |
492 | ("r-tidyr" ,r-tidyr))) | |
493 | (home-page "https://github.com/tidyverse/modelr") | |
494 | (synopsis "Helper functions for modelling in pipelines") | |
495 | (description | |
496 | "Functions for modelling that help you seamlessly integrate modelling | |
497 | into a pipeline of data manipulation and visualisation.") | |
498 | (license license:gpl3))) | |
499 | ||
92ce1883 RW |
500 | (define-public r-httpuv |
501 | (package | |
502 | (name "r-httpuv") | |
a1f43994 | 503 | (version "1.5.2") |
92ce1883 RW |
504 | (source (origin |
505 | (method url-fetch) | |
506 | (uri (cran-uri "httpuv" version)) | |
507 | (sha256 | |
508 | (base32 | |
a1f43994 | 509 | "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk")))) |
92ce1883 | 510 | (build-system r-build-system) |
92ce1883 RW |
511 | (propagated-inputs |
512 | `(("r-bh" ,r-bh) | |
513 | ("r-later" ,r-later) | |
2391e97c RW |
514 | ("r-promises" ,r-promises) |
515 | ("r-r6" ,r-r6) | |
516 | ("r-rcpp" ,r-rcpp))) | |
92ce1883 RW |
517 | (home-page "https://github.com/rstudio/httpuv") |
518 | (synopsis "HTTP and WebSocket server library for R") | |
519 | (description | |
520 | "The httpuv package provides low-level socket and protocol support for | |
521 | handling HTTP and WebSocket requests directly from within R. It is primarily | |
522 | intended as a building block for other packages, rather than making it | |
523 | particularly easy to create complete web applications using httpuv alone.") | |
524 | ;; This package includes third-party code that was originally released | |
525 | ;; under various non-copyleft licenses. Full licensing information can be | |
526 | ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE | |
527 | (license license:gpl3+))) | |
528 | ||
529 | (define-public r-jsonlite | |
530 | (package | |
531 | (name "r-jsonlite") | |
a2315c67 | 532 | (version "1.6") |
92ce1883 RW |
533 | (source (origin |
534 | (method url-fetch) | |
535 | (uri (cran-uri "jsonlite" version)) | |
536 | (sha256 | |
537 | (base32 | |
a2315c67 | 538 | "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8")))) |
92ce1883 RW |
539 | (build-system r-build-system) |
540 | (home-page "http://arxiv.org/abs/1403.2805") | |
541 | (synopsis "Robust, high performance JSON parser and generator for R") | |
542 | (description | |
543 | "The jsonlite package provides a fast JSON parser and generator optimized | |
544 | for statistical data and the web. It offers flexible, robust, high | |
545 | performance tools for working with JSON in R and is particularly powerful for | |
546 | building pipelines and interacting with a web API. In addition to converting | |
547 | JSON data from/to R objects, jsonlite contains functions to stream, validate, | |
548 | and prettify JSON data. The unit tests included with the package verify that | |
549 | all edge cases are encoded and decoded consistently for use with dynamic data | |
550 | in systems and applications.") | |
551 | (license license:expat))) | |
552 | ||
553 | (define-public r-servr | |
554 | (package | |
555 | (name "r-servr") | |
f503ed92 | 556 | (version "0.15") |
92ce1883 RW |
557 | (source (origin |
558 | (method url-fetch) | |
559 | (uri (cran-uri "servr" version)) | |
560 | (sha256 | |
561 | (base32 | |
f503ed92 | 562 | "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi")))) |
92ce1883 RW |
563 | (build-system r-build-system) |
564 | (propagated-inputs | |
565 | `(("r-httpuv" ,r-httpuv) | |
566 | ("r-jsonlite" ,r-jsonlite) | |
567 | ("r-mime" ,r-mime) | |
568 | ("r-xfun" ,r-xfun))) | |
569 | (home-page "https://github.com/yihui/servr") | |
570 | (synopsis "Simple HTTP server to serve static files or dynamic documents") | |
571 | (description | |
572 | "Servr provides an HTTP server in R to serve static files, or dynamic | |
573 | documents that can be converted to HTML files (e.g., R Markdown) under a given | |
574 | directory.") | |
575 | (license license:expat))) | |
576 | ||
577 | (define-public r-htmltools | |
578 | (package | |
579 | (name "r-htmltools") | |
82acc94f | 580 | (version "0.4.0") |
92ce1883 RW |
581 | (source (origin |
582 | (method url-fetch) | |
583 | (uri (cran-uri "htmltools" version)) | |
584 | (sha256 | |
585 | (base32 | |
82acc94f | 586 | "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v")))) |
92ce1883 | 587 | (build-system r-build-system) |
92ce1883 RW |
588 | (propagated-inputs |
589 | `(("r-digest" ,r-digest) | |
82acc94f RW |
590 | ("r-rcpp" ,r-rcpp) |
591 | ("r-rlang" ,r-rlang))) | |
92ce1883 RW |
592 | (home-page "https://cran.r-project.org/web/packages/htmltools") |
593 | (synopsis "R tools for HTML") | |
594 | (description | |
595 | "This package provides tools for HTML generation and output in R.") | |
596 | (license license:expat))) | |
597 | ||
598 | (define-public r-htmlwidgets | |
599 | (package | |
600 | (name "r-htmlwidgets") | |
07b69a0c | 601 | (version "1.5.1") |
92ce1883 RW |
602 | (source (origin |
603 | (method url-fetch) | |
604 | (uri (cran-uri "htmlwidgets" version)) | |
605 | (sha256 | |
606 | (base32 | |
07b69a0c | 607 | "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl")))) |
92ce1883 RW |
608 | (build-system r-build-system) |
609 | (propagated-inputs | |
610 | `(("r-htmltools" ,r-htmltools) | |
611 | ("r-jsonlite" ,r-jsonlite) | |
612 | ("r-yaml" ,r-yaml))) | |
613 | (home-page "https://github.com/ramnathv/htmlwidgets") | |
614 | (synopsis "HTML Widgets for R") | |
615 | (description | |
616 | "HTML widgets is a framework for creating HTML widgets that render in | |
617 | various contexts including the R console, R Markdown documents, and Shiny web | |
618 | applications.") | |
619 | (license license:expat))) | |
620 | ||
621 | (define-public r-htmltable | |
622 | (package | |
623 | (name "r-htmltable") | |
103eef64 | 624 | (version "1.13.3") |
92ce1883 RW |
625 | (source |
626 | (origin | |
627 | (method url-fetch) | |
628 | (uri (cran-uri "htmlTable" version)) | |
629 | (sha256 | |
630 | (base32 | |
103eef64 | 631 | "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl")))) |
92ce1883 RW |
632 | (properties `((upstream-name . "htmlTable"))) |
633 | (build-system r-build-system) | |
634 | (propagated-inputs | |
635 | `(("r-checkmate" ,r-checkmate) | |
636 | ("r-htmltools" ,r-htmltools) | |
637 | ("r-htmlwidgets" ,r-htmlwidgets) | |
638 | ("r-knitr" ,r-knitr) | |
639 | ("r-magrittr" ,r-magrittr) | |
640 | ("r-rstudioapi" ,r-rstudioapi) | |
641 | ("r-stringr" ,r-stringr))) | |
642 | (home-page "http://gforge.se/packages/") | |
643 | (synopsis "Advanced tables for Markdown/HTML") | |
644 | (description | |
645 | "This package provides functions to build tables with advanced layout | |
646 | elements such as row spanners, column spanners, table spanners, zebra | |
647 | striping, and more. While allowing advanced layout, the underlying | |
648 | CSS-structure is simple in order to maximize compatibility with word | |
649 | processors such as LibreOffice. The package also contains a few text | |
650 | formatting functions that help outputting text compatible with HTML or | |
651 | LaTeX.") | |
652 | (license license:gpl3+))) | |
653 | ||
654 | (define-public r-curl | |
655 | (package | |
656 | (name "r-curl") | |
ea5af6e7 | 657 | (version "4.3") |
92ce1883 RW |
658 | (source (origin |
659 | (method url-fetch) | |
660 | (uri (cran-uri "curl" version)) | |
661 | (sha256 | |
662 | (base32 | |
ea5af6e7 | 663 | "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl")))) |
92ce1883 RW |
664 | (build-system r-build-system) |
665 | (arguments | |
666 | `(#:phases | |
667 | (modify-phases %standard-phases | |
668 | ;; The environment variable CURL_CA_BUNDLE is only respected when | |
669 | ;; running Windows, so we disable the platform checks. | |
670 | ;; This can be removed once the libcurl has been patched. | |
671 | (add-after 'unpack 'allow-CURL_CA_BUNDLE | |
672 | (lambda _ | |
673 | (substitute* "R/onload.R" | |
674 | (("if \\(!grepl\\(\"mingw\".*") | |
675 | "if (FALSE)\n")) | |
676 | (substitute* "src/handle.c" | |
677 | (("#ifdef _WIN32") "#if 1")) | |
678 | #t))))) | |
679 | (inputs | |
646e1ef0 RW |
680 | `(("libcurl" ,curl) |
681 | ("zlib" ,zlib))) | |
682 | (native-inputs | |
683 | `(("pkg-config" ,pkg-config))) | |
92ce1883 RW |
684 | (home-page "https://github.com/jeroenooms/curl") |
685 | (synopsis "HTTP client for R") | |
686 | (description | |
687 | "The @code{curl()} and @code{curl_download()} functions provide highly | |
688 | configurable drop-in replacements for base @code{url()} and | |
689 | @code{download.file()} with better performance, support for encryption, gzip | |
690 | compression, authentication, and other @code{libcurl} goodies. The core of | |
691 | the package implements a framework for performing fully customized requests | |
692 | where data can be processed either in memory, on disk, or streaming via the | |
693 | callback or connection interfaces.") | |
694 | (license license:expat))) | |
695 | ||
696 | (define-public r-hwriter | |
697 | (package | |
698 | (name "r-hwriter") | |
699 | (version "1.3.2") | |
700 | (source | |
701 | (origin | |
702 | (method url-fetch) | |
703 | (uri (cran-uri "hwriter" version)) | |
704 | (sha256 | |
705 | (base32 | |
706 | "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb")))) | |
707 | (build-system r-build-system) | |
708 | (home-page "https://cran.r-project.org/web/packages/hwriter") | |
709 | (synopsis "Output R objects in HTML format") | |
710 | (description | |
711 | "This package provides easy-to-use and versatile functions to output R | |
712 | objects in HTML format.") | |
713 | (license license:lgpl2.1+))) | |
714 | ||
715 | (define-public r-rjson | |
716 | (package | |
717 | (name "r-rjson") | |
718 | (version "0.2.20") | |
719 | (source | |
720 | (origin | |
721 | (method url-fetch) | |
722 | (uri (cran-uri "rjson" version)) | |
723 | (sha256 | |
724 | (base32 | |
725 | "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) | |
726 | (build-system r-build-system) | |
727 | (home-page "https://cran.r-project.org/web/packages/rjson") | |
728 | (synopsis "JSON library for R") | |
729 | (description | |
730 | "This package provides functions to convert R objects into JSON objects | |
731 | and vice-versa.") | |
732 | (license license:gpl2+))) | |
733 | ||
c20a81ee RW |
734 | (define-public r-fastmap |
735 | (package | |
736 | (name "r-fastmap") | |
737 | (version "1.0.1") | |
738 | (source | |
739 | (origin | |
740 | (method url-fetch) | |
741 | (uri (cran-uri "fastmap" version)) | |
742 | (sha256 | |
743 | (base32 | |
744 | "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27")))) | |
745 | (properties `((upstream-name . "fastmap"))) | |
746 | (build-system r-build-system) | |
747 | (home-page "https://r-lib.github.io/fastmap/") | |
748 | (synopsis "Fast implementation of a key-value store") | |
749 | (description | |
750 | "This package provides a fast implementation of a key-value store. | |
751 | Environments are commonly used as key-value stores, but every time a new key | |
752 | is used, it is added to R's global symbol table, causing a small amount of | |
753 | memory leakage. This can be problematic in cases where many different keys | |
754 | are used. Fastmap avoids this memory leak issue by implementing the map using | |
755 | data structures in C++.") | |
756 | (license license:expat))) | |
757 | ||
92ce1883 RW |
758 | (define-public r-shiny |
759 | (package | |
760 | (name "r-shiny") | |
6e6fa954 | 761 | (version "1.4.0") |
92ce1883 RW |
762 | (source |
763 | (origin | |
764 | (method git-fetch) | |
765 | (uri (git-reference | |
766 | (url "https://github.com/rstudio/shiny.git") | |
767 | (commit (string-append "v" version)))) | |
768 | (file-name (git-file-name name version)) | |
769 | (sha256 | |
770 | (base32 | |
6e6fa954 | 771 | "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7")))) |
92ce1883 RW |
772 | (build-system r-build-system) |
773 | (arguments | |
774 | `(#:modules ((guix build r-build-system) | |
775 | (guix build minify-build-system) | |
776 | (guix build utils) | |
777 | (ice-9 match)) | |
778 | #:imported-modules (,@%r-build-system-modules | |
779 | (guix build minify-build-system)) | |
780 | #:phases | |
781 | (modify-phases (@ (guix build r-build-system) %standard-phases) | |
782 | (add-after 'unpack 'replace-bundled-minified-JavaScript | |
783 | (lambda* (#:key inputs #:allow-other-keys) | |
784 | (let ((replace-file (lambda (old new) | |
785 | (format #t "replacing ~a with ~a\n" old new) | |
786 | (delete-file old) | |
787 | (symlink new old)))) | |
788 | ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ | |
789 | ;; contain just data. They are not minified code, so we don't | |
790 | ;; replace them. | |
791 | (with-directory-excursion "inst/www/shared" | |
792 | (replace-file "bootstrap/shim/respond.min.js" | |
793 | (string-append (assoc-ref inputs "js-respond") | |
794 | "/share/javascript/respond.min.js")) | |
795 | (replace-file "bootstrap/shim/html5shiv.min.js" | |
796 | (string-append (assoc-ref inputs "js-html5shiv") | |
797 | "/share/javascript/html5shiv.min.js")) | |
798 | (replace-file "json2-min.js" | |
799 | (string-append (assoc-ref inputs "js-json2") | |
6e6fa954 | 800 | "/share/javascript/json2-min.js")) |
92ce1883 RW |
801 | (replace-file "strftime/strftime-min.js" |
802 | (string-append (assoc-ref inputs "js-strftime") | |
803 | "/share/javascript/strftime.min.js")) | |
804 | (replace-file "highlight/highlight.pack.js" | |
805 | (string-append (assoc-ref inputs "js-highlight") | |
806 | "/share/javascript/highlight.min.js")) | |
807 | (replace-file "datatables/js/jquery.dataTables.min.js" | |
808 | (string-append (assoc-ref inputs "js-datatables") | |
809 | "/share/javascript/jquery.dataTables.min.js")) | |
810 | (replace-file "selectize/js/selectize.min.js" | |
811 | (string-append (assoc-ref inputs "js-selectize") | |
812 | "/share/javascript/selectize.min.js")) | |
813 | (replace-file "selectize/js/es5-shim.min.js" | |
814 | (string-append (assoc-ref inputs "js-es5-shim") | |
815 | "/share/javascript/es5-shim.min.js")) | |
816 | (for-each (match-lambda | |
817 | ((source . target) | |
818 | (delete-file target) | |
819 | (minify source #:target target))) | |
820 | '(("jqueryui/jquery-ui.js" . | |
821 | "jqueryui/jquery-ui.min.js") | |
92ce1883 RW |
822 | ("datepicker/js/bootstrap-datepicker.js" . |
823 | "datepicker/js/bootstrap-datepicker.min.js") | |
824 | ("ionrangeslider/js/ion.rangeSlider.js" . | |
825 | "ionrangeslider/js/ion.rangeSlider.min.js") | |
826 | ("bootstrap/js/bootstrap.js" . | |
827 | "bootstrap/js/bootstrap.min.js") | |
828 | ("shiny.js" . | |
829 | "shiny.min.js") | |
830 | ("jquery.js" . | |
6e6fa954 RW |
831 | "jquery.min.js") |
832 | ("legacy/jquery.js" . | |
833 | "legacy/jquery.min.js") | |
834 | ("showdown/src/showdown.js" . | |
835 | "showdown/compressed/showdown.js"))))) | |
92ce1883 RW |
836 | #t))))) |
837 | (propagated-inputs | |
838 | `(("r-crayon" ,r-crayon) | |
6e6fa954 | 839 | ("r-fastmap" ,r-fastmap) |
92ce1883 RW |
840 | ("r-httpuv" ,r-httpuv) |
841 | ("r-mime" ,r-mime) | |
842 | ("r-jsonlite" ,r-jsonlite) | |
843 | ("r-xtable" ,r-xtable) | |
844 | ("r-digest" ,r-digest) | |
845 | ("r-htmltools" ,r-htmltools) | |
846 | ("r-r6" ,r-r6) | |
847 | ("r-sourcetools" ,r-sourcetools))) | |
848 | (inputs | |
849 | `(("js-datatables" ,js-datatables) | |
850 | ("js-html5shiv" ,js-html5shiv) | |
851 | ("js-json2" ,js-json2) | |
852 | ("js-respond" ,js-respond) | |
853 | ("js-selectize" ,js-selectize) | |
854 | ("js-strftime" ,js-strftime) | |
855 | ("js-highlight" ,js-highlight) | |
856 | ("js-es5-shim" ,js-es5-shim))) | |
8916034a RW |
857 | (native-inputs |
858 | `(("uglify-js" ,uglify-js))) | |
92ce1883 RW |
859 | (home-page "http://shiny.rstudio.com") |
860 | (synopsis "Easy interactive web applications with R") | |
861 | (description | |
862 | "Makes it incredibly easy to build interactive web applications | |
863 | with R. Automatic \"reactive\" binding between inputs and outputs and | |
864 | extensive prebuilt widgets make it possible to build beautiful, | |
865 | responsive, and powerful applications with minimal effort.") | |
866 | (license license:artistic2.0))) | |
867 | ||
41b8b05c RW |
868 | ;; This package includes minified JavaScript files. When upgrading please |
869 | ;; check that there are no new minified JavaScript files. | |
870 | (define-public r-shinytree | |
871 | (package | |
872 | (name "r-shinytree") | |
873 | (version "0.2.7") | |
874 | (source | |
875 | (origin | |
876 | (method url-fetch) | |
877 | (uri (cran-uri "shinyTree" version)) | |
878 | (sha256 | |
879 | (base32 | |
880 | "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3")) | |
881 | (modules '((guix build utils))) | |
882 | (snippet | |
883 | '(begin | |
884 | ;; Delete minified JavaScript | |
885 | (for-each delete-file | |
886 | '("inst/www/jsTree-3.3.7/libs/require.js" | |
887 | "inst/www/jsTree-3.3.7/libs/jquery.js" | |
888 | "inst/www/jsTree-3.3.7/jstree.min.js")) | |
889 | #t)))) | |
890 | (properties `((upstream-name . "shinyTree"))) | |
891 | (build-system r-build-system) | |
892 | (arguments | |
893 | `(#:modules ((guix build utils) | |
894 | (guix build r-build-system) | |
895 | (srfi srfi-1) | |
896 | (ice-9 popen)) | |
897 | #:phases | |
898 | (modify-phases %standard-phases | |
899 | (add-after 'unpack 'replace-minified-javascript | |
900 | (lambda* (#:key inputs #:allow-other-keys) | |
901 | (with-directory-excursion "inst/www/jsTree-3.3.7/" | |
902 | (symlink (string-append (assoc-ref inputs "js-requirejs") | |
903 | "/share/javascript/require.min.js") | |
904 | "libs/require.js") | |
905 | (call-with-values | |
906 | (lambda () | |
907 | (unzip2 | |
908 | `((,(assoc-ref inputs "js-jquery") | |
909 | "libs/jquery.js") | |
910 | ("jstree.js" | |
911 | "jstree.min.js")))) | |
912 | (lambda (sources targets) | |
913 | (for-each (lambda (source target) | |
914 | (format #t "Processing ~a --> ~a~%" | |
915 | source target) | |
916 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
917 | (call-with-output-file target | |
918 | (lambda (port) | |
919 | (dump-port minified port))))) | |
920 | sources targets)))) | |
921 | #t))))) | |
922 | (propagated-inputs | |
923 | `(("r-htmlwidgets" ,r-htmlwidgets) | |
924 | ("r-jsonlite" ,r-jsonlite) | |
925 | ("r-promises" ,r-promises) | |
926 | ("r-shiny" ,r-shiny) | |
927 | ("r-stringr" ,r-stringr))) | |
928 | (inputs | |
929 | `(("js-requirejs" ,js-requirejs))) | |
930 | (native-inputs | |
931 | `(("uglify-js" ,uglify-js) | |
932 | ("js-jquery" | |
933 | ,(origin | |
934 | (method url-fetch) | |
935 | (uri "https://code.jquery.com/jquery-3.3.1.js") | |
936 | (sha256 | |
937 | (base32 | |
938 | "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))))) | |
939 | (home-page "https://cran.r-project.org/web/packages/shinyTree/") | |
940 | (synopsis "jsTree bindings for Shiny") | |
941 | (description | |
942 | "This package exposes R bindings to jsTree, a JavaScript library that | |
943 | supports interactive trees, to enable rich, editable trees in Shiny.") | |
944 | (license license:expat))) | |
945 | ||
92ce1883 RW |
946 | (define-public r-shinydashboard |
947 | (package | |
948 | (name "r-shinydashboard") | |
949 | (version "0.7.1") | |
950 | (source (origin | |
951 | (method url-fetch) | |
952 | (uri (cran-uri "shinydashboard" version)) | |
953 | (sha256 | |
954 | (base32 | |
955 | "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) | |
956 | (build-system r-build-system) | |
957 | ;; The directory inst/AdminLTE/ contains a minified JavaScript file. | |
958 | ;; Regenerate it from the included sources. | |
959 | (arguments | |
960 | `(#:modules ((guix build utils) | |
961 | (guix build r-build-system) | |
962 | (ice-9 popen)) | |
963 | #:phases | |
964 | (modify-phases %standard-phases | |
965 | (add-after 'unpack 'generate-minified-javascript | |
966 | (lambda _ | |
967 | (with-directory-excursion "inst/AdminLTE" | |
968 | (delete-file "app.min.js") | |
969 | (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js"))) | |
970 | (call-with-output-file "app.min.js" | |
971 | (lambda (port) | |
972 | (dump-port minified port)))))))))) | |
973 | (propagated-inputs | |
974 | `(("r-htmltools" ,r-htmltools) | |
975 | ("r-promises" ,r-promises) | |
976 | ("r-shiny" ,r-shiny))) | |
977 | (native-inputs | |
978 | `(("uglify-js" ,uglify-js))) | |
979 | (home-page "http://rstudio.github.io/shinydashboard/") | |
980 | (synopsis "Create dashboards with shiny") | |
981 | (description "This package provides an extension to the Shiny web | |
982 | application framework for R, making it easy to create attractive dashboards.") | |
983 | ;; This package includes software that was released under the Expat | |
984 | ;; license, but the whole package is released under GPL version 2 or | |
985 | ;; later. | |
986 | (license license:gpl2+))) | |
987 | ||
988 | (define-public r-shinyfiles | |
989 | (package | |
990 | (name "r-shinyfiles") | |
9a3d4216 | 991 | (version "0.7.5") |
92ce1883 RW |
992 | (source |
993 | (origin | |
994 | (method url-fetch) | |
995 | (uri (cran-uri "shinyFiles" version)) | |
996 | (sha256 | |
9a3d4216 | 997 | (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a")))) |
92ce1883 RW |
998 | (properties `((upstream-name . "shinyFiles"))) |
999 | (build-system r-build-system) | |
1000 | (propagated-inputs | |
1001 | `(("r-fs" ,r-fs) | |
1002 | ("r-htmltools" ,r-htmltools) | |
1003 | ("r-jsonlite" ,r-jsonlite) | |
1004 | ("r-shiny" ,r-shiny) | |
1005 | ("r-tibble" ,r-tibble))) | |
1006 | (home-page "https://github.com/thomasp85/shinyFiles") | |
1007 | (synopsis "Server-side file system viewer for Shiny") | |
1008 | (description | |
1009 | "This package provides functionality for client-side navigation of the | |
1010 | server side file system in shiny apps. In case the app is running locally | |
1011 | this gives the user direct access to the file system without the need to | |
1012 | \"download\" files to a temporary location. Both file and folder selection as | |
1013 | well as file saving is available.") | |
1014 | (license license:gpl2+))) | |
1015 | ||
fc3719cc RW |
1016 | (define-public r-shinythemes |
1017 | (package | |
1018 | (name "r-shinythemes") | |
1019 | (version "1.1.2") | |
1020 | (source | |
1021 | (origin | |
1022 | (method url-fetch) | |
1023 | (uri (cran-uri "shinythemes" version)) | |
1024 | (sha256 | |
1025 | (base32 | |
1026 | "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf")))) | |
1027 | (properties `((upstream-name . "shinythemes"))) | |
1028 | (build-system r-build-system) | |
1029 | (propagated-inputs `(("r-shiny" ,r-shiny))) | |
1030 | (home-page "http://rstudio.github.io/shinythemes/") | |
1031 | (synopsis "Themes for Shiny") | |
1032 | (description | |
1033 | "This package provides themes for use with Shiny. It includes several | |
1034 | Bootstrap themes, which are packaged for use with Shiny applications.") | |
1035 | ;; The package is released under version 3 of the GPL, but it includes | |
1036 | ;; source files that are covered by the Expat license. It also includes | |
1037 | ;; fonts under SIL or the ASL. | |
1038 | (license (list license:gpl3 license:expat | |
1039 | license:silofl1.1 license:asl2.0)))) | |
1040 | ||
983906bb RW |
1041 | ;; The package sources include minified variants of d3.js and non-minified |
1042 | ;; source code of d3-jetpack. | |
1043 | (define-public r-d3r | |
1044 | (package | |
1045 | (name "r-d3r") | |
52aacfbd | 1046 | (version "0.8.7") |
983906bb RW |
1047 | (source |
1048 | (origin | |
1049 | (method url-fetch) | |
1050 | (uri (cran-uri "d3r" version)) | |
1051 | (sha256 | |
1052 | (base32 | |
52aacfbd | 1053 | "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a")))) |
983906bb RW |
1054 | (build-system r-build-system) |
1055 | (arguments | |
1056 | `(#:modules ((guix build utils) | |
1057 | (guix build r-build-system) | |
1058 | (srfi srfi-1) | |
1059 | (ice-9 popen)) | |
1060 | #:phases | |
1061 | (modify-phases %standard-phases | |
1062 | (add-after 'unpack 'process-javascript | |
1063 | (lambda* (#:key inputs #:allow-other-keys) | |
1064 | (with-directory-excursion "inst/www/d3/" | |
1065 | (call-with-values | |
1066 | (lambda () | |
1067 | (unzip2 | |
1068 | `((,(assoc-ref inputs "d3.v3.js") | |
1069 | "v3/dist/d3.min.js") | |
1070 | (,(assoc-ref inputs "d3.v4.js") | |
1071 | "v4/dist/d3.min.js") | |
1072 | (,(assoc-ref inputs "d3.v5.js") | |
1073 | "v5/dist/d3.min.js")))) | |
1074 | (lambda (sources targets) | |
1075 | (for-each (lambda (source target) | |
1076 | (format #t "Processing ~a --> ~a~%" | |
1077 | source target) | |
1078 | (delete-file target) | |
1079 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
1080 | (call-with-output-file target | |
1081 | (lambda (port) | |
1082 | (dump-port minified port))))) | |
1083 | sources targets)))) | |
1084 | #t))))) | |
1085 | (propagated-inputs | |
1086 | `(("r-dplyr" ,r-dplyr) | |
1087 | ("r-htmltools" ,r-htmltools) | |
1088 | ("r-tidyr" ,r-tidyr))) | |
1089 | (native-inputs | |
1090 | `(("uglify-js" ,uglify-js) | |
1091 | ("d3.v3.js" | |
1092 | ,(origin | |
1093 | (method url-fetch) | |
1094 | (uri "https://d3js.org/d3.v3.js") | |
1095 | (sha256 | |
1096 | (base32 | |
1097 | "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) | |
1098 | ("d3.v4.js" | |
1099 | ,(origin | |
1100 | (method url-fetch) | |
1101 | (uri "https://d3js.org/d3.v4.js") | |
1102 | (sha256 | |
1103 | (base32 | |
1104 | "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))) | |
1105 | ("d3.v5.js" | |
1106 | ,(origin | |
1107 | (method url-fetch) | |
1108 | (uri "https://d3js.org/d3.v5.js") | |
1109 | (sha256 | |
1110 | (base32 | |
1111 | "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))))) | |
1112 | (home-page "https://github.com/timelyportfolio/d3r") | |
1113 | (synopsis "d3.js utilities for R") | |
1114 | (description | |
1115 | "This package provides a suite of functions to help ease the use of the | |
1116 | d3.js visualization library in R. These helpers include | |
1117 | @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion | |
1118 | tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame} | |
1119 | R objects into the JSON format that the d3.js library expects.") | |
1120 | (license license:bsd-3))) | |
1121 | ||
b03dd5cf RW |
1122 | ;; We use the latest commit here because the last release was in 2016 while |
1123 | ;; the latest commit was in 2018. | |
1124 | (define-public r-sankeyd3 | |
1125 | (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc") | |
1126 | (revision "1")) | |
1127 | (package | |
1128 | (name "r-sankeyd3") | |
1129 | (version (git-version "0.3.2" revision commit)) | |
1130 | (source | |
1131 | (origin | |
1132 | (method git-fetch) | |
1133 | (uri (git-reference | |
1134 | (url "https://github.com/fbreitwieser/sankeyD3.git") | |
1135 | (commit commit))) | |
1136 | (file-name (git-file-name name version)) | |
1137 | (sha256 | |
1138 | (base32 | |
1139 | "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) | |
1140 | (build-system r-build-system) | |
1141 | (propagated-inputs | |
1142 | `(("r-d3r" ,r-d3r) | |
1143 | ("r-htmlwidgets" ,r-htmlwidgets) | |
1144 | ("r-shiny" ,r-shiny) | |
1145 | ("r-magrittr" ,r-magrittr))) | |
1146 | (home-page "https://github.com/fbreitwieser/sankeyD3") | |
1147 | (synopsis "Sankey network graphs from R") | |
1148 | (description | |
1149 | "This package provides an R library to generate Sankey network graphs | |
1150 | in R and Shiny via the D3 visualization library.") | |
1151 | ;; The R code is licensed under GPLv3+. It includes the non-minified | |
1152 | ;; JavaScript source code of d3-sankey, which is released under the | |
1153 | ;; 3-clause BSD license. | |
1154 | (license (list license:gpl3+ license:bsd-3))))) | |
1155 | ||
92ce1883 RW |
1156 | (define-public r-crosstalk |
1157 | (package | |
1158 | (name "r-crosstalk") | |
1159 | (version "1.0.0") | |
1160 | (source | |
1161 | (origin | |
1162 | (method url-fetch) | |
1163 | (uri (cran-uri "crosstalk" version)) | |
1164 | (sha256 | |
1165 | (base32 | |
1166 | "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk")))) | |
1167 | (build-system r-build-system) | |
1168 | (propagated-inputs | |
1169 | `(("r-ggplot2" ,r-ggplot2) | |
1170 | ("r-htmltools" ,r-htmltools) | |
1171 | ("r-jsonlite" ,r-jsonlite) | |
1172 | ("r-lazyeval" ,r-lazyeval) | |
1173 | ("r-r6" ,r-r6) | |
1174 | ("r-shiny" ,r-shiny))) | |
1175 | (home-page "https://rstudio.github.io/crosstalk/") | |
1176 | (synopsis "Inter-widget interactivity for HTML widgets") | |
1177 | (description | |
1178 | "This package provides building blocks for allowing HTML widgets to | |
1179 | communicate with each other, with Shiny or without (i.e. static @code{.html} | |
1180 | files). It currently supports linked brushing and filtering.") | |
1181 | (license license:expat))) | |
1182 | ||
1183 | (define-public r-rook | |
1184 | (package | |
1185 | (name "r-rook") | |
1186 | (version "1.1-1") | |
1187 | (source | |
1188 | (origin | |
1189 | (method url-fetch) | |
1190 | (uri (cran-uri "Rook" version)) | |
1191 | (sha256 | |
1192 | (base32 | |
1193 | "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) | |
1194 | (properties `((upstream-name . "Rook"))) | |
1195 | (build-system r-build-system) | |
1196 | (propagated-inputs `(("r-brew" ,r-brew))) | |
1197 | (home-page "https://cran.r-project.org/web/packages/Rook") | |
1198 | (synopsis "Web server interface for R") | |
1199 | (description | |
1200 | "This package contains the Rook specification and convenience software | |
1201 | for building and running Rook applications. A Rook application is an R | |
1202 | reference class object that implements a @code{call} method or an R closure | |
1203 | that takes exactly one argument, an environment, and returns a list with three | |
1204 | named elements: the @code{status}, the @code{headers}, and the @code{body}.") | |
1205 | (license license:gpl2))) | |
1206 | ||
1207 | (define-public r-miniui | |
1208 | (package | |
1209 | (name "r-miniui") | |
1210 | (version "0.1.1.1") | |
1211 | (source | |
1212 | (origin | |
1213 | (method url-fetch) | |
1214 | (uri (cran-uri "miniUI" version)) | |
1215 | (sha256 | |
1216 | (base32 | |
1217 | "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) | |
1218 | (properties `((upstream-name . "miniUI"))) | |
1219 | (build-system r-build-system) | |
1220 | (propagated-inputs | |
1221 | `(("r-htmltools" ,r-htmltools) | |
1222 | ("r-shiny" ,r-shiny))) | |
1223 | (home-page "https://cran.r-project.org/web/packages/miniUI/") | |
1224 | (synopsis "Shiny UI widgets for small screens") | |
1225 | (description | |
1226 | "This package provides UI widget and layout functions for writing Shiny apps that | |
1227 | work well on small screens.") | |
1228 | (license license:gpl3))) | |
1229 | ||
60a166c6 RW |
1230 | (define-public r-feather |
1231 | (package | |
1232 | (name "r-feather") | |
e48e476f | 1233 | (version "0.3.5") |
60a166c6 RW |
1234 | (source |
1235 | (origin | |
1236 | (method url-fetch) | |
1237 | (uri (cran-uri "feather" version)) | |
1238 | (sha256 | |
1239 | (base32 | |
e48e476f | 1240 | "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh")))) |
60a166c6 RW |
1241 | (build-system r-build-system) |
1242 | (propagated-inputs | |
1243 | `(("r-hms" ,r-hms) | |
1244 | ("r-rcpp" ,r-rcpp) | |
1245 | ("r-tibble" ,r-tibble))) | |
1246 | (home-page "https://github.com/wesm/feather") | |
1247 | (synopsis "R Bindings to the Feather API") | |
1248 | (description "Read and write feather files, a lightweight binary columnar | |
1249 | data store designed for maximum speed.") | |
1250 | (license license:asl2.0))) | |
1251 | ||
2a2760a0 RW |
1252 | (define-public r-maps |
1253 | (package | |
1254 | (name "r-maps") | |
1255 | (version "3.3.0") | |
1256 | (source | |
1257 | (origin | |
1258 | (method url-fetch) | |
1259 | (uri (cran-uri "maps" version)) | |
1260 | (sha256 | |
1261 | (base32 | |
1262 | "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr")))) | |
1263 | (build-system r-build-system) | |
1264 | (home-page "https://cran.r-project.org/web/packages/maps") | |
1265 | (synopsis "Draw geographical maps") | |
1266 | (description "This package provides an R module for display of maps. | |
36a4366d EF |
1267 | Projection code and larger maps are in separate packages (@code{mapproj} and |
1268 | @code{mapdata}).") | |
2a2760a0 RW |
1269 | (license license:gpl2))) |
1270 | ||
1271 | (define-public r-mapproj | |
1272 | (package | |
1273 | (name "r-mapproj") | |
1274 | (version "1.2.6") | |
1275 | (source | |
1276 | (origin | |
1277 | (method url-fetch) | |
1278 | (uri (cran-uri "mapproj" version)) | |
1279 | (sha256 | |
1280 | (base32 | |
1281 | "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2")))) | |
1282 | (build-system r-build-system) | |
1283 | (propagated-inputs `(("r-maps" ,r-maps))) | |
1284 | (home-page "https://cran.r-project.org/web/packages/mapproj") | |
1285 | (synopsis "Map projection in R") | |
1286 | (description "This package converts latitude/longitude into projected | |
1287 | coordinates.") | |
1288 | (license (list license:gpl2 ; The R interface | |
1289 | (license:non-copyleft ; The C code | |
1290 | "https://www.gnu.org/licenses/license-list.en.html#lucent102" | |
1291 | "Lucent Public License Version 1.02"))))) | |
1292 | ||
1293 | (define-public r-rgooglemaps | |
1294 | (package | |
1295 | (name "r-rgooglemaps") | |
0128a9df | 1296 | (version "1.4.5") |
2a2760a0 RW |
1297 | (source |
1298 | (origin | |
1299 | (method url-fetch) | |
1300 | (uri (cran-uri "RgoogleMaps" version)) | |
1301 | (sha256 | |
1302 | (base32 | |
0128a9df | 1303 | "1acf0qc9597apcidjzrpvwhg9ihypr38jigc10jvqn33qbn1i9s7")))) |
2a2760a0 RW |
1304 | (properties `((upstream-name . "RgoogleMaps"))) |
1305 | (build-system r-build-system) | |
1306 | (propagated-inputs `(("r-png" ,r-png))) | |
1307 | (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") | |
1308 | (synopsis "Use Google Maps in R") | |
1309 | (description "This package serves two purposes: | |
1310 | @enumerate | |
1311 | @item Provide a comfortable R interface to query the Google server for static | |
1312 | maps, and | |
1313 | @item Use the map as a background image to overlay plots within R. This | |
1314 | requires proper coordinate scaling. | |
1315 | @end enumerate\n") | |
1316 | (license license:gpl2+))) | |
1317 | ||
1318 | (define-public r-geosphere | |
1319 | (package | |
1320 | (name "r-geosphere") | |
f43ec9e9 | 1321 | (version "1.5-10") |
2a2760a0 RW |
1322 | (source |
1323 | (origin | |
1324 | (method url-fetch) | |
1325 | (uri (cran-uri "geosphere" version)) | |
1326 | (sha256 | |
1327 | (base32 | |
f43ec9e9 | 1328 | "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan")))) |
2a2760a0 RW |
1329 | (build-system r-build-system) |
1330 | (propagated-inputs `(("r-sp" ,r-sp))) | |
1331 | (home-page "https://cran.r-project.org/web/packages/geosphere") | |
1332 | (synopsis "Spherical trigonometry") | |
1333 | (description "This package computes spherical trigonometry for geographic | |
1334 | applications. That is, compute distances and related measures for angular | |
1335 | (longitude/latitude) locations.") | |
1336 | (license license:gpl3+))) | |
1337 | ||
77e7158c RW |
1338 | (define-public r-jpeg |
1339 | (package | |
1340 | (name "r-jpeg") | |
1341 | (version "0.1-8.1") | |
1342 | (source | |
1343 | (origin | |
1344 | (method url-fetch) | |
1345 | (uri (cran-uri "jpeg" version)) | |
1346 | (sha256 | |
1347 | (base32 | |
1348 | "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x")))) | |
1349 | (build-system r-build-system) | |
1350 | (inputs `(("libjpeg" ,libjpeg))) | |
1351 | (home-page "http://www.rforge.net/jpeg/") | |
1352 | (synopsis "Read and write JPEG images with R") | |
1353 | (description "This package provides a way to read, write and display | |
1354 | bitmap images stored in the JPEG format with R. It can read and write both | |
1355 | files and in-memory raw vectors.") | |
1356 | (license license:gpl2+))) | |
1357 | ||
2a2760a0 RW |
1358 | (define-public r-ggmap |
1359 | (package | |
1360 | (name "r-ggmap") | |
20662a30 | 1361 | (version "3.0.0") |
2a2760a0 RW |
1362 | (source |
1363 | (origin | |
1364 | (method url-fetch) | |
1365 | (uri (cran-uri "ggmap" version)) | |
1366 | (sha256 | |
1367 | (base32 | |
20662a30 | 1368 | "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) |
2a2760a0 RW |
1369 | (build-system r-build-system) |
1370 | (propagated-inputs | |
20662a30 RW |
1371 | `(("r-bitops" ,r-bitops) |
1372 | ("r-digest" ,r-digest) | |
1373 | ("r-dplyr" ,r-dplyr) | |
2a2760a0 | 1374 | ("r-ggplot2" ,r-ggplot2) |
20662a30 RW |
1375 | ("r-glue" ,r-glue) |
1376 | ("r-httr" ,r-httr) | |
2a2760a0 | 1377 | ("r-jpeg" ,r-jpeg) |
20662a30 | 1378 | ("r-magrittr" ,r-magrittr) |
2a2760a0 RW |
1379 | ("r-plyr" ,r-plyr) |
1380 | ("r-png" ,r-png) | |
20662a30 | 1381 | ("r-purrr" ,r-purrr) |
2a2760a0 RW |
1382 | ("r-rgooglemaps" ,r-rgooglemaps) |
1383 | ("r-rjson" ,r-rjson) | |
20662a30 RW |
1384 | ("r-scales" ,r-scales) |
1385 | ("r-stringr" ,r-stringr) | |
1386 | ("r-tibble" ,r-tibble) | |
1387 | ("r-tidyr" ,r-tidyr))) | |
2a2760a0 RW |
1388 | (home-page "https://github.com/dkahle/ggmap") |
1389 | (synopsis "Spatial visualization with ggplot2") | |
1390 | (description "This package provides a collection of functions to visualize | |
1391 | spatial data and models on top of static maps from various online sources (e.g | |
1392 | Google Maps and Stamen Maps). It includes tools common to those tasks, | |
1393 | including functions for geolocation and routing.") | |
1394 | (license license:gpl2))) | |
1395 | ||
d2a507ef CR |
1396 | (define-public r-haven |
1397 | (package | |
1398 | (name "r-haven") | |
65d81e75 | 1399 | (version "2.2.0") |
d2a507ef CR |
1400 | (source |
1401 | (origin | |
1402 | (method url-fetch) | |
1403 | (uri (cran-uri "haven" version)) | |
1404 | (sha256 | |
1405 | (base32 | |
65d81e75 | 1406 | "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr")))) |
d2a507ef | 1407 | (build-system r-build-system) |
35b32367 TGR |
1408 | (inputs |
1409 | `(("zlib" ,zlib))) | |
d2a507ef CR |
1410 | (propagated-inputs |
1411 | `(("r-forcats" ,r-forcats) | |
1412 | ("r-hms" ,r-hms) | |
1413 | ("r-rcpp" ,r-rcpp) | |
65d81e75 | 1414 | ("r-rlang" ,r-rlang) |
d2a507ef | 1415 | ("r-readr" ,r-readr) |
65d81e75 RW |
1416 | ("r-tibble" ,r-tibble) |
1417 | ("r-tidyselect" ,r-tidyselect))) | |
d2a507ef CR |
1418 | (home-page "https://haven.tidyverse.org") |
1419 | (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files") | |
1420 | (description | |
1421 | "This package lets you mport foreign statistical formats into R via the | |
1422 | embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") | |
1423 | (license license:expat))) | |
1424 | ||
996bed06 RJ |
1425 | (define-public r-amap |
1426 | (package | |
1427 | (name "r-amap") | |
3dc1d433 | 1428 | (version "0.8-18") |
996bed06 RJ |
1429 | (source (origin |
1430 | (method url-fetch) | |
1431 | (uri (cran-uri "amap" version)) | |
1432 | (sha256 | |
1433 | (base32 | |
3dc1d433 | 1434 | "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) |
996bed06 | 1435 | (build-system r-build-system) |
c86da03a | 1436 | (native-inputs |
996bed06 RJ |
1437 | `(("gfortran" ,gfortran))) |
1438 | (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") | |
1439 | (synopsis "Another multidimensional analysis package") | |
1440 | (description "This package provides tools for clustering and principal | |
1441 | component analysis (with robust methods, and parallelized functions).") | |
1442 | (license license:gpl2+))) | |
1443 | ||
53cc59a1 RW |
1444 | (define-public r-ape |
1445 | (package | |
1446 | (name "r-ape") | |
8e91ad0b | 1447 | (version "5.3") |
53cc59a1 RW |
1448 | (source |
1449 | (origin | |
1450 | (method url-fetch) | |
1451 | (uri (cran-uri "ape" version)) | |
1452 | (sha256 | |
1453 | (base32 | |
8e91ad0b | 1454 | "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08")))) |
53cc59a1 RW |
1455 | (build-system r-build-system) |
1456 | (propagated-inputs | |
1457 | `(("r-lattice" ,r-lattice) | |
1458 | ("r-nlme" ,r-nlme) | |
1459 | ("r-rcpp" ,r-rcpp))) | |
1460 | (home-page "http://ape-package.ird.fr/") | |
1461 | (synopsis "Analyses of phylogenetics and evolution") | |
1462 | (description | |
1463 | "This package provides functions for reading, writing, plotting, and | |
1464 | manipulating phylogenetic trees, analyses of comparative data in a | |
1465 | phylogenetic framework, ancestral character analyses, analyses of | |
1466 | diversification and macroevolution, computing distances from DNA sequences, | |
1467 | and several other tools.") | |
1468 | (license license:gpl2+))) | |
1469 | ||
109b2f7c VV |
1470 | (define-public r-abbyyr |
1471 | (package | |
1472 | (name "r-abbyyr") | |
4ae5f18a | 1473 | (version "0.5.5") |
109b2f7c VV |
1474 | (source |
1475 | (origin | |
1476 | (method url-fetch) | |
1477 | (uri (cran-uri "abbyyR" version)) | |
1478 | (sha256 | |
1479 | (base32 | |
4ae5f18a | 1480 | "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r")))) |
109b2f7c VV |
1481 | (properties `((upstream-name . "abbyyR"))) |
1482 | (build-system r-build-system) | |
1483 | (propagated-inputs | |
1484 | `(("r-curl" ,r-curl) | |
1485 | ("r-httr" ,r-httr) | |
1486 | ("r-plyr" ,r-plyr) | |
1487 | ("r-progress" ,r-progress) | |
1488 | ("r-readr" ,r-readr) | |
1489 | ("r-xml" ,r-xml))) | |
1490 | (home-page "https://github.com/soodoku/abbyyR") | |
1491 | (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") | |
1492 | (description | |
1493 | "This package provides tools to get text from images of text using Abbyy | |
1494 | Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily | |
1495 | OCR images, barcodes, forms, documents with machine readable zones, e.g. | |
1496 | passports and get the results in a variety of formats including plain text and | |
1497 | XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") | |
1498 | (license license:expat))) | |
1499 | ||
056468dc RW |
1500 | (define-public r-colorspace |
1501 | (package | |
1502 | (name "r-colorspace") | |
f9bc918b | 1503 | (version "1.4-1") |
056468dc RW |
1504 | (source |
1505 | (origin | |
1506 | (method url-fetch) | |
1507 | (uri (cran-uri "colorspace" version)) | |
1508 | (sha256 | |
f9bc918b | 1509 | (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9")))) |
056468dc | 1510 | (build-system r-build-system) |
e9960d8c | 1511 | (home-page "https://cran.r-project.org/web/packages/colorspace") |
056468dc RW |
1512 | (synopsis "Color space manipulation") |
1513 | (description | |
1514 | "This package carries out a mapping between assorted color spaces | |
1515 | including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar | |
1516 | CIELAB. Qualitative, sequential, and diverging color palettes based on HCL | |
1517 | colors are provided.") | |
1518 | (license license:bsd-3))) | |
5bee6bf4 RW |
1519 | |
1520 | (define-public r-glue | |
1521 | (package | |
1522 | (name "r-glue") | |
b21eb347 | 1523 | (version "1.3.1") |
5bee6bf4 RW |
1524 | (source |
1525 | (origin | |
1526 | (method url-fetch) | |
1527 | (uri (cran-uri "glue" version)) | |
1528 | (sha256 | |
1529 | (base32 | |
b21eb347 | 1530 | "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag")))) |
5bee6bf4 RW |
1531 | (build-system r-build-system) |
1532 | (home-page "https://github.com/tidyverse/glue") | |
1533 | (synopsis "Interpreted string literals") | |
1534 | (description | |
1535 | "This package provides an implementation of interpreted string literals, | |
1536 | inspired by Python's Literal String Interpolation (PEP-0498) and | |
1537 | Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") | |
1538 | (license license:expat))) | |
847b4572 | 1539 | |
ddbf2a98 RJ |
1540 | (define-public r-pastecs |
1541 | (package | |
1542 | (name "r-pastecs") | |
1543 | (version "1.3.21") | |
1544 | (source (origin | |
1545 | (method url-fetch) | |
1546 | (uri (cran-uri "pastecs" version)) | |
1547 | (sha256 | |
1548 | (base32 | |
1549 | "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) | |
1550 | (build-system r-build-system) | |
1551 | (propagated-inputs | |
1552 | `(("r-boot" ,r-boot))) | |
1553 | (home-page "http://www.sciviews.org/pastecs") | |
1554 | (synopsis "Analysis of space-time ecological series") | |
1555 | (description | |
1556 | "This package provides functions for regulation, decomposition and analysis | |
1557 | of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER | |
1558 | initiative to bring PASSTEC 2000 functionalities to R.") | |
1559 | (license license:gpl2+))) | |
1560 | ||
847b4572 RW |
1561 | (define-public r-plogr |
1562 | (package | |
1563 | (name "r-plogr") | |
0e947804 | 1564 | (version "0.2.0") |
847b4572 RW |
1565 | (source |
1566 | (origin | |
1567 | (method url-fetch) | |
1568 | (uri (cran-uri "plogr" version)) | |
1569 | (sha256 | |
1570 | (base32 | |
0e947804 | 1571 | "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf")))) |
847b4572 RW |
1572 | (build-system r-build-system) |
1573 | (home-page "https://github.com/krlmlr/plogr") | |
1574 | (synopsis "R bindings for the plog C++ logging library") | |
1575 | (description | |
1576 | "This package provides the header files for a stripped-down version of | |
1577 | the plog header-only C++ logging library, and a method to log to R's standard | |
1578 | error stream.") | |
1579 | (license license:expat))) | |
a8cba9dd | 1580 | |
a86049d9 TGR |
1581 | (define-public r-pls |
1582 | (package | |
1583 | (name "r-pls") | |
4c9a3173 | 1584 | (version "2.7-2") |
a86049d9 TGR |
1585 | (source |
1586 | (origin | |
1587 | (method url-fetch) | |
1588 | (uri (cran-uri "pls" version)) | |
1589 | (sha256 | |
4c9a3173 | 1590 | (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7")))) |
a86049d9 TGR |
1591 | (build-system r-build-system) |
1592 | (home-page "http://mevik.net/work/software/pls.html") | |
1593 | (synopsis "Partial Least Squares and Principal Component Regression") | |
1594 | (description | |
1595 | "The pls package implements multivariate regression methods: Partial Least | |
1596 | Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and | |
1597 | Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports: | |
1598 | ||
1599 | @itemize | |
1600 | @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS | |
1601 | algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd} | |
1602 | @item multi-response models (or @dfn{PLS2}) | |
1603 | @item flexible cross-validation | |
1604 | @item Jackknife variance estimates of regression coefficients | |
1605 | @item extensive and flexible plots: scores, loadings, predictions, coefficients, | |
1606 | (R)MSEP, R², and correlation loadings | |
1607 | @item formula interface, modelled after @code{lm()}, with methods for predict, | |
1608 | print, summary, plot, update, etc. | |
1609 | @item extraction functions for coefficients, scores, and loadings | |
1610 | @item MSEP, RMSEP, and R² estimates | |
1611 | @item multiplicative scatter correction (@dfn{MSC}) | |
1612 | @end itemize\n") | |
1613 | (license license:gpl2))) | |
1614 | ||
b55e64d4 TGR |
1615 | (define-public r-ps |
1616 | (package | |
1617 | (name "r-ps") | |
422dea17 | 1618 | (version "1.3.0") |
b55e64d4 TGR |
1619 | (source |
1620 | (origin | |
1621 | (method url-fetch) | |
1622 | (uri (cran-uri "ps" version)) | |
1623 | (sha256 | |
422dea17 | 1624 | (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498")))) |
b55e64d4 TGR |
1625 | (build-system r-build-system) |
1626 | (home-page "http://ps.r-lib.org") | |
1627 | (synopsis "List, query, and manipulate system processes") | |
1628 | (description | |
1629 | "The ps package implements an API to list, query, and manipulate system | |
1630 | processes. Most of its code is based on the @code{psutil} Python package.") | |
1631 | (license license:bsd-3))) | |
1632 | ||
4f8247b5 RW |
1633 | (define-public r-pkgbuild |
1634 | (package | |
1635 | (name "r-pkgbuild") | |
34ac6089 | 1636 | (version "1.0.6") |
4f8247b5 RW |
1637 | (source |
1638 | (origin | |
1639 | (method url-fetch) | |
1640 | (uri (cran-uri "pkgbuild" version)) | |
1641 | (sha256 | |
34ac6089 | 1642 | (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx")))) |
4f8247b5 RW |
1643 | (build-system r-build-system) |
1644 | (propagated-inputs | |
1645 | `(("r-callr" ,r-callr) | |
2657e666 | 1646 | ("r-cli" ,r-cli) |
4f8247b5 RW |
1647 | ("r-crayon" ,r-crayon) |
1648 | ("r-desc" ,r-desc) | |
2657e666 | 1649 | ("r-prettyunits" ,r-prettyunits) |
4f8247b5 RW |
1650 | ("r-r6" ,r-r6) |
1651 | ("r-rprojroot" ,r-rprojroot) | |
1652 | ("r-withr" ,r-withr))) | |
1653 | (home-page "https://github.com/r-pkgs/pkgbuild") | |
1654 | (synopsis "Find tools needed to build R packages") | |
1655 | (description | |
1656 | "This package provides functions used to build R packages. It locates | |
1657 | compilers needed to build R packages on various platforms and ensures the PATH | |
1658 | is configured appropriately so R can use them.") | |
1659 | (license license:gpl3))) | |
1660 | ||
e362be8e RW |
1661 | (define-public r-pkgload |
1662 | (package | |
1663 | (name "r-pkgload") | |
65dd0e67 | 1664 | (version "1.0.2") |
e362be8e RW |
1665 | (source |
1666 | (origin | |
1667 | (method url-fetch) | |
1668 | (uri (cran-uri "pkgload" version)) | |
1669 | (sha256 | |
1670 | (base32 | |
65dd0e67 | 1671 | "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii")))) |
e362be8e RW |
1672 | (build-system r-build-system) |
1673 | (propagated-inputs | |
1674 | `(("r-desc" ,r-desc) | |
1675 | ("r-pkgbuild" ,r-pkgbuild) | |
1676 | ("r-rlang" ,r-rlang) | |
1677 | ("r-rprojroot" ,r-rprojroot) | |
1678 | ("r-rstudioapi" ,r-rstudioapi) | |
1679 | ("r-withr" ,r-withr))) | |
1680 | (home-page "https://github.com/r-lib/pkgload") | |
1681 | (synopsis "Simulate package installation and attach") | |
1682 | (description | |
1683 | "This package simulates the process of installing a package and then | |
1684 | attaching it. This is a key part of the @code{devtools} package as it allows | |
1685 | you to rapidly iterate while developing a package.") | |
1686 | (license license:gpl3))) | |
1687 | ||
a8cba9dd RW |
1688 | (define-public r-rcpp |
1689 | (package | |
1690 | (name "r-rcpp") | |
8b4178cd | 1691 | (version "1.0.3") |
a8cba9dd RW |
1692 | (source |
1693 | (origin | |
1694 | (method url-fetch) | |
1695 | (uri (cran-uri "Rcpp" version)) | |
1696 | (sha256 | |
8b4178cd | 1697 | (base32 "03h3zyjq948y0hrrs95lfk4zgx6wfrg64hjlrfrzf5na7bfh0d9b")))) |
a8cba9dd | 1698 | (build-system r-build-system) |
f87a18e6 RW |
1699 | (native-inputs |
1700 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
a8cba9dd RW |
1701 | (home-page "http://www.rcpp.org") |
1702 | (synopsis "Seamless R and C++ integration") | |
1703 | (description | |
1704 | "The Rcpp package provides R functions as well as C++ classes which offer | |
1705 | a seamless integration of R and C++. Many R data types and objects can be | |
1706 | mapped back and forth to C++ equivalents which facilitates both writing of new | |
1707 | code as well as easier integration of third-party libraries. Documentation | |
1708 | about Rcpp is provided by several vignettes included in this package, via the | |
36a4366d | 1709 | @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel |
a8cba9dd | 1710 | and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see |
36a4366d | 1711 | @code{citation(\"Rcpp\")} for details on these last two.") |
a8cba9dd | 1712 | (license license:gpl2+))) |
eed58a08 RW |
1713 | |
1714 | (define-public r-bindr | |
1715 | (package | |
1716 | (name "r-bindr") | |
eb575e95 | 1717 | (version "0.1.1") |
eed58a08 RW |
1718 | (source |
1719 | (origin | |
1720 | (method url-fetch) | |
1721 | (uri (cran-uri "bindr" version)) | |
1722 | (sha256 | |
1723 | (base32 | |
eb575e95 | 1724 | "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) |
eed58a08 RW |
1725 | (build-system r-build-system) |
1726 | (home-page "https://github.com/krlmlr/bindr") | |
1727 | (synopsis "Parametrized active bindings") | |
1728 | (description | |
1729 | "This package provides a simple interface for creating active bindings | |
1730 | where the bound function accepts additional arguments.") | |
1731 | (license license:expat))) | |
4bb0b4cc RW |
1732 | |
1733 | (define-public r-bindrcpp | |
1734 | (package | |
1735 | (name "r-bindrcpp") | |
9f17c056 | 1736 | (version "0.2.2") |
4bb0b4cc RW |
1737 | (source |
1738 | (origin | |
1739 | (method url-fetch) | |
1740 | (uri (cran-uri "bindrcpp" version)) | |
1741 | (sha256 | |
1742 | (base32 | |
9f17c056 | 1743 | "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) |
4bb0b4cc RW |
1744 | (build-system r-build-system) |
1745 | (propagated-inputs | |
1746 | `(("r-bindr" ,r-bindr) | |
1747 | ("r-plogr" ,r-plogr) | |
1748 | ("r-rcpp" ,r-rcpp))) | |
1749 | (home-page "https://github.com/krlmlr/bindrcpp") | |
1750 | (synopsis "Rcpp interface to active bindings") | |
1751 | (description | |
1752 | "This package provides an easy way to fill an environment with active | |
1753 | bindings that call a C++ function.") | |
1754 | (license license:expat))) | |
33ce12e2 RW |
1755 | |
1756 | (define-public r-auc | |
1757 | (package | |
1758 | (name "r-auc") | |
1759 | (version "0.3.0") | |
1760 | (source | |
1761 | (origin | |
1762 | (method url-fetch) | |
1763 | (uri (cran-uri "AUC" version)) | |
1764 | (sha256 | |
1765 | (base32 | |
1766 | "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7")))) | |
1767 | (properties `((upstream-name . "AUC"))) | |
1768 | (build-system r-build-system) | |
e9960d8c | 1769 | (home-page "https://cran.r-project.org/web/packages/AUC") |
33ce12e2 RW |
1770 | (synopsis "Compute the area under the curve of selected measures") |
1771 | (description | |
1772 | "This package includes functions to compute the area under the curve of | |
1773 | selected measures: the area under the sensitivity curve (AUSEC), the area | |
1774 | under the specificity curve (AUSPC), the area under the accuracy | |
1775 | curve (AUACC), and the area under the receiver operating characteristic | |
1776 | curve (AUROC). The curves can also be visualized. Support for partial areas | |
1777 | is provided.") | |
1778 | (license license:gpl2+))) | |
c69d27db RW |
1779 | |
1780 | (define-public r-calibrate | |
1781 | (package | |
1782 | (name "r-calibrate") | |
934f7e31 | 1783 | (version "1.7.5") |
c69d27db RW |
1784 | (source |
1785 | (origin | |
1786 | (method url-fetch) | |
1787 | (uri (cran-uri "calibrate" version)) | |
1788 | (sha256 | |
934f7e31 | 1789 | (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k")))) |
c69d27db RW |
1790 | (build-system r-build-system) |
1791 | (propagated-inputs | |
1792 | `(("r-mass" ,r-mass))) | |
e9960d8c | 1793 | (home-page "https://cran.r-project.org/web/packages/calibrate") |
c69d27db RW |
1794 | (synopsis "Calibration of scatterplot and biplot axes") |
1795 | (description | |
1796 | "This is a package for drawing calibrated scales with tick marks | |
1797 | on (non-orthogonal) variable vectors in scatterplots and biplots.") | |
1798 | (license license:gpl2))) | |
2bdb5c3f RW |
1799 | |
1800 | (define-public r-shape | |
1801 | (package | |
1802 | (name "r-shape") | |
fe5b8893 | 1803 | (version "1.4.4") |
2bdb5c3f RW |
1804 | (source |
1805 | (origin | |
1806 | (method url-fetch) | |
1807 | (uri (cran-uri "shape" version)) | |
1808 | (sha256 | |
1809 | (base32 | |
fe5b8893 | 1810 | "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl")))) |
2bdb5c3f | 1811 | (build-system r-build-system) |
e9960d8c | 1812 | (home-page "https://cran.r-project.org/web/packages/shape") |
2bdb5c3f RW |
1813 | (synopsis "Functions for plotting graphical shapes") |
1814 | (description | |
1815 | "This package provides functions for plotting graphical shapes such as | |
1816 | ellipses, circles, cylinders, arrows, ...") | |
1817 | (license license:gpl3+))) | |
4847a62e RW |
1818 | |
1819 | (define-public r-globaloptions | |
1820 | (package | |
1821 | (name "r-globaloptions") | |
bc11837c | 1822 | (version "0.1.1") |
4847a62e RW |
1823 | (source |
1824 | (origin | |
1825 | (method url-fetch) | |
1826 | (uri (cran-uri "GlobalOptions" version)) | |
1827 | (sha256 | |
bc11837c | 1828 | (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2")))) |
4847a62e RW |
1829 | (properties `((upstream-name . "GlobalOptions"))) |
1830 | (build-system r-build-system) | |
1831 | (home-page "https://github.com/jokergoo/GlobalOptions") | |
1832 | (synopsis "Generate functions to get or set global options") | |
1833 | (description | |
1834 | "This package provides more controls on the option values such as | |
1835 | validation and filtering on the values, making options invisible or private.") | |
1836 | (license license:gpl2+))) | |
2856369f RW |
1837 | |
1838 | (define-public r-circlize | |
1839 | (package | |
1840 | (name "r-circlize") | |
4557f447 | 1841 | (version "0.4.8") |
2856369f RW |
1842 | (source |
1843 | (origin | |
1844 | (method url-fetch) | |
1845 | (uri (cran-uri "circlize" version)) | |
1846 | (sha256 | |
1847 | (base32 | |
4557f447 | 1848 | "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2")))) |
2856369f RW |
1849 | (build-system r-build-system) |
1850 | (propagated-inputs | |
1851 | `(("r-colorspace" ,r-colorspace) | |
1852 | ("r-globaloptions" ,r-globaloptions) | |
1853 | ("r-shape" ,r-shape))) | |
1854 | (home-page "https://github.com/jokergoo/circlize") | |
1855 | (synopsis "Circular visualization") | |
1856 | (description | |
031462ba TGR |
1857 | "Circular layout is an efficient way to visualise huge amounts of |
1858 | information. This package provides an implementation of circular layout | |
1859 | generation in R as well as an enhancement of available software. Its | |
1860 | flexibility is based on the usage of low-level graphics functions such that | |
1861 | self-defined high-level graphics can be easily implemented by users for | |
1862 | specific purposes. Together with the seamless connection between the powerful | |
1863 | computational and visual environment in R, it gives users more convenience and | |
1864 | freedom to design figures for better understanding complex patterns behind | |
1865 | multi-dimensional data.") | |
2856369f | 1866 | (license license:gpl2+))) |
5cc79c9c RW |
1867 | |
1868 | (define-public r-powerlaw | |
1869 | (package | |
1870 | (name "r-powerlaw") | |
397dba01 | 1871 | (version "0.70.2") |
5cc79c9c RW |
1872 | (source |
1873 | (origin | |
1874 | (method url-fetch) | |
1875 | (uri (cran-uri "poweRlaw" version)) | |
1876 | (sha256 | |
1877 | (base32 | |
397dba01 | 1878 | "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4")))) |
5cc79c9c RW |
1879 | (properties `((upstream-name . "poweRlaw"))) |
1880 | (build-system r-build-system) | |
1881 | (propagated-inputs | |
1882 | `(("r-vgam" ,r-vgam))) | |
1883 | (home-page "https://github.com/csgillespie/poweRlaw") | |
1884 | (synopsis "Tools for the analysis of heavy tailed distributions") | |
1885 | (description | |
1886 | "This package provides an implementation of maximum likelihood estimators | |
1887 | for a variety of heavy tailed distributions, including both the discrete and | |
1888 | continuous power law distributions. Additionally, a goodness-of-fit based | |
1889 | approach is used to estimate the lower cut-off for the scaling region.") | |
1890 | ;; Any of these GPL versions. | |
1891 | (license (list license:gpl2 license:gpl3)))) | |
05486604 RW |
1892 | |
1893 | (define-public r-compare | |
1894 | (package | |
1895 | (name "r-compare") | |
1896 | (version "0.2-6") | |
1897 | (source | |
1898 | (origin | |
1899 | (method url-fetch) | |
1900 | (uri (cran-uri "compare" version)) | |
1901 | (sha256 | |
1902 | (base32 | |
1903 | "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw")))) | |
1904 | (build-system r-build-system) | |
e9960d8c | 1905 | (home-page "https://cran.r-project.org/web/packages/compare") |
05486604 RW |
1906 | (synopsis "Comparing objects for differences") |
1907 | (description | |
1908 | "This package provides functions to compare a model object to a | |
1909 | comparison object. If the objects are not identical, the functions can be | |
1910 | instructed to explore various modifications of the objects (e.g., sorting | |
1911 | rows, dropping names) to see if the modified versions are identical.") | |
1912 | (license license:gpl2+))) | |
d3c67e1b RW |
1913 | |
1914 | (define-public r-dendextend | |
1915 | (package | |
1916 | (name "r-dendextend") | |
bce0fcae | 1917 | (version "1.13.2") |
d3c67e1b RW |
1918 | (source |
1919 | (origin | |
1920 | (method url-fetch) | |
1921 | (uri (cran-uri "dendextend" version)) | |
1922 | (sha256 | |
1923 | (base32 | |
bce0fcae | 1924 | "1iclvd9cyckd4djpa87ynm05fk6zl4b4m735za1w4irimc130m3r")))) |
d3c67e1b RW |
1925 | (build-system r-build-system) |
1926 | (propagated-inputs | |
089ac9af | 1927 | `(("r-ggplot2" ,r-ggplot2) |
d3c67e1b | 1928 | ("r-magrittr" ,r-magrittr) |
089ac9af | 1929 | ("r-viridis" ,r-viridis))) |
d3c67e1b RW |
1930 | (home-page "https://cran.r-project.org/web/packages/dendextend") |
1931 | (synopsis "Extending 'dendrogram' functionality in R") | |
1932 | (description | |
1933 | "This package offers a set of functions for extending @code{dendrogram} | |
1934 | objects in R, letting you visualize and compare trees of hierarchical | |
1935 | clusterings. You can adjust a tree's graphical parameters (the color, size, | |
1936 | type, etc of its branches, nodes and labels) and visually and statistically | |
1937 | compare different dendrograms to one another.") | |
1938 | ;; Any of these versions | |
1939 | (license (list license:gpl2 license:gpl3)))) | |
e0268ff2 RW |
1940 | |
1941 | (define-public r-getoptlong | |
1942 | (package | |
1943 | (name "r-getoptlong") | |
5fa9be11 | 1944 | (version "0.1.7") |
e0268ff2 RW |
1945 | (source |
1946 | (origin | |
1947 | (method url-fetch) | |
1948 | (uri (cran-uri "GetoptLong" version)) | |
1949 | (sha256 | |
1950 | (base32 | |
5fa9be11 | 1951 | "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr")))) |
e0268ff2 RW |
1952 | (properties `((upstream-name . "GetoptLong"))) |
1953 | (build-system r-build-system) | |
1954 | (inputs | |
1955 | `(("perl" ,perl))) | |
1956 | (propagated-inputs | |
1957 | `(("r-globaloptions" ,r-globaloptions) | |
1958 | ("r-rjson" ,r-rjson))) | |
1959 | (home-page "https://github.com/jokergoo/GetoptLong") | |
1960 | (synopsis "Parsing command-line arguments and variable interpolation") | |
1961 | (description | |
1962 | "This is yet another command-line argument parser which wraps the | |
1963 | powerful Perl module @code{Getopt::Long} and with some adaptation for easier | |
1964 | use in R. It also provides a simple way for variable interpolation in R.") | |
1965 | (license license:gpl2+))) | |
f2e974e1 RW |
1966 | |
1967 | (define-public r-fastmatch | |
1968 | (package | |
1969 | (name "r-fastmatch") | |
1970 | (version "1.1-0") | |
1971 | (source | |
1972 | (origin | |
1973 | (method url-fetch) | |
1974 | (uri (cran-uri "fastmatch" version)) | |
1975 | (sha256 | |
1976 | (base32 | |
1977 | "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) | |
1978 | (build-system r-build-system) | |
1979 | (home-page "http://www.rforge.net/fastmatch") | |
1980 | (synopsis "Fast match function") | |
1981 | (description | |
1982 | "This package provides a fast @code{match} replacement for cases that | |
1983 | require repeated look-ups. It is slightly faster that R's built-in | |
1984 | @code{match} function on first match against a table, but extremely fast on | |
1985 | any subsequent lookup as it keeps the hash table in memory.") | |
1986 | (license license:gpl2))) | |
a7f0faa2 RW |
1987 | |
1988 | (define-public r-ff | |
1989 | (package | |
1990 | (name "r-ff") | |
207c497e | 1991 | (version "2.2-14") |
a7f0faa2 RW |
1992 | (source |
1993 | (origin | |
1994 | (method url-fetch) | |
1995 | (uri (cran-uri "ff" version)) | |
1996 | (sha256 | |
1997 | (base32 | |
207c497e | 1998 | "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw")))) |
a7f0faa2 RW |
1999 | (build-system r-build-system) |
2000 | (propagated-inputs `(("r-bit" ,r-bit))) | |
2001 | (home-page "http://ff.r-forge.r-project.org/") | |
2002 | (synopsis "Memory-efficient storage of large data on disk and access functions") | |
2003 | (description | |
2004 | "This package provides data structures that are stored on disk but | |
2005 | behave (almost) as if they were in RAM by transparently mapping only a section | |
2006 | in main memory.") | |
a6e67d86 EF |
2007 | ;; error Architecture not supported. |
2008 | (supported-systems (delete "aarch64-linux" %supported-systems)) | |
a7f0faa2 | 2009 | (license license:gpl2))) |
49c9c297 RW |
2010 | |
2011 | (define-public r-ffbase | |
2012 | (package | |
2013 | (name "r-ffbase") | |
ec0ee085 | 2014 | (version "0.12.7") |
49c9c297 RW |
2015 | (source |
2016 | (origin | |
2017 | (method url-fetch) | |
2018 | (uri (cran-uri "ffbase" version)) | |
2019 | (sha256 | |
2020 | (base32 | |
ec0ee085 | 2021 | "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw")))) |
49c9c297 RW |
2022 | (build-system r-build-system) |
2023 | (propagated-inputs | |
2024 | `(("r-bit" ,r-bit) | |
2025 | ("r-fastmatch" ,r-fastmatch) | |
2026 | ("r-ff" ,r-ff))) | |
2027 | (home-page "http://github.com/edwindj/ffbase") | |
2028 | (synopsis "Basic statistical functions for package 'ff'") | |
2029 | (description | |
2030 | "This package extends the out of memory vectors of @code{ff} with | |
2031 | statistical functions and other utilities to ease their usage.") | |
2032 | (license license:gpl3))) | |
18a16ceb RW |
2033 | |
2034 | (define-public r-prettyunits | |
2035 | (package | |
2036 | (name "r-prettyunits") | |
2037 | (version "1.0.2") | |
2038 | (source | |
2039 | (origin | |
2040 | (method url-fetch) | |
2041 | (uri (cran-uri "prettyunits" version)) | |
2042 | (sha256 | |
2043 | (base32 | |
2044 | "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m")))) | |
2045 | (build-system r-build-system) | |
2046 | (propagated-inputs | |
2047 | `(("r-assertthat" ,r-assertthat) | |
2048 | ("r-magrittr" ,r-magrittr))) | |
2049 | (home-page "https://github.com/gaborcsardi/prettyunits") | |
2050 | (synopsis "Pretty, human readable formatting of quantities") | |
2051 | (description | |
2052 | "This package provides tools for pretty, human readable formatting of | |
2053 | quantities.") | |
2054 | (license license:expat))) | |
71be51d5 RW |
2055 | |
2056 | (define-public r-reshape | |
2057 | (package | |
2058 | (name "r-reshape") | |
2b8126a4 | 2059 | (version "0.8.8") |
71be51d5 RW |
2060 | (source |
2061 | (origin | |
2062 | (method url-fetch) | |
2063 | (uri (cran-uri "reshape" version)) | |
2064 | (sha256 | |
2065 | (base32 | |
2b8126a4 | 2066 | "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) |
71be51d5 RW |
2067 | (build-system r-build-system) |
2068 | (propagated-inputs | |
2069 | `(("r-plyr" ,r-plyr) | |
2070 | ("r-rcpp" ,r-rcpp))) | |
2071 | (home-page "http://had.co.nz/reshape") | |
2072 | (synopsis "Flexibly reshape data") | |
2073 | (description | |
2074 | "Flexibly restructure and aggregate data using just two functions: | |
2075 | @code{melt} and @code{cast}. This package provides them.") | |
2076 | (license license:expat))) | |
c9c6f4b5 RW |
2077 | |
2078 | (define-public r-progress | |
2079 | (package | |
2080 | (name "r-progress") | |
7e8ac56a | 2081 | (version "1.2.2") |
c9c6f4b5 RW |
2082 | (source |
2083 | (origin | |
2084 | (method url-fetch) | |
2085 | (uri (cran-uri "progress" version)) | |
2086 | (sha256 | |
2087 | (base32 | |
7e8ac56a | 2088 | "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l")))) |
c9c6f4b5 RW |
2089 | (build-system r-build-system) |
2090 | (propagated-inputs | |
9de9dcd9 RW |
2091 | `(("r-crayon" ,r-crayon) |
2092 | ("r-hms" ,r-hms) | |
2093 | ("r-prettyunits" ,r-prettyunits) | |
c9c6f4b5 RW |
2094 | ("r-r6" ,r-r6))) |
2095 | (home-page "https://github.com/gaborcsardi/progress") | |
2096 | (synopsis "Terminal progress bars") | |
2097 | (description | |
2098 | "This package provides configurable progress bars. They may include | |
2099 | percentage, elapsed time, and/or the estimated completion time. They work in | |
2100 | terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The | |
2101 | package also provides a C++ API, that works with or without Rcpp.") | |
2102 | (license license:expat))) | |
ac840207 RW |
2103 | |
2104 | (define-public r-ggally | |
2105 | (package | |
2106 | (name "r-ggally") | |
9944399a | 2107 | (version "1.4.0") |
ac840207 RW |
2108 | (source |
2109 | (origin | |
2110 | (method url-fetch) | |
2111 | (uri (cran-uri "GGally" version)) | |
2112 | (sha256 | |
2113 | (base32 | |
9944399a | 2114 | "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws")))) |
ac840207 RW |
2115 | (properties `((upstream-name . "GGally"))) |
2116 | (build-system r-build-system) | |
9944399a RW |
2117 | (inputs |
2118 | `(("libressl" ,libressl))) | |
ac840207 RW |
2119 | (propagated-inputs |
2120 | `(("r-ggplot2" ,r-ggplot2) | |
2121 | ("r-gtable" ,r-gtable) | |
2122 | ("r-plyr" ,r-plyr) | |
2123 | ("r-progress" ,r-progress) | |
2124 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9944399a RW |
2125 | ("r-reshape" ,r-reshape) |
2126 | ("r-rlang" ,r-rlang))) | |
ac840207 RW |
2127 | (home-page "https://ggobi.github.io/ggally") |
2128 | (synopsis "Extension to ggplot2") | |
2129 | (description | |
2130 | "The R package ggplot2 is a plotting system based on the grammar of | |
2131 | graphics. GGally extends ggplot2 by adding several functions to reduce the | |
2132 | complexity of combining geometric objects with transformed data. Some of | |
2133 | these functions include a pairwise plot matrix, a two group pairwise plot | |
2134 | matrix, a parallel coordinates plot, a survival plot, and several functions to | |
2135 | plot networks.") | |
2136 | (license license:gpl2+))) | |
3349faec RW |
2137 | |
2138 | (define-public r-proxy | |
2139 | (package | |
2140 | (name "r-proxy") | |
e190d9af | 2141 | (version "0.4-23") |
3349faec RW |
2142 | (source |
2143 | (origin | |
2144 | (method url-fetch) | |
2145 | (uri (cran-uri "proxy" version)) | |
2146 | (sha256 | |
2147 | (base32 | |
e190d9af | 2148 | "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x")))) |
3349faec | 2149 | (build-system r-build-system) |
e9960d8c | 2150 | (home-page "https://cran.r-project.org/web/packages/proxy") |
3349faec RW |
2151 | (synopsis "Distance and similarity measures") |
2152 | (description | |
2153 | "This package provides an extensible framework for the efficient | |
2154 | calculation of auto- and cross-proximities, along with implementations of the | |
2155 | most popular ones.") | |
2156 | (license license:gpl2))) | |
bc0081e7 RW |
2157 | |
2158 | (define-public r-sp | |
2159 | (package | |
2160 | (name "r-sp") | |
5d78d47b | 2161 | (version "1.3-2") |
bc0081e7 RW |
2162 | (source |
2163 | (origin | |
2164 | (method url-fetch) | |
2165 | (uri (cran-uri "sp" version)) | |
2166 | (sha256 | |
5d78d47b | 2167 | (base32 "0kpjsqh3lzqp1m0avsvm54lazlgwfx3hyf0av3mvbyslsanj42ll")))) |
bc0081e7 RW |
2168 | (build-system r-build-system) |
2169 | (propagated-inputs | |
2170 | `(("r-lattice" ,r-lattice))) | |
e9960d8c | 2171 | (home-page "https://cran.r-project.org/web/packages/sp") |
bc0081e7 RW |
2172 | (synopsis "Classes and methods for spatial data") |
2173 | (description | |
2174 | "This package provides classes and methods for spatial data; the classes | |
2175 | document where the spatial location information resides, for 2D or 3D data. | |
2176 | Utility functions are provided, e.g. for plotting data as maps, spatial | |
2177 | selection, as well as methods for retrieving coordinates, for subsetting, | |
2178 | print, summary, etc.") | |
2179 | (license license:gpl2+))) | |
e389d10f RW |
2180 | |
2181 | (define-public r-rmtstat | |
2182 | (package | |
2183 | (name "r-rmtstat") | |
2184 | (version "0.3") | |
2185 | (source | |
2186 | (origin | |
2187 | (method url-fetch) | |
2188 | (uri (cran-uri "RMTstat" version)) | |
2189 | (sha256 | |
2190 | (base32 | |
2191 | "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1")))) | |
2192 | (properties `((upstream-name . "RMTstat"))) | |
2193 | (build-system r-build-system) | |
e9960d8c | 2194 | (home-page "https://cran.r-project.org/web/packages/RMTstat") |
e389d10f RW |
2195 | (synopsis "Distributions, statistics and tests derived from random matrix theory") |
2196 | (description | |
2197 | "This package provides functions for working with the Tracy-Widom laws | |
2198 | and other distributions related to the eigenvalues of large Wishart | |
2199 | matrices.") | |
2200 | (license license:bsd-3))) | |
6427e620 | 2201 | |
94989d4b RJ |
2202 | (define-public r-rmpi |
2203 | (package | |
2204 | (name "r-rmpi") | |
5e8282a4 | 2205 | (version "0.6-9") |
94989d4b RJ |
2206 | (source (origin |
2207 | (method url-fetch) | |
2208 | (uri (cran-uri "Rmpi" version)) | |
2209 | (sha256 | |
2210 | (base32 | |
5e8282a4 | 2211 | "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) |
94989d4b RJ |
2212 | (properties `((upstream-name . "Rmpi"))) |
2213 | (build-system r-build-system) | |
2214 | (arguments | |
56d447ba EB |
2215 | `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"") |
2216 | #:phases (modify-phases %standard-phases | |
2217 | (add-before 'install 'mpi-setup | |
2218 | ,%openmpi-setup)))) | |
94989d4b RJ |
2219 | (inputs |
2220 | `(("openmpi" ,openmpi))) | |
9ebfdcd3 RW |
2221 | (native-inputs |
2222 | `(("pkg-config" ,pkg-config))) | |
94989d4b RJ |
2223 | (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") |
2224 | (synopsis "R interface to message-passing interface (MPI)") | |
2225 | (description | |
2226 | "This package provides an interface (wrapper) to MPI APIs. It also | |
2227 | provides an interactive R manager and worker environment.") | |
2228 | (license license:gpl2+))) | |
2229 | ||
6427e620 RW |
2230 | (define-public r-lmoments |
2231 | (package | |
2232 | (name "r-lmoments") | |
739135b2 | 2233 | (version "1.3-1") |
6427e620 RW |
2234 | (source |
2235 | (origin | |
2236 | (method url-fetch) | |
2237 | (uri (cran-uri "Lmoments" version)) | |
2238 | (sha256 | |
2239 | (base32 | |
739135b2 | 2240 | "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw")))) |
6427e620 RW |
2241 | (properties `((upstream-name . "Lmoments"))) |
2242 | (build-system r-build-system) | |
739135b2 RW |
2243 | (propagated-inputs |
2244 | `(("r-rcpp" ,r-rcpp) | |
2245 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
6427e620 RW |
2246 | (home-page "http://www.tilastotiede.fi/juha_karvanen.html") |
2247 | (synopsis "L-moments and quantile mixtures") | |
2248 | (description | |
2249 | "This package contains functions to estimate L-moments and trimmed | |
2250 | L-moments from the data. It also contains functions to estimate the | |
2251 | parameters of the normal polynomial quantile mixture and the Cauchy polynomial | |
2252 | quantile mixture from L-moments and trimmed L-moments.") | |
2253 | (license license:gpl2))) | |
28476b4b RW |
2254 | |
2255 | (define-public r-distillery | |
2256 | (package | |
2257 | (name "r-distillery") | |
5686da76 | 2258 | (version "1.0-6") |
28476b4b RW |
2259 | (source |
2260 | (origin | |
2261 | (method url-fetch) | |
2262 | (uri (cran-uri "distillery" version)) | |
2263 | (sha256 | |
2264 | (base32 | |
5686da76 | 2265 | "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429")))) |
28476b4b RW |
2266 | (build-system r-build-system) |
2267 | (home-page "http://www.ral.ucar.edu/staff/ericg") | |
2268 | (synopsis "Functions for confidence intervals and object information") | |
2269 | (description | |
2270 | "This package provides some very simple method functions for confidence | |
2271 | interval calculation and to distill pertinent information from a potentially | |
2272 | complex object; primarily used in common with the packages extRemes and | |
2273 | SpatialVx.") | |
2274 | (license license:gpl2+))) | |
58db98c9 RW |
2275 | |
2276 | (define-public r-extremes | |
2277 | (package | |
2278 | (name "r-extremes") | |
7055c62d | 2279 | (version "2.0-11") |
58db98c9 RW |
2280 | (source |
2281 | (origin | |
2282 | (method url-fetch) | |
2283 | (uri (cran-uri "extRemes" version)) | |
2284 | (sha256 | |
2285 | (base32 | |
7055c62d | 2286 | "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm")))) |
58db98c9 RW |
2287 | (properties `((upstream-name . "extRemes"))) |
2288 | (build-system r-build-system) | |
2289 | (propagated-inputs | |
987b0804 | 2290 | `(("r-distillery" ,r-distillery) |
58db98c9 RW |
2291 | ("r-lmoments" ,r-lmoments))) |
2292 | (home-page "http://www.assessment.ucar.edu/toolkit/") | |
2293 | (synopsis "Extreme value analysis") | |
2294 | (description | |
2295 | "ExtRemes is a suite of functions for carrying out analyses on the | |
2296 | extreme values of a process of interest; be they block maxima over long blocks | |
2297 | or excesses over a high threshold.") | |
2298 | (license license:gpl2+))) | |
062b6dbd RW |
2299 | |
2300 | (define-public r-lmtest | |
2301 | (package | |
2302 | (name "r-lmtest") | |
0b5b9d69 | 2303 | (version "0.9-37") |
062b6dbd RW |
2304 | (source |
2305 | (origin | |
2306 | (method url-fetch) | |
2307 | (uri (cran-uri "lmtest" version)) | |
2308 | (sha256 | |
2309 | (base32 | |
0b5b9d69 | 2310 | "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx")))) |
062b6dbd RW |
2311 | (build-system r-build-system) |
2312 | (propagated-inputs | |
2313 | `(("r-zoo" ,r-zoo))) | |
2314 | (native-inputs | |
2315 | `(("gfortran" ,gfortran))) | |
e9960d8c | 2316 | (home-page "https://cran.r-project.org/web/packages/lmtest") |
062b6dbd RW |
2317 | (synopsis "Testing linear regression models") |
2318 | (description | |
2319 | "This package provides a collection of tests, data sets, and examples for | |
2320 | diagnostic checking in linear regression models. Furthermore, some generic | |
2321 | tools for inference in parametric models are provided.") | |
2322 | ;; Either version is okay | |
2323 | (license (list license:gpl2 license:gpl3)))) | |
d6b156dc | 2324 | |
c974008d RJ |
2325 | (define-public r-idr |
2326 | (package | |
2327 | (name "r-idr") | |
2328 | (version "1.2") | |
2329 | (source (origin | |
2330 | (method url-fetch) | |
2331 | (uri (cran-uri "idr" version)) | |
2332 | (sha256 | |
2333 | (base32 | |
2334 | "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb")))) | |
2335 | (build-system r-build-system) | |
2336 | (home-page "https://cran.r-project.org/web/packages/idr/") | |
2337 | (synopsis "Irreproducible discovery rate") | |
2338 | (description | |
2339 | "This is a package for estimating the copula mixture model and plotting | |
2340 | correspondence curves in \"Measuring reproducibility of high-throughput | |
2341 | experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, | |
2342 | by Li, Brown, Huang, and Bickel") | |
2343 | (license license:gpl2+))) | |
2344 | ||
d6b156dc RW |
2345 | (define-public r-inline |
2346 | (package | |
2347 | (name "r-inline") | |
0acbf8bb | 2348 | (version "0.3.15") |
d6b156dc RW |
2349 | (source (origin |
2350 | (method url-fetch) | |
2351 | (uri (cran-uri "inline" version)) | |
2352 | (sha256 | |
2353 | (base32 | |
0acbf8bb | 2354 | "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z")))) |
d6b156dc | 2355 | (build-system r-build-system) |
e9960d8c | 2356 | (home-page "https://cran.r-project.org/web/packages/inline") |
d6b156dc RW |
2357 | (synopsis "Functions to inline C, C++, Fortran function calls from R") |
2358 | (description | |
2359 | "This package provides functionality to dynamically define R functions | |
2360 | and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and | |
2361 | @code{.Call} calling conventions.") | |
2362 | ;; Any version of the LGPL. | |
2363 | (license license:lgpl3+))) | |
8c72b830 | 2364 | |
a3569a32 RW |
2365 | (define-public r-bdsmatrix |
2366 | (package | |
2367 | (name "r-bdsmatrix") | |
2368 | (version "1.3-3") | |
2369 | (source | |
2370 | (origin | |
2371 | (method url-fetch) | |
2372 | (uri (cran-uri "bdsmatrix" version)) | |
2373 | (sha256 | |
2374 | (base32 | |
2375 | "17ddvz4gnih7rx0lr1gzk280xyh6x796cf2x794dvplpiiq83skh")))) | |
2376 | (properties `((upstream-name . "bdsmatrix"))) | |
2377 | (build-system r-build-system) | |
2378 | (home-page "https://cran.r-project.org/web/packages/bdsmatrix/") | |
2379 | (synopsis "Routines for block diagonal symmetric matrices") | |
2380 | (description | |
2381 | "This package provides procedures to work with block diagonal symmetric | |
2382 | matrices, a special case of sparse matrices.") | |
2383 | (license license:lgpl2.0))) | |
2384 | ||
8c72b830 RW |
2385 | (define-public r-bbmle |
2386 | (package | |
2387 | (name "r-bbmle") | |
6b662ce3 | 2388 | (version "1.0.22") |
8c72b830 RW |
2389 | (source |
2390 | (origin | |
2391 | (method url-fetch) | |
2392 | (uri (cran-uri "bbmle" version)) | |
2393 | (sha256 | |
2394 | (base32 | |
6b662ce3 | 2395 | "1idn55w5f3iw4r0ydyww8xyinninw07sxlwfqb565vmdrs87dwl4")))) |
8c72b830 RW |
2396 | (build-system r-build-system) |
2397 | (propagated-inputs | |
6b662ce3 RW |
2398 | `(("r-bdsmatrix" ,r-bdsmatrix) |
2399 | ("r-lattice" ,r-lattice) | |
8c72b830 | 2400 | ("r-mass" ,r-mass) |
6b662ce3 RW |
2401 | ("r-matrix" ,r-matrix) |
2402 | ("r-mvtnorm" ,r-mvtnorm) | |
8c72b830 | 2403 | ("r-numderiv" ,r-numderiv))) |
e9960d8c | 2404 | (home-page "https://cran.r-project.org/web/packages/bbmle") |
8c72b830 RW |
2405 | (synopsis "Tools for General Maximum Likelihood Estimation") |
2406 | (description | |
c151b0b6 RW |
2407 | "This package provides methods and functions for fitting maximum |
2408 | likelihood models in R. This package modifies and extends the @code{mle} | |
2409 | classes in the @code{stats4} package.") | |
8c72b830 | 2410 | ;; Any version of the GPL |
c151b0b6 | 2411 | (license license:gpl2+))) |
b31e4a96 RW |
2412 | |
2413 | (define-public r-emdbook | |
2414 | (package | |
2415 | (name "r-emdbook") | |
59c51342 | 2416 | (version "1.3.11") |
b31e4a96 RW |
2417 | (source |
2418 | (origin | |
2419 | (method url-fetch) | |
2420 | (uri (cran-uri "emdbook" version)) | |
2421 | (sha256 | |
2422 | (base32 | |
59c51342 | 2423 | "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q")))) |
b31e4a96 RW |
2424 | (build-system r-build-system) |
2425 | (propagated-inputs | |
2426 | `(("r-bbmle" ,r-bbmle) | |
2427 | ("r-coda" ,r-coda) | |
2428 | ("r-lattice" ,r-lattice) | |
2429 | ("r-mass" ,r-mass) | |
2430 | ("r-plyr" ,r-plyr) | |
2431 | ("r-rcpp" ,r-rcpp))) | |
2432 | (home-page "http://www.math.mcmaster.ca/bolker/emdbook") | |
2433 | (synopsis "Support functions and data for \"Ecological Models and Data\"") | |
2434 | (description | |
2435 | "This package provides auxiliary functions and data sets for \"Ecological | |
2436 | Models and Data\", a book presenting maximum likelihood estimation and related | |
2437 | topics for ecologists (ISBN 978-0-691-12522-0).") | |
2438 | ;; Any GPL version | |
2439 | (license (list license:gpl2 license:gpl3)))) | |
a3e36d37 RW |
2440 | |
2441 | (define-public r-lpsolve | |
2442 | (package | |
2443 | (name "r-lpsolve") | |
bf9a8236 | 2444 | (version "5.6.13.3") |
a3e36d37 RW |
2445 | (source |
2446 | (origin | |
2447 | (method url-fetch) | |
2448 | (uri (cran-uri "lpSolve" version)) | |
2449 | (sha256 | |
2450 | (base32 | |
bf9a8236 | 2451 | "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6")))) |
a3e36d37 RW |
2452 | (properties `((upstream-name . "lpSolve"))) |
2453 | (build-system r-build-system) | |
e9960d8c | 2454 | (home-page "https://cran.r-project.org/web/packages/lpSolve") |
a3e36d37 RW |
2455 | (synopsis "R interface to Lp_solve to solve linear/integer programs") |
2456 | (description | |
2457 | "Lp_solve is software for solving linear, integer and mixed integer | |
2458 | programs. This implementation supplies a \"wrapper\" function in C and some R | |
2459 | functions that solve general linear/integer problems, assignment problems, and | |
2460 | transportation problems.") | |
2461 | (license license:lgpl2.0))) | |
521e0703 RW |
2462 | |
2463 | (define-public r-limsolve | |
2464 | (package | |
2465 | (name "r-limsolve") | |
f94705d6 | 2466 | (version "1.5.6") |
521e0703 RW |
2467 | (source |
2468 | (origin | |
2469 | (method url-fetch) | |
2470 | (uri (cran-uri "limSolve" version)) | |
2471 | (sha256 | |
2472 | (base32 | |
f94705d6 | 2473 | "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr")))) |
521e0703 RW |
2474 | (properties `((upstream-name . "limSolve"))) |
2475 | (build-system r-build-system) | |
2476 | (propagated-inputs | |
2477 | `(("r-lpsolve" ,r-lpsolve) | |
2478 | ("r-mass" ,r-mass) | |
2479 | ("r-quadprog" ,r-quadprog))) | |
2480 | (native-inputs `(("gfortran" ,gfortran))) | |
e9960d8c | 2481 | (home-page "https://cran.r-project.org/web/packages/limSolve") |
521e0703 RW |
2482 | (synopsis "Solving linear inverse models") |
2483 | (description | |
2484 | "This package provides functions that: | |
2485 | ||
2486 | @enumerate | |
2487 | @item find the minimum/maximum of a linear or quadratic function, | |
2488 | @item sample an underdetermined or overdetermined system, | |
2489 | @item solve a linear system Ax=B for the unknown x. | |
2490 | @end enumerate | |
2491 | ||
2492 | It includes banded and tridiagonal linear systems. The package calls Fortran | |
2493 | functions from LINPACK.") | |
2494 | ;; Any GPL version. | |
2495 | (license (list license:gpl2+ license:gpl3+)))) | |
6b4a9aec RW |
2496 | |
2497 | (define-public r-fitdistrplus | |
2498 | (package | |
2499 | (name "r-fitdistrplus") | |
9e0162df | 2500 | (version "1.0-14") |
6b4a9aec RW |
2501 | (source |
2502 | (origin | |
2503 | (method url-fetch) | |
2504 | (uri (cran-uri "fitdistrplus" version)) | |
2505 | (sha256 | |
2506 | (base32 | |
9e0162df | 2507 | "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245")))) |
6b4a9aec RW |
2508 | (build-system r-build-system) |
2509 | (propagated-inputs | |
2510 | `(("r-mass" ,r-mass) | |
8c456dff | 2511 | ("r-npsurv" ,r-npsurv) |
6b4a9aec RW |
2512 | ("r-survival" ,r-survival))) |
2513 | (home-page "http://riskassessment.r-forge.r-project.org") | |
2514 | (synopsis "Fitting a parametric distribution from data") | |
2515 | (description | |
2516 | "This package extends the @code{fitdistr} function of the MASS package | |
2517 | with several functions to help the fit of a parametric distribution to | |
2518 | non-censored or censored data. Censored data may contain left-censored, | |
2519 | right-censored and interval-censored values, with several lower and upper | |
2520 | bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package | |
2521 | provides moment matching (MME), quantile matching (QME) and maximum | |
2522 | goodness-of-fit estimation (MGE) methods (available only for non-censored | |
2523 | data). Weighted versions of MLE, MME and QME are available.") | |
2524 | (license license:gpl2+))) | |
8d220073 RW |
2525 | |
2526 | (define-public r-energy | |
2527 | (package | |
2528 | (name "r-energy") | |
73827e84 | 2529 | (version "1.7-7") |
8d220073 RW |
2530 | (source |
2531 | (origin | |
2532 | (method url-fetch) | |
2533 | (uri (cran-uri "energy" version)) | |
2534 | (sha256 | |
2535 | (base32 | |
73827e84 | 2536 | "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37")))) |
8d220073 RW |
2537 | (build-system r-build-system) |
2538 | (propagated-inputs | |
2539 | `(("r-boot" ,r-boot) | |
2540 | ("r-rcpp" ,r-rcpp))) | |
e9960d8c | 2541 | (home-page "https://cran.r-project.org/web/packages/energy") |
8d220073 RW |
2542 | (synopsis "Multivariate inference via the energy of data") |
2543 | (description | |
2544 | "This package provides e-statistics (energy) tests and statistics for | |
2545 | multivariate and univariate inference, including distance correlation, | |
2546 | one-sample, two-sample, and multi-sample tests for comparing multivariate | |
2547 | distributions, are implemented. Measuring and testing multivariate | |
2548 | independence based on distance correlation, partial distance correlation, | |
2549 | multivariate goodness-of-fit tests, clustering based on energy distance, | |
2550 | testing for multivariate normality, distance components (disco) for | |
2551 | non-parametric analysis of structured data, and other energy | |
2552 | statistics/methods are implemented.") | |
2553 | (license license:gpl2+))) | |
abcb8494 RW |
2554 | |
2555 | (define-public r-suppdists | |
2556 | (package | |
2557 | (name "r-suppdists") | |
2558 | (version "1.1-9.4") | |
2559 | (source | |
2560 | (origin | |
2561 | (method url-fetch) | |
2562 | (uri (cran-uri "SuppDists" version)) | |
2563 | (sha256 | |
2564 | (base32 | |
2565 | "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw")))) | |
2566 | (properties `((upstream-name . "SuppDists"))) | |
2567 | (build-system r-build-system) | |
e9960d8c | 2568 | (home-page "https://cran.r-project.org/web/packages/SuppDists") |
abcb8494 RW |
2569 | (synopsis "Supplementary distributions") |
2570 | (description | |
2571 | "This package provides ten distributions supplementing those built into | |
2572 | R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, | |
2573 | Spearman's rho, maximum F ratio, the Pearson product moment correlation | |
2574 | coefficient, Johnson distributions, normal scores and generalized | |
2575 | hypergeometric distributions. In addition two random number generators of | |
2576 | George Marsaglia are included.") | |
2577 | (license license:gpl2+))) | |
05e8a3ef RW |
2578 | |
2579 | (define-public r-ksamples | |
2580 | (package | |
2581 | (name "r-ksamples") | |
beb82eb9 | 2582 | (version "1.2-9") |
05e8a3ef RW |
2583 | (source |
2584 | (origin | |
2585 | (method url-fetch) | |
2586 | (uri (cran-uri "kSamples" version)) | |
2587 | (sha256 | |
2588 | (base32 | |
beb82eb9 | 2589 | "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms")))) |
05e8a3ef RW |
2590 | (properties `((upstream-name . "kSamples"))) |
2591 | (build-system r-build-system) | |
2592 | (propagated-inputs | |
2593 | `(("r-suppdists" ,r-suppdists))) | |
e9960d8c | 2594 | (home-page "https://cran.r-project.org/web/packages/kSamples") |
05e8a3ef RW |
2595 | (synopsis "K-Sample rank tests and their combinations") |
2596 | (description | |
2597 | "This package provides tools to compares k samples using the | |
2598 | Anderson-Darling test, Kruskal-Wallis type tests with different rank score | |
2599 | criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) | |
2600 | test. It computes asymptotic, simulated or (limited) exact P-values, all | |
2601 | valid under randomization, with or without ties, or conditionally under random | |
2602 | sampling from populations, given the observed tie pattern. Except for Steel's | |
2603 | test and the JT test it also combines these tests across several blocks of | |
2604 | samples.") | |
2605 | (license license:gpl2+))) | |
f97ce815 RW |
2606 | |
2607 | (define-public r-cvst | |
2608 | (package | |
2609 | (name "r-cvst") | |
b13b5674 | 2610 | (version "0.2-2") |
f97ce815 RW |
2611 | (source |
2612 | (origin | |
2613 | (method url-fetch) | |
2614 | (uri (cran-uri "CVST" version)) | |
2615 | (sha256 | |
2616 | (base32 | |
b13b5674 | 2617 | "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5")))) |
f97ce815 RW |
2618 | (properties `((upstream-name . "CVST"))) |
2619 | (build-system r-build-system) | |
2620 | (propagated-inputs | |
2621 | `(("r-kernlab" ,r-kernlab) | |
2622 | ("r-matrix" ,r-matrix))) | |
e9960d8c | 2623 | (home-page "https://cran.r-project.org/web/packages/CVST") |
f97ce815 RW |
2624 | (synopsis "Fast cross-validation via sequential testing") |
2625 | (description | |
2626 | "This package implements the fast cross-validation via sequential | |
2627 | testing (CVST) procedure. CVST is an improved cross-validation procedure | |
2628 | which uses non-parametric testing coupled with sequential analysis to | |
2629 | determine the best parameter set on linearly increasing subsets of the data. | |
2630 | Additionally to the CVST the package contains an implementation of the | |
2631 | ordinary k-fold cross-validation with a flexible and powerful set of helper | |
2632 | objects and methods to handle the overall model selection process. The | |
2633 | implementations of the Cochran's Q test with permutations and the sequential | |
2634 | testing framework of Wald are generic and can therefore also be used in other | |
2635 | contexts.") | |
2636 | (license license:gpl2+))) | |
797e1dfb | 2637 | |
c5f033e0 RW |
2638 | (define-public r-squarem |
2639 | (package | |
2640 | (name "r-squarem") | |
2641 | (version "2017.10-1") | |
2642 | (source | |
2643 | (origin | |
2644 | (method url-fetch) | |
2645 | (uri (cran-uri "SQUAREM" version)) | |
2646 | (sha256 | |
2647 | (base32 | |
2648 | "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv")))) | |
2649 | (properties `((upstream-name . "SQUAREM"))) | |
2650 | (build-system r-build-system) | |
2651 | (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html") | |
2652 | (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms") | |
2653 | (description | |
2654 | "This package provides algorithms for accelerating the convergence of | |
2655 | slow, monotone sequences from smooth, contraction mapping such as the EM | |
2656 | algorithm. It can be used to accelerate any smooth, linearly convergent | |
2657 | acceleration scheme. A tutorial style introduction to this package is | |
2658 | available in a vignette.") | |
2659 | (license license:gpl2+))) | |
2660 | ||
797e1dfb RW |
2661 | (define-public r-lava |
2662 | (package | |
2663 | (name "r-lava") | |
099b7c55 | 2664 | (version "1.6.6") |
797e1dfb RW |
2665 | (source |
2666 | (origin | |
2667 | (method url-fetch) | |
2668 | (uri (cran-uri "lava" version)) | |
2669 | (sha256 | |
2670 | (base32 | |
099b7c55 | 2671 | "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s")))) |
797e1dfb RW |
2672 | (build-system r-build-system) |
2673 | (propagated-inputs | |
2674 | `(("r-numderiv" ,r-numderiv) | |
92e4534c | 2675 | ("r-squarem" ,r-squarem) |
797e1dfb RW |
2676 | ("r-survival" ,r-survival))) |
2677 | (home-page "https://github.com/kkholst/lava") | |
2678 | (synopsis "Latent variable models") | |
2679 | (description | |
2680 | "This package provides tools for the estimation and simulation of latent | |
2681 | variable models.") | |
2682 | (license license:gpl3))) | |
d26b7c1b RW |
2683 | |
2684 | (define-public r-drr | |
2685 | (package | |
2686 | (name "r-drr") | |
0f001b3c | 2687 | (version "0.0.3") |
d26b7c1b RW |
2688 | (source |
2689 | (origin | |
2690 | (method url-fetch) | |
2691 | (uri (cran-uri "DRR" version)) | |
2692 | (sha256 | |
2693 | (base32 | |
0f001b3c | 2694 | "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl")))) |
d26b7c1b RW |
2695 | (properties `((upstream-name . "DRR"))) |
2696 | (build-system r-build-system) | |
2697 | (propagated-inputs | |
2698 | `(("r-cvst" ,r-cvst) | |
2699 | ("r-kernlab" ,r-kernlab) | |
2700 | ("r-matrix" ,r-matrix))) | |
e9960d8c | 2701 | (home-page "https://cran.r-project.org/web/packages/DRR") |
d26b7c1b RW |
2702 | (synopsis "Dimensionality reduction via regression") |
2703 | (description | |
2704 | "This package provides an implementation of dimensionality reduction via | |
2705 | regression using Kernel Ridge Regression.") | |
2706 | (license license:gpl3))) | |
9dd707f0 RW |
2707 | |
2708 | (define-public r-prodlim | |
2709 | (package | |
2710 | (name "r-prodlim") | |
3b2c3878 | 2711 | (version "2019.11.13") |
9dd707f0 RW |
2712 | (source |
2713 | (origin | |
2714 | (method url-fetch) | |
2715 | (uri (cran-uri "prodlim" version)) | |
2716 | (sha256 | |
2717 | (base32 | |
3b2c3878 | 2718 | "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8")))) |
9dd707f0 RW |
2719 | (build-system r-build-system) |
2720 | (propagated-inputs | |
2721 | `(("r-kernsmooth" ,r-kernsmooth) | |
2722 | ("r-lava" ,r-lava) | |
2723 | ("r-rcpp" ,r-rcpp) | |
2724 | ("r-survival" ,r-survival))) | |
e9960d8c | 2725 | (home-page "https://cran.r-project.org/web/packages/prodlim") |
9dd707f0 RW |
2726 | (synopsis "Product-limit estimation for censored event history analysis") |
2727 | (description | |
2728 | "This package provides a fast and user-friendly implementation of | |
2729 | nonparametric estimators for censored event history (survival) analysis with | |
2730 | the Kaplan-Meier and Aalen-Johansen methods.") | |
2731 | (license license:gpl2+))) | |
b561f563 RW |
2732 | |
2733 | (define-public r-dimred | |
2734 | (package | |
2735 | (name "r-dimred") | |
7a67bca1 | 2736 | (version "0.2.3") |
b561f563 RW |
2737 | (source |
2738 | (origin | |
2739 | (method url-fetch) | |
2740 | (uri (cran-uri "dimRed" version)) | |
2741 | (sha256 | |
2742 | (base32 | |
7a67bca1 | 2743 | "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6")))) |
b561f563 RW |
2744 | (properties `((upstream-name . "dimRed"))) |
2745 | (build-system r-build-system) | |
77f97229 RW |
2746 | (propagated-inputs |
2747 | `(("r-drr" ,r-drr) | |
2748 | ("r-magrittr" ,r-magrittr))) | |
b561f563 RW |
2749 | (home-page "https://github.com/gdkrmr/dimRed") |
2750 | (synopsis "Framework for dimensionality reduction") | |
2751 | (description | |
2752 | "This package provides a collection of dimensionality reduction | |
2753 | techniques from R packages and provides a common interface for calling the | |
2754 | methods.") | |
2755 | (license license:gpl3))) | |
1b663184 RW |
2756 | |
2757 | (define-public r-timedate | |
2758 | (package | |
2759 | (name "r-timedate") | |
51b7b0e3 | 2760 | (version "3043.102") |
1b663184 RW |
2761 | (source |
2762 | (origin | |
2763 | (method url-fetch) | |
2764 | (uri (cran-uri "timeDate" version)) | |
2765 | (sha256 | |
2766 | (base32 | |
51b7b0e3 | 2767 | "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p")))) |
1b663184 RW |
2768 | (properties `((upstream-name . "timeDate"))) |
2769 | (build-system r-build-system) | |
2770 | (home-page "https://www.rmetrics.org") | |
2771 | (synopsis "Chronological and calendar objects") | |
2772 | (description | |
2773 | "This package provides an environment for teaching \"Financial | |
2774 | Engineering and Computational Finance\" and for managing chronological and | |
2775 | calendar objects.") | |
2776 | (license license:gpl2+))) | |
f57b883e | 2777 | |
ce4e81cb RW |
2778 | (define-public r-magic |
2779 | (package | |
2780 | (name "r-magic") | |
bba80fad | 2781 | (version "1.5-9") |
ce4e81cb RW |
2782 | (source |
2783 | (origin | |
2784 | (method url-fetch) | |
2785 | (uri (cran-uri "magic" version)) | |
2786 | (sha256 | |
2787 | (base32 | |
bba80fad | 2788 | "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) |
ce4e81cb RW |
2789 | (build-system r-build-system) |
2790 | (propagated-inputs | |
2791 | `(("r-abind" ,r-abind))) | |
2792 | (home-page "https://github.com/RobinHankin/magic.git") | |
2793 | (synopsis "Create and investigate magic squares") | |
2794 | (description | |
2795 | "This package provides a collection of efficient, vectorized algorithms | |
2796 | for the creation and investigation of magic squares and hypercubes, including | |
2797 | a variety of functions for the manipulation and analysis of arbitrarily | |
2798 | dimensioned arrays.") | |
2799 | (license license:gpl2))) | |
2800 | ||
d9bec9a8 RW |
2801 | (define-public r-rmysql |
2802 | (package | |
2803 | (name "r-rmysql") | |
c9a0f610 | 2804 | (version "0.10.18") |
d9bec9a8 RW |
2805 | (source |
2806 | (origin | |
2807 | (method url-fetch) | |
2808 | (uri (cran-uri "RMySQL" version)) | |
2809 | (sha256 | |
2810 | (base32 | |
c9a0f610 | 2811 | "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4")))) |
d9bec9a8 RW |
2812 | (properties `((upstream-name . "RMySQL"))) |
2813 | (build-system r-build-system) | |
d9bec9a8 | 2814 | (inputs |
2b8491fb JL |
2815 | `(("mariadb" ,mariadb "lib") |
2816 | ("mariadb-dev" ,mariadb "dev") | |
d9bec9a8 RW |
2817 | ("zlib" ,zlib))) |
2818 | (propagated-inputs | |
2819 | `(("r-dbi" ,r-dbi))) | |
2820 | (home-page "https://github.com/r-dbi/RMySQL") | |
2821 | (synopsis "Database interface and MySQL driver for R") | |
2822 | (description | |
2823 | "This package provides a DBI interface to MySQL / MariaDB. The RMySQL | |
2824 | package contains an old implementation based on legacy code from S-PLUS which | |
2825 | is being phased out. A modern MySQL client based on Rcpp is available from | |
2826 | the RMariaDB package.") | |
2827 | (license license:gpl2))) | |
2828 | ||
5574cb81 RW |
2829 | (define-public r-rpostgresql |
2830 | (package | |
2831 | (name "r-rpostgresql") | |
2832 | (version "0.6-2") | |
2833 | (source | |
2834 | (origin | |
2835 | (method url-fetch) | |
2836 | (uri (cran-uri "RPostgreSQL" version)) | |
2837 | (sha256 | |
2838 | (base32 | |
2839 | "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) | |
2840 | (properties `((upstream-name . "RPostgreSQL"))) | |
2841 | (build-system r-build-system) | |
2842 | (inputs | |
2843 | `(("postgresql" ,postgresql))) | |
2844 | (propagated-inputs | |
2845 | `(("r-dbi" ,r-dbi))) | |
2846 | (home-page "https://github.com/tomoakin/RPostgreSQL") | |
2847 | (synopsis "R interface to the PostgreSQL database system") | |
2848 | (description | |
2849 | "This package provides a Database Interface (DBI) compliant driver for R | |
2850 | to access PostgreSQL database systems.") | |
2851 | ;; The whole package is released under GPL version 2. It includes code | |
2852 | ;; under the PostgreSQL license. | |
2853 | (license license:gpl2))) | |
2854 | ||
f3640cee RW |
2855 | (define-public r-linprog |
2856 | (package | |
2857 | (name "r-linprog") | |
2858 | (version "0.9-2") | |
2859 | (source | |
2860 | (origin | |
2861 | (method url-fetch) | |
2862 | (uri (cran-uri "linprog" version)) | |
2863 | (sha256 | |
2864 | (base32 | |
2865 | "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9")))) | |
2866 | (build-system r-build-system) | |
2867 | (propagated-inputs `(("r-lpsolve" ,r-lpsolve))) | |
2868 | (home-page "http://linprog.r-forge.r-project.org/") | |
2869 | (synopsis "Linear programming and optimization") | |
2870 | (description | |
2871 | "This package can be used to solve Linear Programming / Linear | |
2872 | Optimization problems by using the simplex algorithm.") | |
2873 | (license license:gpl2+))) | |
2874 | ||
9604429d RW |
2875 | (define-public r-geometry |
2876 | (package | |
2877 | (name "r-geometry") | |
ff653ace | 2878 | (version "0.4.5") |
9604429d RW |
2879 | (source |
2880 | (origin | |
2881 | (method url-fetch) | |
2882 | (uri (cran-uri "geometry" version)) | |
2883 | (sha256 | |
2884 | (base32 | |
ff653ace | 2885 | "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg")))) |
9604429d | 2886 | (build-system r-build-system) |
a023d43d BG |
2887 | (propagated-inputs |
2888 | `(("r-magic" ,r-magic) | |
a80620b9 | 2889 | ("r-linprog" ,r-linprog) |
a023d43d BG |
2890 | ("r-lpsolve" ,r-lpsolve) |
2891 | ("r-rcpp" ,r-rcpp) | |
3d17dc5d | 2892 | ("r-rcppprogress" ,r-rcppprogress))) |
9604429d RW |
2893 | (home-page "http://geometry.r-forge.r-project.org/") |
2894 | (synopsis "Mesh generation and surface tesselation") | |
2895 | (description | |
2896 | "This package makes the qhull library available in R, in a similar manner | |
2897 | as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace | |
2898 | intersections about a point, Voronoi diagrams, furthest-site Delaunay | |
2899 | triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, | |
2900 | and higher dimensions. It implements the Quickhull algorithm for computing | |
2901 | the convex hull. Qhull does not support constrained Delaunay triangulations, | |
2902 | or mesh generation of non-convex objects, but the package does include some R | |
2903 | functions that allow for this. Currently the package only gives access to | |
2904 | Delaunay triangulation and convex hull computation.") | |
2905 | ;; The Qhull sources are included and are distributed under a custom | |
2906 | ;; non-copyleft license. The R sources are released under GPL version 2. | |
2907 | (license (list license:gpl2 | |
2908 | (license:non-copyleft "http://www.qhull.org/COPYING.txt"))))) | |
2909 | ||
f57b883e RW |
2910 | (define-public r-ddalpha |
2911 | (package | |
2912 | (name "r-ddalpha") | |
571f07af | 2913 | (version "1.3.10") |
f57b883e RW |
2914 | (source |
2915 | (origin | |
2916 | (method url-fetch) | |
2917 | (uri (cran-uri "ddalpha" version)) | |
2918 | (sha256 | |
2919 | (base32 | |
571f07af | 2920 | "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz")))) |
f57b883e RW |
2921 | (build-system r-build-system) |
2922 | (propagated-inputs | |
2923 | `(("r-bh" ,r-bh) | |
2924 | ("r-class" ,r-class) | |
4f184233 | 2925 | ("r-geometry" ,r-geometry) |
f57b883e RW |
2926 | ("r-mass" ,r-mass) |
2927 | ("r-rcpp" ,r-rcpp) | |
e90456b9 RW |
2928 | ("r-robustbase" ,r-robustbase) |
2929 | ("r-sfsmisc" ,r-sfsmisc))) | |
2930 | (native-inputs | |
2931 | `(("gfortran" ,gfortran))) | |
e9960d8c | 2932 | (home-page "https://cran.r-project.org/web/packages/ddalpha") |
f57b883e RW |
2933 | (synopsis "Depth-Based classification and calculation of data depth") |
2934 | (description | |
2935 | "This package contains procedures for depth-based supervised learning, | |
2936 | which are entirely non-parametric, in particular the DDalpha-procedure (Lange, | |
2937 | Mosler and Mozharovskyi, 2014). The training data sample is transformed by a | |
2938 | statistical depth function to a compact low-dimensional space, where the final | |
2939 | classification is done. It also offers an extension to functional data and | |
2940 | routines for calculating certain notions of statistical depth functions. 50 | |
2941 | multivariate and 5 functional classification problems are included.") | |
2942 | (license license:gpl2))) | |
5a87093f RW |
2943 | |
2944 | (define-public r-gower | |
2945 | (package | |
2946 | (name "r-gower") | |
1541f0a0 | 2947 | (version "0.2.1") |
5a87093f RW |
2948 | (source |
2949 | (origin | |
2950 | (method url-fetch) | |
2951 | (uri (cran-uri "gower" version)) | |
2952 | (sha256 | |
2953 | (base32 | |
1541f0a0 | 2954 | "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg")))) |
5a87093f | 2955 | (build-system r-build-system) |
5a87093f RW |
2956 | (home-page "https://github.com/markvanderloo/gower") |
2957 | (synopsis "Gower's distance") | |
2958 | (description | |
2959 | "This package provides tools to compute Gower's distance (or similarity) | |
2960 | coefficient between records, and to compute the top-n matches between records. | |
2961 | Core algorithms are executed in parallel on systems supporting OpenMP.") | |
2962 | (license license:gpl3))) | |
649cf27c RW |
2963 | |
2964 | (define-public r-rcpproll | |
2965 | (package | |
2966 | (name "r-rcpproll") | |
d0396c8e | 2967 | (version "0.3.0") |
649cf27c RW |
2968 | (source |
2969 | (origin | |
2970 | (method url-fetch) | |
2971 | (uri (cran-uri "RcppRoll" version)) | |
2972 | (sha256 | |
2973 | (base32 | |
d0396c8e | 2974 | "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) |
649cf27c RW |
2975 | (properties `((upstream-name . "RcppRoll"))) |
2976 | (build-system r-build-system) | |
2977 | (propagated-inputs | |
2978 | `(("r-rcpp" ,r-rcpp))) | |
e9960d8c | 2979 | (home-page "https://cran.r-project.org/web/packages/RcppRoll") |
649cf27c RW |
2980 | (synopsis "Efficient rolling and windowed operations") |
2981 | (description | |
2982 | "This package provides fast and efficient routines for common rolling / | |
2983 | windowed operations. Routines for the efficient computation of windowed mean, | |
2984 | median, sum, product, minimum, maximum, standard deviation and variance are | |
2985 | provided.") | |
2986 | (license license:gpl2+))) | |
6c3d42d6 RW |
2987 | |
2988 | (define-public r-ipred | |
2989 | (package | |
2990 | (name "r-ipred") | |
5fce9013 | 2991 | (version "0.9-9") |
6c3d42d6 RW |
2992 | (source |
2993 | (origin | |
2994 | (method url-fetch) | |
2995 | (uri (cran-uri "ipred" version)) | |
2996 | (sha256 | |
2997 | (base32 | |
5fce9013 | 2998 | "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d")))) |
6c3d42d6 RW |
2999 | (build-system r-build-system) |
3000 | (propagated-inputs | |
3001 | `(("r-class" ,r-class) | |
3002 | ("r-mass" ,r-mass) | |
3003 | ("r-nnet" ,r-nnet) | |
3004 | ("r-prodlim" ,r-prodlim) | |
3005 | ("r-rpart" ,r-rpart) | |
3006 | ("r-survival" ,r-survival))) | |
e9960d8c | 3007 | (home-page "https://cran.r-project.org/web/packages/ipred") |
6c3d42d6 RW |
3008 | (synopsis "Improved predictors") |
3009 | (description | |
3010 | "This package provides improved predictive models by indirect | |
3011 | classification and bagging for classification, regression and survival | |
3012 | problems as well as resampling based estimators of prediction error.") | |
3013 | (license license:gpl2+))) | |
ba4527ab | 3014 | |
cdc129dc RW |
3015 | (define-public r-psych |
3016 | (package | |
3017 | (name "r-psych") | |
571f4689 | 3018 | (version "1.9.12") |
cdc129dc RW |
3019 | (source |
3020 | (origin | |
3021 | (method url-fetch) | |
3022 | (uri (cran-uri "psych" version)) | |
3023 | (sha256 | |
3024 | (base32 | |
571f4689 | 3025 | "13r7fyjsl93m121awnwfhya8a0lw0l2byn60yqdbf9gp3lmb9ny0")))) |
cdc129dc RW |
3026 | (build-system r-build-system) |
3027 | (propagated-inputs | |
3028 | `(("r-foreign" ,r-foreign) | |
3029 | ("r-lattice" ,r-lattice) | |
3030 | ("r-mnormt" ,r-mnormt) | |
3031 | ("r-nlme" ,r-nlme))) | |
e9960d8c | 3032 | (home-page "https://cran.r-project.org/web/packages/psych/") |
cdc129dc RW |
3033 | (synopsis "Procedures for psychological, psychometric, and personality research") |
3034 | (description | |
3035 | "This package provides a general purpose toolbox for personality, | |
3036 | psychometric theory and experimental psychology. Functions are primarily for | |
3037 | multivariate analysis and scale construction using factor analysis, principal | |
3038 | component analysis, cluster analysis and reliability analysis, although others | |
3039 | provide basic descriptive statistics. Item Response Theory is done using | |
3040 | factor analysis of tetrachoric and polychoric correlations. Functions for | |
3041 | analyzing data at multiple levels include within and between group statistics, | |
3042 | including correlations and factor analysis. Functions for simulating and | |
3043 | testing particular item and test structures are included. Several functions | |
3044 | serve as a useful front end for structural equation modeling. Graphical | |
3045 | displays of path diagrams, factor analysis and structural equation models are | |
3046 | created using basic graphics.") | |
3047 | (license license:gpl2+))) | |
3048 | ||
25c67ecf RW |
3049 | (define-public r-generics |
3050 | (package | |
3051 | (name "r-generics") | |
3052 | (version "0.0.2") | |
3053 | (source | |
3054 | (origin | |
3055 | (method url-fetch) | |
3056 | (uri (cran-uri "generics" version)) | |
3057 | (sha256 | |
3058 | (base32 | |
3059 | "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) | |
3060 | (build-system r-build-system) | |
3061 | (home-page "https://github.com/r-lib/generics") | |
3062 | (synopsis "Common S3 generics not provided by base R methods") | |
3063 | (description | |
3064 | "In order to reduce potential package dependencies and conflicts, | |
3065 | generics provides a number of commonly used S3 generics that are not provided | |
3066 | by base R methods related to model fitting.") | |
3067 | (license license:gpl2))) | |
3068 | ||
6c8c8c6b RW |
3069 | (define-public r-broom |
3070 | (package | |
3071 | (name "r-broom") | |
a3b51a34 | 3072 | (version "0.5.3") |
6c8c8c6b RW |
3073 | (source |
3074 | (origin | |
3075 | (method url-fetch) | |
3076 | (uri (cran-uri "broom" version)) | |
3077 | (sha256 | |
3078 | (base32 | |
a3b51a34 | 3079 | "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d")))) |
6c8c8c6b RW |
3080 | (build-system r-build-system) |
3081 | (propagated-inputs | |
45c156bf RW |
3082 | `(("r-backports" ,r-backports) |
3083 | ("r-dplyr" ,r-dplyr) | |
813d9c51 | 3084 | ("r-generics" ,r-generics) |
6c8c8c6b | 3085 | ("r-nlme" ,r-nlme) |
45c156bf | 3086 | ("r-purrr" ,r-purrr) |
6c8c8c6b RW |
3087 | ("r-reshape2" ,r-reshape2) |
3088 | ("r-stringr" ,r-stringr) | |
45c156bf | 3089 | ("r-tibble" ,r-tibble) |
6c8c8c6b | 3090 | ("r-tidyr" ,r-tidyr))) |
6e19d50e | 3091 | (home-page "https://github.com/tidyverse/broom") |
6c8c8c6b RW |
3092 | (synopsis "Convert statistical analysis objects into tidy data frames") |
3093 | (description | |
3094 | "This package provides tools to convert statistical analysis objects from | |
3095 | R into tidy data frames, so that they can more easily be combined, reshaped | |
3096 | and otherwise processed with tools like @code{dplyr}, @code{tidyr} and | |
3097 | @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which | |
3098 | summarizes a model's statistical findings such as coefficients of a | |
3099 | regression; @code{augment}, which adds columns to the original data such as | |
3100 | predictions, residuals and cluster assignments; and @code{glance}, which | |
3101 | provides a one-row summary of model-level statistics.") | |
3102 | (license license:expat))) | |
3103 | ||
ba4527ab RW |
3104 | (define-public r-recipes |
3105 | (package | |
3106 | (name "r-recipes") | |
63b4c779 | 3107 | (version "0.1.8") |
ba4527ab RW |
3108 | (source |
3109 | (origin | |
3110 | (method url-fetch) | |
3111 | (uri (cran-uri "recipes" version)) | |
3112 | (sha256 | |
3113 | (base32 | |
63b4c779 | 3114 | "1n32qc2a3n9cykm8dv9qcr77kdhqfsjiqf6kgfk9s0lnpx2zaldm")))) |
ba4527ab RW |
3115 | (build-system r-build-system) |
3116 | (propagated-inputs | |
decea6ee RW |
3117 | `(("r-dplyr" ,r-dplyr) |
3118 | ("r-generics" ,r-generics) | |
3119 | ("r-glue" ,r-glue) | |
ba4527ab RW |
3120 | ("r-gower" ,r-gower) |
3121 | ("r-ipred" ,r-ipred) | |
3122 | ("r-lubridate" ,r-lubridate) | |
3123 | ("r-magrittr" ,r-magrittr) | |
18a11c6d | 3124 | ("r-matrix" ,r-matrix) |
ba4527ab | 3125 | ("r-purrr" ,r-purrr) |
ba4527ab RW |
3126 | ("r-rlang" ,r-rlang) |
3127 | ("r-tibble" ,r-tibble) | |
decea6ee | 3128 | ("r-tidyr" ,r-tidyr) |
ba4527ab | 3129 | ("r-tidyselect" ,r-tidyselect) |
57039918 RW |
3130 | ("r-timedate" ,r-timedate) |
3131 | ("r-withr" ,r-withr))) | |
ba4527ab RW |
3132 | (home-page "https://github.com/topepo/recipes") |
3133 | (synopsis "Preprocessing tools to create design matrices") | |
3134 | (description | |
3135 | "Recipes is an extensible framework to create and preprocess design | |
3136 | matrices. Recipes consist of one or more data manipulation and analysis | |
3137 | \"steps\". Statistical parameters for the steps can be estimated from an | |
3138 | initial data set and then applied to other data sets. The resulting design | |
3139 | matrices can then be used as inputs into statistical or machine learning | |
3140 | models.") | |
3141 | (license license:gpl2))) | |
1ab867be RW |
3142 | |
3143 | (define-public r-pdist | |
3144 | (package | |
3145 | (name "r-pdist") | |
3146 | (version "1.2") | |
3147 | (source | |
3148 | (origin | |
3149 | (method url-fetch) | |
3150 | (uri (cran-uri "pdist" version)) | |
3151 | (sha256 | |
3152 | (base32 | |
3153 | "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd")))) | |
3154 | (build-system r-build-system) | |
3155 | (home-page "https://github.com/jeffwong/pdist") | |
3156 | (synopsis "Partitioned distance function") | |
3157 | (description | |
3158 | "Pdist computes the euclidean distance between rows of a matrix X and | |
3159 | rows of another matrix Y. Previously, this could be done by binding the two | |
3160 | matrices together and calling @code{dist}, but this creates unnecessary | |
3161 | computation by computing the distances between a row of X and another row of | |
3162 | X, and likewise for Y. Pdist strictly computes distances across the two | |
3163 | matrices, not within the same matrix, making computations significantly faster | |
3164 | for certain use cases.") | |
3165 | (license license:gpl3+))) | |
81e0b625 RW |
3166 | |
3167 | (define-public r-ggrepel | |
3168 | (package | |
3169 | (name "r-ggrepel") | |
00399a78 | 3170 | (version "0.8.1") |
81e0b625 RW |
3171 | (source |
3172 | (origin | |
3173 | (method url-fetch) | |
3174 | (uri (cran-uri "ggrepel" version)) | |
3175 | (sha256 | |
3176 | (base32 | |
00399a78 | 3177 | "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m")))) |
81e0b625 RW |
3178 | (build-system r-build-system) |
3179 | (propagated-inputs | |
3180 | `(("r-ggplot2" ,r-ggplot2) | |
3181 | ("r-rcpp" ,r-rcpp) | |
3182 | ("r-scales" ,r-scales))) | |
3183 | (home-page "http://github.com/slowkow/ggrepel") | |
3184 | (synopsis "Repulsive text and label geometries for ggplot2") | |
3185 | (description | |
3186 | "This package provides text and label geometries for ggplot2 that help to | |
3187 | avoid overlapping text labels. Labels repel away from each other and away | |
3188 | from the data points.") | |
3189 | (license license:gpl3))) | |
6b968c4c RW |
3190 | |
3191 | (define-public r-corrplot | |
3192 | (package | |
3193 | (name "r-corrplot") | |
3194 | (version "0.84") | |
3195 | (source | |
3196 | (origin | |
3197 | (method url-fetch) | |
3198 | (uri (cran-uri "corrplot" version)) | |
3199 | (sha256 | |
3200 | (base32 | |
3201 | "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd")))) | |
3202 | (build-system r-build-system) | |
3203 | (home-page "https://github.com/taiyun/corrplot") | |
3204 | (synopsis "Visualization of a correlation matrix") | |
3205 | (description | |
3206 | "This package provides a graphical display of a correlation matrix or | |
3207 | general matrix. It also contains some algorithms to do matrix reordering. In | |
3208 | addition, corrplot is good at details, including choosing color, text labels, | |
3209 | color labels, layout, etc.") | |
3210 | ;; Any version of the GPL | |
3211 | (license license:gpl2+))) | |
a40a04fd RW |
3212 | |
3213 | (define-public r-stringdist | |
3214 | (package | |
3215 | (name "r-stringdist") | |
252bb462 | 3216 | (version "0.9.5.5") |
a40a04fd RW |
3217 | (source |
3218 | (origin | |
3219 | (method url-fetch) | |
3220 | (uri (cran-uri "stringdist" version)) | |
3221 | (sha256 | |
252bb462 | 3222 | (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi")))) |
a40a04fd RW |
3223 | (build-system r-build-system) |
3224 | (home-page "https://github.com/markvanderloo/stringdist") | |
3225 | (synopsis "Approximate string matching and string distance functions") | |
3226 | (description | |
3227 | "This package implements an approximate string matching version of R's | |
3228 | native @code{match} function. It can calculate various string distances based | |
3229 | on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), | |
3230 | qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, | |
3231 | Jaro-Winkler). An implementation of soundex is provided as well. Distances | |
3232 | can be computed between character vectors while taking proper care of encoding | |
3233 | or between integer vectors representing generic sequences.") | |
3234 | (license license:gpl3+))) | |
10e16fa9 | 3235 | |
dc668352 RW |
3236 | (define-public r-ucminf |
3237 | (package | |
3238 | (name "r-ucminf") | |
3239 | (version "1.1-4") | |
3240 | (source | |
3241 | (origin | |
3242 | (method url-fetch) | |
3243 | (uri (cran-uri "ucminf" version)) | |
3244 | (sha256 | |
3245 | (base32 | |
3246 | "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) | |
3247 | (build-system r-build-system) | |
3248 | (native-inputs `(("gfortran" ,gfortran))) | |
3249 | (home-page "https://cran.r-project.org/web/packages/ucminf/") | |
3250 | (synopsis "General-purpose unconstrained non-linear optimization") | |
3251 | (description | |
3252 | "This package provides an implementation of an algorithm for | |
3253 | general-purpose unconstrained non-linear optimization. The algorithm is of | |
3254 | quasi-Newton type with BFGS updating of the inverse Hessian and soft line | |
3255 | search with a trust region type monitoring of the input to the line search | |
3256 | algorithm. The interface of @code{ucminf} is designed for easy interchange | |
3257 | with the package @code{optim}.") | |
3258 | (license license:gpl2+))) | |
3259 | ||
b8f6e2f8 RW |
3260 | (define-public r-ordinal |
3261 | (package | |
3262 | (name "r-ordinal") | |
f87c6727 | 3263 | (version "2019.12-10") |
b8f6e2f8 RW |
3264 | (source |
3265 | (origin | |
3266 | (method url-fetch) | |
3267 | (uri (cran-uri "ordinal" version)) | |
3268 | (sha256 | |
3269 | (base32 | |
f87c6727 | 3270 | "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) |
b8f6e2f8 RW |
3271 | (build-system r-build-system) |
3272 | (propagated-inputs | |
3273 | `(("r-mass" ,r-mass) | |
3274 | ("r-matrix" ,r-matrix) | |
3275 | ("r-numderiv" ,r-numderiv) | |
3276 | ("r-ucminf" ,r-ucminf))) | |
3277 | (home-page "https://github.com/runehaubo/ordinal") | |
3278 | (synopsis "Regression models for ordinal data") | |
3279 | (description | |
3280 | "This package provides an implementation of cumulative link (mixed) | |
3281 | models also known as ordered regression models, proportional odds models, | |
3282 | proportional hazards models for grouped survival times and ordered models. | |
3283 | Estimation is via maximum likelihood and mixed models are fitted with the | |
3284 | Laplace approximation and adaptive Gauss-Hermite quadrature.") | |
3285 | (license license:gpl2+))) | |
3286 | ||
fe1495e3 RW |
3287 | (define-public r-jomo |
3288 | (package | |
3289 | (name "r-jomo") | |
7195db02 | 3290 | (version "2.6-10") |
fe1495e3 RW |
3291 | (source |
3292 | (origin | |
3293 | (method url-fetch) | |
3294 | (uri (cran-uri "jomo" version)) | |
3295 | (sha256 | |
3296 | (base32 | |
7195db02 | 3297 | "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0")))) |
fe1495e3 RW |
3298 | (build-system r-build-system) |
3299 | (propagated-inputs | |
3300 | `(("r-lme4" ,r-lme4) | |
fccb2450 | 3301 | ("r-mass" ,r-mass) |
e7630cc9 | 3302 | ("r-ordinal" ,r-ordinal) |
fe1495e3 RW |
3303 | ("r-survival" ,r-survival))) |
3304 | (home-page "https://cran.r-project.org/web/packages/jomo/") | |
3305 | (synopsis "Multilevel Joint Modelling Multiple Imputation") | |
3306 | (description | |
3307 | "Similarly to Schafer's package pan, jomo is a package for multilevel | |
3308 | joint modelling multiple imputation @url{Carpenter and Kenward (2013), | |
3309 | http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the | |
3310 | possibility of handling binary and categorical data through latent normal | |
3311 | variables, the option to use cluster-specific covariance matrices and to | |
3312 | impute compatibly with the substantive model.") | |
3313 | (license license:gpl2))) | |
3314 | ||
03e718fb RW |
3315 | (define-public r-pan |
3316 | (package | |
3317 | (name "r-pan") | |
a7265593 | 3318 | (version "1.6") |
03e718fb RW |
3319 | (source |
3320 | (origin | |
3321 | (method url-fetch) | |
3322 | (uri (cran-uri "pan" version)) | |
3323 | (sha256 | |
3324 | (base32 | |
a7265593 | 3325 | "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) |
03e718fb RW |
3326 | (build-system r-build-system) |
3327 | (native-inputs `(("gfortran" ,gfortran))) | |
3328 | (home-page "https://cran.r-project.org/web/packages/pan/") | |
3329 | (synopsis "Multiple imputation for multivariate panel or clustered data") | |
3330 | (description | |
3331 | "This package implements multiple imputation for multivariate panel or | |
3332 | clustered data.") | |
3333 | (license license:gpl3))) | |
3334 | ||
84e7147a RW |
3335 | (define-public r-mitml |
3336 | (package | |
3337 | (name "r-mitml") | |
1c6d199e | 3338 | (version "0.3-7") |
84e7147a RW |
3339 | (source |
3340 | (origin | |
3341 | (method url-fetch) | |
3342 | (uri (cran-uri "mitml" version)) | |
3343 | (sha256 | |
3344 | (base32 | |
1c6d199e | 3345 | "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) |
84e7147a RW |
3346 | (build-system r-build-system) |
3347 | (propagated-inputs | |
3348 | `(("r-haven" ,r-haven) | |
3349 | ("r-jomo" ,r-jomo) | |
3350 | ("r-pan" ,r-pan))) | |
3351 | (home-page "https://cran.r-project.org/web/packages/mitml/") | |
3352 | (synopsis "Tools for multiple imputation in multilevel modeling") | |
3353 | (description | |
3354 | "This package provides tools for multiple imputation of missing data in | |
3355 | multilevel modeling. It includes a user-friendly interface to the packages | |
3356 | pan and jomo, and several functions for visualization, data management and the | |
3357 | analysis of multiply imputed data sets.") | |
3358 | (license license:gpl2+))) | |
3359 | ||
10e16fa9 RW |
3360 | (define-public r-mice |
3361 | (package | |
3362 | (name "r-mice") | |
c79e80f8 | 3363 | (version "3.7.0") |
10e16fa9 RW |
3364 | (source |
3365 | (origin | |
3366 | (method url-fetch) | |
3367 | (uri (cran-uri "mice" version)) | |
3368 | (sha256 | |
3369 | (base32 | |
c79e80f8 | 3370 | "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf")))) |
10e16fa9 RW |
3371 | (build-system r-build-system) |
3372 | (propagated-inputs | |
aea3be25 RW |
3373 | `(("r-broom" ,r-broom) |
3374 | ("r-dplyr" ,r-dplyr) | |
3375 | ("r-lattice" ,r-lattice) | |
10e16fa9 | 3376 | ("r-mass" ,r-mass) |
aea3be25 | 3377 | ("r-mitml" ,r-mitml) |
10e16fa9 RW |
3378 | ("r-nnet" ,r-nnet) |
3379 | ("r-rcpp" ,r-rcpp) | |
aea3be25 | 3380 | ("r-rlang" ,r-rlang) |
10e16fa9 RW |
3381 | ("r-rpart" ,r-rpart) |
3382 | ("r-survival" ,r-survival))) | |
3383 | (home-page "https://cran.r-project.org/web/packages/mice/") | |
3384 | (synopsis "Multivariate imputation by chained equations") | |
3385 | (description | |
3386 | "Multiple imputation using @dfn{Fully Conditional Specification} (FCS) | |
3387 | implemented by the MICE algorithm as described in @url{Van Buuren and | |
3388 | Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each | |
3389 | variable has its own imputation model. Built-in imputation models are | |
3390 | provided for continuous data (predictive mean matching, normal), binary | |
3391 | data (logistic regression), unordered categorical data (polytomous logistic | |
3392 | regression) and ordered categorical data (proportional odds). MICE can also | |
3393 | impute continuous two-level data (normal model, pan, second-level variables). | |
3394 | Passive imputation can be used to maintain consistency between variables. | |
3395 | Various diagnostic plots are available to inspect the quality of the | |
3396 | imputations.") | |
3397 | ;; Any of these two versions. | |
3398 | (license (list license:gpl2 license:gpl3)))) | |
7fd5f60b | 3399 | |
02cdb45f RW |
3400 | (define-public r-truncnorm |
3401 | (package | |
3402 | (name "r-truncnorm") | |
9d6f3925 | 3403 | (version "1.0-8") |
02cdb45f RW |
3404 | (source |
3405 | (origin | |
3406 | (method url-fetch) | |
3407 | (uri (cran-uri "truncnorm" version)) | |
3408 | (sha256 | |
3409 | (base32 | |
9d6f3925 | 3410 | "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9")))) |
02cdb45f | 3411 | (build-system r-build-system) |
e9960d8c | 3412 | (home-page "https://cran.r-project.org/web/packages/truncnorm/") |
02cdb45f RW |
3413 | (synopsis "Truncated normal distribution") |
3414 | (description "This package provides functions for the truncated normal | |
3415 | distribution with mean equal to @code{mean} and standard deviation equal to | |
3416 | @code{sd}. It includes density, distribution, quantile, and expected value | |
3417 | functions, as well as a random generation function.") | |
3418 | (license license:gpl2))) | |
3419 | ||
cb8b4c11 RW |
3420 | (define-public r-rsolnp |
3421 | (package | |
3422 | (name "r-rsolnp") | |
3423 | (version "1.16") | |
3424 | (source | |
3425 | (origin | |
3426 | (method url-fetch) | |
3427 | (uri (cran-uri "Rsolnp" version)) | |
3428 | (sha256 | |
3429 | (base32 | |
3430 | "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii")))) | |
3431 | (properties `((upstream-name . "Rsolnp"))) | |
3432 | (build-system r-build-system) | |
3433 | (propagated-inputs | |
3434 | `(("r-truncnorm" ,r-truncnorm))) | |
e9960d8c | 3435 | (home-page "https://cran.r-project.org/web/packages/Rsolnp/") |
cb8b4c11 RW |
3436 | (synopsis "General non-linear optimization") |
3437 | (description "The Rsolnp package implements a general non-linear augmented | |
3438 | Lagrange multiplier method solver, a @dfn{sequential quadratic | |
3439 | programming} (SQP) based solver).") | |
3440 | ;; Any version of the GPL. | |
3441 | (license license:gpl2+))) | |
3442 | ||
7fd5f60b RW |
3443 | (define-public r-hardyweinberg |
3444 | (package | |
3445 | (name "r-hardyweinberg") | |
83e3e72a | 3446 | (version "1.6.3") |
7fd5f60b RW |
3447 | (source |
3448 | (origin | |
3449 | (method url-fetch) | |
3450 | (uri (cran-uri "HardyWeinberg" version)) | |
3451 | (sha256 | |
3452 | (base32 | |
83e3e72a | 3453 | "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f")))) |
7fd5f60b RW |
3454 | (properties `((upstream-name . "HardyWeinberg"))) |
3455 | (build-system r-build-system) | |
3456 | (propagated-inputs | |
3457 | `(("r-mice" ,r-mice) | |
d0394944 RW |
3458 | ("r-rcpp" ,r-rcpp) |
3459 | ("r-rsolnp" ,r-rsolnp))) | |
7fd5f60b RW |
3460 | (home-page "https://cran.r-project.org/package=HardyWeinberg") |
3461 | (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") | |
3462 | (description | |
3463 | "This package contains tools for exploring Hardy-Weinberg equilibrium for | |
3464 | diallelic genetic marker data. All classical tests (chi-square, exact, | |
3465 | likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are | |
3466 | included in the package, as well as functions for power computation and for | |
3467 | the simulation of marker data under equilibrium and disequilibrium. Routines | |
3468 | for dealing with markers on the X-chromosome are included. Functions for | |
3469 | testing equilibrium in the presence of missing data by using multiple | |
3470 | imputation are also provided. Implements several graphics for exploring the | |
3471 | equilibrium status of a large set of diallelic markers: ternary plots with | |
3472 | acceptance regions, log-ratio plots and Q-Q plots.") | |
3473 | (license license:gpl2+))) | |
3a22732c RW |
3474 | |
3475 | (define-public r-sm | |
3476 | (package | |
3477 | (name "r-sm") | |
5621b840 | 3478 | (version "2.2-5.6") |
3a22732c RW |
3479 | (source |
3480 | (origin | |
3481 | (method url-fetch) | |
3482 | (uri (cran-uri "sm" version)) | |
3483 | (sha256 | |
3484 | (base32 | |
5621b840 | 3485 | "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q")))) |
3a22732c RW |
3486 | (build-system r-build-system) |
3487 | (native-inputs `(("gfortran" ,gfortran))) | |
3488 | (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") | |
3489 | (synopsis "Smoothing methods for nonparametric regression and density estimation") | |
3490 | (description | |
3491 | "This is software accompanying the book 'Applied Smoothing Techniques for | |
3492 | Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford | |
3493 | University Press. It provides smoothing methods for nonparametric regression | |
3494 | and density estimation") | |
3495 | (license license:gpl2+))) | |
9232cac4 | 3496 | |
6174db2b RJ |
3497 | (define-public r-venndiagram |
3498 | (package | |
3499 | (name "r-venndiagram") | |
3500 | (version "1.6.20") | |
3501 | (source (origin | |
3502 | (method url-fetch) | |
3503 | (uri (cran-uri "VennDiagram" version)) | |
3504 | (sha256 | |
3505 | (base32 | |
3506 | "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775")))) | |
3507 | (properties `((upstream-name . "VennDiagram"))) | |
3508 | (build-system r-build-system) | |
3509 | (propagated-inputs | |
3510 | `(("r-futile-logger" ,r-futile-logger))) | |
3511 | (home-page "https://cran.r-project.org/web/packages/VennDiagram/") | |
3512 | (synopsis "Generate High-Resolution Venn and Euler Plots") | |
3513 | (description | |
3514 | "This package provides a set of functions to generate high-resolution | |
3515 | Venn and Euler plots. It includes handling for several special cases, | |
3516 | including two-case scaling, and extensive customization of plot shape and | |
3517 | structure.") | |
3518 | (license license:gpl2+))) | |
3519 | ||
9232cac4 RW |
3520 | (define-public r-vioplot |
3521 | (package | |
3522 | (name "r-vioplot") | |
2899a9d4 | 3523 | (version "0.3.4") |
9232cac4 RW |
3524 | (source |
3525 | (origin | |
3526 | (method url-fetch) | |
3527 | (uri (cran-uri "vioplot" version)) | |
3528 | (sha256 | |
3529 | (base32 | |
2899a9d4 | 3530 | "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529")))) |
9232cac4 | 3531 | (build-system r-build-system) |
7d4b9818 RW |
3532 | (propagated-inputs |
3533 | `(("r-sm" ,r-sm) | |
3534 | ("r-zoo" ,r-zoo))) | |
9232cac4 RW |
3535 | (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") |
3536 | (synopsis "Violin plot") | |
3537 | (description | |
3538 | "This package provides a violin plot, which is a combination of a box | |
3539 | plot and a kernel density plot.") | |
3540 | (license license:bsd-3))) | |
7b0569c0 RW |
3541 | |
3542 | (define-public r-rsofia | |
3543 | (package | |
3544 | (name "r-rsofia") | |
3545 | (version "1.1") | |
3546 | (source (origin | |
3547 | (method url-fetch) | |
3548 | ;; This package has been removed from CRAN, so we can | |
3549 | ;; only fetch it from the archives. | |
3550 | (uri (string-append "https://cran.r-project.org/src/" | |
3551 | "contrib/Archive/RSofia/RSofia_" | |
3552 | version ".tar.gz")) | |
3553 | (sha256 | |
3554 | (base32 | |
3555 | "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn")))) | |
3556 | (properties `((upstream-name . "RSofia"))) | |
3557 | (build-system r-build-system) | |
3558 | (propagated-inputs | |
3559 | `(("r-rcpp" ,r-rcpp))) | |
3560 | (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") | |
3561 | (synopsis "Port of sofia-ml to R") | |
3562 | (description "This package is a port of sofia-ml to R. Sofia-ml is a | |
3563 | suite of fast incremental algorithms for machine learning that can be used for | |
3564 | training models for classification or ranking.") | |
3565 | (license license:asl2.0))) | |
738dda83 | 3566 | |
3699383e RW |
3567 | (define-public r-xts |
3568 | (package | |
3569 | (name "r-xts") | |
cea8a607 | 3570 | (version "0.11-2") |
3699383e RW |
3571 | (source |
3572 | (origin | |
3573 | (method url-fetch) | |
3574 | (uri (cran-uri "xts" version)) | |
3575 | (sha256 | |
3576 | (base32 | |
cea8a607 | 3577 | "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj")))) |
3699383e RW |
3578 | (build-system r-build-system) |
3579 | (propagated-inputs `(("r-zoo" ,r-zoo))) | |
3699383e RW |
3580 | (home-page "https://github.com/joshuaulrich/xts") |
3581 | (synopsis "Extensible time series") | |
3582 | (description | |
3583 | "This package provides for uniform handling of R's different time-based | |
3584 | data classes by extending @code{zoo}, maximizing native format information | |
3585 | preservation and allowing for user-level customization and extension, while | |
3586 | simplifying cross-class interoperability.") | |
3587 | (license license:gpl2+))) | |
b72b42cf RW |
3588 | |
3589 | (define-public r-performanceanalytics | |
3590 | (package | |
3591 | (name "r-performanceanalytics") | |
1f7e8d49 | 3592 | (version "1.5.3") |
b72b42cf RW |
3593 | (source |
3594 | (origin | |
3595 | (method url-fetch) | |
3596 | (uri (cran-uri "PerformanceAnalytics" version)) | |
3597 | (sha256 | |
3598 | (base32 | |
1f7e8d49 | 3599 | "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd")))) |
b72b42cf RW |
3600 | (properties |
3601 | `((upstream-name . "PerformanceAnalytics"))) | |
3602 | (build-system r-build-system) | |
3603 | (propagated-inputs | |
081d143d RW |
3604 | `(("r-quadprog" ,r-quadprog) |
3605 | ("r-xts" ,r-xts) | |
b72b42cf | 3606 | ("r-zoo" ,r-zoo))) |
d062957a | 3607 | (home-page "https://r-forge.r-project.org/projects/returnanalytics/") |
b72b42cf RW |
3608 | (synopsis "Econometric tools for performance and risk analysis") |
3609 | (description "This is a collection of econometric functions for | |
3610 | performance and risk analysis. This package aims to aid practitioners and | |
3611 | researchers in utilizing the latest research in analysis of non-normal return | |
3612 | streams. In general, it is most tested on return (rather than price) data on | |
3613 | a regular scale, but most functions will work with irregular return data as | |
3614 | well, and increasing numbers of functions will work with P&L or price data | |
3615 | where possible.") | |
3616 | ;; Either version may be picked. | |
3617 | (license (list license:gpl2 license:gpl3)))) | |
018cf270 RW |
3618 | |
3619 | (define-public r-laeken | |
3620 | (package | |
3621 | (name "r-laeken") | |
ed46a05c | 3622 | (version "0.5.0") |
018cf270 RW |
3623 | (source |
3624 | (origin | |
3625 | (method url-fetch) | |
3626 | (uri (cran-uri "laeken" version)) | |
3627 | (sha256 | |
3628 | (base32 | |
ed46a05c | 3629 | "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa")))) |
018cf270 RW |
3630 | (build-system r-build-system) |
3631 | (propagated-inputs | |
3632 | `(("r-boot" ,r-boot) | |
3633 | ("r-mass" ,r-mass))) | |
e9960d8c | 3634 | (home-page "https://cran.r-project.org/web/packages/laeken/") |
018cf270 RW |
3635 | (synopsis "Estimation of indicators on social exclusion and poverty") |
3636 | (description "This package provides tools for the estimation of indicators | |
3637 | on social exclusion and poverty, as well as an implementation of Pareto tail | |
3638 | modeling for empirical income distributions.") | |
3639 | (license license:gpl2+))) | |
e5c17b8d RW |
3640 | |
3641 | (define-public r-vcd | |
3642 | (package | |
3643 | (name "r-vcd") | |
2960f965 | 3644 | (version "1.4-4") |
e5c17b8d RW |
3645 | (source |
3646 | (origin | |
3647 | (method url-fetch) | |
3648 | (uri (cran-uri "vcd" version)) | |
3649 | (sha256 | |
3650 | (base32 | |
2960f965 | 3651 | "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5")))) |
e5c17b8d RW |
3652 | (build-system r-build-system) |
3653 | (propagated-inputs | |
3654 | `(("r-colorspace" ,r-colorspace) | |
3655 | ("r-lmtest" ,r-lmtest) | |
3656 | ("r-mass" ,r-mass))) | |
e9960d8c | 3657 | (home-page "https://cran.r-project.org/web/packages/vcd/") |
e5c17b8d RW |
3658 | (synopsis "Visualizing categorical data") |
3659 | (description "This package provides visualization techniques, data sets, | |
3660 | summary and inference procedures aimed particularly at categorical data. | |
3661 | Special emphasis is given to highly extensible grid graphics. The package was | |
3662 | originally inspired by the book \"Visualizing Categorical Data\" by Michael | |
3663 | Friendly and is now the main support package for a new book, \"Discrete Data | |
3664 | Analysis with R\" by Michael Friendly and David Meyer (2015).") | |
3665 | (license license:gpl2))) | |
ae164260 RW |
3666 | |
3667 | (define-public r-ica | |
3668 | (package | |
3669 | (name "r-ica") | |
fabf0993 | 3670 | (version "1.0-2") |
ae164260 RW |
3671 | (source |
3672 | (origin | |
3673 | (method url-fetch) | |
3674 | (uri (cran-uri "ica" version)) | |
3675 | (sha256 | |
3676 | (base32 | |
fabf0993 | 3677 | "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7")))) |
ae164260 | 3678 | (build-system r-build-system) |
e9960d8c | 3679 | (home-page "https://cran.r-project.org/web/packages/ica/") |
ae164260 RW |
3680 | (synopsis "Independent component analysis") |
3681 | (description "This package provides tools for @dfn{Independent Component | |
3682 | Analysis} (ICA) using various algorithms: FastICA, | |
3683 | Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization | |
3684 | of Eigenmatrices} (JADE).") | |
3685 | (license license:gpl2+))) | |
bf025ff6 RW |
3686 | |
3687 | (define-public r-dtw | |
3688 | (package | |
3689 | (name "r-dtw") | |
fa859675 | 3690 | (version "1.21-3") |
bf025ff6 RW |
3691 | (source |
3692 | (origin | |
3693 | (method url-fetch) | |
3694 | (uri (cran-uri "dtw" version)) | |
3695 | (sha256 | |
3696 | (base32 | |
fa859675 | 3697 | "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s")))) |
bf025ff6 RW |
3698 | (build-system r-build-system) |
3699 | (propagated-inputs `(("r-proxy" ,r-proxy))) | |
3700 | (home-page "http://dtw.r-forge.r-project.org/") | |
3701 | (synopsis "Dynamic Time Warping Algorithms") | |
3702 | (description "This package provides a comprehensive implementation of | |
3703 | @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the | |
3704 | optimal (least cumulative distance) alignment between points of two time | |
3705 | series. Common DTW variants covered include local (slope) and global (window) | |
3706 | constraints, subsequence matches, arbitrary distance definitions, | |
3707 | normalizations, minimum variance matching, and so on.") | |
3708 | (license license:gpl2+))) | |
15ef07f0 RW |
3709 | |
3710 | (define-public r-sdmtools | |
3711 | (package | |
3712 | (name "r-sdmtools") | |
670a0101 | 3713 | (version "1.1-221.2") |
15ef07f0 RW |
3714 | (source |
3715 | (origin | |
3716 | (method url-fetch) | |
3717 | (uri (cran-uri "SDMTools" version)) | |
3718 | (sha256 | |
3719 | (base32 | |
670a0101 | 3720 | "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh")))) |
15ef07f0 RW |
3721 | (properties `((upstream-name . "SDMTools"))) |
3722 | (build-system r-build-system) | |
3723 | (propagated-inputs `(("r-r-utils" ,r-r-utils))) | |
3724 | (home-page "http://www.rforge.net/SDMTools/") | |
3725 | (synopsis "Species distribution modelling tools") | |
9c98e0e7 | 3726 | (description "This package provides a set of tools for post processing |
15ef07f0 RW |
3727 | the outcomes of species distribution modeling exercises. It includes novel |
3728 | methods for comparing models and tracking changes in distributions through | |
3729 | time. It further includes methods for visualizing outcomes, selecting | |
3730 | thresholds, calculating measures of accuracy and landscape fragmentation | |
3731 | statistics, etc.") | |
3732 | (license license:gpl3+))) | |
ae3f2079 RW |
3733 | |
3734 | (define-public r-scatterplot3d | |
3735 | (package | |
3736 | (name "r-scatterplot3d") | |
5ade82bb | 3737 | (version "0.3-41") |
ae3f2079 RW |
3738 | (source |
3739 | (origin | |
3740 | (method url-fetch) | |
3741 | (uri (cran-uri "scatterplot3d" version)) | |
3742 | (sha256 | |
3743 | (base32 | |
5ade82bb | 3744 | "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc")))) |
ae3f2079 | 3745 | (build-system r-build-system) |
e9960d8c | 3746 | (home-page "https://cran.r-project.org/web/packages/scatterplot3d/") |
ae3f2079 RW |
3747 | (synopsis "3D scatter plot") |
3748 | (description "This package provides an implementation of scatter plots for | |
3749 | plotting. a three dimensional point cloud.") | |
3750 | (license license:gpl2))) | |
f90018e5 RW |
3751 | |
3752 | (define-public r-ggridges | |
3753 | (package | |
3754 | (name "r-ggridges") | |
16a39c2d | 3755 | (version "0.5.1") |
f90018e5 RW |
3756 | (source |
3757 | (origin | |
3758 | (method url-fetch) | |
3759 | (uri (cran-uri "ggridges" version)) | |
3760 | (sha256 | |
3761 | (base32 | |
16a39c2d | 3762 | "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01")))) |
f90018e5 RW |
3763 | (build-system r-build-system) |
3764 | (propagated-inputs | |
3765 | `(("r-ggplot2" ,r-ggplot2) | |
3766 | ("r-plyr" ,r-plyr) | |
0edd2fd1 RW |
3767 | ("r-scales" ,r-scales) |
3768 | ("r-withr" ,r-withr))) | |
f90018e5 RW |
3769 | (home-page "https://github.com/clauswilke/ggridges") |
3770 | (synopsis "Ridgeline plots in ggplot2") | |
3771 | (description | |
3772 | "Ridgeline plots provide a convenient way of visualizing changes in | |
3773 | distributions over time or space. This package enables the creation of such | |
3774 | plots in @code{ggplot2}.") | |
3775 | (license license:gpl2))) | |
007f6d98 RW |
3776 | |
3777 | (define-public r-ggjoy | |
3778 | (package | |
3779 | (name "r-ggjoy") | |
c36745cf | 3780 | (version "0.4.1") |
007f6d98 RW |
3781 | (source |
3782 | (origin | |
3783 | (method url-fetch) | |
3784 | (uri (cran-uri "ggjoy" version)) | |
3785 | (sha256 | |
3786 | (base32 | |
c36745cf | 3787 | "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) |
007f6d98 RW |
3788 | (build-system r-build-system) |
3789 | (propagated-inputs | |
3790 | `(("r-ggplot2" ,r-ggplot2) | |
3791 | ("r-ggridges" ,r-ggridges))) | |
3792 | (home-page "https://github.com/clauswilke/ggjoy") | |
3793 | (synopsis "Joyplots in ggplot2") | |
3794 | (description "Joyplots provide a convenient way of visualizing changes in | |
3795 | distributions over time or space. This package enables the creation of such | |
3796 | plots in @code{ggplot2}.") | |
3797 | (license license:gpl2))) | |
2976f304 RW |
3798 | |
3799 | (define-public r-cli | |
3800 | (package | |
3801 | (name "r-cli") | |
59ed55df | 3802 | (version "2.0.0") |
2976f304 RW |
3803 | (source |
3804 | (origin | |
3805 | (method url-fetch) | |
3806 | (uri (cran-uri "cli" version)) | |
3807 | (sha256 | |
3808 | (base32 | |
59ed55df | 3809 | "1gv3zqdipj29ivkw5dsi1qdlra7q4lcrcqvlg9fns7d670yglfki")))) |
2976f304 RW |
3810 | (build-system r-build-system) |
3811 | (propagated-inputs | |
3812 | `(("r-assertthat" ,r-assertthat) | |
59ed55df RW |
3813 | ("r-crayon" ,r-crayon) |
3814 | ("r-fansi" ,r-fansi) | |
3815 | ("r-glue" ,r-glue))) | |
2976f304 RW |
3816 | (home-page "https://github.com/r-lib/cli#readme") |
3817 | (synopsis "Helpers for developing command line interfaces") | |
3818 | (description "This package provides a suite of tools designed to build | |
3819 | attractive command line interfaces (CLIs). It includes tools for drawing | |
3820 | rules, boxes, trees, and Unicode symbols with ASCII alternatives.") | |
3821 | (license license:expat))) | |
55577393 RW |
3822 | |
3823 | (define-public r-argparser | |
3824 | (package | |
3825 | (name "r-argparser") | |
4d6ccb00 | 3826 | (version "0.6") |
55577393 RW |
3827 | (source |
3828 | (origin | |
3829 | (method url-fetch) | |
3830 | (uri (cran-uri "argparser" version)) | |
3831 | (sha256 | |
3832 | (base32 | |
4d6ccb00 | 3833 | "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x")))) |
55577393 RW |
3834 | (build-system r-build-system) |
3835 | (home-page "https://bitbucket.org/djhshih/argparser") | |
3836 | (synopsis "Command-line argument parser") | |
3837 | (description | |
3838 | "This package provides a cross-platform command-line argument parser | |
3839 | written purely in R with no external dependencies. It is useful with the | |
3840 | Rscript front-end and facilitates turning an R script into an executable | |
3841 | script.") | |
3842 | (license license:gpl3+))) | |
a3257d42 RW |
3843 | |
3844 | (define-public r-debugme | |
3845 | (package | |
3846 | (name "r-debugme") | |
3847 | (version "1.1.0") | |
3848 | (source | |
3849 | (origin | |
3850 | (method url-fetch) | |
3851 | (uri (cran-uri "debugme" version)) | |
3852 | (sha256 | |
3853 | (base32 | |
3854 | "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) | |
3855 | (build-system r-build-system) | |
3856 | (propagated-inputs `(("r-crayon" ,r-crayon))) | |
3857 | (home-page "https://github.com/r-lib/debugme#readme") | |
3858 | (synopsis "Debug R packages") | |
3859 | (description | |
3860 | "This package allows the user to specify debug messages as special string | |
3861 | constants, and control debugging of packages via environment variables.") | |
3862 | (license license:expat))) | |
2058e37d RW |
3863 | |
3864 | (define-public r-processx | |
3865 | (package | |
3866 | (name "r-processx") | |
503d5b5a | 3867 | (version "3.4.1") |
2058e37d RW |
3868 | (source |
3869 | (origin | |
3870 | (method url-fetch) | |
3871 | (uri (cran-uri "processx" version)) | |
3872 | (sha256 | |
3873 | (base32 | |
503d5b5a | 3874 | "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi")))) |
2058e37d RW |
3875 | (build-system r-build-system) |
3876 | (propagated-inputs | |
0e87bf01 RW |
3877 | `(("r-ps" ,r-ps) |
3878 | ("r-r6" ,r-r6))) | |
2058e37d RW |
3879 | (home-page "https://github.com/r-lib/processx3") |
3880 | (synopsis "Execute and control system processes") | |
3881 | (description | |
3882 | "This package provides portable tools to run system processes in the | |
3883 | background. It can check if a background process is running; wait on a | |
3884 | background process to finish; get the exit status of finished processes; kill | |
3885 | background processes and their children; restart processes. It can read the | |
3886 | standard output and error of the processes, using non-blocking connections. | |
3887 | @code{processx} can poll a process for standard output or error, with a | |
3888 | timeout. It can also poll several processes at once.") | |
3889 | (license license:expat))) | |
f285346a RW |
3890 | |
3891 | (define-public r-tsp | |
3892 | (package | |
3893 | (name "r-tsp") | |
130314d8 | 3894 | (version "1.1-7") |
f285346a RW |
3895 | (source |
3896 | (origin | |
3897 | (method url-fetch) | |
3898 | (uri (cran-uri "TSP" version)) | |
3899 | (sha256 | |
3900 | (base32 | |
130314d8 | 3901 | "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb")))) |
f285346a RW |
3902 | (properties `((upstream-name . "TSP"))) |
3903 | (build-system r-build-system) | |
3904 | (propagated-inputs `(("r-foreach" ,r-foreach))) | |
3905 | (home-page "https://cran.r-project.org/web/packages/TSP/") | |
3906 | (synopsis "Traveling salesperson problem (TSP)") | |
3907 | (description "This package provides basic infrastructure and some | |
3908 | algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the | |
3909 | traveling salesman problem).") | |
3910 | (license license:gpl3))) | |
ffb59bce RW |
3911 | |
3912 | (define-public r-qap | |
3913 | (package | |
3914 | (name "r-qap") | |
3915 | (version "0.1-1") | |
3916 | (source | |
3917 | (origin | |
3918 | (method url-fetch) | |
3919 | (uri (cran-uri "qap" version)) | |
3920 | (sha256 | |
3921 | (base32 | |
3922 | "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) | |
3923 | (build-system r-build-system) | |
3924 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 3925 | (home-page "https://cran.r-project.org/web/packages/qap/") |
ffb59bce RW |
3926 | (synopsis "Heuristics for the quadratic assignment problem (QAP)") |
3927 | (description "This package implements heuristics for the @dfn{quadratic | |
3928 | assignment problem} (QAP). Currently only a simulated annealing heuristic is | |
3929 | available.") | |
3930 | (license license:gpl3))) | |
7fe49f2a RW |
3931 | |
3932 | (define-public r-gclus | |
3933 | (package | |
3934 | (name "r-gclus") | |
111516f9 | 3935 | (version "1.3.2") |
7fe49f2a RW |
3936 | (source |
3937 | (origin | |
3938 | (method url-fetch) | |
3939 | (uri (cran-uri "gclus" version)) | |
3940 | (sha256 | |
3941 | (base32 | |
111516f9 | 3942 | "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) |
7fe49f2a RW |
3943 | (build-system r-build-system) |
3944 | (propagated-inputs `(("r-cluster" ,r-cluster))) | |
d062957a | 3945 | (home-page "https://cran.r-project.org/web/packages/gclus/") |
7fe49f2a RW |
3946 | (synopsis "Clustering graphics") |
3947 | (description "This package orders panels in scatterplot matrices and | |
3948 | parallel coordinate displays by some merit index. It contains various indices | |
3949 | of merit, ordering functions, and enhanced versions of @code{pairs} and | |
3950 | @code{parcoord} which color panels according to their merit level.") | |
3951 | (license license:gpl2+))) | |
8e5e26d2 RW |
3952 | |
3953 | (define-public r-webshot | |
3954 | (package | |
3955 | (name "r-webshot") | |
3d391d2d | 3956 | (version "0.5.2") |
8e5e26d2 RW |
3957 | (source |
3958 | (origin | |
3959 | (method url-fetch) | |
3960 | (uri (cran-uri "webshot" version)) | |
3961 | (sha256 | |
3962 | (base32 | |
3d391d2d | 3963 | "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi")))) |
8e5e26d2 RW |
3964 | (build-system r-build-system) |
3965 | (propagated-inputs | |
8871a513 RW |
3966 | `(("r-callr" ,r-callr) |
3967 | ("r-jsonlite" ,r-jsonlite) | |
3968 | ("r-magrittr" ,r-magrittr))) | |
8e5e26d2 RW |
3969 | (home-page "https://github.com/wch/webshot/") |
3970 | (synopsis "Take screenshots of web pages") | |
3971 | (description | |
3972 | "Webshot makes it easy to take screenshots of web pages from within R. | |
3973 | It can also run Shiny applications locally and take screenshots of the | |
3974 | application; and it can render and screenshot static as well as interactive R | |
3975 | Markdown documents.") | |
3976 | (license license:gpl2))) | |
2e9d187b RW |
3977 | |
3978 | (define-public r-seriation | |
3979 | (package | |
3980 | (name "r-seriation") | |
bd8710b4 | 3981 | (version "1.2-8") |
2e9d187b RW |
3982 | (source |
3983 | (origin | |
3984 | (method url-fetch) | |
3985 | (uri (cran-uri "seriation" version)) | |
3986 | (sha256 | |
3987 | (base32 | |
bd8710b4 | 3988 | "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk")))) |
2e9d187b RW |
3989 | (build-system r-build-system) |
3990 | (propagated-inputs | |
3991 | `(("r-cluster" ,r-cluster) | |
3992 | ("r-colorspace" ,r-colorspace) | |
3993 | ("r-dendextend" ,r-dendextend) | |
3994 | ("r-gclus" ,r-gclus) | |
3995 | ("r-gplots" ,r-gplots) | |
3996 | ("r-mass" ,r-mass) | |
3997 | ("r-qap" ,r-qap) | |
3998 | ("r-registry" ,r-registry) | |
3999 | ("r-tsp" ,r-tsp))) | |
4000 | (native-inputs `(("gfortran" ,gfortran))) | |
4001 | (home-page "http://s2.smu.edu/IDA/seriation/") | |
4002 | (synopsis "Infrastructure for ordering objects using seriation") | |
4003 | (description | |
4004 | "This package provides infrastructure for seriation with an | |
4005 | implementation of several seriation/sequencing techniques to reorder matrices, | |
4006 | dissimilarity matrices, and dendrograms. It also provides (optimally) | |
4007 | reordered heatmaps, color images and clustering visualizations like | |
4008 | dissimilarity plots, and visual assessment of cluster tendency plots (VAT and | |
4009 | iVAT).") | |
4010 | (license license:gpl3))) | |
e9e78d2c | 4011 | |
f6d2b45c RW |
4012 | (define-public r-xfun |
4013 | (package | |
4014 | (name "r-xfun") | |
58fb4f32 | 4015 | (version "0.11") |
f6d2b45c RW |
4016 | (source |
4017 | (origin | |
4018 | (method url-fetch) | |
4019 | (uri (cran-uri "xfun" version)) | |
4020 | (sha256 | |
58fb4f32 | 4021 | (base32 "0dncw6bqkal7nyarrrrj9arxy0y3nkdzmrbibcjh84m1cxd4phiw")))) |
f6d2b45c RW |
4022 | (build-system r-build-system) |
4023 | (home-page "https://github.com/yihui/xfun") | |
4024 | (synopsis "Miscellaneous functions") | |
4025 | (description | |
4026 | "This package provides miscellaneous functions commonly used in other | |
4027 | packages maintained by Yihui Xie.") | |
4028 | (license license:expat))) | |
f2442968 RW |
4029 | |
4030 | (define-public r-utf8 | |
4031 | (package | |
4032 | (name "r-utf8") | |
65ea783f | 4033 | (version "1.1.4") |
f2442968 RW |
4034 | (source |
4035 | (origin | |
4036 | (method url-fetch) | |
4037 | (uri (cran-uri "utf8" version)) | |
4038 | (sha256 | |
4039 | (base32 | |
65ea783f | 4040 | "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) |
f2442968 RW |
4041 | (build-system r-build-system) |
4042 | (home-page "https://github.com/patperry/r-utf8") | |
4043 | (synopsis "Unicode text processing") | |
4044 | (description | |
4045 | "This package provides tools to process and print UTF-8 encoded | |
4046 | international text (Unicode). Input, validate, normalize, encode, format, and | |
4047 | display.") | |
4048 | (license license:asl2.0))) | |
c555ccab | 4049 | |
c87a3358 RW |
4050 | (define-public r-zeallot |
4051 | (package | |
4052 | (name "r-zeallot") | |
4053 | (version "0.1.0") | |
4054 | (source | |
4055 | (origin | |
4056 | (method url-fetch) | |
4057 | (uri (cran-uri "zeallot" version)) | |
4058 | (sha256 | |
4059 | (base32 | |
4060 | "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3")))) | |
4061 | (build-system r-build-system) | |
4062 | (home-page "https://github.com/nteetor/zeallot") | |
4063 | (synopsis "Multiple, unpacking, and destructuring assignment") | |
4064 | (description | |
4065 | "This package provides a @code{%<-%} operator to perform multiple, | |
4066 | unpacking, and destructuring assignment in R. The operator unpacks the | |
4067 | right-hand side of an assignment into multiple values and assigns these values | |
4068 | to variables on the left-hand side of the assignment.") | |
4069 | (license license:expat))) | |
4070 | ||
6004bc1a RW |
4071 | (define-public r-vctrs |
4072 | (package | |
4073 | (name "r-vctrs") | |
bdf552ee | 4074 | (version "0.2.1") |
6004bc1a RW |
4075 | (source |
4076 | (origin | |
4077 | (method url-fetch) | |
4078 | (uri (cran-uri "vctrs" version)) | |
4079 | (sha256 | |
4080 | (base32 | |
bdf552ee | 4081 | "0rlwjfvvhv3s5mj4lqhwlqwddpizyp46i1qbcvw0mzb5q8b0nkz0")))) |
6004bc1a RW |
4082 | (build-system r-build-system) |
4083 | (propagated-inputs | |
4084 | `(("r-backports" ,r-backports) | |
4085 | ("r-digest" ,r-digest) | |
56444d18 | 4086 | ("r-ellipsis" ,r-ellipsis) |
6004bc1a RW |
4087 | ("r-glue" ,r-glue) |
4088 | ("r-rlang" ,r-rlang) | |
4089 | ("r-zeallot" ,r-zeallot))) | |
4090 | (home-page "https://github.com/r-lib/vctrs") | |
4091 | (synopsis "Vector helpers") | |
4092 | (description | |
4093 | "There are three main goals to the @code{vctrs} package: | |
4094 | ||
4095 | @enumerate | |
4096 | @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to | |
4097 | @code{length()} and @code{class()}. These definitions are paired with a | |
4098 | framework for type-coercion and size-recycling. | |
4099 | @item To define type- and size-stability as desirable function properties, use | |
4100 | them to analyse existing base function, and to propose better alternatives. | |
4101 | This work has been particularly motivated by thinking about the ideal | |
4102 | properties of @code{c()}, @code{ifelse()}, and @code{rbind()}. | |
4103 | @item To provide a new @code{vctr} base class that makes it easy to create new | |
4104 | S3 vectors. @code{vctrs} provides methods for many base generics in terms of | |
4105 | a few new @code{vctrs} generics, making implementation considerably simpler | |
4106 | and more robust. | |
4107 | @end enumerate\n") | |
4108 | (license license:gpl3))) | |
4109 | ||
c555ccab RW |
4110 | (define-public r-pillar |
4111 | (package | |
4112 | (name "r-pillar") | |
cd2652f6 | 4113 | (version "1.4.3") |
c555ccab RW |
4114 | (source |
4115 | (origin | |
4116 | (method url-fetch) | |
4117 | (uri (cran-uri "pillar" version)) | |
4118 | (sha256 | |
4119 | (base32 | |
cd2652f6 | 4120 | "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss")))) |
c555ccab RW |
4121 | (build-system r-build-system) |
4122 | (propagated-inputs | |
4123 | `(("r-cli" ,r-cli) | |
4124 | ("r-crayon" ,r-crayon) | |
6f5b157e | 4125 | ("r-fansi" ,r-fansi) |
c555ccab | 4126 | ("r-rlang" ,r-rlang) |
33ba8135 RW |
4127 | ("r-utf8" ,r-utf8) |
4128 | ("r-vctrs" ,r-vctrs))) | |
c555ccab RW |
4129 | (home-page "https://github.com/r-lib/pillar") |
4130 | (synopsis "Coloured formatting for columns") | |
4131 | (description | |
4132 | "This package provides a @code{pillar} generic designed for formatting | |
4133 | columns of data using the full range of colours provided by modern | |
4134 | terminals.") | |
4135 | (license license:gpl3))) | |
1c791925 RW |
4136 | |
4137 | (define-public r-uuid | |
4138 | (package | |
4139 | (name "r-uuid") | |
4140 | (version "0.1-2") | |
4141 | (source | |
4142 | (origin | |
4143 | (method url-fetch) | |
4144 | (uri (cran-uri "uuid" version)) | |
4145 | (sha256 | |
4146 | (base32 | |
4147 | "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx")))) | |
4148 | (build-system r-build-system) | |
4149 | (home-page "http://www.rforge.net/uuid") | |
4150 | (synopsis "Tools for generating and handling of UUIDs") | |
4151 | (description | |
4152 | "This package provides tools for generating and handling of | |
4153 | @dfn{Universally Unique Identifiers} (UUIDs).") | |
4154 | (license license:expat))) | |
846f4c23 RW |
4155 | |
4156 | (define-public r-tinytex | |
4157 | (package | |
4158 | (name "r-tinytex") | |
a8e8a10a | 4159 | (version "0.18") |
846f4c23 RW |
4160 | (source |
4161 | (origin | |
4162 | (method url-fetch) | |
4163 | (uri (cran-uri "tinytex" version)) | |
4164 | (sha256 | |
4165 | (base32 | |
a8e8a10a | 4166 | "04mpbhadixbxmnazj0q6cj973cajchscvyh1k6a5b3qk26dp5krr")))) |
846f4c23 | 4167 | (build-system r-build-system) |
8b0701d9 TGR |
4168 | (propagated-inputs |
4169 | `(("r-xfun" ,r-xfun))) | |
846f4c23 RW |
4170 | (home-page "https://github.com/yihui/tinytex") |
4171 | (synopsis "Helper functions for TeX Live and compiling LaTeX documents") | |
4172 | (description | |
4173 | "This package provides helper functions to install and maintain the LaTeX | |
4174 | distribution named TinyTeX, a lightweight, cross-platform, portable, and | |
4175 | easy-to-maintain version of TeX Live. This package also contains helper | |
4176 | functions to compile LaTeX documents, and install missing LaTeX packages | |
4177 | automatically.") | |
4178 | (license license:expat))) | |
4376166b | 4179 | |
5f4565b1 RW |
4180 | (define-public r-network |
4181 | (package | |
4182 | (name "r-network") | |
a477a5c3 | 4183 | (version "1.16.0") |
5f4565b1 RW |
4184 | (source |
4185 | (origin | |
4186 | (method url-fetch) | |
4187 | (uri (cran-uri "network" version)) | |
4188 | (sha256 | |
4189 | (base32 | |
a477a5c3 | 4190 | "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2")))) |
5f4565b1 | 4191 | (build-system r-build-system) |
75cbc800 RW |
4192 | (propagated-inputs |
4193 | `(("r-magrittr" ,r-magrittr) | |
4194 | ("r-tibble" ,r-tibble))) | |
40862677 | 4195 | (home-page "https://statnet.org/") |
5f4565b1 RW |
4196 | (synopsis "Classes for relational data") |
4197 | (description | |
4198 | "This package provides tools to create and modify network objects. The | |
4199 | @code{network} class can represent a range of relational data types, and | |
4200 | supports arbitrary vertex/edge/graph attributes.") | |
4201 | (license license:gpl2+))) | |
07a2f34d RW |
4202 | |
4203 | (define-public r-statnet-common | |
4204 | (package | |
4205 | (name "r-statnet-common") | |
f7f65cba | 4206 | (version "4.3.0") |
07a2f34d RW |
4207 | (source |
4208 | (origin | |
4209 | (method url-fetch) | |
4210 | (uri (cran-uri "statnet.common" version)) | |
4211 | (sha256 | |
4212 | (base32 | |
f7f65cba | 4213 | "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3")))) |
07a2f34d RW |
4214 | (properties |
4215 | `((upstream-name . "statnet.common"))) | |
4216 | (build-system r-build-system) | |
1268a995 RW |
4217 | (propagated-inputs |
4218 | `(("r-coda" ,r-coda))) | |
40862677 | 4219 | (home-page "https://statnet.org") |
07a2f34d RW |
4220 | (synopsis "R scripts and utilities used by the Statnet software") |
4221 | (description "This package provides non-statistical utilities used by the | |
4222 | software developed by the Statnet Project.") | |
4223 | (license license:gpl3))) | |
1088744d | 4224 | |
5d387030 NB |
4225 | (define-public r-statcheck |
4226 | (package | |
4227 | (name "r-statcheck") | |
4228 | (version "1.3.0") | |
4229 | (source | |
4230 | (origin | |
4231 | (method url-fetch) | |
4232 | (uri (cran-uri "statcheck" version)) | |
4233 | (sha256 | |
4234 | (base32 | |
4235 | "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp")))) | |
4236 | (build-system r-build-system) | |
4237 | (propagated-inputs | |
4238 | `(("r-ggplot2" ,r-ggplot2) | |
4239 | ("r-plyr" ,r-plyr) | |
4240 | ("r-rmarkdown" ,r-rmarkdown))) | |
4241 | (home-page "https://cran.r-project.org/web/packages/statcheck/") | |
4242 | (synopsis "Extract statistics from articles and recompute p-values") | |
4243 | (description "This package can automatically extract statistical | |
4244 | null-hypothesis significant testing (NHST) results from articles and recompute | |
4245 | the p-values based on the reported test statistic and degrees of freedom to | |
4246 | detect possible inconsistencies.") | |
4247 | (license license:gpl2))) | |
4248 | ||
1088744d RW |
4249 | (define-public r-sna |
4250 | (package | |
4251 | (name "r-sna") | |
2beb585c | 4252 | (version "2.5") |
1088744d RW |
4253 | (source |
4254 | (origin | |
4255 | (method url-fetch) | |
4256 | (uri (cran-uri "sna" version)) | |
4257 | (sha256 | |
4258 | (base32 | |
2beb585c | 4259 | "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k")))) |
1088744d RW |
4260 | (build-system r-build-system) |
4261 | (propagated-inputs | |
4262 | `(("r-network" ,r-network) | |
4263 | ("r-statnet-common" ,r-statnet-common))) | |
40862677 | 4264 | (home-page "https://statnet.org") |
1088744d RW |
4265 | (synopsis "Tools for social network analysis") |
4266 | (description | |
4267 | "This package provides a range of tools for social network analysis, | |
4268 | including node and graph-level indices, structural distance and covariance | |
4269 | methods, structural equivalence detection, network regression, random graph | |
4270 | generation, and 2D/3D network visualization.") | |
4271 | (license license:gpl2+))) | |
93c21ddc | 4272 | |
151965fa RW |
4273 | (define-public r-tfisher |
4274 | (package | |
4275 | (name "r-tfisher") | |
4276 | (version "0.2.0") | |
4277 | (source | |
4278 | (origin | |
4279 | (method url-fetch) | |
4280 | (uri (cran-uri "TFisher" version)) | |
4281 | (sha256 | |
4282 | (base32 | |
4283 | "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx")))) | |
4284 | (properties `((upstream-name . "TFisher"))) | |
4285 | (build-system r-build-system) | |
4286 | (propagated-inputs | |
4287 | `(("r-matrix" ,r-matrix) | |
4288 | ("r-mvtnorm" ,r-mvtnorm) | |
4289 | ("r-sn" ,r-sn))) | |
4290 | (home-page "https://cran.r-project.org/web/packages/TFisher/") | |
4291 | (synopsis "Optimal thresholding Fisher's p-value combination method") | |
4292 | (description | |
4293 | "This package provides the @dfn{cumulative distribution function} (CDF), | |
4294 | quantile, and statistical power calculator for a collection of thresholding | |
4295 | Fisher's p-value combination methods, including Fisher's p-value combination | |
4296 | method, truncated product method and, in particular, soft-thresholding | |
4297 | Fisher's p-value combination method which is proven to be optimal in some | |
4298 | context of signal detection. The p-value calculator for the omnibus version | |
4299 | of these tests are also included.") | |
4300 | (license license:gpl2))) | |
4301 | ||
93c21ddc RW |
4302 | (define-public r-ttr |
4303 | (package | |
4304 | (name "r-ttr") | |
6e963260 | 4305 | (version "0.23-6") |
93c21ddc RW |
4306 | (source |
4307 | (origin | |
4308 | (method url-fetch) | |
4309 | (uri (cran-uri "TTR" version)) | |
4310 | (sha256 | |
4311 | (base32 | |
6e963260 | 4312 | "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg")))) |
93c21ddc RW |
4313 | (properties `((upstream-name . "TTR"))) |
4314 | (build-system r-build-system) | |
4315 | (propagated-inputs | |
4316 | `(("r-curl" ,r-curl) | |
4317 | ("r-xts" ,r-xts) | |
4318 | ("r-zoo" ,r-zoo))) | |
93c21ddc RW |
4319 | (home-page "https://github.com/joshuaulrich/TTR") |
4320 | (synopsis "Technical trading rules") | |
4321 | (description | |
4322 | "This package provides functions and data to construct technical trading | |
4323 | rules with R.") | |
4324 | (license license:gpl2))) | |
0b64332c RW |
4325 | |
4326 | (define-public r-leaps | |
4327 | (package | |
4328 | (name "r-leaps") | |
4329 | (version "3.0") | |
4330 | (source | |
4331 | (origin | |
4332 | (method url-fetch) | |
4333 | (uri (cran-uri "leaps" version)) | |
4334 | (sha256 | |
4335 | (base32 | |
4336 | "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m")))) | |
4337 | (build-system r-build-system) | |
4338 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4339 | (home-page "https://cran.r-project.org/web/packages/leaps/") |
0b64332c RW |
4340 | (synopsis "Regression subset selection") |
4341 | (description | |
4342 | "This package provides tools for regression subset selection, including | |
4343 | exhaustive search.") | |
4344 | (license license:gpl2+))) | |
d3cb62e5 RW |
4345 | |
4346 | (define-public r-splus2r | |
4347 | (package | |
4348 | (name "r-splus2r") | |
4349 | (version "1.2-2") | |
4350 | (source | |
4351 | (origin | |
4352 | (method url-fetch) | |
4353 | (uri (cran-uri "splus2R" version)) | |
4354 | (sha256 | |
4355 | (base32 | |
4356 | "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz")))) | |
4357 | (properties `((upstream-name . "splus2R"))) | |
4358 | (build-system r-build-system) | |
4359 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4360 | (home-page "https://cran.r-project.org/web/packages/splus2R/") |
d3cb62e5 RW |
4361 | (synopsis "Supplemental S-PLUS functionality in R") |
4362 | (description | |
4363 | "Currently there are many functions in S-PLUS that are missing in R. To | |
4364 | facilitate the conversion of S-PLUS packages to R packages, this package | |
4365 | provides some missing S-PLUS functionality in R.") | |
4366 | (license license:gpl2))) | |
034ac9d6 RW |
4367 | |
4368 | (define-public r-ifultools | |
4369 | (package | |
4370 | (name "r-ifultools") | |
d8787b33 | 4371 | (version "2.0-5") |
034ac9d6 RW |
4372 | (source |
4373 | (origin | |
4374 | (method url-fetch) | |
4375 | (uri (cran-uri "ifultools" version)) | |
4376 | (sha256 | |
4377 | (base32 | |
d8787b33 | 4378 | "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j")))) |
034ac9d6 RW |
4379 | (build-system r-build-system) |
4380 | (propagated-inputs | |
4381 | `(("r-mass" ,r-mass) | |
4382 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 4383 | (home-page "https://cran.r-project.org/web/packages/ifultools/") |
034ac9d6 RW |
4384 | (synopsis "Insightful research tools") |
4385 | (description "This package provides C code used by the wmtsa, fractal, and | |
4386 | sapa R packages.") | |
4387 | (license license:gpl2))) | |
0be7effe RW |
4388 | |
4389 | (define-public r-sapa | |
4390 | (package | |
4391 | (name "r-sapa") | |
4392 | (version "2.0-2") | |
4393 | (source | |
4394 | (origin | |
4395 | (method url-fetch) | |
4396 | (uri (cran-uri "sapa" version)) | |
4397 | (sha256 | |
4398 | (base32 | |
4399 | "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds")))) | |
4400 | (build-system r-build-system) | |
4401 | (propagated-inputs | |
4402 | `(("r-ifultools" ,r-ifultools) | |
4403 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 4404 | (home-page "https://cran.r-project.org/web/packages/sapa/") |
0be7effe RW |
4405 | (synopsis "Spectral analysis for physical applications") |
4406 | (description "This package provides software for the book Spectral | |
4407 | Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, | |
4408 | Cambridge University Press, 1993.") | |
4409 | (license license:gpl2))) | |
dceb1592 | 4410 | |
3a4c6288 RW |
4411 | (define-public r-aggregation |
4412 | (package | |
4413 | (name "r-aggregation") | |
4414 | (version "1.0.1") | |
4415 | (source | |
4416 | (origin | |
4417 | (method url-fetch) | |
4418 | (uri (cran-uri "aggregation" version)) | |
4419 | (sha256 | |
4420 | (base32 | |
4421 | "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46")))) | |
4422 | (build-system r-build-system) | |
4423 | (home-page "https://cran.r-project.org/web/packages/aggregation/") | |
4424 | (synopsis "Methods for p-value aggregation") | |
4425 | (description | |
4426 | "This package contains functionality for performing the following methods | |
4427 | of p-value aggregation: Fisher's method, the Lancaster method (weighted | |
4428 | Fisher's method), and Sidak correction.") | |
4429 | (license license:gpl3))) | |
4430 | ||
dceb1592 RW |
4431 | (define-public r-quantmod |
4432 | (package | |
4433 | (name "r-quantmod") | |
22b2d8b9 | 4434 | (version "0.4-15") |
dceb1592 RW |
4435 | (source |
4436 | (origin | |
4437 | (method url-fetch) | |
4438 | (uri (cran-uri "quantmod" version)) | |
4439 | (sha256 | |
4440 | (base32 | |
22b2d8b9 | 4441 | "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky")))) |
dceb1592 RW |
4442 | (build-system r-build-system) |
4443 | (propagated-inputs | |
4444 | `(("r-curl" ,r-curl) | |
4445 | ("r-ttr" ,r-ttr) | |
4446 | ("r-xts" ,r-xts) | |
4447 | ("r-zoo" ,r-zoo))) | |
d062957a | 4448 | (home-page "https://cran.r-project.org/web/packages/quantmod/") |
dceb1592 RW |
4449 | (synopsis "Quantitative financial modelling framework") |
4450 | (description "This package provides a quantitative financial modelling | |
4451 | framework to allow users to specify, build, trade, and analyse quantitative | |
4452 | financial trading strategies.") | |
4453 | (license license:gpl3))) | |
b6dc3255 RW |
4454 | |
4455 | (define-public r-tseries | |
4456 | (package | |
4457 | (name "r-tseries") | |
9ce3d17e | 4458 | (version "0.10-47") |
b6dc3255 RW |
4459 | (source |
4460 | (origin | |
4461 | (method url-fetch) | |
4462 | (uri (cran-uri "tseries" version)) | |
4463 | (sha256 | |
4464 | (base32 | |
9ce3d17e | 4465 | "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0")))) |
b6dc3255 RW |
4466 | (build-system r-build-system) |
4467 | (propagated-inputs | |
4468 | `(("r-quadprog" ,r-quadprog) | |
4469 | ("r-quantmod" ,r-quantmod) | |
4470 | ("r-zoo" ,r-zoo))) | |
4471 | (native-inputs | |
4472 | `(("gfortran" ,gfortran))) | |
d062957a | 4473 | (home-page "https://cran.r-project.org/web/packages/tseries/") |
b6dc3255 RW |
4474 | (synopsis "Time series analysis and computational finance") |
4475 | (description | |
4476 | "This package provides functions relating to time series analysis and | |
4477 | computational finance.") | |
4478 | (license license:gpl2))) | |
a2c079a7 RW |
4479 | |
4480 | (define-public r-wmtsa | |
4481 | (package | |
4482 | (name "r-wmtsa") | |
4483 | (version "2.0-3") | |
4484 | (source | |
4485 | (origin | |
4486 | (method url-fetch) | |
4487 | (uri (cran-uri "wmtsa" version)) | |
4488 | (sha256 | |
4489 | (base32 | |
4490 | "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) | |
4491 | (build-system r-build-system) | |
4492 | (propagated-inputs | |
4493 | `(("r-ifultools" ,r-ifultools) | |
4494 | ("r-mass" ,r-mass) | |
4495 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 4496 | (home-page "https://cran.r-project.org/web/packages/wmtsa/") |
a2c079a7 RW |
4497 | (synopsis "Wavelet methods for time series analysis") |
4498 | (description | |
4499 | "This package provides software to accompany the book \"Wavelet Methods | |
4500 | for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge | |
4501 | University Press, 2000.") | |
4502 | (license license:gpl2))) | |
4993a02a RW |
4503 | |
4504 | (define-public r-tsa | |
4505 | (package | |
4506 | (name "r-tsa") | |
1fe9919a | 4507 | (version "1.2") |
4993a02a RW |
4508 | (source |
4509 | (origin | |
4510 | (method url-fetch) | |
4511 | (uri (cran-uri "TSA" version)) | |
4512 | (sha256 | |
4513 | (base32 | |
1fe9919a | 4514 | "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q")))) |
4993a02a RW |
4515 | (properties `((upstream-name . "TSA"))) |
4516 | (build-system r-build-system) | |
4517 | (propagated-inputs | |
4518 | `(("r-leaps" ,r-leaps) | |
4519 | ("r-locfit" ,r-locfit) | |
1fe9919a | 4520 | ("r-mgcv" ,r-mgcv))) |
4993a02a RW |
4521 | (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm") |
4522 | (synopsis "Time series analysis") | |
4523 | (description | |
4524 | "This package contains R functions and datasets detailed in the book | |
4525 | \"Time Series Analysis with Applications in R (second edition)\" by Jonathan | |
4526 | Cryer and Kung-Sik Chan.") | |
4527 | (license license:gpl2+))) | |
19da7fe3 RW |
4528 | |
4529 | (define-public r-extradistr | |
4530 | (package | |
4531 | (name "r-extradistr") | |
e0cd8f73 | 4532 | (version "1.8.11") |
19da7fe3 RW |
4533 | (source |
4534 | (origin | |
4535 | (method url-fetch) | |
4536 | (uri (cran-uri "extraDistr" version)) | |
4537 | (sha256 | |
4538 | (base32 | |
e0cd8f73 | 4539 | "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3")))) |
19da7fe3 RW |
4540 | (properties `((upstream-name . "extraDistr"))) |
4541 | (build-system r-build-system) | |
4542 | (propagated-inputs | |
4543 | `(("r-rcpp" ,r-rcpp))) | |
4544 | (home-page "https://github.com/twolodzko/extraDistr") | |
4545 | (synopsis "Additional univariate and multivariate distributions") | |
4546 | (description | |
4547 | "This package implements density, distribution functions, quantile | |
4548 | functions and random generation functions for a large number of univariate and | |
4549 | multivariate distributions.") | |
4550 | (license license:gpl2))) | |
5b25bc55 RW |
4551 | |
4552 | (define-public r-fractal | |
4553 | (package | |
4554 | (name "r-fractal") | |
4555 | (version "2.0-4") | |
4556 | (source | |
4557 | (origin | |
4558 | (method url-fetch) | |
4559 | (uri (cran-uri "fractal" version)) | |
4560 | (sha256 | |
4561 | (base32 | |
4562 | "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) | |
4563 | (build-system r-build-system) | |
4564 | (propagated-inputs | |
4565 | `(("r-ifultools" ,r-ifultools) | |
4566 | ("r-mass" ,r-mass) | |
4567 | ("r-sapa" ,r-sapa) | |
4568 | ("r-scatterplot3d" ,r-scatterplot3d) | |
4569 | ("r-splus2r" ,r-splus2r) | |
4570 | ("r-wmtsa" ,r-wmtsa))) | |
d062957a | 4571 | (home-page "https://cran.r-project.org/web/packages/fractal/") |
5b25bc55 RW |
4572 | (synopsis "Fractal time series modeling and analysis") |
4573 | (description | |
4574 | "This package provides tools for stochastic fractal and deterministic | |
4575 | chaotic time series analysis.") | |
4576 | (license license:gpl2))) | |
6615a364 RW |
4577 | |
4578 | (define-public r-urca | |
4579 | (package | |
4580 | (name "r-urca") | |
4581 | (version "1.3-0") | |
4582 | (source | |
4583 | (origin | |
4584 | (method url-fetch) | |
4585 | (uri (cran-uri "urca" version)) | |
4586 | (sha256 | |
4587 | (base32 | |
4588 | "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732")))) | |
4589 | (build-system r-build-system) | |
4590 | (propagated-inputs `(("r-nlme" ,r-nlme))) | |
4591 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4592 | (home-page "https://cran.r-project.org/web/packages/urca/") |
6615a364 RW |
4593 | (synopsis "Unit root and cointegration tests for time series data") |
4594 | (description | |
4595 | "This package provides unit root and cointegration tests encountered in | |
4596 | applied econometric analysis.") | |
4597 | (license license:gpl2+))) | |
d32e5724 RW |
4598 | |
4599 | (define-public r-cubature | |
4600 | (package | |
4601 | (name "r-cubature") | |
75f021f4 | 4602 | (version "2.0.4") |
d32e5724 RW |
4603 | (source |
4604 | (origin | |
4605 | (method url-fetch) | |
4606 | (uri (cran-uri "cubature" version)) | |
4607 | (sha256 | |
4608 | (base32 | |
75f021f4 | 4609 | "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r")))) |
d32e5724 RW |
4610 | (build-system r-build-system) |
4611 | (propagated-inputs | |
4612 | `(("r-rcpp" ,r-rcpp))) | |
4613 | (home-page "https://github.com/bnaras/cubature") | |
4614 | (synopsis "Adaptive multivariate integration over hypercubes") | |
4615 | (description | |
4616 | "This package is an R wrapper around the cubature C library for adaptive | |
4617 | multivariate integration over hypercubes. This version provides both | |
4618 | @code{hcubature} and @code{pcubature} routines in addition to a vector | |
4619 | interface.") | |
4620 | ;; The included cubature C library is released under GPLv2+, but the | |
4621 | ;; wrapper declares the license to be GPLv3+. | |
4622 | (license (list license:gpl2+ license:gpl3+)))) | |
7531ee84 RW |
4623 | |
4624 | (define-public r-trend | |
4625 | (package | |
4626 | (name "r-trend") | |
cd4abb6d | 4627 | (version "1.1.1") |
7531ee84 RW |
4628 | (source |
4629 | (origin | |
4630 | (method url-fetch) | |
4631 | (uri (cran-uri "trend" version)) | |
4632 | (sha256 | |
4633 | (base32 | |
cd4abb6d | 4634 | "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q")))) |
7531ee84 RW |
4635 | (build-system r-build-system) |
4636 | (propagated-inputs | |
4637 | `(("r-extradistr" ,r-extradistr))) | |
4638 | (native-inputs | |
4639 | `(("gfortran" ,gfortran))) | |
d062957a | 4640 | (home-page "https://cran.r-project.org/web/packages/trend/") |
7531ee84 RW |
4641 | (synopsis "Non-parametric trend tests and change-point detection") |
4642 | (description | |
4643 | "The analysis of environmental data often requires the detection of | |
4644 | trends and change-points. This package includes tests for trend | |
4645 | detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) | |
4646 | Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) | |
4647 | Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman | |
4648 | correlation trend test), change-point detection (Lanzante's test procedures, | |
4649 | Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal | |
4650 | Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency | |
4651 | Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two | |
4652 | sample Robust Rank-Order Distributional Test.") | |
4653 | (license license:gpl3))) | |
f96eda90 RW |
4654 | |
4655 | (define-public r-expm | |
4656 | (package | |
4657 | (name "r-expm") | |
a11d29b4 | 4658 | (version "0.999-4") |
f96eda90 RW |
4659 | (source |
4660 | (origin | |
4661 | (method url-fetch) | |
4662 | (uri (cran-uri "expm" version)) | |
4663 | (sha256 | |
4664 | (base32 | |
a11d29b4 | 4665 | "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q")))) |
f96eda90 RW |
4666 | (build-system r-build-system) |
4667 | (propagated-inputs `(("r-matrix" ,r-matrix))) | |
4668 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4669 | (home-page "https://r-forge.r-project.org/projects/expm/") |
f96eda90 RW |
4670 | (synopsis "Tools for matrix exponentials and related quantities") |
4671 | (description | |
4672 | "This package provides tools for the computation of the matrix | |
4673 | exponential, logarithm, square root, and related quantities.") | |
4674 | (license license:gpl2+))) | |
68b6a67e RW |
4675 | |
4676 | (define-public r-complexplus | |
4677 | (package | |
4678 | (name "r-complexplus") | |
4679 | (version "2.1") | |
4680 | (source | |
4681 | (origin | |
4682 | (method url-fetch) | |
4683 | (uri (cran-uri "complexplus" version)) | |
4684 | (sha256 | |
4685 | (base32 | |
4686 | "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) | |
4687 | (build-system r-build-system) | |
4688 | (propagated-inputs | |
4689 | `(("r-expm" ,r-expm) | |
4690 | ("r-matrix" ,r-matrix))) | |
d062957a | 4691 | (home-page "https://cran.r-project.org/web/packages/complexplus/") |
68b6a67e RW |
4692 | (synopsis "Functions of complex or real variables") |
4693 | (description | |
4694 | "This package extends several functions to the complex domain, including | |
4695 | the matrix exponential and logarithm, and the determinant.") | |
4696 | (license license:gpl2))) | |
7b81a7ea RW |
4697 | |
4698 | (define-public r-phontools | |
4699 | (package | |
4700 | (name "r-phontools") | |
4701 | (version "0.2-2.1") | |
4702 | (source | |
4703 | (origin | |
4704 | (method url-fetch) | |
4705 | (uri (cran-uri "phonTools" version)) | |
4706 | (sha256 | |
4707 | (base32 | |
4708 | "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7")))) | |
4709 | (properties `((upstream-name . "phonTools"))) | |
4710 | (build-system r-build-system) | |
4711 | (home-page "http://www.santiagobarreda.com/rscripts.html") | |
4712 | (synopsis "Tools for phonetic and acoustic analyses") | |
4713 | (description | |
4714 | "This package contains tools for the organization, display, and analysis | |
4715 | of the sorts of data frequently encountered in phonetics research and | |
4716 | experimentation, including the easy creation of IPA vowel plots, and the | |
4717 | creation and manipulation of WAVE audio files.") | |
4718 | (license license:bsd-2))) | |
d976454c RW |
4719 | |
4720 | (define-public r-np | |
4721 | (package | |
4722 | (name "r-np") | |
02c57c01 | 4723 | (version "0.60-9") |
d976454c RW |
4724 | (source |
4725 | (origin | |
4726 | (method url-fetch) | |
4727 | (uri (cran-uri "np" version)) | |
4728 | (sha256 | |
4729 | (base32 | |
02c57c01 | 4730 | "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy")))) |
d976454c RW |
4731 | (build-system r-build-system) |
4732 | (propagated-inputs | |
4733 | `(("r-boot" ,r-boot) | |
4734 | ("r-cubature" ,r-cubature) | |
65d66b3e | 4735 | ("r-quadprog" ,r-quadprog) |
d976454c RW |
4736 | ("r-quantreg" ,r-quantreg))) |
4737 | (home-page "https://github.com/JeffreyRacine/R-Package-np") | |
4738 | (synopsis "Non-parametric kernel smoothing methods for mixed data types") | |
4739 | (description "This package provides non-parametric (and semi-parametric) | |
4740 | kernel methods that seamlessly handle a mix of continuous, unordered, and | |
4741 | ordered factor data types.") | |
4742 | ;; Any version of the GPL. | |
4743 | (license license:gpl3+))) | |
2a112be0 RW |
4744 | |
4745 | (define-public r-powerplus | |
4746 | (package | |
4747 | (name "r-powerplus") | |
4748 | (version "3.1") | |
4749 | (source | |
4750 | (origin | |
4751 | (method url-fetch) | |
4752 | (uri (cran-uri "powerplus" version)) | |
4753 | (sha256 | |
4754 | (base32 | |
4755 | "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) | |
4756 | (build-system r-build-system) | |
4757 | (propagated-inputs | |
4758 | `(("r-complexplus" ,r-complexplus) | |
4759 | ("r-expm" ,r-expm) | |
4760 | ("r-mass" ,r-mass) | |
4761 | ("r-matrix" ,r-matrix) | |
4762 | ("r-phontools" ,r-phontools))) | |
d062957a | 4763 | (home-page "https://cran.r-project.org/web/packages/powerplus/") |
2a112be0 RW |
4764 | (synopsis "Exponentiation operations") |
4765 | (description | |
4766 | "This package provides tools for the computation of matrix and scalar | |
4767 | exponentiation.") | |
4768 | (license license:gpl2))) | |
021caafa | 4769 | |
0c836f58 RW |
4770 | (define-public r-egg |
4771 | (package | |
4772 | (name "r-egg") | |
4773 | (version "0.4.5") | |
4774 | (source | |
4775 | (origin | |
4776 | (method url-fetch) | |
4777 | (uri (cran-uri "egg" version)) | |
4778 | (sha256 | |
4779 | (base32 | |
4780 | "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m")))) | |
4781 | (properties `((upstream-name . "egg"))) | |
4782 | (build-system r-build-system) | |
4783 | (propagated-inputs | |
4784 | `(("r-ggplot2" ,r-ggplot2) | |
4785 | ("r-gridextra" ,r-gridextra) | |
4786 | ("r-gtable" ,r-gtable))) | |
4787 | (home-page "https://cran.r-project.org/web/packages/egg") | |
4788 | (synopsis "Extensions for ggplot2") | |
4789 | (description | |
4790 | "This package provides miscellaneous functions to help customize ggplot2 | |
4791 | objects. High-level functions are provided to post-process ggplot2 layouts | |
4792 | and allow alignment between plot panels, as well as setting panel sizes to | |
4793 | fixed values. Other functions include a custom @code{geom}, and helper | |
4794 | functions to enforce symmetric scales or add tags to facetted plots.") | |
4795 | (license license:gpl3))) | |
4796 | ||
021caafa RW |
4797 | (define-public r-heatmaply |
4798 | (package | |
4799 | (name "r-heatmaply") | |
91a38c56 | 4800 | (version "1.0.0") |
021caafa RW |
4801 | (source |
4802 | (origin | |
4803 | (method url-fetch) | |
4804 | (uri (cran-uri "heatmaply" version)) | |
4805 | (sha256 | |
4806 | (base32 | |
91a38c56 | 4807 | "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g")))) |
021caafa RW |
4808 | (build-system r-build-system) |
4809 | (propagated-inputs | |
4810 | `(("r-assertthat" ,r-assertthat) | |
4811 | ("r-colorspace" ,r-colorspace) | |
4812 | ("r-dendextend" ,r-dendextend) | |
91a38c56 | 4813 | ("r-egg" ,r-egg) |
021caafa | 4814 | ("r-ggplot2" ,r-ggplot2) |
021caafa RW |
4815 | ("r-htmlwidgets" ,r-htmlwidgets) |
4816 | ("r-magrittr" ,r-magrittr) | |
4817 | ("r-plotly" ,r-plotly) | |
4818 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4819 | ("r-reshape2" ,r-reshape2) | |
4820 | ("r-scales" ,r-scales) | |
4821 | ("r-seriation" ,r-seriation) | |
4822 | ("r-viridis" ,r-viridis) | |
4823 | ("r-webshot" ,r-webshot))) | |
4824 | (home-page "https://cran.r-project.org/package=heatmaply") | |
4825 | (synopsis "Interactive cluster heat maps using plotly") | |
4826 | (description | |
4827 | "This package enables you to create interactive cluster heatmaps that can | |
4828 | be saved as a stand-alone HTML file, embedded in R Markdown documents or in a | |
4829 | Shiny app, and made available in the RStudio viewer pane. Hover the mouse | |
4830 | pointer over a cell to show details or drag a rectangle to zoom. A heatmap is | |
4831 | a popular graphical method for visualizing high-dimensional data, in which a | |
4832 | table of numbers is encoded as a grid of colored cells. The rows and columns | |
4833 | of the matrix are ordered to highlight patterns and are often accompanied by | |
4834 | dendrograms.") | |
4835 | ;; Either version of the license. | |
4836 | (license (list license:gpl2 license:gpl3)))) | |
b2dc4cb4 | 4837 | |
ff939ef4 RW |
4838 | (define-public r-h5 |
4839 | (package | |
4840 | (name "r-h5") | |
4841 | (version "0.9.9") | |
4842 | (source | |
4843 | (origin | |
4844 | (method url-fetch) | |
4845 | (uri (cran-uri "h5" version)) | |
4846 | (sha256 | |
4847 | (base32 | |
4848 | "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) | |
4849 | (build-system r-build-system) | |
4850 | (inputs | |
4851 | `(("zlib" ,zlib) | |
4852 | ("hdf5" ,hdf5))) | |
4853 | (native-inputs | |
4854 | `(("which" ,which))) | |
4855 | (propagated-inputs | |
4856 | `(("r-rcpp" ,r-rcpp))) | |
4857 | (home-page "https://github.com/mannau/h5") | |
4858 | (synopsis "Interface to the HDF5 Library") | |
4859 | (description | |
4860 | "This package provides an S4 interface to the HDF5 library supporting | |
4861 | fast storage and retrieval of R-objects like vectors, matrices and arrays to | |
4862 | binary files in a language independent format. The HDF5 format can therefore | |
4863 | be used as an alternative to R's save/load mechanism. Since h5 is able to | |
4864 | access only subsets of stored data it can also handle data sets which do not | |
4865 | fit into memory.") | |
4866 | (license license:bsd-2))) | |
4867 | ||
b2dc4cb4 RW |
4868 | (define-public r-cgdsr |
4869 | (package | |
4870 | (name "r-cgdsr") | |
dacf52e0 | 4871 | (version "1.3.0") |
b2dc4cb4 RW |
4872 | (source |
4873 | (origin | |
4874 | (method url-fetch) | |
4875 | (uri (cran-uri "cgdsr" version)) | |
4876 | (sha256 | |
4877 | (base32 | |
dacf52e0 | 4878 | "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) |
b2dc4cb4 RW |
4879 | (build-system r-build-system) |
4880 | (propagated-inputs | |
dacf52e0 RW |
4881 | `(("r-httr" ,r-httr) |
4882 | ("r-r-methodss3" ,r-r-methodss3) | |
b2dc4cb4 RW |
4883 | ("r-r-oo" ,r-r-oo))) |
4884 | (home-page "https://github.com/cBioPortal/cgdsr") | |
4885 | (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") | |
4886 | (description | |
4887 | "This package provides a basic set of R functions for querying the Cancer | |
4888 | Genomics Data Server (CGDS), hosted by the Computational Biology Center at | |
4889 | Memorial-Sloan-Kettering Cancer Center (MSKCC).") | |
4890 | (license license:lgpl3))) | |
a00968b7 RW |
4891 | |
4892 | (define-public r-import | |
4893 | (package | |
4894 | (name "r-import") | |
4895 | (version "1.1.0") | |
4896 | (source | |
4897 | (origin | |
4898 | (method url-fetch) | |
4899 | (uri (cran-uri "import" version)) | |
4900 | (sha256 | |
4901 | (base32 | |
4902 | "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji")))) | |
4903 | (build-system r-build-system) | |
4904 | (home-page "https://github.com/smbache/import") | |
4905 | (synopsis "Import mechanism for R") | |
4906 | (description | |
4907 | "This is an alternative mechanism for importing objects from packages. | |
4908 | The syntax allows for importing multiple objects from a package with a single | |
4909 | command in an expressive way. The import package bridges some of the gap | |
4910 | between using @code{library} (or @code{require}) and direct (single-object) | |
4911 | imports. Furthermore the imported objects are not placed in the current | |
4912 | environment. It is also possible to import objects from stand-alone @code{.R} | |
4913 | files.") | |
4914 | (license license:expat))) | |
5d9b82ac RW |
4915 | |
4916 | (define-public r-shinyace | |
4917 | (package | |
4918 | (name "r-shinyace") | |
cd5d6e26 | 4919 | (version "0.4.1") |
5d9b82ac RW |
4920 | (source |
4921 | (origin | |
4922 | (method url-fetch) | |
4923 | (uri (cran-uri "shinyAce" version)) | |
4924 | (sha256 | |
4925 | (base32 | |
cd5d6e26 | 4926 | "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn")))) |
5d9b82ac RW |
4927 | (properties `((upstream-name . "shinyAce"))) |
4928 | (build-system r-build-system) | |
4929 | (propagated-inputs | |
e86d3cc5 RW |
4930 | `(("r-shiny" ,r-shiny) |
4931 | ("r-jsonlite" ,r-jsonlite))) | |
5d9b82ac RW |
4932 | (home-page "http://cran.r-project.org/web/packages/shinyAce") |
4933 | (synopsis "Ace editor bindings for Shiny") | |
4934 | (description | |
4935 | "This package provides Ace editor bindings to enable a rich text editing | |
4936 | environment within Shiny.") | |
4937 | (license license:expat))) | |
f64fea1d | 4938 | |
72032c9d RW |
4939 | (define-public r-base64url |
4940 | (package | |
4941 | (name "r-base64url") | |
4942 | (version "1.4") | |
4943 | (source | |
4944 | (origin | |
4945 | (method url-fetch) | |
4946 | (uri (cran-uri "base64url" version)) | |
4947 | (sha256 | |
4948 | (base32 | |
4949 | "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x")))) | |
4950 | (build-system r-build-system) | |
4951 | (propagated-inputs | |
4952 | `(("r-backports" ,r-backports))) | |
4953 | (home-page "https://github.com/mllg/base64url") | |
4954 | (synopsis "Fast and URL-safe base64 encoder and decoder") | |
4955 | (description | |
4956 | "This package provides a URL-safe base64 encoder and decoder. In | |
4957 | contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-}, | |
4958 | the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the | |
4959 | encoder does not fill the string with trailing @code{=}. The resulting | |
4960 | encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]} | |
4961 | and thus are safe to use in URLs or for file names. The package also comes | |
4962 | with a simple base32 encoder/decoder suited for case insensitive file | |
4963 | systems.") | |
4964 | (license license:gpl3))) | |
4965 | ||
f64fea1d RW |
4966 | (define-public r-radiant-data |
4967 | (package | |
4968 | (name "r-radiant-data") | |
a7146013 | 4969 | (version "1.0.6") |
f64fea1d RW |
4970 | (source |
4971 | (origin | |
4972 | (method url-fetch) | |
4973 | (uri (cran-uri "radiant.data" version)) | |
4974 | (sha256 | |
4975 | (base32 | |
a7146013 | 4976 | "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg")) |
f64fea1d RW |
4977 | (modules '((guix build utils))) |
4978 | (snippet | |
4979 | '(begin | |
4980 | ;; Delete files that are under CC-NC-SA. | |
4981 | (delete-file-recursively "inst/app/tools/help") | |
4982 | #t)))) | |
4983 | (properties `((upstream-name . "radiant.data"))) | |
4984 | (build-system r-build-system) | |
4985 | (propagated-inputs | |
4986 | `(("r-base64enc" ,r-base64enc) | |
4987 | ("r-broom" ,r-broom) | |
4988 | ("r-car" ,r-car) | |
4989 | ("r-curl" ,r-curl) | |
4990 | ("r-dplyr" ,r-dplyr) | |
4991 | ("r-dt" ,r-dt) | |
36dc3591 | 4992 | ("r-glue" ,r-glue) |
f64fea1d RW |
4993 | ("r-ggplot2" ,r-ggplot2) |
4994 | ("r-gridextra" ,r-gridextra) | |
4995 | ("r-import" ,r-import) | |
4996 | ("r-jsonlite" ,r-jsonlite) | |
4997 | ("r-knitr" ,r-knitr) | |
4998 | ("r-lubridate" ,r-lubridate) | |
4999 | ("r-magrittr" ,r-magrittr) | |
5000 | ("r-markdown" ,r-markdown) | |
36dc3591 | 5001 | ("r-plotly" ,r-plotly) |
f64fea1d RW |
5002 | ("r-psych" ,r-psych) |
5003 | ("r-readr" ,r-readr) | |
36dc3591 RW |
5004 | ("r-readxl" ,r-readxl) |
5005 | ("r-rlang" ,r-rlang) | |
f64fea1d RW |
5006 | ("r-rmarkdown" ,r-rmarkdown) |
5007 | ("r-rstudioapi" ,r-rstudioapi) | |
5008 | ("r-scales" ,r-scales) | |
5009 | ("r-shiny" ,r-shiny) | |
e5f9e9fa | 5010 | ("r-shinyfiles" ,r-shinyfiles) |
f64fea1d | 5011 | ("r-shinyace" ,r-shinyace) |
cb40b6eb | 5012 | ("r-stringi" ,r-stringi) |
f64fea1d | 5013 | ("r-tibble" ,r-tibble) |
36dc3591 RW |
5014 | ("r-tidyr" ,r-tidyr) |
5015 | ("r-writexl" ,r-writexl))) | |
f64fea1d RW |
5016 | (home-page "https://github.com/radiant-rstats/radiant.data") |
5017 | (synopsis "Data menu for Radiant: business analytics using R and Shiny") | |
5018 | (description | |
5019 | "The Radiant Data menu includes interfaces for loading, saving, viewing, | |
5020 | visualizing, summarizing, transforming, and combining data. It also contains | |
5021 | functionality to generate reproducible reports of the analyses conducted in | |
5022 | the application.") | |
5023 | (license license:agpl3))) | |
e2cafc24 RW |
5024 | |
5025 | (define-public r-algdesign | |
5026 | (package | |
5027 | (name "r-algdesign") | |
3e3fd3b0 | 5028 | (version "1.2.0") |
e2cafc24 RW |
5029 | (source |
5030 | (origin | |
5031 | (method url-fetch) | |
5032 | (uri (cran-uri "AlgDesign" version)) | |
5033 | (sha256 | |
3e3fd3b0 | 5034 | (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz")))) |
e2cafc24 RW |
5035 | (properties `((upstream-name . "AlgDesign"))) |
5036 | (build-system r-build-system) | |
5037 | (home-page "https://github.com/jvbraun/AlgDesign") | |
5038 | (synopsis "Algorithmic experimental design") | |
5039 | (description | |
5040 | "This package provides tools to calculate exact and approximate theory | |
5041 | experimental designs for D, A, and I criteria. Very large designs may be | |
5042 | created. Experimental designs may be blocked or blocked designs created from | |
5043 | a candidate list, using several criteria. The blocking can be done when whole | |
5044 | and within plot factors interact.") | |
5045 | (license license:gpl2+))) | |
35b0c051 RW |
5046 | |
5047 | (define-public r-signal | |
5048 | (package | |
5049 | (name "r-signal") | |
5050 | (version "0.7-6") | |
5051 | (source | |
5052 | (origin | |
5053 | (method url-fetch) | |
5054 | (uri (cran-uri "signal" version)) | |
5055 | (sha256 | |
5056 | (base32 | |
5057 | "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b")))) | |
5058 | (build-system r-build-system) | |
5059 | (propagated-inputs `(("r-mass" ,r-mass))) | |
5060 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 5061 | (home-page "https://cran.r-project.org/web/packages/signal/") |
35b0c051 RW |
5062 | (synopsis "Signal processing") |
5063 | (description | |
5064 | "This package provides a set of signal processing functions originally | |
5065 | written for Matlab and GNU Octave. It includes filter generation utilities, | |
5066 | filtering functions, resampling routines, and visualization of filter models. | |
5067 | It also includes interpolation functions.") | |
5068 | (license license:gpl2))) | |
db80dd4a | 5069 | |
3dab50d9 RW |
5070 | (define-public r-gsubfn |
5071 | (package | |
5072 | (name "r-gsubfn") | |
2acc0e5f | 5073 | (version "0.7") |
3dab50d9 RW |
5074 | (source |
5075 | (origin | |
5076 | (method url-fetch) | |
5077 | (uri (cran-uri "gsubfn" version)) | |
5078 | (sha256 | |
5079 | (base32 | |
2acc0e5f | 5080 | "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) |
3dab50d9 RW |
5081 | (build-system r-build-system) |
5082 | (propagated-inputs `(("r-proto" ,r-proto))) | |
5083 | (home-page "http://gsubfn.googlecode.com") | |
5084 | (synopsis "Utilities for strings and function arguments.") | |
5085 | (description | |
5086 | "This package provides @code{gsubfn} which is like @code{gsub} but can | |
5087 | take a replacement function or certain other objects instead of the | |
5088 | replacement string. Matches and back references are input to the replacement | |
5089 | function and replaced by the function output. @code{gsubfn} can be used to | |
5090 | split strings based on content rather than delimiters and for quasi-perl-style | |
5091 | string interpolation. The package also has facilities for translating | |
5092 | formulas to functions and allowing such formulas in function calls instead of | |
5093 | functions.") | |
5094 | (license license:gpl2+))) | |
3a563a41 RW |
5095 | |
5096 | (define-public r-sqldf | |
5097 | (package | |
5098 | (name "r-sqldf") | |
5099 | (version "0.4-11") | |
5100 | (source | |
5101 | (origin | |
5102 | (method url-fetch) | |
5103 | (uri (cran-uri "sqldf" version)) | |
5104 | (sha256 | |
5105 | (base32 | |
5106 | "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff")))) | |
5107 | (build-system r-build-system) | |
5108 | (propagated-inputs | |
5109 | `(("r-chron" ,r-chron) | |
5110 | ("r-dbi" ,r-dbi) | |
5111 | ("r-gsubfn" ,r-gsubfn) | |
5112 | ("r-proto" ,r-proto) | |
5113 | ("r-rsqlite" ,r-rsqlite))) | |
5114 | (home-page "https://github.com/ggrothendieck/sqldf") | |
5115 | (synopsis "Manipulate R data frames using SQL") | |
5116 | (description | |
5117 | "The @code{sqldf} function is typically passed a single argument which is | |
5118 | an SQL select statement where the table names are ordinary R data frame names. | |
5119 | @code{sqldf} transparently sets up a database, imports the data frames into | |
5120 | that database, performs the SQL statement and returns the result using a | |
5121 | heuristic to determine which class to assign to each column of the returned | |
5122 | data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be | |
5123 | used to read filtered files into R even if the original files are larger than | |
5124 | R itself can handle.") | |
5125 | (license license:gpl2))) | |
94e46cab RW |
5126 | |
5127 | (define-public r-abind | |
5128 | (package | |
5129 | (name "r-abind") | |
5130 | (version "1.4-5") | |
5131 | (source | |
5132 | (origin | |
5133 | (method url-fetch) | |
5134 | (uri (cran-uri "abind" version)) | |
5135 | (sha256 | |
5136 | (base32 | |
5137 | "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) | |
5138 | (build-system r-build-system) | |
d062957a | 5139 | (home-page "https://cran.r-project.org/web/packages/abind/") |
94e46cab RW |
5140 | (synopsis "Combine multidimensional arrays") |
5141 | (description | |
5142 | "This package provides tools to combine multidimensional arrays into a | |
5143 | single array. This is a generalization of @code{cbind} and @code{rbind}. It | |
5144 | works with vectors, matrices, and higher-dimensional arrays. It also provides | |
5145 | the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating, | |
5146 | extracting and replacing data in arrays.") | |
5147 | (license license:lgpl2.0+))) | |
fc784b66 RW |
5148 | |
5149 | (define-public r-prroc | |
5150 | (package | |
5151 | (name "r-prroc") | |
0430eb66 | 5152 | (version "1.3.1") |
fc784b66 RW |
5153 | (source |
5154 | (origin | |
5155 | (method url-fetch) | |
5156 | (uri (cran-uri "PRROC" version)) | |
5157 | (sha256 | |
5158 | (base32 | |
0430eb66 | 5159 | "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7")))) |
fc784b66 RW |
5160 | (properties `((upstream-name . "PRROC"))) |
5161 | (build-system r-build-system) | |
d062957a | 5162 | (home-page "https://cran.r-project.org/web/packages/PRROC/") |
fc784b66 RW |
5163 | (synopsis "Precision-Recall and ROC curves for weighted and unweighted data") |
5164 | (description | |
5165 | "This package computes the areas under the @dfn{precision-recall} (PR) | |
5166 | and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In | |
5167 | contrast to other implementations, the interpolation between points of the PR | |
5168 | curve is done by a non-linear piecewise function. In addition to the areas | |
5169 | under the curves, the curves themselves can also be computed and plotted by a | |
5170 | specific S3-method.") | |
5171 | (license license:gpl3))) | |
661bb51e RW |
5172 | |
5173 | (define-public r-vim | |
5174 | (package | |
5175 | (name "r-vim") | |
8b2c80b8 | 5176 | (version "4.8.0") |
661bb51e RW |
5177 | (source |
5178 | (origin | |
5179 | (method url-fetch) | |
5180 | (uri (cran-uri "VIM" version)) | |
5181 | (sha256 | |
5182 | (base32 | |
8b2c80b8 | 5183 | "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw")))) |
661bb51e RW |
5184 | (properties `((upstream-name . "VIM"))) |
5185 | (build-system r-build-system) | |
5186 | (propagated-inputs | |
5187 | `(("r-car" ,r-car) | |
5188 | ("r-colorspace" ,r-colorspace) | |
5189 | ("r-data-table" ,r-data-table) | |
5190 | ("r-e1071" ,r-e1071) | |
5191 | ("r-laeken" ,r-laeken) | |
5192 | ("r-mass" ,r-mass) | |
5193 | ("r-nnet" ,r-nnet) | |
8b2c80b8 | 5194 | ("r-ranger" ,r-ranger) |
661bb51e RW |
5195 | ("r-rcpp" ,r-rcpp) |
5196 | ("r-robustbase" ,r-robustbase) | |
5197 | ("r-sp" ,r-sp) | |
5198 | ("r-vcd" ,r-vcd))) | |
5199 | (home-page "https://github.com/alexkowa/VIM") | |
5200 | (synopsis "Visualization and imputation of missing values") | |
5201 | (description | |
5202 | "This package provides tools for the visualization of missing and/or | |
5203 | imputed values are introduced, which can be used for exploring the data and | |
5204 | the structure of the missing and/or imputed values. Depending on this | |
5205 | structure of the missing values, the corresponding methods may help to | |
5206 | identify the mechanism generating the missing values and allows to explore the | |
5207 | data including missing values. In addition, the quality of imputation can be | |
5208 | visually explored using various univariate, bivariate, multiple and | |
5209 | multivariate plot methods.") | |
5210 | (license license:gpl2+))) | |
d10b0952 RW |
5211 | |
5212 | (define-public r-fnn | |
5213 | (package | |
5214 | (name "r-fnn") | |
b9b10413 | 5215 | (version "1.1.3") |
d10b0952 RW |
5216 | (source |
5217 | (origin | |
5218 | (method url-fetch) | |
5219 | (uri (cran-uri "FNN" version)) | |
5220 | (sha256 | |
5221 | (base32 | |
b9b10413 | 5222 | "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny")))) |
d10b0952 RW |
5223 | (properties `((upstream-name . "FNN"))) |
5224 | (build-system r-build-system) | |
1b5905fe | 5225 | (home-page "https://cran.r-project.org/web/packages/FNN") |
d10b0952 RW |
5226 | (synopsis "Fast nearest neighbor search algorithms and applications") |
5227 | (description | |
5228 | "This package provides cover-tree and kd-tree fast k-nearest neighbor | |
5229 | search algorithms. Related applications including KNN classification, | |
5230 | regression and information measures are implemented.") | |
5231 | ;; The DESCRIPTION file erroneously states that GPL version 2.1 or | |
5232 | ;; later can be used. | |
5233 | (license license:gpl2+))) | |
be815dbd RW |
5234 | |
5235 | (define-public r-smoother | |
5236 | (package | |
5237 | (name "r-smoother") | |
5238 | (version "1.1") | |
5239 | (source | |
5240 | (origin | |
5241 | (method url-fetch) | |
5242 | (uri (cran-uri "smoother" version)) | |
5243 | (sha256 | |
5244 | (base32 | |
5245 | "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci")))) | |
5246 | (build-system r-build-system) | |
5247 | (propagated-inputs | |
5248 | `(("r-ttr" ,r-ttr))) | |
5249 | (home-page "http://cran.r-project.org/web/packages/smoother") | |
5250 | (synopsis "Functions relating to the smoothing of numerical data") | |
5251 | (description | |
5252 | "This package provides a collection of methods for smoothing numerical | |
5253 | data, commencing with a port of the Matlab gaussian window smoothing function. | |
5254 | In addition, several functions typically used in smoothing of financial data | |
5255 | are included.") | |
5256 | (license license:gpl2))) | |
0efd09ac RW |
5257 | |
5258 | (define-public r-riverplot | |
5259 | (package | |
5260 | (name "r-riverplot") | |
5261 | (version "0.6") | |
5262 | (source | |
5263 | (origin | |
5264 | (method url-fetch) | |
5265 | (uri (cran-uri "riverplot" version)) | |
5266 | (sha256 | |
5267 | (base32 | |
5268 | "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z")))) | |
5269 | (build-system r-build-system) | |
5270 | (home-page "https://logfc.wordpress.com") | |
5271 | (synopsis "Sankey or ribbon plots") | |
5272 | (description | |
5273 | "Sankey plots are a type of diagram that is convenient to illustrate how | |
5274 | flow of information, resources etc. separates and joins, much like observing | |
5275 | how rivers split and merge. For example, they can be used to compare | |
5276 | different clusterings. This package provides an implementation of Sankey | |
5277 | plots for R.") | |
5278 | (license license:gpl2+))) | |
c56739df SY |
5279 | |
5280 | (define-public r-dyn | |
5281 | (package | |
5282 | (name "r-dyn") | |
5283 | (version "0.2-9.6") | |
5284 | (source | |
5285 | (origin | |
5286 | (method url-fetch) | |
5287 | (uri (cran-uri "dyn" version)) | |
5288 | (sha256 | |
5289 | (base32 | |
5290 | "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb")))) | |
5291 | (build-system r-build-system) | |
5292 | (propagated-inputs | |
5293 | `(("r-zoo" ,r-zoo))) | |
5294 | (home-page "https://cran.r-project.org/web/packages/dyn") | |
5295 | (synopsis "Time series regression") | |
5296 | (description | |
5297 | "This package provides the dyn class interfaces @code{ts}, @code{irts}, | |
5298 | @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm}, | |
5299 | @code{loess}, @code{quantreg::rq}, @code{MASS::rlm}, | |
5300 | @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()}, | |
5301 | @code{randomForest::randomForest()} and other regression functions, allowing | |
5302 | those functions to be used with time series including specifications that may | |
5303 | contain lags, diffs and missing values.") | |
5304 | ;; Any GPL version. | |
5305 | (license license:gpl2+))) | |
24fa6bca SY |
5306 | |
5307 | (define-public r-catdap | |
5308 | (package | |
5309 | (name "r-catdap") | |
5310 | (version "1.3.4") | |
5311 | (source | |
5312 | (origin | |
5313 | (method url-fetch) | |
5314 | (uri (cran-uri "catdap" version)) | |
5315 | (sha256 | |
5316 | (base32 | |
5317 | "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2")))) | |
5318 | (build-system r-build-system) | |
5319 | (native-inputs | |
5320 | `(("gfortran" ,gfortran))) | |
5321 | (home-page "https://cran.r-project.org/web/packages/catdap/") | |
5322 | (synopsis "Tools for categorical data analysis") | |
5323 | (description | |
5324 | "This package provides functions for analyzing multivariate data. | |
5325 | Dependencies of the distribution of the specified variable (response | |
5326 | variable) to other variables (explanatory variables) are derived and | |
5327 | evaluated by the @dfn{Akaike Information Criterion} (AIC).") | |
5328 | (license license:gpl2+))) | |
96e22362 SS |
5329 | |
5330 | (define-public r-arules | |
5331 | (package | |
5332 | (name "r-arules") | |
2586cfd3 | 5333 | (version "1.6-4") |
96e22362 SS |
5334 | (source |
5335 | (origin | |
5336 | (method url-fetch) | |
5337 | (uri (cran-uri "arules" version)) | |
5338 | (sha256 | |
5339 | (base32 | |
2586cfd3 | 5340 | "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n")))) |
96e22362 SS |
5341 | (build-system r-build-system) |
5342 | (propagated-inputs | |
5343 | `(("r-matrix" ,r-matrix))) | |
5344 | (home-page "https://github.com/mhahsler/arules") | |
5345 | (synopsis "Mining association rules and frequent itemsets") | |
5346 | (description | |
5347 | "This package provides an infrastructure for representing, manipulating | |
5348 | and analyzing transaction data and patterns (frequent itemsets and association rules). | |
5349 | It also provides C implementations of the association mining algorithms Apriori | |
5350 | and Eclat.") | |
5351 | (license license:gpl3))) | |
1cde7467 KH |
5352 | |
5353 | (define-public r-parsedate | |
5354 | (package | |
5355 | (name "r-parsedate") | |
86ad5dbc | 5356 | (version "1.2.0") |
1cde7467 KH |
5357 | (source |
5358 | (origin | |
5359 | (method url-fetch) | |
5360 | (uri (cran-uri "parsedate" version)) | |
5361 | (sha256 | |
5362 | (base32 | |
86ad5dbc | 5363 | "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr")))) |
1cde7467 | 5364 | (build-system r-build-system) |
86ad5dbc RW |
5365 | (propagated-inputs |
5366 | `(("r-rematch2" ,r-rematch2))) | |
1cde7467 KH |
5367 | (home-page "https://github.com/gaborcsardi/parsedate") |
5368 | (synopsis | |
5369 | "Recognize and parse dates in various formats") | |
5370 | (description | |
5371 | "This package provides three functions for dealing with dates: | |
5372 | @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and | |
5373 | time formats, @code{parse_date} parses dates in unspecified formats, | |
5374 | and @code{format_iso_8601} formats a date in ISO 8601 format.") | |
5375 | (license license:gpl2))) | |
2a27c0bb SY |
5376 | |
5377 | (define-public r-abc-data | |
5378 | (package | |
5379 | (name "r-abc-data") | |
5380 | (version "1.0") | |
5381 | (source | |
5382 | (origin | |
5383 | (method url-fetch) | |
5384 | (uri (cran-uri "abc.data" version)) | |
5385 | (sha256 | |
5386 | (base32 | |
5387 | "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj")))) | |
5388 | (properties `((upstream-name . "abc.data"))) | |
5389 | (build-system r-build-system) | |
5390 | (home-page "https://cran.r-project.org/web/packages/abc.data/") | |
5391 | (synopsis "Data for Approximate Bayesian Computation (ABC) package") | |
5392 | (description | |
5393 | "This package contains data which are used by functions of the abc | |
5394 | package which implements several @dfn{Approximate Bayesian Computation} (ABC) | |
5395 | algorithms for performing parameter estimation, model selection, and | |
5396 | goodness-of-fit.") | |
5397 | (license license:gpl3+))) | |
82c8e0ae SY |
5398 | |
5399 | (define-public r-abc | |
5400 | (package | |
5401 | (name "r-abc") | |
5402 | (version "2.1") | |
5403 | (source | |
5404 | (origin | |
5405 | (method url-fetch) | |
5406 | (uri (cran-uri "abc" version)) | |
5407 | (sha256 | |
5408 | (base32 | |
5409 | "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) | |
5410 | (build-system r-build-system) | |
5411 | (propagated-inputs | |
5412 | `(("r-abc-data" ,r-abc-data) | |
5413 | ("r-locfit" ,r-locfit) | |
5414 | ("r-mass" ,r-mass) | |
5415 | ("r-nnet" ,r-nnet) | |
5416 | ("r-quantreg" ,r-quantreg))) | |
5417 | (home-page "https://cran.r-project.org/web/packages/abc/") | |
5418 | (synopsis "Tools for Approximate Bayesian Computation (ABC)") | |
5419 | (description | |
5420 | "This package implements several @dfn{Approximate Bayesian | |
5421 | Computation} (ABC) algorithms for performing parameter estimation, model | |
5422 | selection, and goodness-of-fit. Cross-validation tools are also available for | |
5423 | measuring the accuracy of ABC estimates, and to calculate the | |
5424 | misclassification probabilities of different models.") | |
5425 | (license license:gpl3+))) | |
4b1f7a3e | 5426 | |
d182828f RW |
5427 | (define-public r-zip |
5428 | (package | |
5429 | (name "r-zip") | |
59fd6915 | 5430 | (version "2.0.4") |
d182828f RW |
5431 | (source |
5432 | (origin | |
5433 | (method url-fetch) | |
5434 | (uri (cran-uri "zip" version)) | |
5435 | (sha256 | |
5436 | (base32 | |
59fd6915 | 5437 | "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb")))) |
d182828f RW |
5438 | (build-system r-build-system) |
5439 | (home-page "https://github.com/gaborcsardi/zip") | |
5440 | (synopsis "Cross-platform Zip compression") | |
5441 | (description | |
5442 | "This package provides a cross-platform Zip compression library for R. | |
5443 | It is a replacement for the @code{zip} function, that does not require any | |
5444 | additional external tools on any platform.") | |
5445 | (license license:cc0))) | |
5446 | ||
4b1f7a3e RW |
5447 | (define-public r-openxlsx |
5448 | (package | |
5449 | (name "r-openxlsx") | |
e8ae22a6 | 5450 | (version "4.1.4") |
4b1f7a3e RW |
5451 | (source |
5452 | (origin | |
5453 | (method url-fetch) | |
5454 | (uri (cran-uri "openxlsx" version)) | |
5455 | (sha256 | |
5456 | (base32 | |
e8ae22a6 | 5457 | "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7")))) |
4b1f7a3e | 5458 | (build-system r-build-system) |
a8b4677b RW |
5459 | (propagated-inputs |
5460 | `(("r-rcpp" ,r-rcpp) | |
383ab0da | 5461 | ("r-stringi" ,r-stringi) |
a8b4677b | 5462 | ("r-zip" ,r-zip))) |
4b1f7a3e RW |
5463 | (home-page "https://github.com/awalker89/openxlsx") |
5464 | (synopsis "Read, write and edit XLSX files") | |
5465 | (description | |
5466 | "This package simplifies the creation of Excel @code{.xlsx} files by | |
5467 | providing a high level interface to writing, styling and editing worksheets. | |
5468 | Through the use of Rcpp, read/write times are comparable to the @code{xlsx} | |
5469 | and @code{XLConnect} packages with the added benefit of removing the | |
5470 | dependency on Java.") | |
5471 | (license license:gpl3))) | |
c9920f25 RW |
5472 | |
5473 | (define-public r-rio | |
5474 | (package | |
5475 | (name "r-rio") | |
1417d5f1 | 5476 | (version "0.5.16") |
c9920f25 RW |
5477 | (source |
5478 | (origin | |
5479 | (method url-fetch) | |
5480 | (uri (cran-uri "rio" version)) | |
5481 | (sha256 | |
5482 | (base32 | |
1417d5f1 | 5483 | "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) |
c9920f25 RW |
5484 | (build-system r-build-system) |
5485 | (propagated-inputs | |
5486 | `(("r-curl" ,r-curl) | |
5487 | ("r-data-table" ,r-data-table) | |
5488 | ("r-foreign" ,r-foreign) | |
5489 | ("r-haven" ,r-haven) | |
5490 | ("r-openxlsx" ,r-openxlsx) | |
5491 | ("r-readxl" ,r-readxl) | |
5492 | ("r-tibble" ,r-tibble))) | |
5493 | (home-page "https://github.com/leeper/rio") | |
5494 | (synopsis "Swiss-army knife for data I/O") | |
5495 | (description | |
5496 | "This package provides streamlined data import and export infrastructure | |
5497 | by making assumptions that the user is probably willing to make: @code{import} | |
5498 | and @code{export} determine the data structure from the file extension, | |
5499 | reasonable defaults are used for data import and export (e.g., | |
5500 | @code{stringsAsFactors=FALSE}), web-based import is natively | |
5501 | supported (including from SSL/HTTPS), compressed files can be read directly | |
5502 | without explicit decompression, and fast import packages are used where | |
5503 | appropriate. An additional convenience function, @code{convert}, provides a | |
5504 | simple method for converting between file types.") | |
5505 | (license license:gpl2))) | |
08dac3d9 RW |
5506 | |
5507 | (define-public r-maptools | |
5508 | (package | |
5509 | (name "r-maptools") | |
27c2a6a1 | 5510 | (version "0.9-9") |
08dac3d9 RW |
5511 | (source |
5512 | (origin | |
5513 | (method url-fetch) | |
5514 | (uri (cran-uri "maptools" version)) | |
5515 | (sha256 | |
5516 | (base32 | |
27c2a6a1 | 5517 | "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9")))) |
08dac3d9 RW |
5518 | (build-system r-build-system) |
5519 | (propagated-inputs | |
5520 | `(("r-foreign" ,r-foreign) | |
5521 | ("r-lattice" ,r-lattice) | |
5522 | ("r-sp" ,r-sp))) | |
5523 | (home-page "http://r-forge.r-project.org/projects/maptools/") | |
5524 | (synopsis "Tools for reading and handling spatial objects") | |
5525 | (description | |
5526 | "This package provides a set of tools for manipulating and reading | |
5527 | geographic data, in particular ESRI Shapefiles. It includes binary access to | |
5528 | GSHHG shoreline files. The package also provides interface wrappers for | |
5529 | exchanging spatial objects with other R packages.") | |
5530 | ;; The C source files from shapelib are released under the Expat license. | |
5531 | ;; The R code is released under GPL version 2 or later. | |
5532 | (license (list license:gpl2+ | |
5533 | license:expat)))) | |
284179bb RW |
5534 | |
5535 | (define-public r-later | |
5536 | (package | |
5537 | (name "r-later") | |
ab99236e | 5538 | (version "1.0.0") |
284179bb RW |
5539 | (source |
5540 | (origin | |
5541 | (method url-fetch) | |
5542 | (uri (cran-uri "later" version)) | |
5543 | (sha256 | |
5544 | (base32 | |
ab99236e | 5545 | "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7")))) |
284179bb RW |
5546 | (build-system r-build-system) |
5547 | (propagated-inputs | |
5548 | `(("r-bh" ,r-bh) | |
5549 | ("r-rcpp" ,r-rcpp) | |
5550 | ("r-rlang" ,r-rlang))) | |
5551 | (home-page "https://github.com/r-lib/later") | |
5552 | (synopsis "Utilities for delaying function execution") | |
5553 | (description | |
5554 | "This package provides tools to execute arbitrary R or C functions some | |
5555 | time after the current time, after the R execution stack has emptied.") | |
5556 | (license license:gpl2+))) | |
d9d66ba9 RW |
5557 | |
5558 | (define-public r-promises | |
5559 | (package | |
5560 | (name "r-promises") | |
2e6ccd6c | 5561 | (version "1.1.0") |
d9d66ba9 RW |
5562 | (source |
5563 | (origin | |
5564 | (method url-fetch) | |
5565 | (uri (cran-uri "promises" version)) | |
5566 | (sha256 | |
5567 | (base32 | |
2e6ccd6c | 5568 | "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8")))) |
d9d66ba9 RW |
5569 | (build-system r-build-system) |
5570 | (propagated-inputs | |
5571 | `(("r-later" ,r-later) | |
5572 | ("r-magrittr" ,r-magrittr) | |
5573 | ("r-r6" ,r-r6) | |
5574 | ("r-rcpp" ,r-rcpp) | |
5575 | ("r-rlang" ,r-rlang))) | |
5576 | (home-page "https://rstudio.github.io/promises") | |
5577 | (synopsis "Abstractions for promise-based asynchronous programming") | |
5578 | (description | |
5579 | "This package provides fundamental abstractions for doing asynchronous | |
5580 | programming in R using promises. Asynchronous programming is useful for | |
5581 | allowing a single R process to orchestrate multiple tasks in the background | |
5582 | while also attending to something else. Semantics are similar to JavaScript | |
5583 | promises, but with a syntax that is idiomatic R.") | |
5584 | (license license:expat))) | |
3cf9ae2f RW |
5585 | |
5586 | (define-public r-dosnow | |
5587 | (package | |
5588 | (name "r-dosnow") | |
e3abc134 | 5589 | (version "1.0.18") |
3cf9ae2f RW |
5590 | (source |
5591 | (origin | |
5592 | (method url-fetch) | |
5593 | (uri (cran-uri "doSNOW" version)) | |
5594 | (sha256 | |
5595 | (base32 | |
e3abc134 | 5596 | "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh")))) |
3cf9ae2f RW |
5597 | (properties `((upstream-name . "doSNOW"))) |
5598 | (build-system r-build-system) | |
5599 | (propagated-inputs | |
5600 | `(("r-foreach" ,r-foreach) | |
5601 | ("r-iterators" ,r-iterators) | |
5602 | ("r-snow" ,r-snow))) | |
5603 | (home-page "https://cran.r-project.org/web/packages/doSNOW") | |
5604 | (synopsis "Foreach parallel adaptor for the snow package") | |
5605 | (description | |
5606 | "This package provides a parallel backend for the @code{%dopar%} function | |
5607 | using the @code{snow} package.") | |
5608 | (license license:gpl2))) | |
fdc3a05d RJ |
5609 | |
5610 | (define-public r-snowfall | |
5611 | (package | |
5612 | (name "r-snowfall") | |
5613 | (version "1.84-6.1") | |
5614 | (source (origin | |
5615 | (method url-fetch) | |
5616 | (uri (cran-uri "snowfall" version)) | |
5617 | (sha256 | |
5618 | (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) | |
5619 | (build-system r-build-system) | |
5620 | (propagated-inputs | |
5621 | `(("r-snow" ,r-snow))) | |
5622 | (home-page "http://cran.r-project.org/web/packages/snowfall/") | |
5623 | (synopsis "Easier cluster computing") | |
5624 | (description "This package is a usability wrapper around snow for easier | |
5625 | development of parallel R programs. This package offers e.g. extended error | |
5626 | checks, and additional functions. All functions work in sequential mode, too, | |
5627 | if no cluster is present or wished. The package is also designed as connector | |
5628 | to the cluster management tool @code{sfCluster}, but can also used without | |
5629 | it.") | |
5630 | (license license:gpl2+))) | |
e09d74ec | 5631 | |
94a8990f RW |
5632 | (define-public r-rappdirs |
5633 | (package | |
5634 | (name "r-rappdirs") | |
5635 | (version "0.3.1") | |
5636 | (source | |
5637 | (origin | |
5638 | (method url-fetch) | |
5639 | (uri (cran-uri "rappdirs" version)) | |
5640 | (sha256 | |
5641 | (base32 | |
5642 | "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g")))) | |
5643 | (build-system r-build-system) | |
5644 | (home-page "https://cran.r-project.org/web/packages/rappdirs/") | |
5645 | (synopsis "Determine where to save data, caches, and logs") | |
5646 | (description | |
5647 | "This package provides an easy way to determine which directories on the | |
5648 | user's computer should be used to save data, caches and logs. It is a port of | |
5649 | Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") | |
5650 | (license license:expat))) | |
2b47ebe1 | 5651 | |
a9b66019 RW |
5652 | (define-public r-renv |
5653 | (package | |
5654 | (name "r-renv") | |
98ce8a31 | 5655 | (version "0.9.2") |
a9b66019 RW |
5656 | (source |
5657 | (origin | |
5658 | (method url-fetch) | |
5659 | (uri (cran-uri "renv" version)) | |
5660 | (sha256 | |
5661 | (base32 | |
98ce8a31 | 5662 | "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr")))) |
a9b66019 RW |
5663 | (properties `((upstream-name . "renv"))) |
5664 | (build-system r-build-system) | |
5665 | (home-page "https://rstudio.github.io/renv") | |
5666 | (synopsis "Project environments") | |
5667 | (description | |
5668 | "This package provides a dependency management toolkit for R. Using | |
5669 | renv, you can create and manage project-local R libraries, save the state of | |
5670 | these libraries to a lockfile, and later restore your library as required. | |
5671 | Together, these tools can help make your projects more isolated, portable, and | |
5672 | reproducible.") | |
5673 | (license license:expat))) | |
5674 | ||
2b47ebe1 RW |
5675 | (define-public r-learnr |
5676 | (package | |
5677 | (name "r-learnr") | |
389f169a | 5678 | (version "0.10.0") |
2b47ebe1 RW |
5679 | (source |
5680 | (origin | |
5681 | (method url-fetch) | |
5682 | (uri (cran-uri "learnr" version)) | |
5683 | (sha256 | |
5684 | (base32 | |
389f169a | 5685 | "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6")))) |
2b47ebe1 RW |
5686 | (build-system r-build-system) |
5687 | (propagated-inputs | |
389f169a RW |
5688 | `(("r-checkmate" ,r-checkmate) |
5689 | ("r-ellipsis" ,r-ellipsis) | |
5690 | ("r-evaluate" ,r-evaluate) | |
2b47ebe1 RW |
5691 | ("r-htmltools" ,r-htmltools) |
5692 | ("r-htmlwidgets" ,r-htmlwidgets) | |
5693 | ("r-jsonlite" ,r-jsonlite) | |
5694 | ("r-knitr" ,r-knitr) | |
5695 | ("r-markdown" ,r-markdown) | |
5696 | ("r-rappdirs" ,r-rappdirs) | |
389f169a | 5697 | ("r-renv" ,r-renv) |
2b47ebe1 RW |
5698 | ("r-rmarkdown" ,r-rmarkdown) |
5699 | ("r-rprojroot" ,r-rprojroot) | |
5700 | ("r-shiny" ,r-shiny) | |
5701 | ("r-withr" ,r-withr))) | |
5702 | (home-page "https://rstudio.github.io/learnr/") | |
5703 | (synopsis "Interactive tutorials for R") | |
5704 | (description | |
5705 | "This package provides tools to create interactive tutorials using R | |
5706 | Markdown. Use a combination of narrative, figures, videos, exercises, and | |
5707 | quizzes to create self-paced tutorials for learning about R and R packages.") | |
5708 | (license license:asl2.0))) | |
12591673 RW |
5709 | |
5710 | (define-public r-analytics | |
5711 | (package | |
5712 | (name "r-analytics") | |
7a06cdfa | 5713 | (version "3.0") |
12591673 RW |
5714 | (source |
5715 | (origin | |
5716 | (method url-fetch) | |
5717 | (uri (cran-uri "analytics" version)) | |
5718 | (sha256 | |
5719 | (base32 | |
7a06cdfa | 5720 | "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) |
12591673 RW |
5721 | (build-system r-build-system) |
5722 | (propagated-inputs | |
5723 | `(("r-car" ,r-car) | |
5724 | ("r-cluster" ,r-cluster) | |
5725 | ("r-fractal" ,r-fractal) | |
5726 | ("r-lmtest" ,r-lmtest) | |
5727 | ("r-mass" ,r-mass) | |
5728 | ("r-np" ,r-np) | |
5729 | ("r-powerplus" ,r-powerplus) | |
5730 | ("r-robust" ,r-robust) | |
5731 | ("r-trend" ,r-trend) | |
5732 | ("r-tsa" ,r-tsa) | |
7a06cdfa RW |
5733 | ("r-urca" ,r-urca) |
5734 | ("r-vim" ,r-vim))) | |
12591673 RW |
5735 | (home-page "https://cran.r-project.org/web/packages/analytics/") |
5736 | (synopsis "Collection of data analysis tools") | |
5737 | (description | |
5738 | "This package is a collection of data analysis tools. It includes tools | |
5739 | for regression outlier detection in a fitted linear model, stationary | |
5740 | bootstrap using a truncated geometric distribution, a comprehensive test for | |
5741 | weak stationarity, column means by group, weighted biplots, and a heuristic to | |
5742 | obtain a better initial configuration in non-metric MDS.") | |
5743 | (license license:gpl2))) | |
9f56ceec RW |
5744 | |
5745 | (define-public r-reticulate | |
5746 | (package | |
5747 | (name "r-reticulate") | |
4aeb0a2b | 5748 | (version "1.14") |
9f56ceec RW |
5749 | (source |
5750 | (origin | |
5751 | (method url-fetch) | |
5752 | (uri (cran-uri "reticulate" version)) | |
5753 | (sha256 | |
5754 | (base32 | |
4aeb0a2b | 5755 | "0icb9zl9zlx75njv7y1dr450k0yw2n3q2jkr4nicnphdyfn69gkn")))) |
9f56ceec RW |
5756 | (build-system r-build-system) |
5757 | (inputs `(("python" ,python))) | |
5758 | (propagated-inputs | |
4aeb0a2b RW |
5759 | `(("r-rappdirs" ,r-rappdirs) |
5760 | ("r-jsonlite" ,r-jsonlite) | |
9f56ceec RW |
5761 | ("r-matrix" ,r-matrix) |
5762 | ("r-rcpp" ,r-rcpp))) | |
5763 | (home-page "https://github.com/rstudio/reticulate") | |
5764 | (synopsis "R interface to Python") | |
5765 | (description | |
5766 | "This package provides an interface from R to Python modules, classes, | |
5767 | and functions. When calling into Python, R data types are automatically | |
5768 | converted to their equivalent Python types. When values are returned from | |
5769 | Python to R they are converted back to R types.") | |
5770 | (license license:asl2.0))) | |
11de8673 RW |
5771 | |
5772 | (define-public r-bibtex | |
5773 | (package | |
5774 | (name "r-bibtex") | |
1d3c31a2 | 5775 | (version "0.4.2.1") |
11de8673 RW |
5776 | (source |
5777 | (origin | |
5778 | (method url-fetch) | |
5779 | (uri (cran-uri "bibtex" version)) | |
5780 | (sha256 | |
5781 | (base32 | |
1d3c31a2 | 5782 | "1ks1w59ldwmfd1sj8ap7smyhf8dhykv7xnwrl8z9xzkcfpv1rbc0")))) |
11de8673 RW |
5783 | (build-system r-build-system) |
5784 | (propagated-inputs `(("r-stringr" ,r-stringr))) | |
5785 | (home-page "https://github.com/romainfrancois/bibtex") | |
5786 | (synopsis "Bibtex parser") | |
5787 | (description "This package provides a utility for R to parse a bibtex | |
5788 | file.") | |
5789 | (license license:gpl2+))) | |
e67acae7 RW |
5790 | |
5791 | (define-public r-ggseqlogo | |
5792 | (package | |
5793 | (name "r-ggseqlogo") | |
5794 | (version "0.1") | |
5795 | (source | |
5796 | (origin | |
5797 | (method url-fetch) | |
5798 | (uri (cran-uri "ggseqlogo" version)) | |
5799 | (sha256 | |
5800 | (base32 | |
5801 | "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1")))) | |
5802 | (build-system r-build-system) | |
5803 | (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) | |
5804 | (home-page "https://github.com/omarwagih/ggseqlogo") | |
5805 | (synopsis "ggplot2 extension for drawing genetic sequence logos") | |
5806 | (description | |
5807 | "The range of functions provided by this package makes it possible to | |
5808 | draw highly versatile genomic sequence logos. Features include, but are not | |
5809 | limited to, modifying colour schemes and fonts used to draw the logo, | |
5810 | generating multiple logo plots, and aiding the visualisation with annotations. | |
5811 | Sequence logos can easily be combined with other ggplot2 plots.") | |
5812 | ;; Unspecified version of the LGPL. | |
5813 | (license license:lgpl3+))) | |
85df1a86 RW |
5814 | |
5815 | (define-public r-ggsci | |
5816 | (package | |
5817 | (name "r-ggsci") | |
5818 | (version "2.9") | |
5819 | (source | |
5820 | (origin | |
5821 | (method url-fetch) | |
5822 | (uri (cran-uri "ggsci" version)) | |
5823 | (sha256 | |
5824 | (base32 | |
5825 | "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) | |
5826 | (build-system r-build-system) | |
5827 | (propagated-inputs | |
5828 | `(("r-ggplot2" ,r-ggplot2) | |
5829 | ("r-scales" ,r-scales))) | |
5830 | (home-page "https://nanx.me/ggsci/") | |
5831 | (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") | |
5832 | (description | |
5833 | "This package provides a collection of ggplot2 color palettes inspired by | |
5834 | plots in scientific journals, data visualization libraries, science fiction | |
5835 | movies, and TV shows.") | |
5836 | (license license:gpl3))) | |
5219c5c5 RW |
5837 | |
5838 | (define-public r-ggsignif | |
5839 | (package | |
5840 | (name "r-ggsignif") | |
d099499e | 5841 | (version "0.6.0") |
5219c5c5 RW |
5842 | (source |
5843 | (origin | |
5844 | (method url-fetch) | |
5845 | (uri (cran-uri "ggsignif" version)) | |
5846 | (sha256 | |
5847 | (base32 | |
d099499e | 5848 | "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg")))) |
5219c5c5 RW |
5849 | (build-system r-build-system) |
5850 | (propagated-inputs | |
5851 | `(("r-ggplot2" ,r-ggplot2))) | |
5852 | (home-page "https://github.com/const-ae/ggsignif") | |
5853 | (synopsis "Significance brackets for ggplot2") | |
5854 | (description | |
5855 | "Enrich your ggplots with group-wise comparisons. This package provides | |
5856 | an easy way to indicate if two groups are significantly different. Commonly | |
5857 | this is shown by a bracket on top connecting the groups of interest which | |
5858 | itself is annotated with the level of significance. The package provides a | |
5859 | single layer that takes the groups for comparison and the test as arguments | |
5860 | and adds the annotation to the plot.") | |
5861 | (license license:gpl3))) | |
5cbaaee8 RW |
5862 | |
5863 | (define-public r-ggpubr | |
5864 | (package | |
5865 | (name "r-ggpubr") | |
1ca04927 | 5866 | (version "0.2.4") |
5cbaaee8 RW |
5867 | (source |
5868 | (origin | |
5869 | (method url-fetch) | |
5870 | (uri (cran-uri "ggpubr" version)) | |
5871 | (sha256 | |
5872 | (base32 | |
1ca04927 | 5873 | "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf")))) |
5cbaaee8 RW |
5874 | (build-system r-build-system) |
5875 | (propagated-inputs | |
5876 | `(("r-cowplot" ,r-cowplot) | |
5877 | ("r-dplyr" ,r-dplyr) | |
5878 | ("r-ggplot2" ,r-ggplot2) | |
5879 | ("r-ggrepel" ,r-ggrepel) | |
5880 | ("r-ggsci" ,r-ggsci) | |
5881 | ("r-ggsignif" ,r-ggsignif) | |
caaec886 | 5882 | ("r-glue" ,r-glue) |
5cbaaee8 RW |
5883 | ("r-gridextra" ,r-gridextra) |
5884 | ("r-magrittr" ,r-magrittr) | |
caaec886 | 5885 | ("r-polynom" ,r-polynom) |
5cbaaee8 | 5886 | ("r-purrr" ,r-purrr) |
2132e922 | 5887 | ("r-rlang" ,r-rlang) |
5cbaaee8 RW |
5888 | ("r-scales" ,r-scales) |
5889 | ("r-tidyr" ,r-tidyr))) | |
5890 | (home-page "http://www.sthda.com/english/rpkgs/ggpubr") | |
5891 | (synopsis "ggplot2-based publication-ready plots") | |
5892 | (description | |
5893 | "The ggplot2 package is an excellent and flexible package for elegant | |
5894 | data visualization in R. However the default generated plots require some | |
5895 | formatting before we can send them for publication. The ggpubr package | |
5896 | provides some easy-to-use functions for creating and customizing ggplot2-based | |
5897 | publication-ready plots.") | |
5898 | (license license:gpl2))) | |
141e43bd RW |
5899 | |
5900 | (define-public r-ellipse | |
5901 | (package | |
5902 | (name "r-ellipse") | |
5903 | (version "0.4.1") | |
5904 | (source | |
5905 | (origin | |
5906 | (method url-fetch) | |
5907 | (uri (cran-uri "ellipse" version)) | |
5908 | (sha256 | |
5909 | (base32 | |
5910 | "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs")))) | |
5911 | (build-system r-build-system) | |
5912 | (home-page "https://cran.r-project.org/web/packages/ellipse/") | |
5913 | (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") | |
5914 | (description | |
5915 | "This package contains various routines for drawing ellipses and | |
5916 | ellipse-like confidence regions, implementing the plots described in Murdoch | |
5917 | and Chow (1996), A graphical display of large correlation matrices, The | |
5918 | American Statistician 50, 178-180. There are also routines implementing the | |
5919 | profile plots described in Bates and Watts (1988), Nonlinear Regression | |
5920 | Analysis and its Applications.") | |
5921 | (license license:gpl2+))) | |
cbf6017d RW |
5922 | |
5923 | (define-public r-flashclust | |
5924 | (package | |
5925 | (name "r-flashclust") | |
5926 | (version "1.01-2") | |
5927 | (source | |
5928 | (origin | |
5929 | (method url-fetch) | |
5930 | (uri (cran-uri "flashClust" version)) | |
5931 | (sha256 | |
5932 | (base32 | |
5933 | "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) | |
5934 | (properties `((upstream-name . "flashClust"))) | |
5935 | (build-system r-build-system) | |
5936 | (native-inputs `(("gfortran" ,gfortran))) | |
5937 | (home-page "https://cran.r-project.org/web/packages/flashClust/") | |
5938 | (synopsis "Implementation of optimal hierarchical clustering") | |
5939 | (description | |
5940 | "This package provides a fast implementation of hierarchical | |
5941 | clustering.") | |
5942 | (license license:gpl2+))) | |
e83841a2 RW |
5943 | |
5944 | (define-public r-factominer | |
5945 | (package | |
5946 | (name "r-factominer") | |
efec58e7 | 5947 | (version "2.0") |
e83841a2 RW |
5948 | (source |
5949 | (origin | |
5950 | (method url-fetch) | |
5951 | (uri (cran-uri "FactoMineR" version)) | |
5952 | (sha256 | |
5953 | (base32 | |
efec58e7 | 5954 | "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8")))) |
e83841a2 RW |
5955 | (properties `((upstream-name . "FactoMineR"))) |
5956 | (build-system r-build-system) | |
5957 | (propagated-inputs | |
5958 | `(("r-car" ,r-car) | |
5959 | ("r-cluster" ,r-cluster) | |
5960 | ("r-ellipse" ,r-ellipse) | |
5961 | ("r-flashclust" ,r-flashclust) | |
efec58e7 RW |
5962 | ("r-ggplot2" ,r-ggplot2) |
5963 | ("r-ggrepel" ,r-ggrepel) | |
e83841a2 RW |
5964 | ("r-lattice" ,r-lattice) |
5965 | ("r-leaps" ,r-leaps) | |
5966 | ("r-mass" ,r-mass) | |
5967 | ("r-scatterplot3d" ,r-scatterplot3d))) | |
5968 | (home-page "http://factominer.free.fr") | |
5969 | (synopsis "Multivariate exploratory data analysis and data mining") | |
5970 | (description | |
5971 | "This package provides exploratory data analysis methods to summarize, | |
5972 | visualize and describe datasets. The main principal component methods are | |
5973 | available, those with the largest potential in terms of applications: | |
5974 | principal component analysis (PCA) when variables are quantitative, | |
5975 | correspondence analysis (CA) and multiple correspondence analysis (MCA) when | |
5976 | variables are categorical, Multiple Factor Analysis when variables are | |
5977 | structured in groups, etc. and hierarchical cluster analysis.") | |
5978 | (license license:gpl2+))) | |
f22bfee9 RW |
5979 | |
5980 | (define-public r-factoextra | |
5981 | (package | |
5982 | (name "r-factoextra") | |
60512680 | 5983 | (version "1.0.6") |
f22bfee9 RW |
5984 | (source |
5985 | (origin | |
5986 | (method url-fetch) | |
5987 | (uri (cran-uri "factoextra" version)) | |
5988 | (sha256 | |
5989 | (base32 | |
60512680 | 5990 | "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8")))) |
f22bfee9 RW |
5991 | (build-system r-build-system) |
5992 | (propagated-inputs | |
5993 | `(("r-abind" ,r-abind) | |
5994 | ("r-cluster" ,r-cluster) | |
5995 | ("r-dendextend" ,r-dendextend) | |
5996 | ("r-factominer" ,r-factominer) | |
5997 | ("r-ggplot2" ,r-ggplot2) | |
5998 | ("r-ggpubr" ,r-ggpubr) | |
5999 | ("r-ggrepel" ,r-ggrepel) | |
6000 | ("r-reshape2" ,r-reshape2) | |
6001 | ("r-tidyr" ,r-tidyr))) | |
6002 | (home-page "http://www.sthda.com/english/rpkgs/factoextra") | |
6003 | (synopsis "Extract and visualize the results of multivariate data analyses") | |
6004 | (description | |
6005 | "This package provides some easy-to-use functions to extract and | |
6006 | visualize the output of multivariate data analyses, including | |
6ccd88e8 RW |
6007 | @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence |
6008 | Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor | |
6009 | Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and | |
f22bfee9 RW |
6010 | @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R |
6011 | packages. It contains also functions for simplifying some clustering analysis | |
6012 | steps and provides ggplot2-based elegant data visualization.") | |
6013 | (license license:gpl2))) | |
0c9868aa | 6014 | |
356230da RW |
6015 | (define-public r-fansi |
6016 | (package | |
6017 | (name "r-fansi") | |
08645fcf | 6018 | (version "0.4.0") |
356230da RW |
6019 | (source |
6020 | (origin | |
6021 | (method url-fetch) | |
6022 | (uri (cran-uri "fansi" version)) | |
6023 | (sha256 | |
6024 | (base32 | |
08645fcf | 6025 | "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171")))) |
356230da RW |
6026 | (build-system r-build-system) |
6027 | (native-inputs | |
6028 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
6029 | (home-page "https://github.com/brodieG/fansi") | |
6030 | (synopsis "ANSI control sequence aware string functions") | |
6031 | (description | |
6032 | "This package provides counterparts to R string manipulation functions | |
6033 | that account for the effects of ANSI text formatting control sequences.") | |
6034 | (license license:gpl2+))) | |
6035 | ||
0c9868aa RW |
6036 | (define-public r-nbclust |
6037 | (package | |
6038 | (name "r-nbclust") | |
6039 | (version "3.0") | |
6040 | (source | |
6041 | (origin | |
6042 | (method url-fetch) | |
6043 | (uri (cran-uri "NbClust" version)) | |
6044 | (sha256 | |
6045 | (base32 | |
6046 | "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c")))) | |
6047 | (properties `((upstream-name . "NbClust"))) | |
6048 | (build-system r-build-system) | |
6049 | (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package") | |
6050 | (synopsis "Determine the best number of clusters in a data set") | |
6051 | (description | |
6052 | "NbClust provides 30 indexes for determining the optimal number of | |
6053 | clusters in a data set and offers the best clustering scheme from different | |
6054 | results to the user.") | |
6055 | (license license:gpl2))) | |
546fc4aa RW |
6056 | |
6057 | (define-public r-hdf5r | |
6058 | (package | |
6059 | (name "r-hdf5r") | |
77032118 | 6060 | (version "1.3.0") |
546fc4aa RW |
6061 | (source |
6062 | (origin | |
6063 | (method url-fetch) | |
6064 | (uri (cran-uri "hdf5r" version)) | |
6065 | (sha256 | |
6066 | (base32 | |
77032118 | 6067 | "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f")))) |
546fc4aa RW |
6068 | (build-system r-build-system) |
6069 | (inputs | |
6070 | `(("hdf5" ,hdf5) | |
6071 | ("zlib" ,zlib))) | |
6072 | (propagated-inputs | |
6073 | `(("r-bit64" ,r-bit64) | |
6074 | ("r-r6" ,r-r6))) | |
6075 | (home-page "https://hhoeflin.github.io/hdf5r") | |
6076 | (synopsis "Interface to the HDF5 binary data format") | |
6077 | (description | |
6078 | "HDF5 is a data model, library and file format for storing and managing | |
6079 | large amounts of data. This package provides a nearly feature complete, | |
6080 | object oriented wrapper for the HDF5 API using R6 classes. Additionally, | |
6081 | functionality is added so that HDF5 objects behave very similar to their | |
6082 | corresponding R counterparts.") | |
6083 | (license license:asl2.0))) | |
846325a8 | 6084 | |
3568b823 RW |
6085 | (define-public r-itertools |
6086 | (package | |
6087 | (name "r-itertools") | |
6088 | (version "0.1-3") | |
6089 | (source | |
6090 | (origin | |
6091 | (method url-fetch) | |
6092 | (uri (cran-uri "itertools" version)) | |
6093 | (sha256 | |
6094 | (base32 | |
6095 | "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn")))) | |
6096 | (build-system r-build-system) | |
6097 | (propagated-inputs | |
6098 | `(("r-iterators" ,r-iterators))) | |
6099 | (home-page "https://cran.r-project.org/web/packages/itertools/") | |
6100 | (synopsis "Iterator tools") | |
6101 | (description | |
6102 | "This package provides various tools for creating iterators, many | |
6103 | patterned after functions in the Python @code{itertools} module, and others | |
6104 | patterned after functions in the snow package.") | |
6105 | (license license:gpl2))) | |
6106 | ||
53718658 RW |
6107 | (define-public r-polynom |
6108 | (package | |
6109 | (name "r-polynom") | |
3be585cf | 6110 | (version "1.4-0") |
53718658 RW |
6111 | (source |
6112 | (origin | |
6113 | (method url-fetch) | |
6114 | (uri (cran-uri "polynom" version)) | |
6115 | (sha256 | |
6116 | (base32 | |
3be585cf | 6117 | "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5")))) |
53718658 RW |
6118 | (build-system r-build-system) |
6119 | (home-page "https://cran.r-project.org/web/packages/polynom/") | |
6120 | (synopsis "Functions for univariate polynomial manipulations") | |
6121 | (description | |
6122 | "This package provides a collection of functions to implement a class for | |
6123 | univariate polynomial manipulations.") | |
6124 | (license license:gpl2))) | |
6125 | ||
dd954dd7 RW |
6126 | (define-public r-gbrd |
6127 | (package | |
6128 | (name "r-gbrd") | |
6129 | (version "0.4-11") | |
6130 | (source | |
6131 | (origin | |
6132 | (method url-fetch) | |
6133 | (uri (cran-uri "gbRd" version)) | |
6134 | (sha256 | |
6135 | (base32 | |
6136 | "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82")))) | |
6137 | (properties `((upstream-name . "gbRd"))) | |
6138 | (build-system r-build-system) | |
6139 | (home-page "https://cran.r-project.org/web/packages/gbRd/") | |
6140 | (synopsis "Utilities for processing Rd objects and files") | |
6141 | (description | |
6142 | "This package provides utilities for processing Rd objects and files. | |
6143 | Extract argument descriptions and other parts of the help pages of | |
6144 | functions.") | |
6145 | (license license:gpl2+))) | |
6146 | ||
0c92f373 RW |
6147 | (define-public r-rjags |
6148 | (package | |
6149 | (name "r-rjags") | |
b0fd313e | 6150 | (version "4-10") |
0c92f373 RW |
6151 | (source |
6152 | (origin | |
6153 | (method url-fetch) | |
6154 | (uri (cran-uri "rjags" version)) | |
6155 | (sha256 | |
6156 | (base32 | |
b0fd313e | 6157 | "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx")))) |
0c92f373 RW |
6158 | (build-system r-build-system) |
6159 | (propagated-inputs | |
6160 | `(("r-coda" ,r-coda))) | |
6161 | (inputs | |
6162 | `(("jags" ,jags))) | |
6163 | (native-inputs | |
6164 | `(("pkg-config" ,pkg-config))) | |
6165 | (home-page "http://mcmc-jags.sourceforge.net") | |
6166 | (synopsis "Bayesian graphical models using MCMC") | |
6167 | (description | |
6168 | "This package provides an R interface to the JAGS MCMC library. JAGS is | |
6169 | Just Another Gibbs Sampler. It is a program for analysis of Bayesian | |
6170 | hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") | |
6171 | (license license:gpl2))) | |
6172 | ||
6a846975 RW |
6173 | (define-public r-rdpack |
6174 | (package | |
6175 | (name "r-rdpack") | |
cceb86f9 | 6176 | (version "0.11-1") |
6a846975 RW |
6177 | (source |
6178 | (origin | |
6179 | (method url-fetch) | |
6180 | (uri (cran-uri "Rdpack" version)) | |
6181 | (sha256 | |
6182 | (base32 | |
cceb86f9 | 6183 | "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq")))) |
6a846975 RW |
6184 | (properties `((upstream-name . "Rdpack"))) |
6185 | (build-system r-build-system) | |
6186 | (propagated-inputs | |
6187 | `(("r-bibtex" ,r-bibtex) | |
6188 | ("r-gbrd" ,r-gbrd))) | |
6189 | (home-page "https://github.com/GeoBosh/Rdpack") | |
6190 | (synopsis "Update and manipulate Rd documentation objects") | |
6191 | (description | |
6192 | "This package provides functions for manipulation of R documentation | |
6193 | objects, including functions @code{reprompt()} and @code{ereprompt()} for | |
6194 | updating Rd documentation for functions, methods and classes; it also includes | |
6195 | Rd macros for citations and import of references from bibtex files for use in | |
6196 | Rd files and roxygen2 comments, as well as many functions for manipulation of | |
6197 | references and Rd files.") | |
6198 | (license license:gpl2+))) | |
6199 | ||
c183fa26 RW |
6200 | (define-public r-officer |
6201 | (package | |
6202 | (name "r-officer") | |
7f4025aa | 6203 | (version "0.3.6") |
c183fa26 RW |
6204 | (source |
6205 | (origin | |
6206 | (method url-fetch) | |
6207 | (uri (cran-uri "officer" version)) | |
6208 | (sha256 | |
6209 | (base32 | |
7f4025aa | 6210 | "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4")))) |
c183fa26 RW |
6211 | (build-system r-build-system) |
6212 | (propagated-inputs | |
6213 | `(("r-base64enc" ,r-base64enc) | |
6214 | ("r-digest" ,r-digest) | |
6215 | ("r-htmltools" ,r-htmltools) | |
6216 | ("r-magrittr" ,r-magrittr) | |
6217 | ("r-r6" ,r-r6) | |
6218 | ("r-rcpp" ,r-rcpp) | |
fd1a17a5 | 6219 | ("r-rlang" ,r-rlang) |
c183fa26 RW |
6220 | ("r-uuid" ,r-uuid) |
6221 | ("r-xml2" ,r-xml2) | |
6222 | ("r-zip" ,r-zip))) | |
6223 | (home-page "https://davidgohel.github.io/officer") | |
6224 | (synopsis "Manipulation of Word and PowerPoint documents") | |
6225 | (description | |
6226 | "This package provides tools to access and manipulate Word and PowerPoint | |
6227 | documents from R. The package focuses on tabular and graphical reporting from | |
6228 | R; it also provides two functions that let users get document content into | |
6229 | data objects. A set of functions lets add and remove images, tables and | |
6230 | paragraphs of text in new or existing documents. When working with PowerPoint | |
6231 | presentations, slides can be added or removed; shapes inside slides can also | |
6232 | be added or removed. When working with Word documents, a cursor can be used | |
6233 | to help insert or delete content at a specific location in the document.") | |
6234 | (license license:gpl3))) | |
6235 | ||
488dc4e1 RW |
6236 | (define-public r-abn |
6237 | (package | |
6238 | (name "r-abn") | |
a6828e0b | 6239 | (version "2.2") |
488dc4e1 RW |
6240 | (source |
6241 | (origin | |
6242 | (method url-fetch) | |
6243 | (uri (cran-uri "abn" version)) | |
6244 | (sha256 | |
6245 | (base32 | |
a6828e0b | 6246 | "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d")))) |
488dc4e1 RW |
6247 | (build-system r-build-system) |
6248 | (inputs | |
6249 | `(("gsl" ,gsl))) | |
6250 | (propagated-inputs | |
72c967e2 | 6251 | `(("r-lme4" ,r-lme4) |
488dc4e1 RW |
6252 | ("r-mass" ,r-mass) |
6253 | ("r-nnet" ,r-nnet) | |
6254 | ("r-rcpp" ,r-rcpp) | |
6255 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6256 | ("r-rjags" ,r-rjags))) | |
6257 | (home-page "http://www.r-bayesian-networks.org") | |
6258 | (synopsis "Modelling multivariate data with additive bayesian networks") | |
6259 | (description | |
6260 | "Bayesian network analysis is a form of probabilistic graphical models | |
6261 | which derives from empirical data a directed acyclic graph, DAG, describing | |
6262 | the dependency structure between random variables. An additive Bayesian | |
6263 | network model consists of a form of a DAG where each node comprises a | |
6264 | @dfn{generalized linear model} (GLM). Additive Bayesian network models are | |
6265 | equivalent to Bayesian multivariate regression using graphical modelling, they | |
6266 | generalises the usual multivariable regression, GLM, to multiple dependent | |
6267 | variables. This package provides routines to help determine optimal Bayesian | |
6268 | network models for a given data set, where these models are used to identify | |
6269 | statistical dependencies in messy, complex data.") | |
6270 | (license license:gpl2+))) | |
6271 | ||
ffdeda3c RW |
6272 | (define-public r-acd |
6273 | (package | |
6274 | (name "r-acd") | |
6275 | (version "1.5.3") | |
6276 | (source | |
6277 | (origin | |
6278 | (method url-fetch) | |
6279 | (uri (cran-uri "ACD" version)) | |
6280 | (sha256 | |
6281 | (base32 | |
6282 | "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6")))) | |
6283 | (properties `((upstream-name . "ACD"))) | |
6284 | (build-system r-build-system) | |
6285 | (home-page "https://cran.r-project.org/web/packages/ACD/") | |
6286 | (synopsis "Categorical data analysis with complete or missing responses") | |
6287 | (description | |
6288 | "This package provides tools for categorical data analysis with complete | |
6289 | or missing responses.") | |
6290 | (license license:gpl2+))) | |
6291 | ||
acbf23da RW |
6292 | (define-public r-acdm |
6293 | (package | |
6294 | (name "r-acdm") | |
6295 | (version "1.0.4") | |
6296 | (source | |
6297 | (origin | |
6298 | (method url-fetch) | |
6299 | (uri (cran-uri "ACDm" version)) | |
6300 | (sha256 | |
6301 | (base32 | |
6302 | "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil")))) | |
6303 | (properties `((upstream-name . "ACDm"))) | |
6304 | (build-system r-build-system) | |
6305 | (propagated-inputs | |
6306 | `(("r-dplyr" ,r-dplyr) | |
6307 | ("r-ggplot2" ,r-ggplot2) | |
6308 | ("r-plyr" ,r-plyr) | |
6309 | ("r-rsolnp" ,r-rsolnp) | |
6310 | ("r-zoo" ,r-zoo))) | |
6311 | (home-page "https://cran.r-project.org/web/packages/ACDm/") | |
6312 | (synopsis "Tools for Autoregressive Conditional Duration Models") | |
6313 | (description | |
6314 | "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle | |
6315 | and Russell, 1998) models. It creates trade, price or volume durations from | |
6316 | transactions (tic) data, performs diurnal adjustments, fits various ACD models | |
6317 | and tests them.") | |
6318 | (license license:gpl2+))) | |
6319 | ||
08bf097a RW |
6320 | (define-public r-overlap |
6321 | (package | |
6322 | (name "r-overlap") | |
6323 | (version "0.3.2") | |
6324 | (source | |
6325 | (origin | |
6326 | (method url-fetch) | |
6327 | (uri (cran-uri "overlap" version)) | |
6328 | (sha256 | |
6329 | (base32 | |
6330 | "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy")))) | |
6331 | (build-system r-build-system) | |
6332 | (home-page "https://cran.r-project.org/web/packages/overlap/") | |
6333 | (synopsis "Estimates of coefficient of overlapping for animal activity patterns") | |
6334 | (description | |
6335 | "This package provides functions to fit kernel density functions to data | |
6336 | on temporal activity patterns of animals; estimate coefficients of overlapping | |
6337 | of densities for two species; and calculate bootstrap estimates of confidence | |
6338 | intervals.") | |
6339 | (license license:gpl3+))) | |
6340 | ||
bfee9ce8 RW |
6341 | (define-public r-snakecase |
6342 | (package | |
6343 | (name "r-snakecase") | |
794c9e7d | 6344 | (version "0.11.0") |
bfee9ce8 RW |
6345 | (source |
6346 | (origin | |
6347 | (method url-fetch) | |
6348 | (uri (cran-uri "snakecase" version)) | |
6349 | (sha256 | |
6350 | (base32 | |
794c9e7d | 6351 | "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r")))) |
bfee9ce8 RW |
6352 | (build-system r-build-system) |
6353 | (propagated-inputs | |
6354 | `(("r-stringi" ,r-stringi) | |
6355 | ("r-stringr" ,r-stringr))) | |
6356 | (home-page "https://github.com/Tazinho/snakecase") | |
6357 | (synopsis "Convert strings into any case") | |
6358 | (description | |
6359 | "This package provides a consistent, flexible and easy to use tool to | |
6360 | parse and convert strings into cases like snake or camel among others.") | |
6361 | (license license:gpl3))) | |
6362 | ||
de059e4b RW |
6363 | (define-public r-prediction |
6364 | (package | |
6365 | (name "r-prediction") | |
c3447a92 | 6366 | (version "0.3.14") |
de059e4b RW |
6367 | (source |
6368 | (origin | |
6369 | (method url-fetch) | |
6370 | (uri (cran-uri "prediction" version)) | |
6371 | (sha256 | |
6372 | (base32 | |
c3447a92 | 6373 | "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx")))) |
de059e4b RW |
6374 | (build-system r-build-system) |
6375 | (propagated-inputs | |
6376 | `(("r-data-table" ,r-data-table))) | |
6377 | (home-page "https://github.com/leeper/prediction") | |
6378 | (synopsis "Tidy, type-safe prediction methods") | |
6379 | (description | |
6380 | "This package provides the @code{prediction()} function, a type-safe | |
6381 | alternative to @code{predict()} that always returns a data frame. The package | |
6382 | currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"}) | |
6383 | from the @code{stats} package, as well as numerous other model classes from | |
6384 | other add-on packages.") | |
6385 | (license license:expat))) | |
6386 | ||
d14c770d RW |
6387 | (define-public r-insight |
6388 | (package | |
6389 | (name "r-insight") | |
a346c936 | 6390 | (version "0.7.1") |
d14c770d RW |
6391 | (source |
6392 | (origin | |
6393 | (method url-fetch) | |
6394 | (uri (cran-uri "insight" version)) | |
6395 | (sha256 | |
6396 | (base32 | |
a346c936 | 6397 | "0scjmr8qvwaswb9wfq2lxp1v5fl72way8cid9agrf0z1agp0adad")))) |
d14c770d RW |
6398 | (build-system r-build-system) |
6399 | (home-page "https://easystats.github.io/insight/") | |
6400 | (synopsis "Easy access to model information for various model objects") | |
6401 | (description | |
6402 | "This package provides a tool to provide an easy, intuitive and | |
6403 | consistent access to information contained in various R models, like model | |
6404 | formulas, model terms, information about random effects, data that was used to | |
6405 | fit the model or data from response variables. The package mainly revolves | |
6406 | around two types of functions: Functions that find (the names of) information, | |
6407 | starting with @code{find_}, and functions that get the underlying data, | |
6408 | starting with @code{get_}. The package has a consistent syntax and works with | |
6409 | many different model objects, where otherwise functions to access these | |
6410 | information are missing.") | |
6411 | (license license:gpl3))) | |
6412 | ||
cfc06314 RW |
6413 | (define-public r-sjlabelled |
6414 | (package | |
6415 | (name "r-sjlabelled") | |
3ab3f7f3 | 6416 | (version "1.1.1") |
cfc06314 RW |
6417 | (source |
6418 | (origin | |
6419 | (method url-fetch) | |
6420 | (uri (cran-uri "sjlabelled" version)) | |
6421 | (sha256 | |
6422 | (base32 | |
3ab3f7f3 | 6423 | "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz")))) |
cfc06314 RW |
6424 | (build-system r-build-system) |
6425 | (propagated-inputs | |
bc418c97 | 6426 | `(("r-haven" ,r-haven) |
5e16dff9 | 6427 | ("r-insight" ,r-insight) |
cfc06314 | 6428 | ("r-magrittr" ,r-magrittr) |
cfc06314 | 6429 | ("r-purrr" ,r-purrr) |
bc418c97 RW |
6430 | ("r-rlang" ,r-rlang) |
6431 | ("r-tidyselect" ,r-tidyselect))) | |
cfc06314 RW |
6432 | (home-page "https://github.com/strengejacke/sjlabelled") |
6433 | (synopsis "Labelled data utility functions") | |
6434 | (description | |
6435 | "This package provides a collection of functions dealing with labelled | |
6436 | data, like reading and writing data between R and other statistical software | |
6437 | packages. This includes easy ways to get, set or change value and variable | |
6438 | label attributes, to convert labelled vectors into factors or numeric (and | |
6439 | vice versa), or to deal with multiple declared missing values.") | |
6440 | (license license:gpl3))) | |
6441 | ||
1f560b9c RW |
6442 | (define-public r-sjmisc |
6443 | (package | |
6444 | (name "r-sjmisc") | |
14c3e7bb | 6445 | (version "2.8.2") |
1f560b9c RW |
6446 | (source |
6447 | (origin | |
6448 | (method url-fetch) | |
6449 | (uri (cran-uri "sjmisc" version)) | |
6450 | (sha256 | |
6451 | (base32 | |
14c3e7bb | 6452 | "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2")))) |
1f560b9c RW |
6453 | (build-system r-build-system) |
6454 | (propagated-inputs | |
31af2e7f | 6455 | `(("r-dplyr" ,r-dplyr) |
45dcc89d | 6456 | ("r-insight" ,r-insight) |
1f560b9c | 6457 | ("r-magrittr" ,r-magrittr) |
1f560b9c RW |
6458 | ("r-purrr" ,r-purrr) |
6459 | ("r-rlang" ,r-rlang) | |
14c3e7bb RW |
6460 | ("r-sjlabelled" ,r-sjlabelled) |
6461 | ("r-tidyselect" ,r-tidyselect))) | |
1f560b9c RW |
6462 | (home-page "https://github.com/strengejacke/sjmisc") |
6463 | (synopsis "Data and variable transformation functions") | |
6464 | (description | |
6465 | "This package is a collection of miscellaneous utility functions, | |
6466 | supporting data transformation tasks like recoding, dichotomizing or grouping | |
6467 | variables, setting and replacing missing values. The data transformation | |
6468 | functions also support labelled data, and all integrate seamlessly into a | |
6469 | tidyverse workflow.") | |
6470 | (license license:gpl3))) | |
6471 | ||
aaed237d RW |
6472 | (define-public r-nortest |
6473 | (package | |
6474 | (name "r-nortest") | |
6475 | (version "1.0-4") | |
6476 | (source | |
6477 | (origin | |
6478 | (method url-fetch) | |
6479 | (uri (cran-uri "nortest" version)) | |
6480 | (sha256 | |
6481 | (base32 | |
6482 | "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3")))) | |
6483 | (build-system r-build-system) | |
6484 | (home-page "https://cran.r-project.org/web/packages/nortest/") | |
6485 | (synopsis "Tests for normality") | |
6486 | (description | |
6487 | "This package provides five omnibus tests for testing the composite | |
6488 | hypothesis of normality.") | |
6489 | (license license:gpl2+))) | |
6490 | ||
0fd7d59d RW |
6491 | (define-public r-moonbook |
6492 | (package | |
6493 | (name "r-moonbook") | |
6494 | (version "0.2.3") | |
6495 | (source | |
6496 | (origin | |
6497 | (method url-fetch) | |
6498 | (uri (cran-uri "moonBook" version)) | |
6499 | (sha256 | |
6500 | (base32 | |
6501 | "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6")))) | |
6502 | (properties `((upstream-name . "moonBook"))) | |
6503 | (build-system r-build-system) | |
6504 | (propagated-inputs | |
6505 | `(("r-magrittr" ,r-magrittr) | |
6506 | ("r-nortest" ,r-nortest) | |
6507 | ("r-purrr" ,r-purrr) | |
6508 | ("r-sjmisc" ,r-sjmisc) | |
6509 | ("r-stringr" ,r-stringr) | |
6510 | ("r-survival" ,r-survival))) | |
6511 | (home-page "https://github.com/cardiomoon/moonBook") | |
6512 | (synopsis "Functions and datasets for the book by Keon-Woong Moon") | |
6513 | (description | |
6514 | "This package provides several analysis-related functions for the book | |
6515 | entitled \"R statistics and graph for medical articles\" (written in Korean), | |
6516 | version 1, by Keon-Woong Moon with Korean demographic data with several plot | |
6517 | functions.") | |
6518 | (license license:gpl2))) | |
6519 | ||
589bd1c4 RW |
6520 | (define-public r-flextable |
6521 | (package | |
6522 | (name "r-flextable") | |
56b88f6c | 6523 | (version "0.5.6") |
589bd1c4 RW |
6524 | (source |
6525 | (origin | |
6526 | (method url-fetch) | |
6527 | (uri (cran-uri "flextable" version)) | |
6528 | (sha256 | |
6529 | (base32 | |
56b88f6c | 6530 | "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w")))) |
589bd1c4 RW |
6531 | (build-system r-build-system) |
6532 | (propagated-inputs | |
30918ce8 RW |
6533 | `(("r-base64enc" ,r-base64enc) |
6534 | ("r-data-table" ,r-data-table) | |
e89d5427 | 6535 | ("r-gdtools" ,r-gdtools) |
589bd1c4 RW |
6536 | ("r-htmltools" ,r-htmltools) |
6537 | ("r-knitr" ,r-knitr) | |
6538 | ("r-officer" ,r-officer) | |
e89d5427 | 6539 | ("r-rlang" ,r-rlang) |
589bd1c4 | 6540 | ("r-rmarkdown" ,r-rmarkdown) |
589bd1c4 RW |
6541 | ("r-xml2" ,r-xml2))) |
6542 | (home-page "https://davidgohel.github.io/flextable") | |
6543 | (synopsis "Functions for tabular reporting") | |
6544 | (description | |
6545 | "This package provides tools to create pretty tables for HTML documents | |
6546 | and other formats. Functions are provided to let users create tables, modify | |
6547 | and format their content. It extends the @code{officer} package and can be | |
6548 | used within R markdown documents when rendering to HTML and to Word | |
6549 | documents.") | |
6550 | (license license:gpl3))) | |
6551 | ||
846325a8 RW |
6552 | (define-public r-writexl |
6553 | (package | |
6554 | (name "r-writexl") | |
fda807da | 6555 | (version "1.2") |
846325a8 RW |
6556 | (source |
6557 | (origin | |
6558 | (method url-fetch) | |
6559 | (uri (cran-uri "writexl" version)) | |
6560 | (sha256 | |
6561 | (base32 | |
fda807da | 6562 | "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3")))) |
846325a8 RW |
6563 | (build-system r-build-system) |
6564 | (inputs `(("zlib" ,zlib))) | |
6565 | (home-page "https://github.com/ropensci/writexl") | |
6566 | (synopsis "Export data frames to xlsx format") | |
6567 | (description | |
6568 | "This package provides a data frame to xlsx exporter based on | |
6569 | libxlsxwriter.") | |
6570 | (license license:bsd-2))) | |
64abd245 RW |
6571 | |
6572 | (define-public r-biasedurn | |
6573 | (package | |
6574 | (name "r-biasedurn") | |
6575 | (version "1.07") | |
6576 | (source | |
6577 | (origin | |
6578 | (method url-fetch) | |
6579 | (uri (cran-uri "BiasedUrn" version)) | |
6580 | (sha256 | |
6581 | (base32 | |
6582 | "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) | |
6583 | (properties `((upstream-name . "BiasedUrn"))) | |
6584 | (build-system r-build-system) | |
6585 | (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") | |
6586 | (synopsis "Biased Urn model distributions") | |
6587 | (description | |
6588 | "This package provides statistical models of biased sampling in the form | |
6589 | of univariate and multivariate noncentral hypergeometric distributions, | |
6590 | including Wallenius' noncentral hypergeometric distribution and Fisher's | |
6591 | noncentral hypergeometric distribution (also called extended hypergeometric | |
6592 | distribution).") | |
6593 | (license license:gpl3))) | |
87ba9508 RW |
6594 | |
6595 | (define-public r-goplot | |
6596 | (package | |
6597 | (name "r-goplot") | |
6598 | (version "1.0.2") | |
6599 | (source | |
6600 | (origin | |
6601 | (method url-fetch) | |
6602 | (uri (cran-uri "GOplot" version)) | |
6603 | (sha256 | |
6604 | (base32 | |
6605 | "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix")))) | |
6606 | (properties `((upstream-name . "GOplot"))) | |
6607 | (build-system r-build-system) | |
6608 | (propagated-inputs | |
6609 | `(("r-ggdendro" ,r-ggdendro) | |
6610 | ("r-ggplot2" ,r-ggplot2) | |
6611 | ("r-gridextra" ,r-gridextra) | |
6612 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
6613 | (home-page "https://github.com/wencke/wencke.github.io") | |
6614 | (synopsis "Visualization of functional analysis data") | |
6615 | (description | |
6616 | "This package provides an implementation of multilayered visualizations | |
6617 | for enhanced graphical representation of functional analysis data. It | |
6618 | combines and integrates omics data derived from expression and functional | |
6619 | annotation enrichment analyses. Its plotting functions have been developed | |
6620 | with an hierarchical structure in mind: starting from a general overview to | |
6621 | identify the most enriched categories (modified bar plot, bubble plot) to a | |
6622 | more detailed one displaying different types of relevant information for the | |
6623 | molecules in a given set of categories (circle plot, chord plot, cluster plot, | |
6624 | Venn diagram, heatmap).") | |
6625 | (license license:gpl2))) | |
aec7d6be RW |
6626 | |
6627 | (define-public r-getopt | |
6628 | (package | |
6629 | (name "r-getopt") | |
104ec4c9 | 6630 | (version "1.20.3") |
aec7d6be RW |
6631 | (source |
6632 | (origin | |
6633 | (method url-fetch) | |
6634 | (uri (cran-uri "getopt" version)) | |
6635 | (sha256 | |
6636 | (base32 | |
104ec4c9 | 6637 | "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk")))) |
aec7d6be RW |
6638 | (build-system r-build-system) |
6639 | (home-page "https://github.com/trevorld/getopt") | |
6640 | (synopsis "Command-line option processor for R") | |
6641 | (description | |
6642 | "This package is designed to be used with Rscript to write shebang | |
6643 | scripts that accept short and long options. Many users will prefer to | |
6644 | use the packages @code{optparse} or @code{argparse} which add extra | |
6645 | features like automatically generated help options and usage texts, | |
6646 | support for default values, positional argument support, etc.") | |
6647 | (license license:gpl2+))) | |
3629622b RW |
6648 | |
6649 | (define-public r-findpython | |
6650 | (package | |
6651 | (name "r-findpython") | |
fcb84565 | 6652 | (version "1.0.5") |
3629622b RW |
6653 | (source |
6654 | (origin | |
6655 | (method url-fetch) | |
6656 | (uri (cran-uri "findpython" version)) | |
6657 | (sha256 | |
6658 | (base32 | |
fcb84565 | 6659 | "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy")))) |
3629622b RW |
6660 | (build-system r-build-system) |
6661 | (home-page "https://github.com/trevorld/findpython") | |
6662 | (synopsis "Functions to find an acceptable Python binary") | |
6663 | (description | |
6664 | "This package was designed to find an acceptable Python binary that | |
6665 | matches version and feature constraints.") | |
6666 | (license license:expat))) | |
fa697599 RW |
6667 | |
6668 | ;; This in not the same as "r-argparser" | |
6669 | (define-public r-argparse | |
6670 | (package | |
6671 | (name "r-argparse") | |
37317189 | 6672 | (version "2.0.1") |
fa697599 RW |
6673 | (source |
6674 | (origin | |
6675 | (method url-fetch) | |
6676 | (uri (cran-uri "argparse" version)) | |
6677 | (sha256 | |
6678 | (base32 | |
37317189 | 6679 | "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l")))) |
fa697599 RW |
6680 | (build-system r-build-system) |
6681 | (inputs `(("python" ,python))) | |
6682 | (propagated-inputs | |
6683 | `(("r-findpython" ,r-findpython) | |
fa697599 | 6684 | ("r-jsonlite" ,r-jsonlite) |
11a36548 | 6685 | ("r-r6" ,r-r6))) |
fa697599 RW |
6686 | (home-page "https://github.com/trevorld/argparse") |
6687 | (synopsis "Command line optional and positional argument parser") | |
6688 | (description | |
6689 | "This package provides a command line parser to be used with Rscript to | |
6690 | write shebang scripts that gracefully accept positional and optional arguments | |
6691 | and automatically generate usage notices.") | |
6692 | (license license:gpl2+))) | |
4646d18e RW |
6693 | |
6694 | (define-public r-hash | |
6695 | (package | |
6696 | (name "r-hash") | |
a431c381 | 6697 | (version "2.2.6.1") |
4646d18e RW |
6698 | (source |
6699 | (origin | |
6700 | (method url-fetch) | |
6701 | (uri (cran-uri "hash" version)) | |
6702 | (sha256 | |
6703 | (base32 | |
a431c381 | 6704 | "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056")))) |
4646d18e RW |
6705 | (build-system r-build-system) |
6706 | (home-page "https://cran.r-project.org/web/packages/hash/") | |
6707 | (synopsis "Implementation of hash/associated arrays/dictionaries") | |
6708 | (description | |
6709 | "This package implements a data structure similar to hashes in Perl and | |
6710 | dictionaries in Python but with a purposefully R flavor. For objects of | |
6711 | appreciable size, access using hashes outperforms native named lists and | |
6712 | vectors.") | |
6713 | (license license:gpl2+))) | |
06a45ad6 RW |
6714 | |
6715 | (define-public r-orddom | |
6716 | (package | |
6717 | (name "r-orddom") | |
6718 | (version "3.1") | |
6719 | (source | |
6720 | (origin | |
6721 | (method url-fetch) | |
6722 | (uri (cran-uri "orddom" version)) | |
6723 | (sha256 | |
6724 | (base32 | |
6725 | "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) | |
6726 | (build-system r-build-system) | |
6727 | (propagated-inputs `(("r-psych" ,r-psych))) | |
6728 | (home-page "https://cran.r-project.org/web/packages/orddom/") | |
6729 | (synopsis "Ordinal dominance statistics") | |
6730 | (description | |
6731 | "This package provides tools to compute ordinal, statistics and effect | |
6732 | sizes as an alternative to mean comparison: Cliff's delta or success rate | |
6733 | difference (SRD), Vargha and Delaney's A or the Area Under a Receiver | |
6734 | Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's | |
6735 | Common Language Effect Size (CLES) or Grissom & Kim's Probability of | |
6736 | Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover, | |
6737 | comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of | |
6738 | Group (Non-)Overlap considerations.") | |
6739 | (license license:gpl2))) | |
0fccd15f | 6740 | |
6f921bfd RW |
6741 | (define-public r-deriv |
6742 | (package | |
6743 | (name "r-deriv") | |
31fa45b6 | 6744 | (version "4.0") |
6f921bfd RW |
6745 | (source |
6746 | (origin | |
6747 | (method url-fetch) | |
6748 | (uri (cran-uri "Deriv" version)) | |
6749 | (sha256 | |
6750 | (base32 | |
31fa45b6 | 6751 | "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n")))) |
6f921bfd RW |
6752 | (properties `((upstream-name . "Deriv"))) |
6753 | (build-system r-build-system) | |
6754 | (home-page "https://cran.r-project.org/web/packages/Deriv") | |
6755 | (synopsis "Symbolic differentiation") | |
6756 | (description | |
6757 | "This package provides an R-based solution for symbolic differentiation. | |
6758 | It admits user-defined functions as well as function substitution in arguments | |
6759 | of functions to be differentiated. Some symbolic simplification is part of | |
6760 | the work.") | |
6761 | (license license:gpl3+))) | |
6762 | ||
0fccd15f RW |
6763 | (define-public r-doby |
6764 | (package | |
6765 | (name "r-doby") | |
dcbeae60 | 6766 | (version "4.6-3") |
0fccd15f RW |
6767 | (source |
6768 | (origin | |
6769 | (method url-fetch) | |
6770 | (uri (cran-uri "doBy" version)) | |
6771 | (sha256 | |
6772 | (base32 | |
dcbeae60 | 6773 | "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635")))) |
0fccd15f RW |
6774 | (properties `((upstream-name . "doBy"))) |
6775 | (build-system r-build-system) | |
6776 | (propagated-inputs | |
dcbeae60 RW |
6777 | `(("r-broom" ,r-broom) |
6778 | ("r-deriv" ,r-deriv) | |
6779 | ("r-dplyr" ,r-dplyr) | |
0fccd15f RW |
6780 | ("r-magrittr" ,r-magrittr) |
6781 | ("r-mass" ,r-mass) | |
6782 | ("r-matrix" ,r-matrix) | |
dcbeae60 RW |
6783 | ("r-plyr" ,r-plyr) |
6784 | ("r-pbkrtest" ,r-pbkrtest) | |
6785 | ("r-tibble" ,r-tibble))) | |
0fccd15f RW |
6786 | (home-page "http://people.math.aau.dk/~sorenh/software/doBy/") |
6787 | (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") | |
6788 | (description | |
6789 | "This package contains: | |
6790 | ||
6791 | @itemize | |
6792 | @item facilities for working with grouped data: @code{do} | |
6793 | something to data stratified @code{by} some variables. | |
6794 | @item implementations of least-squares means, general linear contrasts, and | |
6795 | @item miscellaneous other utilities. | |
6796 | @end itemize\n") | |
6797 | (license license:gpl2+))) | |
5850c5b3 RW |
6798 | |
6799 | (define-public r-refgenome | |
6800 | (package | |
6801 | (name "r-refgenome") | |
27abdb11 | 6802 | (version "1.7.7") |
5850c5b3 RW |
6803 | (source |
6804 | (origin | |
6805 | (method url-fetch) | |
6806 | (uri (cran-uri "refGenome" version)) | |
6807 | (sha256 | |
6808 | (base32 | |
27abdb11 | 6809 | "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5")))) |
5850c5b3 RW |
6810 | (properties `((upstream-name . "refGenome"))) |
6811 | (build-system r-build-system) | |
6812 | (propagated-inputs | |
6813 | `(("r-dbi" ,r-dbi) | |
6814 | ("r-doby" ,r-doby) | |
6815 | ("r-rsqlite" ,r-rsqlite))) | |
6816 | (home-page "https://cran.r-project.org/web/packages/refGenome/") | |
6817 | (synopsis | |
6818 | "Gene and splice site annotation using annotation data from Ensembl and UCSC") | |
6819 | (description | |
6820 | "This package contains functionality for importing and managing of | |
6821 | downloaded genome annotation data from the Ensembl genome browser (European | |
6822 | Bioinformatics Institute) and from the UCSC genome browser (University of | |
6823 | California, Santa Cruz) and annotation routines for genomic positions and | |
6824 | splice site positions.") | |
6825 | (license license:gpl2))) | |
ff7d53a7 RW |
6826 | |
6827 | (define-public r-basix | |
6828 | (package | |
6829 | (name "r-basix") | |
6830 | (version "1.1") | |
6831 | (source | |
6832 | (origin | |
6833 | (method url-fetch) | |
6834 | (uri (cran-uri "BASIX" version)) | |
6835 | (sha256 | |
6836 | (base32 | |
6837 | "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id")))) | |
6838 | (properties `((upstream-name . "BASIX"))) | |
6839 | (build-system r-build-system) | |
6840 | (home-page "https://cran.r-project.org/web/packages/BASIX/") | |
6841 | (synopsis "Efficient C/C++ toolset for R") | |
6842 | (description | |
6843 | "BASIX provides some efficient C/C++ implementations of native R | |
6844 | procedures to speed up calculations in R.") | |
6845 | (license license:gpl2))) | |
65e74814 RW |
6846 | |
6847 | (define-public r-blockfest | |
6848 | (package | |
6849 | (name "r-blockfest") | |
6850 | (version "1.6") | |
6851 | (source | |
6852 | (origin | |
6853 | (method url-fetch) | |
6854 | (uri (cran-uri "BlockFeST" version)) | |
6855 | (sha256 | |
6856 | (base32 | |
6857 | "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) | |
6858 | (properties `((upstream-name . "BlockFeST"))) | |
6859 | (build-system r-build-system) | |
6860 | (propagated-inputs `(("r-basix" ,r-basix))) | |
6861 | (home-page "https://cran.r-project.org/web/packages/BlockFeST/") | |
6862 | (synopsis "Bayesian calculation of region-specific fixation index") | |
6863 | (description | |
6864 | "This package provides an R implementation of an extension of the | |
6865 | BayeScan software for codominant markers, adding the option to group | |
6866 | individual SNPs into pre-defined blocks. A typical application of this new | |
6867 | approach is the identification of genomic regions, genes, or gene sets | |
6868 | containing one or more SNPs that evolved under directional selection.") | |
6869 | (license license:gpl2))) | |
b9ff2599 | 6870 | |
fbdf05b1 RW |
6871 | (define-public r-proc |
6872 | (package | |
6873 | (name "r-proc") | |
a510dc60 | 6874 | (version "1.15.3") |
fbdf05b1 RW |
6875 | (source |
6876 | (origin | |
6877 | (method url-fetch) | |
6878 | (uri (cran-uri "pROC" version)) | |
6879 | (sha256 | |
6880 | (base32 | |
a510dc60 | 6881 | "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h")))) |
fbdf05b1 RW |
6882 | (properties `((upstream-name . "pROC"))) |
6883 | (build-system r-build-system) | |
6884 | (propagated-inputs | |
a3daf011 | 6885 | `(("r-plyr" ,r-plyr) |
fbdf05b1 RW |
6886 | ("r-rcpp" ,r-rcpp))) |
6887 | (home-page "http://expasy.org/tools/pROC/") | |
6888 | (synopsis "Display and analyze ROC curves") | |
6889 | (description | |
6890 | "This package provides tools for visualizing, smoothing and comparing | |
6891 | receiver operating characteristic (ROC curves). The area under the | |
6892 | curve (AUC) can be compared with statistical tests based on U-statistics or | |
6893 | bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") | |
6894 | (license license:gpl3+))) | |
cea4d360 RW |
6895 | |
6896 | (define-public r-rootsolve | |
6897 | (package | |
6898 | (name "r-rootsolve") | |
550a1e01 | 6899 | (version "1.8.2") |
cea4d360 RW |
6900 | (source |
6901 | (origin | |
6902 | (method url-fetch) | |
6903 | (uri (cran-uri "rootSolve" version)) | |
6904 | (sha256 | |
6905 | (base32 | |
550a1e01 | 6906 | "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l")))) |
cea4d360 RW |
6907 | (properties `((upstream-name . "rootSolve"))) |
6908 | (build-system r-build-system) | |
6909 | (native-inputs `(("gfortran" ,gfortran))) | |
6910 | (home-page "https://cran.r-project.org/web/packages/rootSolve/") | |
6911 | (synopsis "Tools for the analysis of ordinary differential equations") | |
6912 | (description | |
6913 | "This package provides routines to find the root of nonlinear functions, | |
6914 | and to perform steady-state and equilibrium analysis of @dfn{ordinary | |
6915 | differential equations} (ODE). It includes routines that: | |
6916 | ||
6917 | @enumerate | |
6918 | @item generate gradient and jacobian matrices (full and banded), | |
6919 | @item find roots of non-linear equations by the Newton-Raphson method, | |
6920 | @item estimate steady-state conditions of a system of (differential) equations | |
6921 | in full, banded or sparse form, using the Newton-Raphson method, or by | |
6922 | dynamically running, | |
6923 | @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, | |
6924 | and 3-D partial differential equations, that have been converted to ordinary | |
6925 | differential equations by numerical differencing (using the method-of-lines | |
6926 | approach). | |
6927 | @end enumerate\n") | |
6928 | (license license:gpl2+))) | |
c994418b | 6929 | |
6930 | (define-public r-abcanalysis | |
6931 | (package | |
6932 | (name "r-abcanalysis") | |
6933 | (version "1.2.1") | |
6934 | (source | |
6935 | (origin | |
6936 | (method url-fetch) | |
6937 | (uri (cran-uri "ABCanalysis" version)) | |
6938 | (sha256 | |
6939 | (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) | |
6940 | (properties `((upstream-name . "ABCanalysis"))) | |
6941 | (build-system r-build-system) | |
6942 | (propagated-inputs `(("r-plotrix" ,r-plotrix))) | |
6943 | (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") | |
6944 | (synopsis "Computed ABC Analysis") | |
6945 | (description | |
6946 | "Multivariate data sets often differ in several factors or derived statistical | |
6947 | parameters, which have to be selected for a valid interpretation. Basing this | |
6948 | selection on traditional statistical limits leads occasionally to the perception | |
6949 | of losing information from a data set. This package provides tools to calculate | |
6950 | these limits on the basis of the mathematical properties of the distribution of | |
6951 | the analyzed items.") | |
6952 | (license license:gpl3))) | |
87b576aa | 6953 | |
6954 | (define-public r-slam | |
6955 | (package | |
6956 | (name "r-slam") | |
976ef4cd | 6957 | (version "0.1-47") |
87b576aa | 6958 | (source |
6959 | (origin | |
6960 | (method url-fetch) | |
6961 | (uri (cran-uri "slam" version)) | |
6962 | (sha256 | |
976ef4cd | 6963 | (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9")))) |
87b576aa | 6964 | (build-system r-build-system) |
6965 | (home-page "https://cran.r-project.org/web/packages/slam/") | |
6966 | (synopsis "Sparse lightweight arrays and matrices") | |
6967 | (description | |
6968 | "This package contains data structures and algorithms for sparse arrays and matrices, | |
6969 | based on index arrays and simple triplet representations, respectively.") | |
6970 | (license license:gpl2))) | |
881cc61c | 6971 | |
6972 | (define-public r-manipulatewidget | |
6973 | (package | |
6974 | (name "r-manipulatewidget") | |
6975 | (version "0.10.0") | |
6976 | (source | |
6977 | (origin | |
6978 | (method url-fetch) | |
6979 | (uri (cran-uri "manipulateWidget" version)) | |
6980 | (sha256 | |
6981 | (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x")))) | |
6982 | (properties | |
6983 | `((upstream-name . "manipulateWidget"))) | |
6984 | (build-system r-build-system) | |
6985 | (propagated-inputs | |
6986 | `(("r-base64enc" ,r-base64enc) | |
6987 | ("r-codetools" ,r-codetools) | |
6988 | ("r-htmltools" ,r-htmltools) | |
6989 | ("r-htmlwidgets" ,r-htmlwidgets) | |
6990 | ("r-knitr" ,r-knitr) | |
6991 | ("r-miniui" ,r-miniui) | |
6992 | ("r-shiny" ,r-shiny) | |
6993 | ("r-webshot" ,r-webshot))) | |
6994 | (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") | |
6995 | (synopsis "Add even more interactivity to interactive charts") | |
6996 | (description | |
6997 | "This package lets you create in just a few lines of R code a nice user interface to | |
6998 | modify the data or the graphical parameters of one or multiple interactive | |
6999 | charts. It is useful to quickly explore visually some data or for package | |
7000 | developers to generate user interfaces easy to maintain.") | |
7001 | (license license:gpl2+))) | |
16b0e8da | 7002 | |
7003 | (define-public r-a3 | |
7004 | (package | |
7005 | (name "r-a3") | |
7006 | (version "1.0.0") | |
7007 | (source | |
7008 | (origin | |
7009 | (method url-fetch) | |
7010 | (uri (cran-uri "A3" version)) | |
7011 | (sha256 | |
7012 | (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) | |
7013 | (properties `((upstream-name . "A3"))) | |
7014 | (build-system r-build-system) | |
7015 | (propagated-inputs | |
7016 | `(("r-pbapply" ,r-pbapply) | |
7017 | ("r-xtable" ,r-xtable))) | |
7018 | (home-page "https://cran.r-project.org/web/packages/A3/") | |
7019 | (synopsis "Error metrics for predictive models") | |
7020 | (description | |
7021 | "This package supplies tools for tabulating and analyzing the results of predictive | |
7022 | models. The methods employed are applicable to virtually any predictive model | |
7023 | and make comparisons between different methodologies straightforward.") | |
7024 | (license license:gpl2+))) | |
59b55def RW |
7025 | |
7026 | (define-public r-infotheo | |
7027 | (package | |
7028 | (name "r-infotheo") | |
7029 | (version "1.2.0") | |
7030 | (source | |
7031 | (origin | |
7032 | (method url-fetch) | |
7033 | (uri (cran-uri "infotheo" version)) | |
7034 | (sha256 | |
7035 | (base32 | |
7036 | "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv")))) | |
7037 | (build-system r-build-system) | |
7038 | (home-page "http://homepage.meyerp.com/software") | |
7039 | (synopsis "Information-theoretic measures") | |
7040 | (description | |
7041 | "This package implements various measures of information theory based on | |
7042 | several entropy estimators.") | |
7043 | (license license:gpl3+))) | |
9e21f217 | 7044 | |
7045 | (define-public r-abcoptim | |
7046 | (package | |
7047 | (name "r-abcoptim") | |
7048 | (version "0.15.0") | |
7049 | (source | |
7050 | (origin | |
7051 | (method url-fetch) | |
7052 | (uri (cran-uri "ABCoptim" version)) | |
7053 | (sha256 | |
7054 | (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) | |
7055 | (properties `((upstream-name . "ABCoptim"))) | |
7056 | (build-system r-build-system) | |
7057 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
7058 | (home-page "https://github.com/gvegayon/ABCoptim/") | |
7059 | (synopsis "Optimization of Artificial Bee Colony algorithm") | |
7060 | (description | |
7061 | "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis | |
7062 | Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as | |
7063 | simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) | |
7064 | algorithms, and uses only common control parameters such as colony size and | |
7065 | maximum cycle number. The @code{r-abcoptim} implements the Artificial bee | |
7066 | colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. | |
7067 | This version is a work-in-progress and is written in R code.") | |
7068 | (license license:expat))) | |
40c10917 | 7069 | |
7070 | (define-public r-abcp2 | |
7071 | (package | |
7072 | (name "r-abcp2") | |
7073 | (version "1.2") | |
7074 | (source | |
7075 | (origin | |
7076 | (method url-fetch) | |
7077 | (uri (cran-uri "ABCp2" version)) | |
7078 | (sha256 | |
7079 | (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) | |
7080 | (properties `((upstream-name . "ABCp2"))) | |
7081 | (build-system r-build-system) | |
7082 | (propagated-inputs `(("r-mass" ,r-mass))) | |
7083 | (home-page "https://cran.r-project.org/web/packages/ABCp2/") | |
7084 | (synopsis "Approximate Bayesian Computational Model for Estimating P2") | |
7085 | (description | |
7086 | "This package tests the goodness of fit of a distribution of offspring to the Normal, | |
7087 | Poisson, and Gamma distribution and estimates the proportional paternity of the | |
7088 | second male (P2) based on the best fit distribution.") | |
7089 | (license license:gpl2))) | |
cadc10a5 | 7090 | |
7091 | (define-public r-abcrf | |
7092 | (package | |
7093 | (name "r-abcrf") | |
1a6fe7c9 | 7094 | (version "1.8.1") |
cadc10a5 | 7095 | (source |
7096 | (origin | |
7097 | (method url-fetch) | |
7098 | (uri (cran-uri "abcrf" version)) | |
7099 | (sha256 | |
1a6fe7c9 | 7100 | (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27")))) |
cadc10a5 | 7101 | (build-system r-build-system) |
7102 | (propagated-inputs | |
89afd031 RW |
7103 | `(("r-doparallel" ,r-doparallel) |
7104 | ("r-foreach" ,r-foreach) | |
7105 | ("r-mass" ,r-mass) | |
cadc10a5 | 7106 | ("r-matrixstats" ,r-matrixstats) |
7107 | ("r-ranger" ,r-ranger) | |
7108 | ("r-rcpp" ,r-rcpp) | |
7109 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
7110 | ("r-readr" ,r-readr) | |
7111 | ("r-stringr" ,r-stringr))) | |
7112 | (home-page "https://cran.r-project.org/web/packages/abcrf/") | |
7113 | (synopsis "Approximate bayesian computation via random forests") | |
7114 | (description | |
7115 | "This package performs approximate bayesian computation (ABC) model choice and | |
7116 | parameter inference via random forests. This machine learning tool named random | |
7117 | forests (RF) can conduct selection among the highly complex models covered by | |
7118 | ABC algorithms.") | |
7119 | (license license:gpl2+))) | |
12da2a5e | 7120 | |
7121 | (define-public r-abctools | |
7122 | (package | |
7123 | (name "r-abctools") | |
7124 | (version "1.1.3") | |
7125 | (source | |
7126 | (origin | |
7127 | (method url-fetch) | |
7128 | (uri (cran-uri "abctools" version)) | |
7129 | (sha256 | |
7130 | (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) | |
7131 | (build-system r-build-system) | |
7132 | (propagated-inputs | |
7133 | `(("r-abc" ,r-abc) | |
7134 | ("r-abind" ,r-abind) | |
7135 | ("r-hmisc" ,r-hmisc) | |
7136 | ("r-plyr" ,r-plyr))) | |
7137 | (home-page "https://github.com/dennisprangle/abctools/") | |
7138 | (synopsis "Tools for ABC analyses") | |
7139 | (description | |
7140 | "This @code{r-abctools} package provides tools for approximate Bayesian computation | |
7141 | including summary statistic selection and assessing coverage. This includes | |
7142 | recent dimension reduction algorithms to tune the choice of summary statistics, | |
7143 | and coverage methods to tune the choice of threshold.") | |
7144 | (license license:gpl2+))) | |
77b33e0e | 7145 | |
7146 | (define-public r-ggstance | |
7147 | (package | |
7148 | (name "r-ggstance") | |
b3aa0d2f | 7149 | (version "0.3.3") |
77b33e0e | 7150 | (source |
7151 | (origin | |
7152 | (method url-fetch) | |
7153 | (uri (cran-uri "ggstance" version)) | |
7154 | (sha256 | |
b3aa0d2f | 7155 | (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh")))) |
77b33e0e | 7156 | (build-system r-build-system) |
7157 | (propagated-inputs | |
7158 | `(("r-ggplot2" ,r-ggplot2) | |
7159 | ("r-plyr" ,r-plyr) | |
7160 | ("r-rlang" ,r-rlang) | |
7161 | ("r-withr" ,r-withr))) | |
7162 | (home-page "https://cran.r-project.org/web/packages/ggstance/") | |
7163 | (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") | |
7164 | (description | |
7165 | "This package is a @code{r-ggplot2} extension that provides flipped components: | |
7166 | @enumerate | |
7167 | @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms; | |
7168 | @item vertical versions of @code{r-ggplot2} positions. | |
7169 | @end enumerate") | |
7170 | (license license:gpl3))) | |
c61f7bc5 | 7171 | |
7172 | (define-public r-mosaiccore | |
7173 | (package | |
7174 | (name "r-mosaiccore") | |
7175 | (version "0.6.0") | |
7176 | (source | |
7177 | (origin | |
7178 | (method url-fetch) | |
7179 | (uri (cran-uri "mosaicCore" version)) | |
7180 | (sha256 | |
7181 | (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z")))) | |
7182 | (properties `((upstream-name . "mosaicCore"))) | |
7183 | (build-system r-build-system) | |
7184 | (propagated-inputs | |
7185 | `(("r-dplyr" ,r-dplyr) | |
7186 | ("r-lazyeval" ,r-lazyeval) | |
7187 | ("r-mass" ,r-mass) | |
7188 | ("r-rlang" ,r-rlang) | |
7189 | ("r-tidyr" ,r-tidyr))) | |
7190 | (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") | |
7191 | (synopsis "Common utilities for mosaic family packages") | |
7192 | (description | |
7193 | "Common utilities used in other Mosaic family packages are collected here.") | |
7194 | (license license:gpl2+))) | |
214452ff | 7195 | |
7196 | (define-public r-ggformula | |
7197 | (package | |
7198 | (name "r-ggformula") | |
9a470682 | 7199 | (version "0.9.2") |
214452ff | 7200 | (source |
7201 | (origin | |
7202 | (method url-fetch) | |
7203 | (uri (cran-uri "ggformula" version)) | |
7204 | (sha256 | |
9a470682 | 7205 | (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr")))) |
214452ff | 7206 | (build-system r-build-system) |
7207 | (propagated-inputs | |
7208 | `(("r-ggplot2" ,r-ggplot2) | |
7209 | ("r-ggstance" ,r-ggstance) | |
7210 | ("r-magrittr" ,r-magrittr) | |
7211 | ("r-mosaiccore" ,r-mosaiccore) | |
7212 | ("r-rlang" ,r-rlang) | |
7213 | ("r-stringr" ,r-stringr) | |
7214 | ("r-tibble" ,r-tibble) | |
7215 | ("r-tidyr" ,r-tidyr))) | |
7216 | (home-page "https://github.com/ProjectMOSAIC/ggformula/") | |
7217 | (synopsis "Formula interface for the @code{r-ggplot2}") | |
7218 | (description | |
7219 | "The @code{r-ggformula} introduces a family of graphics functions, gf_point(), | |
7220 | gf_density(), and so on, bring the formula interface to ggplot(). This captures | |
7221 | and extends the excellent simplicity of the lattice-graphics formula interface, | |
7222 | while providing the intuitive capabilities of @code{r-ggplot2}.") | |
7223 | (license license:expat))) | |
2f195b6f | 7224 | |
7225 | (define-public r-mosaicdata | |
7226 | (package | |
7227 | (name "r-mosaicdata") | |
7228 | (version "0.17.0") | |
7229 | (source | |
7230 | (origin | |
7231 | (method url-fetch) | |
7232 | (uri (cran-uri "mosaicData" version)) | |
7233 | (sha256 | |
7234 | (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9")))) | |
7235 | (properties `((upstream-name . "mosaicData"))) | |
7236 | (build-system r-build-system) | |
7237 | (home-page "https://cran.r-project.org/web/packages/mosaicData/") | |
7238 | (synopsis "Data sets for project Mosaic") | |
7239 | (description | |
7240 | "This package provides data sets from project Mosaic @url{http://mosaic-web.org} | |
7241 | used to teach mathematics, statistics, computation and modeling.") | |
7242 | (license license:gpl2+))) | |
6c6ce2d0 | 7243 | |
82acd43c RW |
7244 | (define-public r-raster |
7245 | (package | |
7246 | (name "r-raster") | |
e7c8c685 | 7247 | (version "3.0-7") |
82acd43c RW |
7248 | (source |
7249 | (origin | |
7250 | (method url-fetch) | |
7251 | (uri (cran-uri "raster" version)) | |
7252 | (sha256 | |
7253 | (base32 | |
e7c8c685 | 7254 | "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn")))) |
82acd43c RW |
7255 | (build-system r-build-system) |
7256 | (propagated-inputs | |
7257 | `(("r-rcpp" ,r-rcpp) | |
7258 | ("r-sp" ,r-sp))) | |
aff13de3 | 7259 | (home-page "https://www.rspatial.org/") |
82acd43c RW |
7260 | (synopsis "Geographic data analysis and modeling") |
7261 | (description | |
7262 | "The package implements basic and high-level functions for reading, | |
7263 | writing, manipulating, analyzing and modeling of gridded spatial data. | |
7264 | Processing of very large files is supported.") | |
7265 | (license license:gpl3+))) | |
7266 | ||
6c6ce2d0 | 7267 | (define-public r-mosaic |
7268 | (package | |
7269 | (name "r-mosaic") | |
7270 | (version "1.4.0") | |
7271 | (source | |
7272 | (origin | |
7273 | (method url-fetch) | |
7274 | (uri (cran-uri "mosaic" version)) | |
7275 | (sha256 | |
7276 | (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2")))) | |
7277 | (build-system r-build-system) | |
7278 | (propagated-inputs | |
7279 | `(("r-broom" ,r-broom) | |
7280 | ("r-dplyr" ,r-dplyr) | |
7281 | ("r-ggdendro" ,r-ggdendro) | |
7282 | ("r-ggformula" ,r-ggformula) | |
7283 | ("r-ggplot2" ,r-ggplot2) | |
7284 | ("r-ggrepel" ,r-ggrepel) | |
7285 | ("r-glue" ,r-glue) | |
7286 | ("r-gridextra" ,r-gridextra) | |
7287 | ("r-lattice" ,r-lattice) | |
7288 | ("r-latticeextra" ,r-latticeextra) | |
7289 | ("r-lazyeval" ,r-lazyeval) | |
7290 | ("r-mass" ,r-mass) | |
7291 | ("r-matrix" ,r-matrix) | |
7292 | ("r-mosaiccore" ,r-mosaiccore) | |
7293 | ("r-mosaicdata" ,r-mosaicdata) | |
7294 | ("r-readr" ,r-readr) | |
7295 | ("r-tidyr" ,r-tidyr))) | |
7296 | (home-page "https://github.com/ProjectMOSAIC/mosaic/") | |
7297 | (synopsis "Mathematics, statistics, and computation teaching utilities") | |
7298 | (description | |
7299 | "This package contain data sets and utilities from | |
7300 | @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics, | |
7301 | statistics, computation and modeling. Project MOSAIC is a community of | |
7302 | educators working to tie together aspects of quantitative work that students | |
7303 | in science, technology, engineering and mathematics will need in their | |
7304 | professional lives, but which are usually taught in isolation, if at all.") | |
7305 | (license license:gpl2+))) | |
cbb0edd1 | 7306 | |
7307 | (define-public r-abd | |
7308 | (package | |
7309 | (name "r-abd") | |
7310 | (version "0.2-8") | |
7311 | (source | |
7312 | (origin | |
7313 | (method url-fetch) | |
7314 | (uri (cran-uri "abd" version)) | |
7315 | (sha256 | |
7316 | (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7")))) | |
7317 | (build-system r-build-system) | |
7318 | (propagated-inputs | |
7319 | `(("r-lattice" ,r-lattice) | |
7320 | ("r-mosaic" ,r-mosaic) | |
7321 | ("r-nlme" ,r-nlme))) | |
7322 | (home-page "https://cran.r-project.org/web/packages/abd/") | |
7323 | (synopsis "Analysis of biological data") | |
7324 | (description | |
7325 | "The @code{r-abd} package contains data sets and sample code for the Analysis of | |
7326 | biological data by Michael Whitlock and Dolph Schluter.") | |
7327 | (license license:gpl2))) | |
01af264d MIP |
7328 | |
7329 | (define-public r-svgui | |
7330 | (package | |
7331 | (name "r-svgui") | |
7332 | (version "1.0.0") | |
7333 | (source | |
7334 | (origin | |
7335 | (method url-fetch) | |
7336 | (uri (cran-uri "svGUI" version)) | |
7337 | (sha256 | |
7338 | (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc")))) | |
7339 | (properties `((upstream-name . "svGUI"))) | |
7340 | (build-system r-build-system) | |
7341 | (home-page "https://github.com/SciViews/svGUI/") | |
7342 | (synopsis "Functions for managing GUI clients in R") | |
7343 | (description | |
7344 | "The SciViews @code{svGUI} package eases the management of Graphical User | |
7345 | Interfaces (GUI) in R. It is independent from any particular GUI widgets. It | |
7346 | centralizes info about GUI elements currently used, and it dispatches GUI | |
7347 | calls to the particular toolkits in use in function of the context.") | |
7348 | (license license:gpl2))) | |
d1ca3d72 | 7349 | |
7350 | (define-public r-svdialogs | |
7351 | (package | |
7352 | (name "r-svdialogs") | |
7353 | (version "1.0.0") | |
7354 | (source | |
7355 | (origin | |
7356 | (method url-fetch) | |
7357 | (uri (cran-uri "svDialogs" version)) | |
7358 | (sha256 | |
7359 | (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97")))) | |
7360 | (properties `((upstream-name . "svDialogs"))) | |
7361 | (build-system r-build-system) | |
7362 | (inputs | |
7363 | `(("yad" ,yad) | |
7364 | ("zenity" ,zenity))) | |
7365 | (propagated-inputs | |
7366 | `(("r-rstudioapi" ,r-rstudioapi) | |
7367 | ("r-svgui" ,r-svgui))) | |
7368 | (home-page "https://github.com/SciViews/svDialogs/") | |
7369 | (synopsis "Portable dialog boxes") | |
7370 | (description | |
7371 | "This package helps to construct standard dialog boxes for your GUI, including | |
7372 | message boxes, input boxes, list, file or directory selection, and others. In | |
7373 | case R cannot display GUI dialog boxes, a simpler command line version of these | |
7374 | interactive elements is also provided as a fallback solution.") | |
7375 | (license license:gpl2))) | |
3cadd3ce | 7376 | |
7377 | (define-public r-abe | |
7378 | (package | |
7379 | (name "r-abe") | |
7380 | (version "3.0.1") | |
7381 | (source | |
7382 | (origin | |
7383 | (method url-fetch) | |
7384 | (uri (cran-uri "abe" version)) | |
7385 | (sha256 | |
7386 | (base32 | |
7387 | "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6")))) | |
7388 | (build-system r-build-system) | |
7389 | (home-page "https://cran.r-project.org/web/packages/abe/") | |
7390 | (synopsis "Augmented backward elimination") | |
7391 | (description | |
7392 | "This package performs augmented backward elimination and checks the | |
7393 | stability of the obtained model. Augmented backward elimination combines | |
7394 | significance or information based criteria with the change in estimate to | |
7395 | either select the optimal model for prediction purposes or to serve as a tool | |
7396 | to obtain a practically sound, highly interpretable model.") | |
7397 | (license license:gpl2+))) | |
ef26400b | 7398 | |
7399 | (define-public r-abf2 | |
7400 | (package | |
7401 | (name "r-abf2") | |
7402 | (version "0.7-1") | |
7403 | (source | |
7404 | (origin | |
7405 | (method url-fetch) | |
7406 | (uri (cran-uri "abf2" version)) | |
7407 | (sha256 | |
7408 | (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx")))) | |
7409 | (build-system r-build-system) | |
7410 | (home-page "https://cran.r-project.org/web/packages/abf2/") | |
7411 | (synopsis "Load gap-free axon @code{r-abf2} files") | |
7412 | (description | |
7413 | "This package loads electrophysiology data from ABF2 files, as created by | |
7414 | Axon Instruments/Molecular Devices software. Only files recorded in gap-free | |
7415 | mode are currently supported.") | |
7416 | (license license:artistic2.0))) | |
1efcd0f1 | 7417 | |
7418 | (define-public r-abhgenotyper | |
7419 | (package | |
7420 | (name "r-abhgenotyper") | |
7421 | (version "1.0.1") | |
7422 | (source | |
7423 | (origin | |
7424 | (method url-fetch) | |
7425 | (uri (cran-uri "ABHgenotypeR" version)) | |
7426 | (sha256 | |
7427 | (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l")))) | |
7428 | (properties `((upstream-name . "ABHgenotypeR"))) | |
7429 | (build-system r-build-system) | |
7430 | (propagated-inputs | |
7431 | `(("r-ggplot2" ,r-ggplot2) | |
7432 | ("r-reshape2" ,r-reshape2))) | |
7433 | (home-page "https://github.com/StefanReuscher/ABHgenotypeR/") | |
7434 | (synopsis "Visualize and manipulate ABH genotypes") | |
7435 | (description | |
7436 | "The @code{r-abhgenotyper} package provides simple imputation, | |
7437 | error-correction and plotting capacities for genotype data. The package is | |
7438 | supposed to serve as an intermediate but independent analysis tool between the | |
7439 | TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities | |
7440 | not found in either TASSEL or @code{r-qtl} in addition to visualization of | |
7441 | genotypes as \"graphical genotypes\".") | |
7442 | (license license:gpl3))) | |
ebb3cdb1 | 7443 | |
6e8b38d3 RW |
7444 | (define-public r-furrr |
7445 | (package | |
7446 | (name "r-furrr") | |
7447 | (version "0.1.0") | |
7448 | (source | |
7449 | (origin | |
7450 | (method url-fetch) | |
7451 | (uri (cran-uri "furrr" version)) | |
7452 | (sha256 | |
7453 | (base32 | |
7454 | "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx")))) | |
7455 | (build-system r-build-system) | |
7456 | (propagated-inputs | |
7457 | `(("r-future" ,r-future) | |
7458 | ("r-globals" ,r-globals) | |
7459 | ("r-purrr" ,r-purrr) | |
7460 | ("r-rlang" ,r-rlang))) | |
7461 | (home-page "https://github.com/DavisVaughan/furrr") | |
7462 | (synopsis "Apply mapping functions in parallel using futures") | |
7463 | (description | |
7464 | "This package provides implementations of the family of @code{map()} | |
7465 | functions from the @code{purrr} package that can be resolved using any | |
7466 | @code{future}-supported backend, e.g. parallel on the local machine or | |
7467 | distributed on a compute cluster.") | |
7468 | (license license:lgpl2.1+))) | |
7469 | ||
ebb3cdb1 | 7470 | (define-public r-abjutils |
7471 | (package | |
7472 | (name "r-abjutils") | |
3d5bcae0 | 7473 | (version "0.2.3") |
ebb3cdb1 | 7474 | (source |
7475 | (origin | |
7476 | (method url-fetch) | |
7477 | (uri (cran-uri "abjutils" version)) | |
7478 | (sha256 | |
3d5bcae0 | 7479 | (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv")))) |
ebb3cdb1 | 7480 | (build-system r-build-system) |
7481 | (propagated-inputs | |
7482 | `(("r-devtools" ,r-devtools) | |
7483 | ("r-dplyr" ,r-dplyr) | |
3d5bcae0 RW |
7484 | ("r-furrr" ,r-furrr) |
7485 | ("r-future" ,r-future) | |
ebb3cdb1 | 7486 | ("r-glue" ,r-glue) |
7487 | ("r-httr" ,r-httr) | |
7488 | ("r-magrittr" ,r-magrittr) | |
ebb3cdb1 | 7489 | ("r-progress" ,r-progress) |
7490 | ("r-purrr" ,r-purrr) | |
3d5bcae0 RW |
7491 | ("r-readr" ,r-readr) |
7492 | ("r-rlang" ,r-rlang) | |
ebb3cdb1 | 7493 | ("r-rstudioapi" ,r-rstudioapi) |
7494 | ("r-scales" ,r-scales) | |
7495 | ("r-stringi" ,r-stringi) | |
7496 | ("r-stringr" ,r-stringr) | |
7497 | ("r-tibble" ,r-tibble) | |
7498 | ("r-tidyr" ,r-tidyr))) | |
7499 | (home-page "https://github.com/abjur/abjutils/") | |
7500 | (synopsis "Collection of tools for jurimetrical analysis") | |
7501 | (description | |
7502 | "This package implements general purpose tools, such as functions for | |
7503 | sampling and basic manipulation of Brazilian lawsuits identification number. | |
7504 | It also implements functions for text cleaning, such as accentuation | |
7505 | removal.") | |
7506 | (license license:expat))) | |
b6afe7b7 | 7507 | |
7508 | (define-public r-abnormality | |
7509 | (package | |
7510 | (name "r-abnormality") | |
7511 | (version "0.1.0") | |
7512 | (source | |
7513 | (origin | |
7514 | (method url-fetch) | |
7515 | (uri (cran-uri "abnormality" version)) | |
7516 | (sha256 | |
7517 | (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) | |
7518 | (build-system r-build-system) | |
7519 | (propagated-inputs | |
7520 | `(("r-mass" ,r-mass) | |
7521 | ("r-matrix" ,r-matrix))) | |
7522 | (home-page "https://cran.r-project.org/web/packages/abnormality/") | |
7523 | (synopsis "Measure a subject's abnormality with respect to a reference population") | |
7524 | (description | |
7525 | "This package contains functions to implement the methodology and | |
7526 | considerations laid out by Marks et al. in the article \"Measuring abnormality | |
7527 | in high dimensional spaces: applications in biomechanical gait analysis\". | |
7528 | Using high-dimensional datasets to measure a subject's overall level of | |
7529 | abnormality as compared to a reference population is often needed in outcomes | |
7530 | research.") | |
7531 | (license license:expat))) | |
016cabf7 | 7532 | |
7533 | (define-public r-abodoutlier | |
7534 | (package | |
7535 | (name "r-abodoutlier") | |
7536 | (version "0.1") | |
7537 | (source | |
7538 | (origin | |
7539 | (method url-fetch) | |
7540 | (uri (cran-uri "abodOutlier" version)) | |
7541 | (sha256 | |
7542 | (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj")))) | |
7543 | (properties `((upstream-name . "abodOutlier"))) | |
7544 | (build-system r-build-system) | |
7545 | (propagated-inputs | |
7546 | `(("r-cluster" ,r-cluster))) | |
7547 | (home-page "https://cran.r-project.org/web/packages/abodOutlier/") | |
7548 | (synopsis "Angle-based outlier detection") | |
7549 | (description | |
7550 | "This package performs angle-based outlier detection on a given data | |
7551 | frame. It offers three methods to process data: | |
7552 | @enumerate | |
7553 | @item full but slow implementation using all the data that has cubic | |
7554 | complexity; | |
7555 | @item a fully randomized method; | |
7556 | @item a method using k-nearest neighbours. | |
7557 | @end enumerate | |
7558 | These algorithms are well suited for high dimensional data outlier | |
7559 | detection.") | |
7560 | (license license:expat))) | |
03c95f04 | 7561 | |
7562 | (define-public r-abps | |
7563 | (package | |
7564 | (name "r-abps") | |
bec74196 | 7565 | (version "0.3") |
03c95f04 | 7566 | (source |
7567 | (origin | |
7568 | (method url-fetch) | |
7569 | (uri (cran-uri "ABPS" version)) | |
7570 | (sha256 | |
bec74196 | 7571 | (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) |
03c95f04 | 7572 | (properties `((upstream-name . "ABPS"))) |
7573 | (build-system r-build-system) | |
7574 | (propagated-inputs `(("r-kernlab" ,r-kernlab))) | |
7575 | (home-page "https://cran.r-project.org/web/packages/ABPS/") | |
7576 | (synopsis "Abnormal blood profile score to detect blood doping") | |
7577 | (description | |
7578 | "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS). | |
7579 | The ABPS is a part of the Athlete biological passport program of the World | |
7580 | anti-doping agency, which combines several blood parameters into a single | |
7581 | score in order to detect blood doping. The package also contains functions to | |
7582 | calculate other scores used in anti-doping programs, such as the ratio of | |
7583 | hemoglobin to reticulocytes (OFF-score), as well as example data.") | |
7584 | (license license:gpl2+))) | |
26358ac5 RW |
7585 | |
7586 | (define-public r-parmigene | |
7587 | (package | |
7588 | (name "r-parmigene") | |
7589 | (version "1.0.2") | |
7590 | (source | |
7591 | (origin | |
7592 | (method url-fetch) | |
7593 | (uri (cran-uri "parmigene" version)) | |
7594 | (sha256 | |
7595 | (base32 | |
7596 | "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d")))) | |
7597 | (build-system r-build-system) | |
7598 | (home-page "https://cran.r-project.org/web/packages/parmigene/") | |
7599 | (synopsis "Mutual information estimation for gene network reconstruction") | |
7600 | (description | |
7601 | "This package provides a parallel estimation of the mutual information | |
7602 | based on entropy estimates from k-nearest neighbors distances and algorithms | |
7603 | for the reconstruction of gene regulatory networks.") | |
7604 | (license license:agpl3+))) | |
b2bf43b2 | 7605 | |
7606 | (define-public r-pscl | |
7607 | (package | |
7608 | (name "r-pscl") | |
7609 | (version "1.5.2") | |
7610 | (source | |
7611 | (origin | |
7612 | (method url-fetch) | |
7613 | (uri (cran-uri "pscl" version)) | |
7614 | (sha256 | |
7615 | (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc")))) | |
7616 | (build-system r-build-system) | |
7617 | (propagated-inputs | |
7618 | `(("r-mass" ,r-mass))) | |
7619 | (home-page "https://github.com/atahk/pscl/") | |
7620 | (synopsis "Political science computational laboratory") | |
7621 | (description | |
7622 | "The @code{pscl} is an R package providing classes and methods for: | |
7623 | @enumerate | |
7624 | @item Bayesian analysis of roll call data (item-response models); | |
7625 | @item elementary Bayesian statistics; | |
7626 | @item maximum likelihood estimation of zero-inflated and hurdle models for count | |
7627 | data; | |
7628 | @item utility functions. | |
7629 | @end enumerate") | |
7630 | (license license:gpl2))) | |
e710d1a4 | 7631 | |
7632 | (define-public r-accelmissing | |
7633 | (package | |
7634 | (name "r-accelmissing") | |
7635 | (version "1.4") | |
7636 | (source | |
7637 | (origin | |
7638 | (method url-fetch) | |
7639 | (uri (cran-uri "accelmissing" version)) | |
7640 | (sha256 | |
7641 | (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) | |
7642 | (build-system r-build-system) | |
7643 | (propagated-inputs | |
7644 | `(("r-mice" ,r-mice) | |
7645 | ("r-pscl" ,r-pscl))) | |
7646 | (home-page "https://cran.r-project.org/web/packages/accelmissing/") | |
7647 | (synopsis "Missing value imputation for accelerometer data") | |
7648 | (description | |
7649 | "This package provides a statistical method to impute the missing values in | |
7650 | accelerometer data. The methodology includes both parametric and | |
7651 | semi-parametric multiple imputations under the zero-inflated Poisson lognormal | |
7652 | model. It also provides multiple functions to preprocess the accelerometer data | |
7653 | previous to the missing data imputation. These include detecting the wearing | |
7654 | and the non-wearing time, selecting valid days and subjects, and creating plots.") | |
7655 | (license license:gpl2+))) | |
f359b115 | 7656 | |
7657 | (define-public r-mhsmm | |
7658 | (package | |
7659 | (name "r-mhsmm") | |
7660 | (version "0.4.16") | |
7661 | (source | |
7662 | (origin | |
7663 | (method url-fetch) | |
7664 | (uri (cran-uri "mhsmm" version)) | |
7665 | (sha256 | |
7666 | (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) | |
7667 | (build-system r-build-system) | |
7668 | (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) | |
7669 | (home-page "https://github.com/jaredo/mhsmm/") | |
7670 | (synopsis "Inference for hidden Markov and semi-Markov models") | |
7671 | (description | |
7672 | "The @code{r-mhsmm} package implements estimation and prediction methods for | |
7673 | hidden Markov and semi-Markov models for multiple observation sequences. Such | |
7674 | techniques are of interest when observed data is thought to be dependent on some | |
7675 | unobserved (or hidden) state. Also, this package is suitable for equidistant | |
7676 | time series data, with multivariate and/or missing data. Allows user defined | |
7677 | emission distributions.") | |
7678 | (license license:gpl2+))) | |
16c5285a | 7679 | |
7680 | (define-public r-nleqslv | |
7681 | (package | |
7682 | (name "r-nleqslv") | |
7683 | (version "3.3.2") | |
7684 | (source | |
7685 | (origin | |
7686 | (method url-fetch) | |
7687 | (uri (cran-uri "nleqslv" version)) | |
7688 | (sha256 | |
7689 | (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) | |
7690 | (build-system r-build-system) | |
7691 | (native-inputs `(("gfortran" ,gfortran))) | |
7692 | (home-page "https://cran.r-project.org/web/packages/nleqslv/") | |
7693 | (synopsis "Solve systems of nonlinear equations") | |
7694 | (description | |
7695 | "The @code{r-nleqslv} package solves a system of nonlinear equations using a | |
7696 | Broyden or a Newton method with a choice of global strategies such as line | |
7697 | search and trust region. There are options for using a numerical or user | |
7698 | supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a | |
7699 | singular or ill-conditioned Jacobian.") | |
7700 | (license license:gpl2+))) | |
63ec2c50 | 7701 | |
7702 | (define-public r-physicalactivity | |
7703 | (package | |
7704 | (name "r-physicalactivity") | |
7705 | (version "0.2-2") | |
7706 | (source | |
7707 | (origin | |
7708 | (method url-fetch) | |
7709 | (uri (cran-uri "PhysicalActivity" version)) | |
7710 | (sha256 | |
7711 | (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln")))) | |
7712 | (properties | |
7713 | `((upstream-name . "PhysicalActivity"))) | |
7714 | (build-system r-build-system) | |
7715 | (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") | |
7716 | (synopsis "Procesing accelerometer data for physical activity measurement") | |
7717 | (description | |
7718 | "This @code{r-physicalactivity} package provides a function @code{wearingMarking} | |
7719 | for classification of monitor wear and nonwear time intervals in accelerometer | |
7720 | data collected to assess physical activity. The package also contains functions | |
7721 | for making plots of accelerometer data and obtaining the summary of various | |
7722 | information including daily monitor wear time and the mean monitor wear time | |
7723 | during valid days. The revised package version 0.2-1 improved the functions | |
7724 | regarding speed, robustness and add better support for time zones and daylight | |
7725 | saving. In addition, several functions were added: | |
7726 | @enumerate | |
7727 | @item the @code{markDelivery} can classify days for ActiGraph delivery by mail; | |
7728 | @item the @code{markPAI} can categorize physical activity intensity level based | |
7729 | on user-defined cut-points of accelerometer counts. | |
7730 | @end enumerate | |
7731 | It also supports importing ActiGraph (AGD) files with @code{readActigraph} and | |
7732 | @code{queryActigraph} functions.") | |
7733 | (license license:gpl3+))) | |
f95d4542 | 7734 | |
7735 | (define-public r-acc | |
7736 | (package | |
7737 | (name "r-acc") | |
7738 | (version "1.3.3") | |
7739 | (source | |
7740 | (origin | |
7741 | (method url-fetch) | |
7742 | (uri (cran-uri "acc" version)) | |
7743 | (sha256 | |
7744 | (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) | |
7745 | (build-system r-build-system) | |
7746 | (propagated-inputs | |
7747 | `(("r-circlize" ,r-circlize) | |
7748 | ("r-dbi" ,r-dbi) | |
7749 | ("r-ggplot2" ,r-ggplot2) | |
7750 | ("r-iterators" ,r-iterators) | |
7751 | ("r-mhsmm" ,r-mhsmm) | |
7752 | ("r-nleqslv" ,r-nleqslv) | |
7753 | ("r-physicalactivity" ,r-physicalactivity) | |
7754 | ("r-plyr" ,r-plyr) | |
7755 | ("r-r-utils" ,r-r-utils) | |
7756 | ("r-rcpp" ,r-rcpp) | |
7757 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
7758 | ("r-rsqlite" ,r-rsqlite) | |
7759 | ("r-zoo" ,r-zoo))) | |
7760 | (home-page "https://cran.r-project.org/web/packages/acc/") | |
7761 | (synopsis "Exploring accelerometer data") | |
7762 | (description | |
7763 | "This package processes accelerometer data from uni-axial and tri-axial devices | |
7764 | and generates data summaries. Also, includes functions to plot, analyze, and | |
7765 | simulate accelerometer data.") | |
7766 | (license license:gpl2+))) | |
f6890c08 | 7767 | |
7768 | (define-public r-rbenchmark | |
7769 | (package | |
7770 | (name "r-rbenchmark") | |
7771 | (version "1.0.0") | |
7772 | (source | |
7773 | (origin | |
7774 | (method url-fetch) | |
7775 | (uri (cran-uri "rbenchmark" version)) | |
7776 | (sha256 | |
7777 | (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9")))) | |
7778 | (build-system r-build-system) | |
7779 | (home-page "https://cran.r-project.org/web/packages/rbenchmark/") | |
7780 | (synopsis "Benchmarking routine for R") | |
7781 | (description | |
7782 | "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark, | |
7783 | and is intended to facilitate benchmarking of arbitrary R code. The library | |
7784 | consists of just one function, benchmark, which is a simple wrapper around | |
7785 | system.time. Given a specification of the benchmarking process (counts of | |
7786 | replications, evaluation environment) and an arbitrary number of expressions, | |
7787 | benchmark evaluates each of the expressions in the specified environment, | |
7788 | replicating the evaluation as many times as specified, and returning the results | |
7789 | conveniently wrapped into a data frame.") | |
7790 | (license license:gpl2+))) | |
7791 | ||
9c4f118b RW |
7792 | (define-public r-mitools |
7793 | (package | |
7794 | (name "r-mitools") | |
7795 | (version "2.4") | |
7796 | (source | |
7797 | (origin | |
7798 | (method url-fetch) | |
7799 | (uri (cran-uri "mitools" version)) | |
7800 | (sha256 | |
7801 | (base32 | |
7802 | "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j")))) | |
7803 | (build-system r-build-system) | |
7804 | (propagated-inputs `(("r-dbi" ,r-dbi))) | |
7805 | (home-page "https://cran.r-project.org/web/packages/mitools/") | |
7806 | (synopsis "Tools for multiple imputation of missing data") | |
7807 | (description | |
7808 | "This package provides tools to perform analyses and combine results from | |
7809 | multiple-imputation datasets.") | |
7810 | (license license:gpl2))) | |
7811 | ||
dab3e92c RW |
7812 | (define-public r-magick |
7813 | (package | |
7814 | (name "r-magick") | |
9c2d9780 | 7815 | (version "2.2") |
dab3e92c RW |
7816 | (source |
7817 | (origin | |
7818 | (method url-fetch) | |
7819 | (uri (cran-uri "magick" version)) | |
7820 | (sha256 | |
7821 | (base32 | |
9c2d9780 | 7822 | "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85")))) |
dab3e92c RW |
7823 | (build-system r-build-system) |
7824 | (inputs | |
7825 | `(("imagemagick" ,imagemagick) | |
7826 | ("zlib" ,zlib))) | |
7827 | (propagated-inputs | |
7828 | `(("r-curl" ,r-curl) | |
7829 | ("r-magrittr" ,r-magrittr) | |
7830 | ("r-rcpp" ,r-rcpp))) | |
7831 | (native-inputs | |
7832 | `(("pkg-config" ,pkg-config))) | |
7833 | (home-page "https://github.com/ropensci/magick") | |
7834 | (synopsis "Advanced graphics and image-processing in R") | |
7835 | (description | |
7836 | "This package provides bindings to ImageMagick, a comprehensive image | |
7837 | processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, | |
7838 | etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All | |
7839 | operations are vectorized via the Magick++ STL meaning they operate either on | |
7840 | a single frame or a series of frames for working with layers, collages, or | |
7841 | animation. In RStudio, images are automatically previewed when printed to the | |
7842 | console, resulting in an interactive editing environment.") | |
7843 | (license license:expat))) | |
7844 | ||
f0bff698 RW |
7845 | (define-public r-survey |
7846 | (package | |
7847 | (name "r-survey") | |
7b18fac4 | 7848 | (version "3.36") |
f0bff698 RW |
7849 | (source |
7850 | (origin | |
7851 | (method url-fetch) | |
7852 | (uri (cran-uri "survey" version)) | |
7853 | (sha256 | |
7854 | (base32 | |
7b18fac4 | 7855 | "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh")))) |
f0bff698 RW |
7856 | (build-system r-build-system) |
7857 | (propagated-inputs | |
7858 | `(("r-lattice" ,r-lattice) | |
7859 | ("r-matrix" ,r-matrix) | |
7860 | ("r-minqa" ,r-minqa) | |
7b18fac4 | 7861 | ("r-mitools" ,r-mitools) |
f0bff698 RW |
7862 | ("r-numderiv" ,r-numderiv) |
7863 | ("r-survival" ,r-survival))) | |
7864 | (home-page "http://r-survey.r-forge.r-project.org/survey/") | |
7865 | (synopsis "Analysis of complex survey samples") | |
7866 | (description | |
7867 | "This package provides tools for the analysis of complex survey samples. | |
7868 | The provided features include: summary statistics, two-sample tests, rank | |
7869 | tests, generalised linear models, cumulative link models, Cox models, | |
7870 | loglinear models, and general maximum pseudolikelihood estimation for | |
7871 | multistage stratified, cluster-sampled, unequally weighted survey samples; | |
7872 | variances by Taylor series linearisation or replicate weights; | |
7873 | post-stratification, calibration, and raking; two-phase subsampling designs; | |
7874 | graphics; PPS sampling without replacement; principal components, and factor | |
7875 | analysis.") | |
7876 | ;; Either version of the GPL. | |
7877 | (license (list license:gpl2 license:gpl3)))) | |
7878 | ||
5ba865a7 RW |
7879 | (define-public r-gee |
7880 | (package | |
7881 | (name "r-gee") | |
7882 | (version "4.13-20") | |
7883 | (source | |
7884 | (origin | |
7885 | (method url-fetch) | |
7886 | (uri (cran-uri "gee" version)) | |
7887 | (sha256 | |
7888 | (base32 | |
7889 | "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak")))) | |
7890 | (properties `((upstream-name . "gee"))) | |
7891 | (build-system r-build-system) | |
7892 | (native-inputs | |
7893 | `(("gfortran" ,gfortran))) | |
7894 | (home-page "https://cran.r-project.org/web/packages/gee/") | |
7895 | (synopsis "Generalized estimation equation solver") | |
7896 | (description | |
7897 | "This package provides a solver for generalized estimation equations.") | |
7898 | (license license:gpl2))) | |
7899 | ||
3b21f581 RW |
7900 | (define-public r-tab |
7901 | (package | |
7902 | (name "r-tab") | |
7903 | (version "4.1.1") | |
7904 | (source | |
7905 | (origin | |
7906 | (method url-fetch) | |
7907 | (uri (cran-uri "tab" version)) | |
7908 | (sha256 | |
7909 | (base32 | |
7910 | "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm")))) | |
7911 | (properties `((upstream-name . "tab"))) | |
7912 | (build-system r-build-system) | |
7913 | (propagated-inputs | |
7914 | `(("r-dplyr" ,r-dplyr) | |
7915 | ("r-gee" ,r-gee) | |
7916 | ("r-knitr" ,r-knitr) | |
7917 | ("r-mass" ,r-mass) | |
7918 | ("r-survey" ,r-survey) | |
7919 | ("r-survival" ,r-survival) | |
7920 | ("r-xtable" ,r-xtable))) | |
7921 | (home-page "https://cran.r-project.org/web/packages/tab/") | |
7922 | (synopsis "Create summary tables for statistical reports") | |
7923 | (description | |
7924 | "This package contains functions for creating various types of summary | |
7925 | tables, e.g. comparing characteristics across levels of a categorical variable | |
7926 | and summarizing fitted generalized linear models, generalized estimating | |
7927 | equations, and Cox proportional hazards models. Functions are available to | |
7928 | handle data from simple random samples as well as complex surveys.") | |
7929 | (license license:gpl3+))) | |
7930 | ||
7af2dd38 | 7931 | (define-public r-dvmisc |
7932 | (package | |
7933 | (name "r-dvmisc") | |
f6e75823 | 7934 | (version "1.1.4") |
7af2dd38 | 7935 | (source |
7936 | (origin | |
7937 | (method url-fetch) | |
7938 | (uri (cran-uri "dvmisc" version)) | |
7939 | (sha256 | |
f6e75823 | 7940 | (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) |
7af2dd38 | 7941 | (build-system r-build-system) |
7942 | (propagated-inputs | |
a6a87db8 RW |
7943 | `(("r-cubature" ,r-cubature) |
7944 | ("r-data-table" ,r-data-table) | |
7945 | ("r-dplyr" ,r-dplyr) | |
7946 | ("r-ggplot2" ,r-ggplot2) | |
7947 | ("r-mass" ,r-mass) | |
7948 | ("r-mvtnorm" ,r-mvtnorm) | |
7949 | ("r-pracma" ,r-pracma) | |
7af2dd38 | 7950 | ("r-rbenchmark" ,r-rbenchmark) |
a6a87db8 | 7951 | ("r-rcpp" ,r-rcpp) |
f6e75823 RW |
7952 | ("r-survey" ,r-survey) |
7953 | ("r-tab" ,r-tab))) | |
7af2dd38 | 7954 | (home-page "https://cran.r-project.org/web/packages/dvmisc/") |
7955 | (synopsis "Faster computation of common statistics and miscellaneous functions") | |
7956 | (description | |
7957 | "This package implements faster versions of base R functions (e.g. mean, standard | |
7958 | deviation, covariance, weighted mean), mostly written in C++, along with | |
7959 | miscellaneous functions for various purposes (e.g. create the histogram with | |
7960 | fitted probability density function or probability mass function curve, create | |
7961 | the body mass index groups, assess the linearity assumption in logistic | |
7962 | regression).") | |
7963 | (license license:gpl2))) | |
d8d8844e | 7964 | |
7965 | (define-public r-accelerometry | |
7966 | (package | |
7967 | (name "r-accelerometry") | |
7968 | (version "3.1.2") | |
7969 | (source | |
7970 | (origin | |
7971 | (method url-fetch) | |
7972 | (uri (cran-uri "accelerometry" version)) | |
7973 | (sha256 | |
7974 | (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) | |
7975 | (build-system r-build-system) | |
7976 | (propagated-inputs | |
7977 | `(("r-dvmisc" ,r-dvmisc) | |
7978 | ("r-rcpp" ,r-rcpp))) | |
7979 | (home-page "https://cran.r-project.org/web/packages/accelerometry/") | |
7980 | (synopsis "Functions for processing accelerometer data") | |
7981 | (description | |
7982 | "This package provides a collection of functions that perform operations on | |
7983 | time-series accelerometer data, such as identify the non-wear time, flag minutes | |
7984 | that are part of an activity bout, and find the maximum 10-minute average count | |
7985 | value. The functions are generally very flexible, allowing for a variety of | |
7986 | algorithms to be implemented.") | |
7987 | (license license:gpl3))) | |
1ddb2b5c | 7988 | |
7989 | (define-public r-absim | |
7990 | (package | |
7991 | (name "r-absim") | |
7992 | (version "0.2.6") | |
7993 | (source | |
7994 | (origin | |
7995 | (method url-fetch) | |
7996 | (uri (cran-uri "AbSim" version)) | |
7997 | (sha256 | |
7998 | (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) | |
7999 | (properties `((upstream-name . "AbSim"))) | |
8000 | (build-system r-build-system) | |
8001 | (propagated-inputs | |
8002 | `(("r-ape" ,r-ape) | |
8003 | ("r-powerlaw" ,r-powerlaw))) | |
8004 | (home-page "https://cran.r-project.org/web/packages/AbSim/") | |
8005 | (synopsis "Time resolved simulations of antibody repertoires") | |
8006 | (description | |
8007 | "This package provides simulation methods for the evolution of antibody repertoires. | |
8008 | The heavy and light chain variable region of both human and C57BL/6 mice can | |
8009 | be simulated in a time-dependent fashion. Both single lineages using one set of | |
8010 | V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins | |
8011 | with an initial V-D-J recombination event, starting the first phylogenetic tree. | |
8012 | Upon completion, the main loop of the algorithm begins, with each iteration | |
8013 | representing one simulated time step. Various mutation events are possible at | |
8014 | each time step, contributing to a diverse final repertoire.") | |
8015 | (license license:gpl2))) | |
c2ffc4fb | 8016 | |
b5a31005 MIP |
8017 | (define-public r-quic |
8018 | (package | |
8019 | (name "r-quic") | |
8020 | (version "1.1") | |
8021 | (source | |
8022 | (origin | |
8023 | (method url-fetch) | |
8024 | (uri (cran-uri "QUIC" version)) | |
8025 | (sha256 | |
8026 | (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) | |
8027 | (properties `((upstream-name . "QUIC"))) | |
8028 | (build-system r-build-system) | |
8029 | (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") | |
8030 | (synopsis "Regularized sparse inverse covariance matrix estimation") | |
8031 | (description | |
8032 | "This package implements the regularized Gaussian maximum likelihood | |
8033 | estimation of the inverse of a covariance matrix. It uses Newton's method and | |
8034 | coordinate descent to solve the regularized inverse covariance matrix | |
8035 | estimation problem.") | |
8036 | ;; The project home page states that the release is under GPLv3 or later. | |
8037 | ;; The CRAN page only says GPL-3. | |
8038 | (license license:gpl3+))) | |
8039 | ||
b509df82 MIP |
8040 | (define-public r-abundant |
8041 | (package | |
8042 | (name "r-abundant") | |
8043 | (version "1.1") | |
8044 | (source | |
8045 | (origin | |
8046 | (method url-fetch) | |
8047 | (uri (cran-uri "abundant" version)) | |
8048 | (sha256 | |
8049 | (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) | |
8050 | (build-system r-build-system) | |
8051 | (propagated-inputs | |
8052 | `(("r-quic" ,r-quic))) | |
8053 | (home-page "https://cran.r-project.org/web/packages/abundant/") | |
8054 | (synopsis "Abundant regression and high-dimensional principal fitted components") | |
8055 | (description | |
8056 | "This package provides tools to fit and predict with the high-dimensional | |
8057 | principal fitted components model. This model is described by Cook, Forzani, | |
8058 | and Rothman (2012) @url{doi:10.1214/11-AOS962}.") | |
8059 | ;; The DESCRIPTION file states GPL-2, but since it directly depends on a | |
8060 | ;; GPLv3+ package (QUIC) this likely means GPLv2+. | |
8061 | (license license:gpl2+))) | |
8062 | ||
c2ffc4fb | 8063 | (define-public r-ac3net |
8064 | (package | |
8065 | (name "r-ac3net") | |
8066 | (version "1.2.2") | |
8067 | (source | |
8068 | (origin | |
8069 | (method url-fetch) | |
8070 | (uri (cran-uri "Ac3net" version)) | |
8071 | (sha256 | |
8072 | (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) | |
8073 | (properties `((upstream-name . "Ac3net"))) | |
8074 | (build-system r-build-system) | |
8075 | (propagated-inputs | |
8076 | `(("r-data-table" ,r-data-table))) | |
8077 | (home-page "https://cran.r-project.org/web/packages/Ac3net/") | |
8078 | (synopsis "Inferring directional conservative causal core gene networks") | |
8079 | (description "This package infers directional Conservative causal core | |
8080 | (gene) networks (C3NET). This is a version of the algorithm C3NET with | |
8081 | directional network.") | |
8082 | (license license:gpl3+))) | |
da333859 | 8083 | |
8084 | (define-public r-aca | |
8085 | (package | |
8086 | (name "r-aca") | |
8087 | (version "1.1") | |
8088 | (source | |
8089 | (origin | |
8090 | (method url-fetch) | |
8091 | (uri (cran-uri "ACA" version)) | |
8092 | (sha256 | |
8093 | (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) | |
8094 | (properties `((upstream-name . "ACA"))) | |
8095 | (build-system r-build-system) | |
8096 | (home-page "https://cran.r-project.org/web/packages/ACA/") | |
8097 | (synopsis "Abrupt change-point or aberration detection in point series") | |
8098 | (description | |
8099 | "This package offers an interactive function for the detection of breakpoints in | |
8100 | series.") | |
8101 | ;; Any version of the GPL | |
8102 | (license (list license:gpl2+ license:gpl3+)))) | |
9c1c2108 | 8103 | |
8104 | (define-public r-acceptancesampling | |
8105 | (package | |
8106 | (name "r-acceptancesampling") | |
ddd168ff | 8107 | (version "1.0-6") |
9c1c2108 | 8108 | (source |
8109 | (origin | |
8110 | (method url-fetch) | |
8111 | (uri (cran-uri "AcceptanceSampling" version)) | |
8112 | (sha256 | |
ddd168ff | 8113 | (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9")))) |
9c1c2108 | 8114 | (properties |
8115 | `((upstream-name . "AcceptanceSampling"))) | |
8116 | (build-system r-build-system) | |
8117 | (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") | |
8118 | (synopsis "Creation and evaluation of acceptance sampling plans") | |
8119 | (description | |
8120 | "This @code{r-acceptancesampling} provides functionality for creating and evaluating | |
8121 | acceptance sampling plans. Acceptance sampling is a methodology commonly used | |
8122 | in quality control and improvement. International standards of acceptance | |
8123 | sampling provide sampling plans for specific circumstances. The aim of this | |
8124 | package is to provide an easy-to-use interface to visualize single, double or | |
8125 | multiple sampling plans. In addition, methods have been provided to enable the | |
8126 | user to assess sampling plans against pre-specified levels of performance, as | |
8127 | measured by the probability of acceptance for a given level of quality in the | |
8128 | lot.") | |
8129 | (license license:gpl3+))) | |
8130 | ||
63781c57 LF |
8131 | (define-public r-acclma |
8132 | (package | |
8133 | (name "r-acclma") | |
8134 | (version "1.0") | |
8135 | (source | |
8136 | (origin | |
8137 | (method url-fetch) | |
8138 | (uri (cran-uri "ACCLMA" version)) | |
8139 | (sha256 | |
8140 | (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) | |
8141 | (properties `((upstream-name . "ACCLMA"))) | |
8142 | (build-system r-build-system) | |
8143 | (home-page "https://cran.r-project.org/web/packages/ACCLMA/") | |
8144 | (synopsis "ACC & LMA graph plotting") | |
8145 | (description | |
666fb288 LC |
8146 | "This package contains a function that imports data from a @acronym{CSV, |
8147 | Comma-Separated Values} file, or uses manually entered data from the format (x, | |
8148 | y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration | |
8149 | Curve} vs @acronym{LOI, Line of Independence} graph and | |
8150 | @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main | |
8151 | function is @code{plotLMA} (source file, header) that takes a data set and plots the | |
63781c57 LF |
8152 | appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a |
8153 | string) was passed, a manual data entry window is opened. The header parameter | |
8154 | indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has | |
8155 | a header row or not. The dataset should contain only one independent variable | |
8156 | (x) and one dependent variable (y) and can contain a weight for each | |
8157 | observation.") | |
8158 | (license license:gpl2))) | |
b55697fb LL |
8159 | |
8160 | (define-public r-aspi | |
8161 | (package | |
8162 | (name "r-aspi") | |
8163 | (version "0.2.0") | |
8164 | (source | |
8165 | (origin | |
8166 | (method url-fetch) | |
8167 | (uri (cran-uri "aspi" version)) | |
8168 | (sha256 | |
8169 | (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) | |
8170 | (build-system r-build-system) | |
8171 | (home-page | |
8172 | "https://cran.r-project.org/web/packages/aspi/") | |
8173 | (synopsis | |
8174 | "Analysis of symmetry of parasitic infections") | |
8175 | (description | |
8176 | "This package provides tools for the analysis and visualization of bilateral | |
8177 | asymmetry in parasitic infections.") | |
8178 | (license license:gpl3+))) | |
302db585 RW |
8179 | |
8180 | (define-public r-sandwich | |
8181 | (package | |
8182 | (name "r-sandwich") | |
0eb306d3 | 8183 | (version "2.5-1") |
302db585 RW |
8184 | (source |
8185 | (origin | |
8186 | (method url-fetch) | |
8187 | (uri (cran-uri "sandwich" version)) | |
8188 | (sha256 | |
8189 | (base32 | |
0eb306d3 | 8190 | "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv")))) |
302db585 RW |
8191 | (build-system r-build-system) |
8192 | (propagated-inputs | |
8193 | `(("r-zoo" ,r-zoo))) | |
8194 | (home-page "https://cran.r-project.org/web/packages/sandwich/") | |
8195 | (synopsis "Robust Covariance Matrix Estimators") | |
8196 | (description | |
8197 | "This package provides model-robust standard error estimators for | |
8198 | cross-sectional, time series, clustered, panel, and longitudinal data.") | |
8199 | ;; Either version of the license. | |
8200 | (license (list license:gpl2 license:gpl3)))) | |
6ce07cf9 RW |
8201 | |
8202 | (define-public r-th-data | |
8203 | (package | |
8204 | (name "r-th-data") | |
62595ee3 | 8205 | (version "1.0-10") |
6ce07cf9 RW |
8206 | (source |
8207 | (origin | |
8208 | (method url-fetch) | |
8209 | (uri (cran-uri "TH.data" version)) | |
8210 | (sha256 | |
8211 | (base32 | |
62595ee3 | 8212 | "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1")))) |
6ce07cf9 RW |
8213 | (properties `((upstream-name . "TH.data"))) |
8214 | (build-system r-build-system) | |
8215 | (propagated-inputs | |
8216 | `(("r-mass" ,r-mass) | |
8217 | ("r-survival" ,r-survival))) | |
8218 | (home-page "https://cran.r-project.org/web/packages/TH.data/") | |
8219 | (synopsis "Shared data sets") | |
8220 | (description | |
8221 | "This package contains supporting data sets that are used in other | |
8222 | packages maintained by Torsten Hothorn.") | |
8223 | (license license:gpl3))) | |
7753b543 RW |
8224 | |
8225 | (define-public r-multcomp | |
8226 | (package | |
8227 | (name "r-multcomp") | |
f92c0c1e | 8228 | (version "1.4-11") |
7753b543 RW |
8229 | (source |
8230 | (origin | |
8231 | (method url-fetch) | |
8232 | (uri (cran-uri "multcomp" version)) | |
8233 | (sha256 | |
8234 | (base32 | |
f92c0c1e | 8235 | "0jw9661hs4396wz9vflk3rak0ryzj1cg2pnndsn1gb4fjyf2vlhb")))) |
7753b543 RW |
8236 | (build-system r-build-system) |
8237 | (propagated-inputs | |
8238 | `(("r-codetools" ,r-codetools) | |
8239 | ("r-mvtnorm" ,r-mvtnorm) | |
8240 | ("r-sandwich" ,r-sandwich) | |
8241 | ("r-survival" ,r-survival) | |
8242 | ("r-th-data" ,r-th-data))) | |
8243 | (home-page "https://cran.r-project.org/web/packages/multcomp/") | |
8244 | (synopsis "Simultaneous inference in general parametric models") | |
8245 | (description | |
8246 | "Simultaneous tests and confidence intervals for general linear | |
8247 | hypotheses in parametric models, including linear, generalized linear, linear | |
8248 | mixed effects, and survival models. The package includes demos reproducing | |
8249 | analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, | |
8250 | Hothorn, Westfall, 2010, CRC Press).") | |
8251 | (license license:gpl2))) | |
55a08dce RW |
8252 | |
8253 | (define-public r-emmeans | |
8254 | (package | |
8255 | (name "r-emmeans") | |
f71b16e8 | 8256 | (version "1.4.3.01") |
55a08dce RW |
8257 | (source |
8258 | (origin | |
8259 | (method url-fetch) | |
8260 | (uri (cran-uri "emmeans" version)) | |
8261 | (sha256 | |
8262 | (base32 | |
f71b16e8 | 8263 | "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg")))) |
55a08dce RW |
8264 | (build-system r-build-system) |
8265 | (propagated-inputs | |
8266 | `(("r-estimability" ,r-estimability) | |
8267 | ("r-mvtnorm" ,r-mvtnorm) | |
e0f86164 | 8268 | ("r-numderiv" ,r-numderiv) |
55a08dce RW |
8269 | ("r-plyr" ,r-plyr) |
8270 | ("r-xtable" ,r-xtable))) | |
8271 | (home-page "https://github.com/rvlenth/emmeans") | |
8272 | (synopsis "Estimated marginal means, aka least-squares means") | |
8273 | (description | |
8274 | "This package provides tools to obtain @dfn{estimated marginal | |
8275 | means} (EMMs) for many linear, generalized linear, and mixed models. It can | |
8276 | be used to compute contrasts or linear functions of EMMs, trends, and | |
8277 | comparisons of slopes.") | |
8278 | ;; Either version of the license. | |
8279 | (license (list license:gpl2 license:gpl3)))) | |
63fcb88a RW |
8280 | |
8281 | (define-public r-pwr | |
8282 | (package | |
8283 | (name "r-pwr") | |
8284 | (version "1.2-2") | |
8285 | (source | |
8286 | (origin | |
8287 | (method url-fetch) | |
8288 | (uri (cran-uri "pwr" version)) | |
8289 | (sha256 | |
8290 | (base32 | |
8291 | "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm")))) | |
8292 | (build-system r-build-system) | |
8293 | (native-inputs | |
8294 | `(("r-knitr" ,r-knitr))) | |
8295 | (home-page "https://github.com/heliosdrm/pwr") | |
8296 | (synopsis "Basic functions for power analysis") | |
8297 | (description | |
8298 | "This package provides power analysis functions along the lines of | |
8299 | Cohen (1988).") | |
8300 | (license license:gpl3+))) | |
bd531e83 | 8301 | |
42f344fa RW |
8302 | (define-public r-libcoin |
8303 | (package | |
8304 | (name "r-libcoin") | |
a13f81dd | 8305 | (version "1.0-5") |
42f344fa RW |
8306 | (source |
8307 | (origin | |
8308 | (method url-fetch) | |
8309 | (uri (cran-uri "libcoin" version)) | |
8310 | (sha256 | |
8311 | (base32 | |
a13f81dd | 8312 | "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a")))) |
42f344fa RW |
8313 | (build-system r-build-system) |
8314 | (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) | |
8315 | (home-page "https://cran.r-project.org/web/packages/libcoin") | |
8316 | (synopsis "Linear test statistics for permutation inference") | |
8317 | (description | |
8318 | "This package provides basic infrastructure for linear test statistics | |
8319 | and permutation inference in the framework of Strasser and Weber (1999).") | |
8320 | (license license:gpl2))) | |
8321 | ||
bd531e83 RW |
8322 | (define-public r-coin |
8323 | (package | |
8324 | (name "r-coin") | |
1656a425 | 8325 | (version "1.3-1") |
bd531e83 RW |
8326 | (source |
8327 | (origin | |
8328 | (method url-fetch) | |
8329 | (uri (cran-uri "coin" version)) | |
8330 | (sha256 | |
8331 | (base32 | |
1656a425 | 8332 | "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx")))) |
bd531e83 RW |
8333 | (build-system r-build-system) |
8334 | (propagated-inputs | |
f69ba00f RW |
8335 | `(("r-libcoin" ,r-libcoin) |
8336 | ("r-matrixstats" ,r-matrixstats) | |
8337 | ("r-modeltools" ,r-modeltools) | |
bd531e83 RW |
8338 | ("r-multcomp" ,r-multcomp) |
8339 | ("r-mvtnorm" ,r-mvtnorm) | |
8340 | ("r-survival" ,r-survival))) | |
8341 | (home-page "http://coin.r-forge.r-project.org") | |
8342 | (synopsis "Conditional inference procedures in a permutation test framework") | |
8343 | (description | |
8344 | "This package provides conditional inference procedures for the general | |
8345 | independence problem including two-sample, K-sample (non-parametric ANOVA), | |
8346 | correlation, censored, ordered and multivariate problems.") | |
8347 | (license license:gpl2))) | |
9b3ecb60 RW |
8348 | |
8349 | (define-public r-bayesplot | |
8350 | (package | |
8351 | (name "r-bayesplot") | |
de5092ba | 8352 | (version "1.7.1") |
9b3ecb60 RW |
8353 | (source |
8354 | (origin | |
8355 | (method url-fetch) | |
8356 | (uri (cran-uri "bayesplot" version)) | |
8357 | (sha256 | |
8358 | (base32 | |
de5092ba | 8359 | "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342")))) |
9b3ecb60 RW |
8360 | (build-system r-build-system) |
8361 | (inputs | |
8362 | `(("pandoc" ,ghc-pandoc) | |
8363 | ("pandoc-citeproc" ,ghc-pandoc-citeproc))) | |
8364 | (propagated-inputs | |
8365 | `(("r-dplyr" ,r-dplyr) | |
8366 | ("r-ggplot2" ,r-ggplot2) | |
8367 | ("r-ggridges" ,r-ggridges) | |
1d7bde78 | 8368 | ("r-glue" ,r-glue) |
9b3ecb60 | 8369 | ("r-reshape2" ,r-reshape2) |
1d7bde78 RW |
8370 | ("r-rlang" ,r-rlang) |
8371 | ("r-tibble" ,r-tibble) | |
8372 | ("r-tidyselect" ,r-tidyselect))) | |
9b3ecb60 RW |
8373 | (home-page "http://mc-stan.org/bayesplot") |
8374 | (synopsis "Plotting for Bayesian models") | |
8375 | (description | |
8376 | "This package provides plotting functions for posterior analysis, model | |
8377 | checking, and MCMC diagnostics. The package is designed not only to provide | |
8378 | convenient functionality for users, but also a common set of functions that | |
8379 | can be easily used by developers working on a variety of R packages for | |
8380 | Bayesian modeling.") | |
8381 | (license license:gpl3+))) | |
3b8a3f55 RW |
8382 | |
8383 | (define-public r-tmb | |
8384 | (package | |
8385 | (name "r-tmb") | |
492ec498 | 8386 | (version "1.7.15") |
3b8a3f55 RW |
8387 | (source |
8388 | (origin | |
8389 | (method url-fetch) | |
8390 | (uri (cran-uri "TMB" version)) | |
8391 | (sha256 | |
8392 | (base32 | |
492ec498 | 8393 | "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs")))) |
3b8a3f55 RW |
8394 | (properties `((upstream-name . "TMB"))) |
8395 | (build-system r-build-system) | |
8396 | (propagated-inputs | |
8397 | `(("r-matrix" ,r-matrix) | |
8398 | ("r-rcppeigen" ,r-rcppeigen))) | |
8399 | (home-page "http://tmb-project.org") | |
8400 | (synopsis "Template model builder: a general random effect tool") | |
8401 | (description | |
8402 | "With this tool, a user should be able to quickly implement complex | |
8403 | random effect models through simple C++ templates. The package combines | |
8404 | @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated | |
8405 | matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available | |
8406 | from R) to obtain an efficient implementation of the applied Laplace | |
8407 | approximation with exact derivatives. Key features are: Automatic sparseness | |
8408 | detection, parallelism through BLAS and parallel user templates.") | |
8409 | (license license:gpl2))) | |
aa4bde0b RW |
8410 | |
8411 | (define-public r-sjstats | |
8412 | (package | |
8413 | (name "r-sjstats") | |
ec2014d5 | 8414 | (version "0.17.7") |
aa4bde0b RW |
8415 | (source |
8416 | (origin | |
8417 | (method url-fetch) | |
8418 | (uri (cran-uri "sjstats" version)) | |
8419 | (sha256 | |
ec2014d5 | 8420 | (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6")))) |
aa4bde0b RW |
8421 | (build-system r-build-system) |
8422 | (propagated-inputs | |
a1473cb4 RW |
8423 | `(("r-bayestestr" ,r-bayestestr) |
8424 | ("r-broom" ,r-broom) | |
aa4bde0b RW |
8425 | ("r-dplyr" ,r-dplyr) |
8426 | ("r-emmeans" ,r-emmeans) | |
a7524f70 | 8427 | ("r-insight" ,r-insight) |
aa4bde0b RW |
8428 | ("r-lme4" ,r-lme4) |
8429 | ("r-magrittr" ,r-magrittr) | |
8430 | ("r-mass" ,r-mass) | |
aa4bde0b | 8431 | ("r-modelr" ,r-modelr) |
664e15ed | 8432 | ("r-parameters" ,r-parameters) |
a1473cb4 | 8433 | ("r-performance" ,r-performance) |
aa4bde0b | 8434 | ("r-purrr" ,r-purrr) |
aa4bde0b RW |
8435 | ("r-rlang" ,r-rlang) |
8436 | ("r-sjlabelled" ,r-sjlabelled) | |
8437 | ("r-sjmisc" ,r-sjmisc) | |
8438 | ("r-tidyr" ,r-tidyr))) | |
8439 | (home-page "https://github.com/strengejacke/sjstats") | |
8440 | (synopsis "Functions for common statistical computations") | |
8441 | (description | |
8442 | "This package provides a collection of convenient functions for common | |
8443 | statistical computations, which are not directly provided by R's @code{base} | |
8444 | or @code{stats} packages. This package aims at providing, first, shortcuts | |
8445 | for statistical measures, which otherwise could only be calculated with | |
8446 | additional effort. Second, these shortcut functions are generic, and can be | |
8447 | applied not only to vectors, but also to other objects as well. The focus of | |
8448 | most functions lies on summary statistics or fit measures for regression | |
8449 | models, including generalized linear models, mixed effects models and Bayesian | |
8450 | models.") | |
8451 | (license license:gpl3))) | |
41394423 RW |
8452 | |
8453 | (define-public r-glmmtmb | |
8454 | (package | |
8455 | (name "r-glmmtmb") | |
1afe5644 | 8456 | (version "0.2.3") |
41394423 RW |
8457 | (source |
8458 | (origin | |
8459 | (method url-fetch) | |
8460 | (uri (cran-uri "glmmTMB" version)) | |
8461 | (sha256 | |
8462 | (base32 | |
1afe5644 | 8463 | "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb")))) |
41394423 RW |
8464 | (properties `((upstream-name . "glmmTMB"))) |
8465 | (build-system r-build-system) | |
8466 | (propagated-inputs | |
8467 | `(("r-lme4" ,r-lme4) | |
8468 | ("r-matrix" ,r-matrix) | |
8469 | ("r-nlme" ,r-nlme) | |
8470 | ("r-rcppeigen" ,r-rcppeigen) | |
8471 | ("r-tmb" ,r-tmb))) | |
8472 | (native-inputs | |
1afe5644 | 8473 | `(("r-knitr" ,r-knitr))) ; for vignettes |
41394423 RW |
8474 | (home-page "https://github.com/glmmTMB") |
8475 | (synopsis "Generalized linear mixed models") | |
8476 | (description | |
8477 | "Fit linear and generalized linear mixed models with various extensions, | |
8478 | including zero-inflation. The models are fitted using maximum likelihood | |
8479 | estimation via the Template Model Builder. Random effects are assumed to be | |
8480 | Gaussian on the scale of the linear predictor and are integrated out using the | |
8481 | Laplace approximation. Gradients are calculated using automatic | |
8482 | differentiation.") | |
8483 | (license license:agpl3+))) | |
489a6178 | 8484 | |
c4568c5c RW |
8485 | (define-public r-bayestestr |
8486 | (package | |
8487 | (name "r-bayestestr") | |
18376def | 8488 | (version "0.4.0") |
c4568c5c RW |
8489 | (source |
8490 | (origin | |
8491 | (method url-fetch) | |
8492 | (uri (cran-uri "bayestestR" version)) | |
8493 | (sha256 | |
8494 | (base32 | |
18376def | 8495 | "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc")))) |
c4568c5c RW |
8496 | (properties `((upstream-name . "bayestestR"))) |
8497 | (build-system r-build-system) | |
8498 | (propagated-inputs | |
8499 | `(("r-insight" ,r-insight))) | |
8500 | (home-page "https://github.com/easystats/bayestestR") | |
8501 | (synopsis "Describe Bayesian models and posterior distributions") | |
8502 | (description | |
8503 | "This package provides utilities to understand and describe posterior | |
8504 | distributions and Bayesian models. It includes point-estimates such as | |
8505 | @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest | |
8506 | Density Interval} (HDI), and indices used for null-hypothesis testing (such as | |
8507 | ROPE percentage and pd).") | |
8508 | (license license:gpl3))) | |
8509 | ||
711a2f06 RW |
8510 | (define-public r-performance |
8511 | (package | |
8512 | (name "r-performance") | |
afc1ff2f | 8513 | (version "0.4.2") |
711a2f06 RW |
8514 | (source |
8515 | (origin | |
8516 | (method url-fetch) | |
8517 | (uri (cran-uri "performance" version)) | |
8518 | (sha256 | |
8519 | (base32 | |
afc1ff2f | 8520 | "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p")))) |
711a2f06 RW |
8521 | (build-system r-build-system) |
8522 | (propagated-inputs | |
8523 | `(("r-bayestestr" ,r-bayestestr) | |
8524 | ("r-insight" ,r-insight))) | |
8525 | (home-page "https://easystats.github.io/performance/") | |
8526 | (synopsis "Assessment of regression models performance") | |
8527 | (description | |
8528 | "This package provides utilities for computing measures to assess model | |
8529 | quality, which are not directly provided by R's @code{base} or @code{stats} | |
8530 | packages. These include e.g. measures like r-squared, intraclass correlation | |
8531 | coefficient, root mean squared error or functions to check models for | |
8532 | overdispersion, singularity or zero-inflation and more. Functions apply to a | |
8533 | large variety of regression models, including generalized linear models, mixed | |
8534 | effects models and Bayesian models.") | |
8535 | (license license:gpl3))) | |
8536 | ||
489a6178 RW |
8537 | (define-public r-ggeffects |
8538 | (package | |
8539 | (name "r-ggeffects") | |
cd0e2815 | 8540 | (version "0.14.0") |
489a6178 RW |
8541 | (source |
8542 | (origin | |
8543 | (method url-fetch) | |
8544 | (uri (cran-uri "ggeffects" version)) | |
8545 | (sha256 | |
8546 | (base32 | |
cd0e2815 | 8547 | "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw")))) |
489a6178 RW |
8548 | (build-system r-build-system) |
8549 | (propagated-inputs | |
cd0e2815 | 8550 | `(("r-insight" ,r-insight) |
489a6178 RW |
8551 | ("r-magrittr" ,r-magrittr) |
8552 | ("r-mass" ,r-mass) | |
489a6178 | 8553 | ("r-purrr" ,r-purrr) |
489a6178 | 8554 | ("r-sjlabelled" ,r-sjlabelled) |
fef93da8 | 8555 | ("r-sjmisc" ,r-sjmisc))) |
489a6178 RW |
8556 | (home-page "https://github.com/strengejacke/ggeffects") |
8557 | (synopsis "Create tidy data frames of marginal effects for ggplot") | |
8558 | (description | |
8559 | "This package provides tools to compute marginal effects from statistical | |
8560 | models and return the result as tidy data frames. These data frames are ready | |
8561 | to use with the @code{ggplot2} package. Marginal effects can be calculated | |
8562 | for many different models. Interaction terms, splines and polynomial terms | |
8563 | are also supported. The two main functions are @code{ggpredict()} and | |
8564 | @code{ggeffect()}. There is a generic @code{plot()} method to plot the | |
8565 | results using @code{ggplot2}.") | |
8566 | (license license:gpl3))) | |
7b63047c | 8567 | |
24edd279 RW |
8568 | (define-public r-effectsize |
8569 | (package | |
8570 | (name "r-effectsize") | |
8571 | (version "0.0.1") | |
8572 | (source | |
8573 | (origin | |
8574 | (method url-fetch) | |
8575 | (uri (cran-uri "effectsize" version)) | |
8576 | (sha256 | |
8577 | (base32 | |
8578 | "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb")))) | |
8579 | (properties `((upstream-name . "effectsize"))) | |
8580 | (build-system r-build-system) | |
8581 | (propagated-inputs | |
8582 | `(("r-bayestestr" ,r-bayestestr) | |
8583 | ("r-insight" ,r-insight) | |
8584 | ("r-parameters" ,r-parameters))) | |
8585 | (home-page "https://github.com/easystats/effectsize") | |
8586 | (synopsis "Indices of effect size and standardized parameters") | |
8587 | (description | |
8588 | "This package provides utilities to work with indices of effect size and | |
8589 | standardized parameters for a wide variety of models, allowing computation and | |
8590 | conversion of indices such as Cohen's d, r, odds, etc.") | |
8591 | (license license:gpl3))) | |
8592 | ||
7b63047c RW |
8593 | (define-public r-sjplot |
8594 | (package | |
8595 | (name "r-sjplot") | |
8aab9b98 | 8596 | (version "2.8.1") |
7b63047c RW |
8597 | (source |
8598 | (origin | |
8599 | (method url-fetch) | |
8600 | (uri (cran-uri "sjPlot" version)) | |
8601 | (sha256 | |
8aab9b98 | 8602 | (base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7")))) |
7b63047c RW |
8603 | (properties `((upstream-name . "sjPlot"))) |
8604 | (build-system r-build-system) | |
8605 | (propagated-inputs | |
d22d7904 | 8606 | `(("r-bayestestr" ,r-bayestestr) |
7b63047c | 8607 | ("r-dplyr" ,r-dplyr) |
3356eb51 | 8608 | ("r-effectsize" ,r-effectsize) |
7b63047c RW |
8609 | ("r-forcats" ,r-forcats) |
8610 | ("r-ggeffects" ,r-ggeffects) | |
8611 | ("r-ggplot2" ,r-ggplot2) | |
a5a64814 | 8612 | ("r-ggrepel" ,r-ggrepel) |
7b63047c | 8613 | ("r-glmmtmb" ,r-glmmtmb) |
d22d7904 | 8614 | ("r-insight" ,r-insight) |
7b63047c RW |
8615 | ("r-knitr" ,r-knitr) |
8616 | ("r-lme4" ,r-lme4) | |
8617 | ("r-magrittr" ,r-magrittr) | |
8618 | ("r-mass" ,r-mass) | |
8619 | ("r-modelr" ,r-modelr) | |
3356eb51 | 8620 | ("r-parameters" ,r-parameters) |
d22d7904 | 8621 | ("r-performance" ,r-performance) |
7b63047c RW |
8622 | ("r-psych" ,r-psych) |
8623 | ("r-purrr" ,r-purrr) | |
8624 | ("r-rlang" ,r-rlang) | |
8625 | ("r-scales" ,r-scales) | |
8626 | ("r-sjlabelled" ,r-sjlabelled) | |
8627 | ("r-sjmisc" ,r-sjmisc) | |
8628 | ("r-sjstats" ,r-sjstats) | |
8629 | ("r-tidyr" ,r-tidyr))) | |
8630 | (home-page "https://strengejacke.github.io/sjPlot/") | |
8631 | (synopsis "Data visualization for statistics in social science") | |
8632 | (description | |
8633 | "This package represents a collection of plotting and table output | |
8634 | functions for data visualization. Results of various statistical | |
8635 | analyses (that are commonly used in social sciences) can be visualized using | |
8636 | this package, including simple and cross tabulated frequencies, histograms, | |
8637 | box plots, (generalized) linear models, mixed effects models, principal | |
8638 | component analysis and correlation matrices, cluster analyses, scatter plots, | |
8639 | stacked scales, effects plots of regression models (including interaction | |
8640 | terms) and much more. This package supports labelled data.") | |
8641 | (license license:gpl3))) | |
03f80112 RW |
8642 | |
8643 | (define-public r-ini | |
8644 | (package | |
8645 | (name "r-ini") | |
8646 | (version "0.3.1") | |
8647 | (source | |
8648 | (origin | |
8649 | (method url-fetch) | |
8650 | (uri (cran-uri "ini" version)) | |
8651 | (sha256 | |
8652 | (base32 | |
8653 | "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) | |
8654 | (build-system r-build-system) | |
8655 | (home-page "https://github.com/dvdscripter/ini") | |
8656 | (synopsis "Read and write configuration files") | |
8657 | (description | |
8658 | "This package provides tools to parse simple @code{.ini} configuration | |
8659 | files to an structured list. Users can manipulate this resulting list with | |
8660 | @code{lapply()} functions. This same structured list can be used to write | |
8661 | back to file after modifications.") | |
8662 | (license license:gpl3))) | |
21405e81 RW |
8663 | |
8664 | (define-public r-gh | |
8665 | (package | |
8666 | (name "r-gh") | |
8667 | (version "1.0.1") | |
8668 | (source | |
8669 | (origin | |
8670 | (method url-fetch) | |
8671 | (uri (cran-uri "gh" version)) | |
8672 | (sha256 | |
8673 | (base32 | |
8674 | "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k")))) | |
8675 | (build-system r-build-system) | |
8676 | (propagated-inputs | |
8677 | `(("r-httr" ,r-httr) | |
8678 | ("r-ini" ,r-ini) | |
8679 | ("r-jsonlite" ,r-jsonlite))) | |
8680 | (home-page "https://github.com/r-lib/gh#readme") | |
8681 | (synopsis "Access the GitHub API via R") | |
8682 | (description | |
8683 | "This package provides a minimal R client to access the GitHub API.") | |
8684 | (license license:expat))) | |
d6871153 RW |
8685 | |
8686 | (define-public r-fs | |
8687 | (package | |
8688 | (name "r-fs") | |
c02f574d | 8689 | (version "1.3.1") |
d6871153 RW |
8690 | (source |
8691 | (origin | |
8692 | (method url-fetch) | |
8693 | (uri (cran-uri "fs" version)) | |
8694 | (sha256 | |
8695 | (base32 | |
c02f574d | 8696 | "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn")))) |
d6871153 RW |
8697 | (build-system r-build-system) |
8698 | (propagated-inputs | |
8699 | `(("r-rcpp" ,r-rcpp))) | |
8700 | (native-inputs | |
8701 | `(("pkg-config" ,pkg-config))) | |
8702 | (home-page "http://fs.r-lib.org") | |
8703 | (synopsis "Cross-platform file system operations based on libuv") | |
8704 | (description | |
8705 | "This package provides a cross-platform interface to file system | |
8706 | operations, built on top of the libuv C library.") | |
8707 | (license license:gpl3))) | |
153e5b2d RW |
8708 | |
8709 | (define-public r-clisymbols | |
8710 | (package | |
8711 | (name "r-clisymbols") | |
8712 | (version "1.2.0") | |
8713 | (source | |
8714 | (origin | |
8715 | (method url-fetch) | |
8716 | (uri (cran-uri "clisymbols" version)) | |
8717 | (sha256 | |
8718 | (base32 | |
8719 | "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86")))) | |
8720 | (build-system r-build-system) | |
8721 | (home-page "https://github.com/gaborcsardi/clisymbols") | |
8722 | (synopsis "Unicode symbols at the R prompt") | |
8723 | (description | |
8724 | "This package provides a small subset of Unicode symbols, that are useful | |
8725 | when building command line applications. They fall back to alternatives on | |
8726 | terminals that do not support Unicode.") | |
8727 | (license license:expat))) | |
efefd3ec RW |
8728 | |
8729 | (define-public r-usethis | |
8730 | (package | |
8731 | (name "r-usethis") | |
99765abb | 8732 | (version "1.5.1") |
efefd3ec RW |
8733 | (source |
8734 | (origin | |
8735 | (method url-fetch) | |
8736 | (uri (cran-uri "usethis" version)) | |
8737 | (sha256 | |
8738 | (base32 | |
99765abb | 8739 | "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy")))) |
efefd3ec RW |
8740 | (build-system r-build-system) |
8741 | (propagated-inputs | |
8742 | `(("r-clipr" ,r-clipr) | |
8743 | ("r-clisymbols" ,r-clisymbols) | |
8744 | ("r-crayon" ,r-crayon) | |
8745 | ("r-curl" ,r-curl) | |
8746 | ("r-desc" ,r-desc) | |
8747 | ("r-fs" ,r-fs) | |
8748 | ("r-gh" ,r-gh) | |
8749 | ("r-git2r" ,r-git2r) | |
8750 | ("r-glue" ,r-glue) | |
35171015 | 8751 | ("r-purrr" ,r-purrr) |
efefd3ec RW |
8752 | ("r-rlang" ,r-rlang) |
8753 | ("r-rprojroot" ,r-rprojroot) | |
8754 | ("r-rstudioapi" ,r-rstudioapi) | |
35171015 RW |
8755 | ("r-whisker" ,r-whisker) |
8756 | ("r-withr" ,r-withr) | |
8757 | ("r-yaml" ,r-yaml))) | |
efefd3ec RW |
8758 | (home-page "https://github.com/r-lib/usethis") |
8759 | (synopsis "Automate R package and project setup") | |
8760 | (description | |
8761 | "This package helps you to automate R package and project setup tasks | |
8762 | that are otherwise performed manually. This includes setting up unit testing, | |
8763 | test coverage, continuous integration, Git, GitHub integration, licenses, | |
8764 | Rcpp, RStudio projects, and more.") | |
8765 | (license license:gpl3))) | |
99342624 RW |
8766 | |
8767 | (define-public r-sessioninfo | |
8768 | (package | |
8769 | (name "r-sessioninfo") | |
3d6fa1a3 | 8770 | (version "1.1.1") |
99342624 RW |
8771 | (source |
8772 | (origin | |
8773 | (method url-fetch) | |
8774 | (uri (cran-uri "sessioninfo" version)) | |
8775 | (sha256 | |
8776 | (base32 | |
3d6fa1a3 | 8777 | "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn")))) |
99342624 RW |
8778 | (build-system r-build-system) |
8779 | (propagated-inputs | |
8780 | `(("r-cli" ,r-cli) | |
8781 | ("r-withr" ,r-withr))) | |
8782 | (home-page "https://github.com/r-lib/sessioninfo#readme") | |
8783 | (synopsis "R session information") | |
8784 | (description | |
8785 | "This package provides tools to query and print information about the | |
8786 | current R session. It is similar to @code{utils::sessionInfo()}, but includes | |
8787 | more information about packages, and where they were installed from.") | |
8788 | (license license:gpl2))) | |
cbc8e6dd RW |
8789 | |
8790 | (define-public r-remotes | |
8791 | (package | |
8792 | (name "r-remotes") | |
da4754a3 | 8793 | (version "2.1.0") |
cbc8e6dd RW |
8794 | (source |
8795 | (origin | |
8796 | (method url-fetch) | |
8797 | (uri (cran-uri "remotes" version)) | |
8798 | (sha256 | |
8799 | (base32 | |
da4754a3 | 8800 | "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49")))) |
cbc8e6dd RW |
8801 | (build-system r-build-system) |
8802 | (home-page "https://github.com/r-lib/remotes#readme") | |
8803 | (synopsis "R package installation from remote repositories") | |
8804 | (description | |
8805 | "Download and install R packages stored in GitHub, BitBucket, or plain | |
8806 | subversion or git repositories. This package is a lightweight replacement of | |
8807 | the @code{install_*} functions in the @code{devtools} package. Indeed most of | |
8808 | the code was copied over from @code{devtools}.") | |
8809 | (license license:gpl2+))) | |
7d8f3470 RW |
8810 | |
8811 | (define-public r-xopen | |
8812 | (package | |
8813 | (name "r-xopen") | |
8814 | (version "1.0.0") | |
8815 | (source | |
8816 | (origin | |
8817 | (method url-fetch) | |
8818 | (uri (cran-uri "xopen" version)) | |
8819 | (sha256 | |
8820 | (base32 | |
8821 | "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) | |
8822 | (build-system r-build-system) | |
8823 | (propagated-inputs | |
8824 | `(("r-processx" ,r-processx))) | |
8825 | (home-page "https://github.com/r-lib/xopen#readme") | |
8826 | (synopsis "Open system files, URLs, anything") | |
8827 | (description | |
8828 | "This package provides a cross-platform solution to open files, | |
8829 | directories or URLs with their associated programs.") | |
8830 | (license license:expat))) | |
5df4e27f RW |
8831 | |
8832 | (define-public r-rcmdcheck | |
8833 | (package | |
8834 | (name "r-rcmdcheck") | |
a75c6d9c | 8835 | (version "1.3.3") |
5df4e27f RW |
8836 | (source |
8837 | (origin | |
8838 | (method url-fetch) | |
8839 | (uri (cran-uri "rcmdcheck" version)) | |
8840 | (sha256 | |
8841 | (base32 | |
a75c6d9c | 8842 | "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs")))) |
5df4e27f RW |
8843 | (build-system r-build-system) |
8844 | (propagated-inputs | |
8845 | `(("r-callr" ,r-callr) | |
8846 | ("r-cli" ,r-cli) | |
8847 | ("r-crayon" ,r-crayon) | |
8848 | ("r-desc" ,r-desc) | |
8849 | ("r-digest" ,r-digest) | |
8850 | ("r-pkgbuild" ,r-pkgbuild) | |
8851 | ("r-prettyunits" ,r-prettyunits) | |
8852 | ("r-r6" ,r-r6) | |
8853 | ("r-rprojroot" ,r-rprojroot) | |
7466c3bb | 8854 | ("r-sessioninfo" ,r-sessioninfo) |
5df4e27f RW |
8855 | ("r-withr" ,r-withr) |
8856 | ("r-xopen" ,r-xopen))) | |
8857 | (home-page "https://github.com/r-Lib/rcmdcheck#readme") | |
8858 | (synopsis "Run R CMD check from R and capture results") | |
8859 | (description | |
8860 | "Run @code{R CMD check} from R programmatically, and capture the results | |
8861 | of the individual checks.") | |
8862 | (license license:expat))) | |
9b02d1a1 RW |
8863 | |
8864 | (define-public r-rapportools | |
8865 | (package | |
8866 | (name "r-rapportools") | |
8867 | (version "1.0") | |
8868 | (source | |
8869 | (origin | |
8870 | (method url-fetch) | |
8871 | (uri (cran-uri "rapportools" version)) | |
8872 | (sha256 | |
8873 | (base32 | |
8874 | "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) | |
8875 | (build-system r-build-system) | |
8876 | (propagated-inputs | |
8877 | `(("r-pander" ,r-pander) | |
8878 | ("r-plyr" ,r-plyr) | |
8879 | ("r-reshape" ,r-reshape))) | |
8880 | (home-page "https://cran.r-project.org/web/packages/rapportools/") | |
8881 | (synopsis "Miscellaneous helper functions with sane defaults for reporting") | |
8882 | (description | |
8883 | "This package provides helper functions that act as wrappers to more | |
8884 | advanced statistical methods with the advantage of having sane defaults for | |
8885 | quick reporting.") | |
8886 | (license license:agpl3+))) | |
319a80ce RW |
8887 | |
8888 | (define-public r-pander | |
8889 | (package | |
8890 | (name "r-pander") | |
a44f8b00 | 8891 | (version "0.6.3") |
319a80ce RW |
8892 | (source |
8893 | (origin | |
8894 | (method url-fetch) | |
8895 | (uri (cran-uri "pander" version)) | |
8896 | (sha256 | |
8897 | (base32 | |
a44f8b00 | 8898 | "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi")))) |
319a80ce RW |
8899 | (build-system r-build-system) |
8900 | (propagated-inputs | |
8901 | `(("r-digest" ,r-digest) | |
8902 | ("r-rcpp" ,r-rcpp))) | |
8903 | (home-page "https://rapporter.github.io/pander") | |
8904 | (synopsis "Render R objects into Pandoc's markdown") | |
8905 | (description | |
8906 | "The main aim of the pander R package is to provide a minimal and easy | |
8907 | tool for rendering R objects into Pandoc's markdown. The package is also | |
8908 | capable of exporting/converting complex Pandoc documents (reports) in various | |
8909 | ways.") | |
8910 | ;; This package is licensed under either the AGPLv3+ or the very rarely | |
8911 | ;; used OSL 3.0. | |
8912 | (license license:agpl3+))) | |
74cc74e4 RW |
8913 | |
8914 | (define-public r-summarytools | |
8915 | (package | |
8916 | (name "r-summarytools") | |
084ea348 | 8917 | (version "0.9.4") |
74cc74e4 RW |
8918 | (source |
8919 | (origin | |
8920 | (method url-fetch) | |
8921 | (uri (cran-uri "summarytools" version)) | |
8922 | (sha256 | |
8923 | (base32 | |
084ea348 | 8924 | "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a")))) |
74cc74e4 RW |
8925 | (build-system r-build-system) |
8926 | (propagated-inputs | |
5093cbdc RW |
8927 | `(("r-checkmate" ,r-checkmate) |
8928 | ("r-dplyr" ,r-dplyr) | |
8929 | ("r-htmltools" ,r-htmltools) | |
74cc74e4 | 8930 | ("r-lubridate" ,r-lubridate) |
5093cbdc | 8931 | ("r-magick" ,r-magick) |
74cc74e4 RW |
8932 | ("r-matrixstats" ,r-matrixstats) |
8933 | ("r-pander" ,r-pander) | |
8934 | ("r-pryr" ,r-pryr) | |
8935 | ("r-rapportools" ,r-rapportools) | |
5093cbdc | 8936 | ("r-rcurl" ,r-rcurl) |
4c920fbb | 8937 | ("r-tibble" ,r-tibble) |
5093cbdc | 8938 | ("r-tidyr" ,r-tidyr))) |
74cc74e4 RW |
8939 | (home-page "https://github.com/dcomtois/summarytools") |
8940 | (synopsis "Tools to quickly and neatly summarize data") | |
8941 | (description | |
8942 | "This package provides tools for data frame summaries, cross-tabulations, | |
8943 | weight-enabled frequency tables and common univariate statistics in concise | |
8944 | tables available in a variety of formats (plain ASCII, Markdown and HTML). A | |
8945 | good point-of-entry for exploring data, both for experienced and new R | |
8946 | users.") | |
8947 | (license license:gpl2))) | |
7c7ee6cf RW |
8948 | |
8949 | (define-public r-lsei | |
8950 | (package | |
8951 | (name "r-lsei") | |
8952 | (version "1.2-0") | |
8953 | (source | |
8954 | (origin | |
8955 | (method url-fetch) | |
8956 | (uri (cran-uri "lsei" version)) | |
8957 | (sha256 | |
8958 | (base32 | |
8959 | "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7")))) | |
8960 | (build-system r-build-system) | |
8961 | (native-inputs | |
8962 | `(("gfortran" ,gfortran))) | |
8963 | (home-page "https://www.stat.auckland.ac.nz/~yongwang") | |
8964 | (synopsis "Solve regression problems under equality/inequality constraints") | |
8965 | (description | |
8966 | "It contains functions that solve least squares linear regression | |
8967 | problems under linear equality/inequality constraints. Functions for solving | |
8968 | quadratic programming problems are also available, which transform such | |
8969 | problems into least squares ones first.") | |
8970 | (license license:gpl2+))) | |
2ea75a83 RW |
8971 | |
8972 | (define-public r-npsurv | |
8973 | (package | |
8974 | (name "r-npsurv") | |
8975 | (version "0.4-0") | |
8976 | (source | |
8977 | (origin | |
8978 | (method url-fetch) | |
8979 | (uri (cran-uri "npsurv" version)) | |
8980 | (sha256 | |
8981 | (base32 | |
8982 | "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20")))) | |
8983 | (build-system r-build-system) | |
8984 | (propagated-inputs | |
8985 | `(("r-lsei" ,r-lsei))) | |
8986 | (home-page "https://www.stat.auckland.ac.nz/~yongwang") | |
8987 | (synopsis "Nonparametric survival analysis") | |
8988 | (description | |
8989 | "This package contains functions for non-parametric survival analysis of | |
8990 | exact and interval-censored observations.") | |
8991 | (license license:gpl2+))) | |
32499b26 RW |
8992 | |
8993 | (define-public r-clusteval | |
8994 | (package | |
8995 | (name "r-clusteval") | |
8996 | (version "0.1") | |
8997 | (source | |
8998 | (origin | |
8999 | (method url-fetch) | |
9000 | (uri (cran-uri "clusteval" version)) | |
9001 | (sha256 | |
9002 | (base32 | |
9003 | "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) | |
9004 | (build-system r-build-system) | |
9005 | (propagated-inputs | |
9006 | `(("r-mvtnorm" ,r-mvtnorm) | |
9007 | ("r-rcpp" ,r-rcpp))) | |
9008 | (home-page "https://cran.r-project.org/web/packages/clusteval/") | |
9009 | (synopsis "Evaluation of clustering algorithms") | |
9010 | (description | |
9011 | "This R package provides a suite of tools to evaluate clustering | |
9012 | algorithms, clusterings, and individual clusters.") | |
9013 | (license license:expat))) | |
373cef0a RW |
9014 | |
9015 | (define-public r-tweedie | |
9016 | (package | |
9017 | (name "r-tweedie") | |
9018 | (version "2.3.2") | |
9019 | (source | |
9020 | (origin | |
9021 | (method url-fetch) | |
9022 | (uri (cran-uri "tweedie" version)) | |
9023 | (sha256 | |
9024 | (base32 | |
9025 | "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls")))) | |
9026 | (build-system r-build-system) | |
9027 | (native-inputs `(("gfortran" ,gfortran))) | |
9028 | (home-page "https://cran.r-project.org/web/packages/tweedie/") | |
9029 | (synopsis "Evaluation of Tweedie exponential family models") | |
9030 | (description | |
9031 | "Maximum likelihood computations for Tweedie families, including the | |
9032 | series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and | |
9033 | the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), | |
9034 | and related methods.") | |
9035 | (license license:gpl2+))) | |
4fb35ebd RW |
9036 | |
9037 | (define-public r-rcppgsl | |
9038 | (package | |
9039 | (name "r-rcppgsl") | |
c42625c8 | 9040 | (version "0.3.7") |
4fb35ebd RW |
9041 | (source |
9042 | (origin | |
9043 | (method url-fetch) | |
9044 | (uri (cran-uri "RcppGSL" version)) | |
9045 | (sha256 | |
c42625c8 | 9046 | (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5")))) |
4fb35ebd RW |
9047 | (properties `((upstream-name . "RcppGSL"))) |
9048 | (build-system r-build-system) | |
9049 | (propagated-inputs | |
9050 | `(("r-rcpp" ,r-rcpp) | |
9051 | ("gsl" ,gsl))) | |
9052 | (native-inputs | |
c42625c8 | 9053 | `(("r-knitr" ,r-knitr))) ; for vignettes |
4fb35ebd RW |
9054 | (home-page "https://cran.r-project.org/web/packages/RcppGSL/") |
9055 | (synopsis "Rcpp integration for GSL vectors and matrices") | |
9056 | (description | |
9057 | "The GNU Scientific Library (or GSL) is a collection of numerical | |
9058 | routines for scientific computing. It is particularly useful for C and C++ | |
9059 | programs as it provides a standard C interface to a wide range of mathematical | |
9060 | routines. There are over 1000 functions in total with an extensive test | |
9061 | suite. The RcppGSL package provides an easy-to-use interface between GSL data | |
9062 | structures and R using concepts from Rcpp which is itself a package that eases | |
9063 | the interfaces between R and C++.") | |
9064 | (license license:gpl2+))) | |
20ff6e3a RW |
9065 | |
9066 | (define-public r-mvabund | |
9067 | (package | |
9068 | (name "r-mvabund") | |
48102ce1 | 9069 | (version "4.0.1") |
20ff6e3a RW |
9070 | (source |
9071 | (origin | |
9072 | (method url-fetch) | |
9073 | (uri (cran-uri "mvabund" version)) | |
9074 | (sha256 | |
9075 | (base32 | |
48102ce1 | 9076 | "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k")))) |
20ff6e3a RW |
9077 | (build-system r-build-system) |
9078 | (propagated-inputs | |
9079 | `(("r-mass" ,r-mass) | |
9080 | ("r-rcpp" ,r-rcpp) | |
9081 | ("r-rcppgsl" ,r-rcppgsl) | |
9082 | ("r-statmod" ,r-statmod) | |
9083 | ("r-tweedie" ,r-tweedie))) | |
9084 | (home-page "https://cran.r-project.org/web/packages/mvabund/") | |
9085 | (synopsis "Statistical methods for analysing multivariate abundance data") | |
9086 | (description | |
9087 | "This package provides a set of tools for displaying, modeling and | |
9088 | analysing multivariate abundance data in community ecology.") | |
9089 | (license license:lgpl2.1+))) | |
49863fd6 RW |
9090 | |
9091 | (define-public r-afex | |
9092 | (package | |
9093 | (name "r-afex") | |
0eb28435 | 9094 | (version "0.25-1") |
49863fd6 RW |
9095 | (source |
9096 | (origin | |
9097 | (method url-fetch) | |
9098 | (uri (cran-uri "afex" version)) | |
9099 | (sha256 | |
9100 | (base32 | |
0eb28435 | 9101 | "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf")))) |
49863fd6 RW |
9102 | (build-system r-build-system) |
9103 | (propagated-inputs | |
9104 | `(("r-car" ,r-car) | |
9105 | ("r-lme4" ,r-lme4) | |
9106 | ("r-lmertest" ,r-lmertest) | |
9107 | ("r-pbkrtest" ,r-pbkrtest) | |
9108 | ("r-reshape2" ,r-reshape2))) | |
9109 | (home-page "https://afex.singmann.science/") | |
9110 | (synopsis "Analysis of factorial experiments") | |
9111 | (description | |
9112 | "This package provides convenience functions for analyzing factorial | |
9113 | experiments using ANOVA or mixed models.") | |
9114 | (license license:gpl2+))) | |
7c02dd62 RW |
9115 | |
9116 | (define-public r-lmertest | |
9117 | (package | |
9118 | (name "r-lmertest") | |
d4e8f207 | 9119 | (version "3.1-1") |
7c02dd62 RW |
9120 | (source |
9121 | (origin | |
9122 | (method url-fetch) | |
9123 | (uri (cran-uri "lmerTest" version)) | |
9124 | (sha256 | |
9125 | (base32 | |
d4e8f207 | 9126 | "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj")))) |
7c02dd62 RW |
9127 | (properties `((upstream-name . "lmerTest"))) |
9128 | (build-system r-build-system) | |
9129 | (propagated-inputs | |
9130 | `(("r-ggplot2" ,r-ggplot2) | |
9131 | ("r-lme4" ,r-lme4) | |
9132 | ("r-mass" ,r-mass) | |
9133 | ("r-numderiv" ,r-numderiv))) | |
9134 | (home-page "https://github.com/runehaubo/lmerTestR") | |
9135 | (synopsis "Tests in linear mixed effects models") | |
9136 | (description | |
9137 | "This package provides p-values in type I, II or III anova and summary | |
9138 | tables for @code{lmer} model fits via Satterthwaite's degrees of freedom | |
9139 | method. A Kenward-Roger method is also available via the @code{pbkrtest} | |
9140 | package. Model selection methods include step, drop1 and anova-like tables | |
9141 | for random effects (ranova). Methods for Least-Square means (LS-means) and | |
9142 | tests of linear contrasts of fixed effects are also available.") | |
9143 | (license license:gpl2+))) | |
fd649d1e RW |
9144 | |
9145 | (define-public r-r2glmm | |
9146 | (package | |
9147 | (name "r-r2glmm") | |
9148 | (version "0.1.2") | |
9149 | (source | |
9150 | (origin | |
9151 | (method url-fetch) | |
9152 | (uri (cran-uri "r2glmm" version)) | |
9153 | (sha256 | |
9154 | (base32 | |
9155 | "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) | |
9156 | (build-system r-build-system) | |
9157 | (propagated-inputs | |
9158 | `(("r-afex" ,r-afex) | |
9159 | ("r-data-table" ,r-data-table) | |
9160 | ("r-dplyr" ,r-dplyr) | |
9161 | ("r-ggplot2" ,r-ggplot2) | |
9162 | ("r-gridextra" ,r-gridextra) | |
9163 | ("r-lmertest" ,r-lmertest) | |
9164 | ("r-mass" ,r-mass) | |
9165 | ("r-matrix" ,r-matrix) | |
9166 | ("r-mgcv" ,r-mgcv) | |
9167 | ("r-pbkrtest" ,r-pbkrtest))) | |
9168 | (home-page "https://github.com/bcjaeger/r2glmm") | |
9169 | (synopsis "Compute R squared for mixed (multilevel) models") | |
9170 | (description | |
9171 | "This package computes model and semi partial R squared with confidence | |
9172 | limits for the linear and generalized linear mixed model (LMM and GLMM). The | |
9173 | R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM | |
9174 | using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et | |
9175 | al. (2016)).") | |
9176 | (license license:gpl2))) | |
cddc0300 | 9177 | |
9178 | (define-public r-weights | |
9179 | (package | |
9180 | (name "r-weights") | |
9181 | (version "1.0") | |
9182 | (source | |
9183 | (origin | |
9184 | (method url-fetch) | |
9185 | (uri (cran-uri "weights" version)) | |
9186 | (sha256 | |
9187 | (base32 | |
9188 | "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c")))) | |
9189 | (build-system r-build-system) | |
9190 | (propagated-inputs | |
9191 | `(("r-gdata" ,r-gdata) | |
9192 | ("r-hmisc" ,r-hmisc) | |
9193 | ("r-mice" ,r-mice))) | |
9194 | (home-page | |
9195 | "https://cran.r-project.org/web/packages/weights/") | |
9196 | (synopsis "Weighting and weighted statistics") | |
9197 | (description "This package Provides a variety of functions for producing | |
9198 | simple weighted statistics, such as weighted Pearson's correlations, partial | |
9199 | correlations, Chi-Squared statistics, histograms, and t-tests. Also now | |
9200 | includes some software for quickly recoding survey data and plotting point | |
9201 | estimates from interaction terms in regressions (and multiply imputed | |
9202 | regressions). NOTE: Weighted partial correlation calculations pulled to | |
9203 | address a bug.") | |
9204 | (license license:gpl2+))) | |
bfa5662e RW |
9205 | |
9206 | (define-public r-rcppannoy | |
9207 | (package | |
9208 | (name "r-rcppannoy") | |
0da4cb54 | 9209 | (version "0.0.14") |
bfa5662e RW |
9210 | (source |
9211 | (origin | |
9212 | (method url-fetch) | |
9213 | (uri (cran-uri "RcppAnnoy" version)) | |
9214 | (sha256 | |
9215 | (base32 | |
0da4cb54 | 9216 | "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4")))) |
bfa5662e RW |
9217 | (properties `((upstream-name . "RcppAnnoy"))) |
9218 | (build-system r-build-system) | |
9219 | (propagated-inputs | |
9220 | `(("r-rcpp" ,r-rcpp))) | |
9221 | (native-inputs | |
9222 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
9223 | (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") | |
9224 | (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") | |
9225 | (description | |
9226 | "Annoy is a small C++ library for Approximate Nearest Neighbors written | |
9227 | for efficient memory usage as well an ability to load from and save to disk. | |
9228 | This package provides an R interface.") | |
9229 | ;; Annoy is released under ASL 2.0, but this wrapper is released under | |
9230 | ;; GPLv2+. | |
9231 | (license (list license:gpl2+ license:asl2.0)))) | |
b58940cb | 9232 | |
81281899 RW |
9233 | (define-public r-rcpphnsw |
9234 | (package | |
9235 | (name "r-rcpphnsw") | |
7c27558a | 9236 | (version "0.2.0") |
81281899 RW |
9237 | (source |
9238 | (origin | |
9239 | (method url-fetch) | |
9240 | (uri (cran-uri "RcppHNSW" version)) | |
9241 | (sha256 | |
9242 | (base32 | |
7c27558a | 9243 | "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv")))) |
81281899 RW |
9244 | (properties `((upstream-name . "RcppHNSW"))) |
9245 | (build-system r-build-system) | |
9246 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
9247 | (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") | |
9248 | (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") | |
9249 | (description | |
9250 | "Hnswlib is a C++ library for approximate nearest neighbors. This | |
9251 | package provides a minimal R interface by relying on the Rcpp package.") | |
9252 | ;; hnswlib is released under Version 2.0 of the Apache License. | |
9253 | (license (list license:gpl3 license:asl2.0)))) | |
9254 | ||
c4a5ce46 RW |
9255 | (define-public r-rcppparallel |
9256 | (package | |
9257 | (name "r-rcppparallel") | |
9b112f40 | 9258 | (version "4.4.4") |
c4a5ce46 RW |
9259 | (source |
9260 | (origin | |
9261 | (method url-fetch) | |
9262 | (uri (cran-uri "RcppParallel" version)) | |
9263 | (sha256 | |
9264 | (base32 | |
9b112f40 | 9265 | "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia")))) |
c4a5ce46 RW |
9266 | (properties `((upstream-name . "RcppParallel"))) |
9267 | (build-system r-build-system) | |
9268 | (home-page "http://rcppcore.github.io/RcppParallel") | |
9269 | (synopsis "Parallel programming tools for Rcpp") | |
9270 | (description | |
9271 | "This package provides high level functions for parallel programming with | |
9272 | Rcpp. For example, the @code{parallelFor()} function can be used to convert | |
9273 | the work of a standard serial @code{for} loop into a parallel one and the | |
9274 | @code{parallelReduce()} function can be used for accumulating aggregates or | |
9275 | other values.") | |
9276 | (license license:gpl2))) | |
9277 | ||
b58940cb RW |
9278 | (define-public r-ncdf4 |
9279 | (package | |
9280 | (name "r-ncdf4") | |
883f76b8 | 9281 | (version "1.17") |
b58940cb RW |
9282 | (source |
9283 | (origin | |
9284 | (method url-fetch) | |
9285 | (uri (cran-uri "ncdf4" version)) | |
9286 | (sha256 | |
9287 | (base32 | |
883f76b8 | 9288 | "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv")))) |
b58940cb RW |
9289 | (build-system r-build-system) |
9290 | (inputs | |
9291 | `(("netcdf" ,netcdf) | |
9292 | ("zlib" ,zlib))) | |
9293 | (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") | |
9294 | (synopsis "R interface to Unidata netCDF format data files") | |
9295 | (description | |
9296 | "This package provides a high-level R interface to data files written | |
9297 | using Unidata's netCDF library (version 4 or earlier), which are binary data | |
9298 | files that are portable across platforms and include metadata information in | |
9299 | addition to the data sets. Using this package, netCDF files can be opened and | |
9300 | data sets read in easily. It is also easy to create new netCDF dimensions, | |
9301 | variables, and files, in either version 3 or 4 format, and manipulate existing | |
9302 | netCDF files.") | |
9303 | (license license:gpl3+))) | |
1e605c03 RW |
9304 | |
9305 | (define-public r-biocmanager | |
9306 | (package | |
9307 | (name "r-biocmanager") | |
b93a3297 | 9308 | (version "1.30.10") |
1e605c03 RW |
9309 | (source |
9310 | (origin | |
9311 | (method url-fetch) | |
9312 | (uri (cran-uri "BiocManager" version)) | |
9313 | (sha256 | |
b93a3297 | 9314 | (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk")))) |
1e605c03 RW |
9315 | (properties `((upstream-name . "BiocManager"))) |
9316 | (build-system r-build-system) | |
9317 | (home-page "https://cran.r-project.org/web/packages/BiocManager/") | |
9318 | (synopsis "Access the Bioconductor project package repository") | |
9319 | (description | |
9320 | "This package provides a convenient tool to install and update | |
9321 | Bioconductor packages.") | |
9322 | (license license:artistic2.0))) | |
f338e480 RW |
9323 | |
9324 | (define-public r-rgl | |
9325 | (package | |
9326 | (name "r-rgl") | |
4f1c668d | 9327 | (version "0.100.30") |
f338e480 RW |
9328 | (source |
9329 | (origin | |
9330 | (method url-fetch) | |
9331 | (uri (cran-uri "rgl" version)) | |
9332 | (sha256 | |
9333 | (base32 | |
4f1c668d | 9334 | "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5")))) |
f338e480 RW |
9335 | (build-system r-build-system) |
9336 | (native-inputs | |
9337 | `(("pkg-config" ,pkg-config))) | |
9338 | (inputs | |
9339 | `(("freetype" ,freetype) | |
9340 | ("libpng" ,libpng) | |
9341 | ("glu" ,glu) | |
9342 | ("libx11" ,libx11) | |
9343 | ("ghc-pandoc" ,ghc-pandoc) | |
9344 | ("zlib" ,zlib))) | |
9345 | (propagated-inputs | |
9346 | `(("r-crosstalk" ,r-crosstalk) | |
9347 | ("r-htmltools" ,r-htmltools) | |
9348 | ("r-htmlwidgets" ,r-htmlwidgets) | |
9349 | ("r-jsonlite" ,r-jsonlite) | |
9350 | ("r-knitr" ,r-knitr) | |
9351 | ("r-magrittr" ,r-magrittr) | |
9352 | ("r-manipulatewidget" ,r-manipulatewidget) | |
9353 | ("r-shiny" ,r-shiny))) | |
9354 | (home-page "https://r-forge.r-project.org/projects/rgl/") | |
9355 | (synopsis "3D visualization using OpenGL") | |
9356 | (description | |
9357 | "This package provides medium to high level functions for 3D interactive graphics, | |
9358 | including functions modelled on base graphics (@code{plot3d()}, etc.) as well | |
9359 | as functions for constructing representations of geometric | |
9360 | objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to | |
9361 | various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D | |
9362 | image formats, including PNG, Postscript, SVG, PGF.") | |
9363 | ;; Any version of the GPL. | |
9364 | (license (list license:gpl2+ license:gpl3+)))) | |
213e72a1 RW |
9365 | |
9366 | (define-public r-multicool | |
9367 | (package | |
9368 | (name "r-multicool") | |
b159b8a7 | 9369 | (version "0.1-11") |
213e72a1 RW |
9370 | (source |
9371 | (origin | |
9372 | (method url-fetch) | |
9373 | (uri (cran-uri "multicool" version)) | |
9374 | (sha256 | |
9375 | (base32 | |
b159b8a7 | 9376 | "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w")))) |
213e72a1 RW |
9377 | (build-system r-build-system) |
9378 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
9379 | (home-page "https://cran.r-project.org/web/packages/multicool/") | |
9380 | (synopsis "Permutations of multisets in cool-lex order") | |
9381 | (description | |
9382 | "This package provides a set of tools to permute multisets without loops | |
9383 | or hash tables and to generate integer partitions. Cool-lex order is similar | |
9384 | to colexicographical order.") | |
9385 | (license license:gpl2))) | |
4106e6ad RW |
9386 | |
9387 | (define-public r-misc3d | |
9388 | (package | |
9389 | (name "r-misc3d") | |
9390 | (version "0.8-4") | |
9391 | (source | |
9392 | (origin | |
9393 | (method url-fetch) | |
9394 | (uri (cran-uri "misc3d" version)) | |
9395 | (sha256 | |
9396 | (base32 | |
9397 | "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) | |
9398 | (build-system r-build-system) | |
9399 | (home-page "https://cran.r-project.org/web/packages/misc3d/") | |
9400 | (synopsis "Miscellaneous 3D Plots") | |
9401 | (description | |
9402 | "This package provides a collection of miscellaneous 3d plots, including | |
9403 | isosurfaces.") | |
9404 | ;; Any version of the GPL. | |
9405 | (license (list license:gpl2+ license:gpl3+)))) | |
da256afb RW |
9406 | |
9407 | (define-public r-ks | |
9408 | (package | |
9409 | (name "r-ks") | |
2ac4eb78 | 9410 | (version "1.11.6") |
da256afb RW |
9411 | (source |
9412 | (origin | |
9413 | (method url-fetch) | |
9414 | (uri (cran-uri "ks" version)) | |
9415 | (sha256 | |
2ac4eb78 | 9416 | (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq")))) |
da256afb RW |
9417 | (build-system r-build-system) |
9418 | (propagated-inputs | |
9419 | `(("r-fnn" ,r-fnn) | |
9420 | ("r-kernlab" ,r-kernlab) | |
9421 | ("r-kernsmooth" ,r-kernsmooth) | |
9422 | ("r-matrix" ,r-matrix) | |
9423 | ("r-mclust" ,r-mclust) | |
9424 | ("r-mgcv" ,r-mgcv) | |
da256afb RW |
9425 | ("r-multicool" ,r-multicool) |
9426 | ("r-mvtnorm" ,r-mvtnorm))) | |
9427 | (home-page "http://www.mvstat.net/tduong/") | |
9428 | (synopsis "Kernel smoothing") | |
9429 | (description | |
9430 | "This package provides kernel smoothers for univariate and multivariate | |
9431 | data, including density functions, density derivatives, cumulative | |
9432 | distributions, modal clustering, discriminant analysis, and two-sample | |
9433 | hypothesis testing.") | |
9434 | ;; Either version of the GPL. | |
9435 | (license (list license:gpl2 license:gpl3)))) | |
cf383cf0 RW |
9436 | |
9437 | (define-public r-feature | |
9438 | (package | |
9439 | (name "r-feature") | |
9440 | (version "1.2.13") | |
9441 | (source | |
9442 | (origin | |
9443 | (method url-fetch) | |
9444 | (uri (cran-uri "feature" version)) | |
9445 | (sha256 | |
9446 | (base32 | |
9447 | "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra")))) | |
9448 | (build-system r-build-system) | |
9449 | (propagated-inputs | |
9450 | `(("r-ks" ,r-ks) | |
9451 | ("r-misc3d" ,r-misc3d) | |
9452 | ("r-rgl" ,r-rgl))) | |
9453 | (home-page "http://www.mvstat.net/tduong/") | |
9454 | (synopsis "Inferential feature significance for kernel density estimation") | |
9455 | (description | |
9456 | "The feature package contains functions to display and compute kernel | |
9457 | density estimates, significant gradient and significant curvature regions. | |
9458 | Significant gradient and/or curvature regions often correspond to significant | |
9459 | features (e.g. local modes).") | |
9460 | ;; Either version of the GPL. | |
9461 | (license (list license:gpl2 license:gpl3)))) | |
06bc7b82 RW |
9462 | |
9463 | (define-public r-arm | |
9464 | (package | |
9465 | (name "r-arm") | |
9466 | (version "1.10-1") | |
9467 | (source | |
9468 | (origin | |
9469 | (method url-fetch) | |
9470 | (uri (cran-uri "arm" version)) | |
9471 | (sha256 | |
9472 | (base32 | |
9473 | "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg")))) | |
9474 | (build-system r-build-system) | |
9475 | (propagated-inputs | |
9476 | `(("r-abind" ,r-abind) | |
9477 | ("r-coda" ,r-coda) | |
9478 | ("r-lme4" ,r-lme4) | |
9479 | ("r-mass" ,r-mass) | |
9480 | ("r-matrix" ,r-matrix) | |
9481 | ("r-nlme" ,r-nlme))) | |
9482 | (home-page "https://cran.r-project.org/web/packages/arm/") | |
9483 | (synopsis "Data analysis using regression and multilevel/hierarchical models") | |
9484 | (description | |
9485 | "This package provides functions to accompany A. Gelman and J. Hill, | |
9486 | Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge | |
9487 | University Press, 2007.") | |
9488 | (license license:gpl3+))) | |
3cef715a RW |
9489 | |
9490 | (define-public r-circular | |
9491 | (package | |
9492 | (name "r-circular") | |
9493 | (version "0.4-93") | |
9494 | (source | |
9495 | (origin | |
9496 | (method url-fetch) | |
9497 | (uri (cran-uri "circular" version)) | |
9498 | (sha256 | |
9499 | (base32 | |
9500 | "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) | |
9501 | (build-system r-build-system) | |
9502 | (propagated-inputs | |
9503 | `(("r-boot" ,r-boot) | |
9504 | ("r-mvtnorm" ,r-mvtnorm))) | |
9505 | (native-inputs | |
9506 | `(("gfortran" ,gfortran))) | |
9507 | (home-page "https://cran.r-project.org/web/packages/circular/") | |
9508 | (synopsis "Circular statistics") | |
9509 | (description | |
9510 | "This package provides tools for circular statistics, from \"Topics in | |
9511 | circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World | |
9512 | Scientific.") | |
9513 | (license license:gpl2+))) | |
10483a64 RW |
9514 | |
9515 | (define-public r-activity | |
9516 | (package | |
9517 | (name "r-activity") | |
aef5e2aa | 9518 | (version "1.3") |
10483a64 RW |
9519 | (source |
9520 | (origin | |
9521 | (method url-fetch) | |
9522 | (uri (cran-uri "activity" version)) | |
9523 | (sha256 | |
9524 | (base32 | |
aef5e2aa | 9525 | "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92")))) |
10483a64 RW |
9526 | (build-system r-build-system) |
9527 | (propagated-inputs | |
9528 | `(("r-circular" ,r-circular) | |
aef5e2aa | 9529 | ("r-insol" ,r-insol) |
10483a64 RW |
9530 | ("r-pbapply" ,r-pbapply))) |
9531 | (home-page "https://cran.r-project.org/web/packages/activity/") | |
9532 | (synopsis "Animal activity statistics") | |
9533 | (description | |
9534 | "This package provides functions to fit kernel density functions to | |
9535 | animal activity time data; plot activity distributions; quantify overall | |
9536 | levels of activity; statistically compare activity metrics through | |
9537 | bootstrapping; and evaluate variation in linear variables with time (or other | |
9538 | circular variables).") | |
9539 | (license license:gpl3))) | |
e4f4a04a RW |
9540 | |
9541 | (define-public r-ouch | |
9542 | (package | |
9543 | (name "r-ouch") | |
27b4bfbe | 9544 | (version "2.14-1") |
e4f4a04a RW |
9545 | (source |
9546 | (origin | |
9547 | (method url-fetch) | |
9548 | (uri (cran-uri "ouch" version)) | |
9549 | (sha256 | |
9550 | (base32 | |
27b4bfbe | 9551 | "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b")))) |
e4f4a04a RW |
9552 | (build-system r-build-system) |
9553 | (propagated-inputs `(("r-subplex" ,r-subplex))) | |
9554 | (home-page "http://kingaa.github.io/ouch/") | |
9555 | (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") | |
9556 | (description | |
9557 | "This package provides tools to fit and compare Ornstein-Uhlenbeck models | |
9558 | for evolution along a phylogenetic tree.") | |
9559 | (license license:gpl2+))) | |
705ea5bf RW |
9560 | |
9561 | (define-public r-fmsb | |
9562 | (package | |
9563 | (name "r-fmsb") | |
b744174e | 9564 | (version "0.7.0") |
705ea5bf RW |
9565 | (source |
9566 | (origin | |
9567 | (method url-fetch) | |
9568 | (uri (cran-uri "fmsb" version)) | |
9569 | (sha256 | |
9570 | (base32 | |
b744174e | 9571 | "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45")))) |
705ea5bf RW |
9572 | (build-system r-build-system) |
9573 | (home-page "http://minato.sip21c.org/msb/") | |
9574 | (synopsis "Functions for medical statistics book with demographic data") | |
9575 | (description | |
9576 | "This package provides several utility functions for the book entitled | |
9577 | \"Practices of Medical and Health Data Analysis using R\" (Pearson Education | |
9578 | Japan, 2007) with Japanese demographic data and some demographic analysis | |
9579 | related functions.") | |
9580 | (license license:gpl2+))) | |
ced51a20 RW |
9581 | |
9582 | (define-public r-stabledist | |
9583 | (package | |
9584 | (name "r-stabledist") | |
9585 | (version "0.7-1") | |
9586 | (source | |
9587 | (origin | |
9588 | (method url-fetch) | |
9589 | (uri (cran-uri "stabledist" version)) | |
9590 | (sha256 | |
9591 | (base32 | |
9592 | "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86")))) | |
9593 | (build-system r-build-system) | |
9594 | (home-page "http://www.rmetrics.org") | |
9595 | (synopsis "Stable distribution functions") | |
9596 | (description | |
9597 | "This package provides density, probability and quantile functions, and | |
9598 | random number generation for (skew) stable distributions, using the | |
9599 | parametrizations of Nolan.") | |
9600 | (license license:gpl2+))) | |
a50abb36 RW |
9601 | |
9602 | (define-public r-gsl | |
9603 | (package | |
9604 | (name "r-gsl") | |
6bdce94f | 9605 | (version "2.1-6") |
a50abb36 RW |
9606 | (source |
9607 | (origin | |
9608 | (method url-fetch) | |
9609 | (uri (cran-uri "gsl" version)) | |
9610 | (sha256 | |
9611 | (base32 | |
6bdce94f | 9612 | "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m")))) |
a50abb36 RW |
9613 | (build-system r-build-system) |
9614 | (inputs | |
9615 | `(("gsl" ,gsl))) | |
9616 | (home-page "https://cran.r-project.org/web/packages/gsl") | |
9617 | (synopsis "Wrapper for the GNU Scientific Library") | |
9618 | (description | |
9619 | "This package provides an R wrapper for the special functions and quasi | |
9620 | random number generators of the GNU Scientific Library.") | |
9621 | (license license:gpl2+))) | |
03a3ec5e RW |
9622 | |
9623 | (define-public r-adgoftest | |
9624 | (package | |
9625 | (name "r-adgoftest") | |
9626 | (version "0.3") | |
9627 | (source | |
9628 | (origin | |
9629 | (method url-fetch) | |
9630 | (uri (cran-uri "ADGofTest" version)) | |
9631 | (sha256 | |
9632 | (base32 | |
9633 | "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) | |
9634 | (properties `((upstream-name . "ADGofTest"))) | |
9635 | (build-system r-build-system) | |
9636 | (home-page "https://cran.r-project.org/web/packages/ADGofTest") | |
9637 | (synopsis "Anderson-Darling GoF test") | |
9638 | (description | |
9639 | "This package provides an implementation of the Anderson-Darling GoF test | |
9640 | with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the | |
9641 | Anderson-Darling Distribution\".") | |
9642 | ;; Any version of the GPL. | |
9643 | (license license:gpl3+))) | |
71601a5d RW |
9644 | |
9645 | (define-public r-softimpute | |
9646 | (package | |
9647 | (name "r-softimpute") | |
9648 | (version "1.4") | |
9649 | (source | |
9650 | (origin | |
9651 | (method url-fetch) | |
9652 | (uri (cran-uri "softImpute" version)) | |
9653 | (sha256 | |
9654 | (base32 | |
9655 | "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq")))) | |
9656 | (properties `((upstream-name . "softImpute"))) | |
9657 | (build-system r-build-system) | |
9658 | (propagated-inputs | |
9659 | `(("r-matrix" ,r-matrix))) | |
9660 | (native-inputs | |
9661 | `(("gfortran" ,gfortran))) | |
9662 | (home-page "https://cran.r-project.org/web/packages/softImpute") | |
9663 | (synopsis "Matrix completion via iterative soft-thresholded SVD") | |
9664 | (description | |
9665 | "This package provides iterative methods for matrix completion that use | |
9666 | nuclear-norm regularization. The package includes procedures for centering | |
9667 | and scaling rows, columns or both, and for computing low-rank @dfn{single | |
9668 | value decompositions} (SVDs) on large sparse centered matrices (i.e. principal | |
9669 | components).") | |
9670 | (license license:gpl2))) | |
44b0c5b5 RW |
9671 | |
9672 | (define-public r-fftwtools | |
9673 | (package | |
9674 | (name "r-fftwtools") | |
9675 | (version "0.9-8") | |
9676 | (source | |
9677 | (origin | |
9678 | (method url-fetch) | |
9679 | (uri (cran-uri "fftwtools" version)) | |
9680 | (sha256 | |
9681 | (base32 | |
9682 | "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6")))) | |
9683 | (build-system r-build-system) | |
9684 | (inputs `(("fftw" ,fftw))) | |
9685 | (home-page "https://github.com/krahim/fftwtools") | |
9686 | (synopsis "Wrapper for FFTW3") | |
9687 | (description | |
9688 | "This package provides a wrapper for several FFTW functions. It provides | |
9689 | access to the two-dimensional FFT, the multivariate FFT, and the | |
9690 | one-dimensional real to complex FFT using the FFTW3 library. The package | |
9691 | includes the functions @code{fftw()} and @code{mvfftw()} which are designed to | |
9692 | mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. | |
9693 | The FFT functions have a parameter that allows them to not return the | |
9694 | redundant complex conjugate when the input is real data.") | |
9695 | (license license:gpl2+))) | |
db084d79 RW |
9696 | |
9697 | (define-public r-tiff | |
9698 | (package | |
9699 | (name "r-tiff") | |
9700 | (version "0.1-5") | |
9701 | (source | |
9702 | (origin | |
9703 | (method url-fetch) | |
9704 | (uri (cran-uri "tiff" version)) | |
9705 | (sha256 | |
9706 | (base32 | |
9707 | "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) | |
9708 | (build-system r-build-system) | |
9709 | (inputs | |
9710 | `(("libtiff" ,libtiff) | |
9711 | ("libjpeg" ,libjpeg) | |
9712 | ("zlib" ,zlib))) | |
9713 | (home-page "http://www.rforge.net/tiff/") | |
9714 | (synopsis "Read and write TIFF images") | |
9715 | (description | |
9716 | "This package provides an easy and simple way to read, write and display | |
9717 | bitmap images stored in the TIFF format. It can read and write both files and | |
9718 | in-memory raw vectors.") | |
9719 | ;; Either of these two license versions. | |
9720 | (license (list license:gpl2 license:gpl3)))) | |
f3949fec | 9721 | |
53bd3ab3 RW |
9722 | (define-public r-nlp |
9723 | (package | |
9724 | (name "r-nlp") | |
9725 | (version "0.2-0") | |
9726 | (source | |
9727 | (origin | |
9728 | (method url-fetch) | |
9729 | (uri (cran-uri "NLP" version)) | |
9730 | (sha256 | |
9731 | (base32 | |
9732 | "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w")))) | |
9733 | (properties `((upstream-name . "NLP"))) | |
9734 | (build-system r-build-system) | |
9735 | (home-page "https://cran.r-project.org/web/packages/NLP/") | |
9736 | (synopsis "Natural language processing infrastructure") | |
9737 | (description | |
9738 | "This package provides basic classes and methods for Natural Language | |
9739 | Processing.") | |
9740 | (license license:gpl3))) | |
9741 | ||
f785d546 RW |
9742 | (define-public r-tm |
9743 | (package | |
9744 | (name "r-tm") | |
5f99ffb0 | 9745 | (version "0.7-7") |
f785d546 RW |
9746 | (source |
9747 | (origin | |
9748 | (method url-fetch) | |
9749 | (uri (cran-uri "tm" version)) | |
9750 | (sha256 | |
9751 | (base32 | |
5f99ffb0 | 9752 | "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh")))) |
f785d546 RW |
9753 | (properties `((upstream-name . "tm"))) |
9754 | (build-system r-build-system) | |
9755 | (propagated-inputs | |
9756 | `(("r-bh" ,r-bh) | |
9757 | ("r-nlp" ,r-nlp) | |
9758 | ("r-rcpp" ,r-rcpp) | |
9759 | ("r-slam" ,r-slam) | |
9760 | ("r-xml2" ,r-xml2))) | |
9761 | (home-page "http://tm.r-forge.r-project.org/") | |
9762 | (synopsis "Text mining package") | |
9763 | (description | |
9764 | "This package provides a framework for text mining applications within R.") | |
9765 | (license license:gpl3))) | |
9766 | ||
f3949fec RW |
9767 | (define-public r-waveslim |
9768 | (package | |
9769 | (name "r-waveslim") | |
61cb2e31 | 9770 | (version "1.7.5.1") |
f3949fec RW |
9771 | (source |
9772 | (origin | |
9773 | (method url-fetch) | |
9774 | (uri (cran-uri "waveslim" version)) | |
9775 | (sha256 | |
9776 | (base32 | |
61cb2e31 | 9777 | "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk")))) |
f3949fec RW |
9778 | (build-system r-build-system) |
9779 | (native-inputs | |
9780 | `(("gfortran" ,gfortran))) | |
9781 | (home-page "http://waveslim.blogspot.com") | |
9782 | (synopsis "Basic wavelet routines for signal processing") | |
9783 | (description | |
9784 | "This package provides basic wavelet routines for time series (1D), | |
9785 | image (2D) and array (3D) analysis. The code provided here is based on | |
9786 | wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk | |
9787 | and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from | |
9788 | Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet | |
9789 | pairs (Selesnick 2001, 2002).") | |
9790 | (license license:bsd-3))) | |
e37935e4 RW |
9791 | |
9792 | (define-public r-wordcloud | |
9793 | (package | |
9794 | (name "r-wordcloud") | |
9795 | (version "2.6") | |
9796 | (source | |
9797 | (origin | |
9798 | (method url-fetch) | |
9799 | (uri (cran-uri "wordcloud" version)) | |
9800 | (sha256 | |
9801 | (base32 | |
9802 | "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) | |
9803 | (build-system r-build-system) | |
9804 | (propagated-inputs | |
9805 | `(("r-rcolorbrewer" ,r-rcolorbrewer) | |
f847b659 RW |
9806 | ("r-rcpp" ,r-rcpp) |
9807 | ;; The "tm" package is only "suggested" according to CRAN, but the | |
9808 | ;; wordcloud package cannot be loaded without it. | |
9809 | ("r-tm" ,r-tm))) | |
e37935e4 RW |
9810 | (home-page "https://cran.r-project.org/web/packages/wordcloud") |
9811 | (synopsis "Word clouds") | |
9812 | (description | |
9813 | "This package provides functionality to create pretty word clouds, | |
9814 | visualize differences and similarity between documents, and avoid | |
9815 | over-plotting in scatter plots with text.") | |
9816 | (license license:lgpl2.1))) | |
a6e4413d RW |
9817 | |
9818 | (define-public r-colorramps | |
9819 | (package | |
9820 | (name "r-colorramps") | |
9821 | (version "2.3") | |
9822 | (source | |
9823 | (origin | |
9824 | (method url-fetch) | |
9825 | (uri (cran-uri "colorRamps" version)) | |
9826 | (sha256 | |
9827 | (base32 | |
9828 | "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z")))) | |
9829 | (properties `((upstream-name . "colorRamps"))) | |
9830 | (build-system r-build-system) | |
9831 | (home-page "https://cran.r-project.org/web/packages/colorRamps") | |
9832 | (synopsis "Build color tables") | |
9833 | (description "This package provides features to build gradient color | |
9834 | maps.") | |
9835 | ;; Any version of the GPL | |
9836 | (license license:gpl3+))) | |
61d73349 RW |
9837 | |
9838 | (define-public r-tidytree | |
9839 | (package | |
9840 | (name "r-tidytree") | |
126f027b | 9841 | (version "0.3.1") |
61d73349 RW |
9842 | (source |
9843 | (origin | |
9844 | (method url-fetch) | |
9845 | (uri (cran-uri "tidytree" version)) | |
9846 | (sha256 | |
126f027b | 9847 | (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7")))) |
61d73349 RW |
9848 | (build-system r-build-system) |
9849 | (propagated-inputs | |
9850 | `(("r-ape" ,r-ape) | |
9851 | ("r-dplyr" ,r-dplyr) | |
9852 | ("r-lazyeval" ,r-lazyeval) | |
9853 | ("r-magrittr" ,r-magrittr) | |
9854 | ("r-rlang" ,r-rlang) | |
9855 | ("r-tibble" ,r-tibble))) | |
9856 | (home-page "https://github.com/GuangchuangYu/tidytree") | |
9857 | (synopsis "Tidy tool for phylogenetic tree data manipulation") | |
9858 | (description | |
9859 | "Phylogenetic trees generally contain multiple components including nodes, | |
9860 | edges, branches and associated data. This package provides an approach to | |
9861 | convert tree objects to tidy data frames. It also provides tidy interfaces to | |
9862 | manipulate tree data.") | |
9863 | (license license:artistic2.0))) | |
45b469a4 RW |
9864 | |
9865 | (define-public r-rvcheck | |
9866 | (package | |
9867 | (name "r-rvcheck") | |
5378a1ae | 9868 | (version "0.1.7") |
45b469a4 RW |
9869 | (source |
9870 | (origin | |
9871 | (method url-fetch) | |
9872 | (uri (cran-uri "rvcheck" version)) | |
9873 | (sha256 | |
5378a1ae | 9874 | (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw")))) |
45b469a4 RW |
9875 | (build-system r-build-system) |
9876 | (propagated-inputs | |
9bcd8b68 TGR |
9877 | `(("r-biocmanager" ,r-biocmanager) |
9878 | ("r-rlang" ,r-rlang))) | |
45b469a4 RW |
9879 | (home-page "https://cran.r-project.org/web/packages/rvcheck") |
9880 | (synopsis "R package version check") | |
9881 | (description | |
9882 | "This package provides tools to check the latest release version of R and | |
9883 | R packages (on CRAN, Bioconductor or Github).") | |
9884 | (license license:artistic2.0))) | |
fbebccf7 RW |
9885 | |
9886 | (define-public r-docopt | |
9887 | (package | |
9888 | (name "r-docopt") | |
9889 | (version "0.6.1") | |
9890 | (source | |
9891 | (origin | |
9892 | (method url-fetch) | |
9893 | (uri (cran-uri "docopt" version)) | |
9894 | (sha256 | |
9895 | (base32 | |
9896 | "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068")))) | |
9897 | (build-system r-build-system) | |
9898 | (home-page "https://github.com/docopt/docopt.R") | |
9899 | (synopsis "Command-line interface specification language") | |
9900 | (description | |
9901 | "This package enables you to define a command-line interface by just | |
9902 | giving it a description in the specific format.") | |
9903 | (license license:expat))) | |
b614009e RW |
9904 | |
9905 | (define-public r-sparsesvd | |
9906 | (package | |
9907 | (name "r-sparsesvd") | |
e0f20dce | 9908 | (version "0.2") |
b614009e RW |
9909 | (source |
9910 | (origin | |
9911 | (method url-fetch) | |
9912 | (uri (cran-uri "sparsesvd" version)) | |
9913 | (sha256 | |
9914 | (base32 | |
e0f20dce | 9915 | "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs")))) |
b614009e RW |
9916 | (build-system r-build-system) |
9917 | (propagated-inputs `(("r-matrix" ,r-matrix))) | |
9918 | (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") | |
9919 | (synopsis "Sparse truncated singular value decomposition") | |
9920 | (description | |
9921 | "This package provides a Wrapper around the SVDLIBC library | |
9922 | for (truncated) singular value decomposition of a sparse matrix. Currently, | |
9923 | only sparse real matrices in Matrix package format are supported.") | |
9924 | ;; SVDLIBC is released under BSD-2. The R interface is released under | |
9925 | ;; BSD-3. | |
9926 | (license (list license:bsd-3 license:bsd-2)))) | |
13f5837b | 9927 | |
8f7d7cd0 RW |
9928 | (define-public r-speedglm |
9929 | (package | |
9930 | (name "r-speedglm") | |
9931 | (version "0.3-2") | |
9932 | (source | |
9933 | (origin | |
9934 | (method url-fetch) | |
9935 | (uri (cran-uri "speedglm" version)) | |
9936 | (sha256 | |
9937 | (base32 | |
9938 | "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz")))) | |
9939 | (build-system r-build-system) | |
9940 | (propagated-inputs | |
9941 | `(("r-mass" ,r-mass) | |
9942 | ("r-matrix" ,r-matrix))) | |
9943 | (home-page "https://cran.r-project.org/web/packages/speedglm") | |
9944 | (synopsis "Fit linear and generalized linear models to large data sets") | |
9945 | (description | |
9946 | "This package provides tools for fitting linear models and generalized | |
9947 | linear models to large data sets by updating algorithms.") | |
9948 | ;; Any version of the GPL | |
9949 | (license license:gpl2+))) | |
9950 | ||
13f5837b RW |
9951 | (define-public r-densityclust |
9952 | (package | |
9953 | (name "r-densityclust") | |
9954 | (version "0.3") | |
9955 | (source | |
9956 | (origin | |
9957 | (method url-fetch) | |
9958 | (uri (cran-uri "densityClust" version)) | |
9959 | (sha256 | |
9960 | (base32 | |
9961 | "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13")))) | |
9962 | (properties `((upstream-name . "densityClust"))) | |
9963 | (build-system r-build-system) | |
9964 | (propagated-inputs | |
9965 | `(("r-fnn" ,r-fnn) | |
9966 | ("r-ggplot2" ,r-ggplot2) | |
9967 | ("r-ggrepel" ,r-ggrepel) | |
9968 | ("r-gridextra" ,r-gridextra) | |
9969 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9970 | ("r-rcpp" ,r-rcpp) | |
9971 | ("r-rtsne" ,r-rtsne))) | |
9972 | (home-page "https://cran.r-project.org/web/packages/densityClust") | |
9973 | (synopsis "Clustering by fast search and find of density peaks") | |
9974 | (description | |
9975 | "This package provides an improved implementation (based on k-nearest | |
9976 | neighbors) of the density peak clustering algorithm, originally described by | |
9977 | Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle | |
9978 | large datasets (> 100,000 samples) very efficiently.") | |
9979 | (license license:gpl2+))) | |
58bc8857 RW |
9980 | |
9981 | (define-public r-combinat | |
9982 | (package | |
9983 | (name "r-combinat") | |
9984 | (version "0.0-8") | |
9985 | (source | |
9986 | (origin | |
9987 | (method url-fetch) | |
9988 | (uri (cran-uri "combinat" version)) | |
9989 | (sha256 | |
9990 | (base32 | |
9991 | "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) | |
9992 | (build-system r-build-system) | |
9993 | (home-page "https://cran.r-project.org/web/packages/combinat") | |
9994 | (synopsis "Combinatorics utilities") | |
9995 | (description "This package provides assorted routines for combinatorics.") | |
9996 | (license license:gpl2))) | |
9f33d76c RW |
9997 | |
9998 | (define-public r-qlcmatrix | |
9999 | (package | |
10000 | (name "r-qlcmatrix") | |
10001 | (version "0.9.7") | |
10002 | (source | |
10003 | (origin | |
10004 | (method url-fetch) | |
10005 | (uri (cran-uri "qlcMatrix" version)) | |
10006 | (sha256 | |
10007 | (base32 | |
10008 | "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) | |
10009 | (properties `((upstream-name . "qlcMatrix"))) | |
10010 | (build-system r-build-system) | |
10011 | (propagated-inputs | |
10012 | `(("r-docopt" ,r-docopt) | |
10013 | ("r-matrix" ,r-matrix) | |
10014 | ("r-slam" ,r-slam) | |
10015 | ("r-sparsesvd" ,r-sparsesvd))) | |
10016 | (home-page "https://cran.r-project.org/web/packages/qlcMatrix") | |
10017 | (synopsis "Sparse matrix functions for quantitative language comparison") | |
10018 | (description | |
10019 | "This package provides an extension of the functionality of the Matrix | |
10020 | package for using sparse matrices. Some of the functions are very general, | |
10021 | while other are highly specific for the special data format used for | |
10022 | @dfn{quantitative language comparison} (QLC).") | |
10023 | (license license:gpl3))) | |
e3bb0766 RW |
10024 | |
10025 | (define-public r-ddrtree | |
10026 | (package | |
10027 | (name "r-ddrtree") | |
10028 | (version "0.1.5") | |
10029 | (source | |
10030 | (origin | |
10031 | (method url-fetch) | |
10032 | (uri (cran-uri "DDRTree" version)) | |
10033 | (sha256 | |
10034 | (base32 | |
10035 | "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) | |
10036 | (properties `((upstream-name . "DDRTree"))) | |
10037 | (build-system r-build-system) | |
10038 | (propagated-inputs | |
10039 | `(("r-bh" ,r-bh) | |
10040 | ("r-irlba" ,r-irlba) | |
10041 | ("r-rcpp" ,r-rcpp) | |
10042 | ("r-rcppeigen" ,r-rcppeigen))) | |
10043 | (home-page "https://cran.r-project.org/web/packages/DDRTree") | |
10044 | (synopsis "Learning principal graphs with DDRTree") | |
10045 | (description | |
10046 | "This package provides an implementation of the framework of | |
10047 | @dfn{reversed graph embedding} (RGE) which projects data into a reduced | |
10048 | dimensional space while constructs a principal tree which passes through the | |
10049 | middle of the data simultaneously. DDRTree shows superiority to | |
10050 | alternatives (Wishbone, DPT) for inferring the ordering as well as the | |
10051 | intrinsic structure of single cell genomics data. In general, it could be | |
10052 | used to reconstruct the temporal progression as well as the bifurcation | |
10053 | structure of any data type.") | |
10054 | (license license:asl2.0))) | |
d53b2317 RW |
10055 | |
10056 | (define-public r-corpcor | |
10057 | (package | |
10058 | (name "r-corpcor") | |
10059 | (version "1.6.9") | |
10060 | (source | |
10061 | (origin | |
10062 | (method url-fetch) | |
10063 | (uri (cran-uri "corpcor" version)) | |
10064 | (sha256 | |
10065 | (base32 | |
10066 | "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf")))) | |
10067 | (build-system r-build-system) | |
10068 | (home-page "http://strimmerlab.org/software/corpcor/") | |
10069 | (synopsis "Efficient estimation of covariance and (partial) correlation") | |
10070 | (description | |
10071 | "This package implements a James-Stein-type shrinkage estimator for the | |
10072 | covariance matrix, with separate shrinkage for variances and correlations. | |
10073 | Furthermore, functions are available for fast singular value decomposition, | |
10074 | for computing the pseudoinverse, and for checking the rank and positive | |
10075 | definiteness of a matrix.") | |
10076 | (license license:gpl3+))) | |
3088b3fc RW |
10077 | |
10078 | (define-public r-rspectra | |
10079 | (package | |
10080 | (name "r-rspectra") | |
6a7ac0a8 | 10081 | (version "0.16-0") |
3088b3fc RW |
10082 | (source |
10083 | (origin | |
10084 | (method url-fetch) | |
10085 | (uri (cran-uri "RSpectra" version)) | |
10086 | (sha256 | |
10087 | (base32 | |
6a7ac0a8 | 10088 | "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda")))) |
3088b3fc RW |
10089 | (properties `((upstream-name . "RSpectra"))) |
10090 | (build-system r-build-system) | |
10091 | (propagated-inputs | |
10092 | `(("r-matrix" ,r-matrix) | |
10093 | ("r-rcpp" ,r-rcpp) | |
10094 | ("r-rcppeigen" ,r-rcppeigen))) | |
10095 | (home-page "https://github.com/yixuan/RSpectra") | |
10096 | (synopsis "Solvers for large-scale Eigenvalue and SVD problems") | |
10097 | (description | |
10098 | "This package provides an R interface to the Spectra library for | |
10099 | large-scale eigenvalue and SVD problems. It is typically used to compute a | |
10100 | few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, | |
10101 | which is usually more efficient than @code{eigen()} if k << n.") | |
10102 | ;; MPL 2 or later. | |
10103 | (license license:mpl2.0))) | |
029425cb RW |
10104 | |
10105 | (define-public r-vbsr | |
10106 | (package | |
10107 | (name "r-vbsr") | |
10108 | (version "0.0.5") | |
10109 | (source | |
10110 | (origin | |
10111 | (method url-fetch) | |
10112 | (uri (cran-uri "vbsr" version)) | |
10113 | (sha256 | |
10114 | (base32 | |
10115 | "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) | |
10116 | (build-system r-build-system) | |
10117 | (home-page "https://cran.r-project.org/web/packages/vbsr") | |
10118 | (synopsis "Variational Bayes spike regression regularized linear models") | |
10119 | (description | |
10120 | "This package provides an efficient algorithm for solving ultra-sparse | |
10121 | regularized regression models using a variational Bayes algorithm with a spike | |
10122 | prior. The algorithm is solved on a path, with coordinate updates, and is | |
10123 | capable of generating very sparse models. Very general model | |
10124 | diagnostics for controlling type-1 errors are also provided.") | |
10125 | (license license:gpl2))) | |
3d62d98e RW |
10126 | |
10127 | (define-public r-flare | |
10128 | (package | |
10129 | (name "r-flare") | |
b154b026 | 10130 | (version "1.6.0.2") |
3d62d98e RW |
10131 | (source |
10132 | (origin | |
10133 | (method url-fetch) | |
10134 | (uri (cran-uri "flare" version)) | |
10135 | (sha256 | |
10136 | (base32 | |
b154b026 | 10137 | "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5")))) |
3d62d98e RW |
10138 | (build-system r-build-system) |
10139 | (propagated-inputs | |
10140 | `(("r-igraph" ,r-igraph) | |
10141 | ("r-lattice" ,r-lattice) | |
10142 | ("r-mass" ,r-mass) | |
10143 | ("r-matrix" ,r-matrix))) | |
10144 | (home-page "https://cran.r-project.org/web/packages/flare") | |
10145 | (synopsis "Family of Lasso regression implementations") | |
10146 | (description | |
6a0c3e03 | 10147 | "This package provides implementations of a family of Lasso variants |
3d62d98e RW |
10148 | including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating |
10149 | high dimensional sparse linear models.") | |
10150 | (license license:gpl2))) | |
5f0fbfc0 RW |
10151 | |
10152 | (define-public r-lassopv | |
10153 | (package | |
10154 | (name "r-lassopv") | |
10155 | (version "0.2.0") | |
10156 | (source | |
10157 | (origin | |
10158 | (method url-fetch) | |
10159 | (uri (cran-uri "lassopv" version)) | |
10160 | (sha256 | |
10161 | (base32 | |
10162 | "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) | |
10163 | (build-system r-build-system) | |
10164 | (propagated-inputs `(("r-lars" ,r-lars))) | |
10165 | (home-page "https://github.com/lingfeiwang/lassopv") | |
10166 | (synopsis "Non-parametric p-value estimation for predictors in Lasso") | |
10167 | (description | |
10168 | "This package enables you to estimate the p-values for predictors x | |
10169 | against target variable y in Lasso regression, using the regularization | |
10170 | strength when each predictor enters the active set of regularization path for | |
10171 | the first time as the statistic.") | |
10172 | (license license:gpl3))) | |
adcd0cc8 RW |
10173 | |
10174 | (define-public r-splitstackshape | |
10175 | (package | |
10176 | (name "r-splitstackshape") | |
90325bb1 | 10177 | (version "1.4.8") |
adcd0cc8 RW |
10178 | (source |
10179 | (origin | |
10180 | (method url-fetch) | |
10181 | (uri (cran-uri "splitstackshape" version)) | |
10182 | (sha256 | |
10183 | (base32 | |
90325bb1 | 10184 | "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) |
adcd0cc8 RW |
10185 | (build-system r-build-system) |
10186 | (propagated-inputs | |
10187 | `(("r-data-table" ,r-data-table))) | |
10188 | (home-page "https://github.com/mrdwab/splitstackshape") | |
10189 | (synopsis "Stack and reshape datasets after splitting concatenated values") | |
10190 | (description | |
10191 | "Online data collection tools like Google Forms often export | |
10192 | multiple-response questions with data concatenated in cells. The | |
10193 | @code{concat.split} (cSplit) family of functions provided by this package | |
10194 | splits such data into separate cells. This package also includes functions to | |
10195 | stack groups of columns and to reshape wide data, even when the data are | |
10196 | \"unbalanced\"---something which @code{reshape} (from base R) does not handle, | |
10197 | and which @code{melt} and @code{dcast} from @code{reshape2} do not easily | |
10198 | handle.") | |
10199 | (license license:gpl3))) | |
b2e777b2 RW |
10200 | |
10201 | (define-public r-tfmpvalue | |
10202 | (package | |
10203 | (name "r-tfmpvalue") | |
10204 | (version "0.0.8") | |
10205 | (source | |
10206 | (origin | |
10207 | (method url-fetch) | |
10208 | (uri (cran-uri "TFMPvalue" version)) | |
10209 | (sha256 | |
10210 | (base32 | |
10211 | "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) | |
10212 | (properties `((upstream-name . "TFMPvalue"))) | |
10213 | (build-system r-build-system) | |
10214 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
10215 | (home-page "https://github.com/ge11232002/TFMPvalue") | |
10216 | (synopsis "P-value computation for position weight matrices") | |
10217 | (description | |
10218 | "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) | |
10219 | identification from sequence/alignments, we are interested in the significance | |
10220 | of certain match scores. TFMPvalue provides the accurate calculation of a | |
10221 | p-value with a score threshold for position weight matrices, or the score with | |
10222 | a given p-value. It is an interface to code originally made available by | |
10223 | Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. | |
10224 | Touzet and Varre (2007).") | |
10225 | (license license:gpl2))) | |
f79e63a5 RW |
10226 | |
10227 | (define-public r-rnifti | |
10228 | (package | |
10229 | (name "r-rnifti") | |
04c3fd85 | 10230 | (version "1.0.1") |
f79e63a5 RW |
10231 | (source |
10232 | (origin | |
10233 | (method url-fetch) | |
10234 | (uri (cran-uri "RNifti" version)) | |
10235 | (sha256 | |
10236 | (base32 | |
04c3fd85 | 10237 | "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w")))) |
f79e63a5 RW |
10238 | (properties `((upstream-name . "RNifti"))) |
10239 | (build-system r-build-system) | |
10240 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
10241 | (home-page "https://github.com/jonclayden/RNifti") | |
10242 | (synopsis "Fast R and C++ access to NIfTI images") | |
10243 | (description | |
10244 | "This package provides very fast read and write access to images stored | |
10245 | in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between | |
10246 | compiled C and interpreted R code. It also provides a C/C++ API that can be | |
10247 | used by other packages.") | |
10248 | (license license:gpl2))) | |
6e09f506 RW |
10249 | |
10250 | (define-public r-shades | |
10251 | (package | |
10252 | (name "r-shades") | |
031afc48 | 10253 | (version "1.4.0") |
6e09f506 RW |
10254 | (source |
10255 | (origin | |
10256 | (method url-fetch) | |
10257 | (uri (cran-uri "shades" version)) | |
10258 | (sha256 | |
10259 | (base32 | |
031afc48 | 10260 | "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) |
6e09f506 RW |
10261 | (build-system r-build-system) |
10262 | (home-page "https://github.com/jonclayden/shades") | |
10263 | (synopsis "Simple color manipulation") | |
10264 | (description | |
10265 | "This package provides functions for easily manipulating colors, | |
10266 | creating color scales and calculating color distances.") | |
10267 | (license license:bsd-3))) | |
cb03d6c6 RW |
10268 | |
10269 | (define-public r-ore | |
10270 | (package | |
10271 | (name "r-ore") | |
a8ea0c5e | 10272 | (version "1.6.3") |
cb03d6c6 RW |
10273 | (source |
10274 | (origin | |
10275 | (method url-fetch) | |
10276 | (uri (cran-uri "ore" version)) | |
10277 | (sha256 | |
a8ea0c5e | 10278 | (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv")))) |
cb03d6c6 RW |
10279 | (build-system r-build-system) |
10280 | (home-page "https://github.com/jonclayden/ore") | |
10281 | (synopsis "R interface to the Onigmo regular expression library") | |
10282 | (description | |
10283 | "This package provides an alternative to R's built-in functionality for | |
10284 | handling regular expressions, based on the Onigmo library. It offers | |
10285 | first-class compiled regex objects, partial matching and function-based | |
10286 | substitutions, amongst other features.") | |
10287 | (license license:bsd-3))) | |
b98662c5 RW |
10288 | |
10289 | (define-public r-reportr | |
10290 | (package | |
10291 | (name "r-reportr") | |
10292 | (version "1.3.0") | |
10293 | (source | |
10294 | (origin | |
10295 | (method url-fetch) | |
10296 | (uri (cran-uri "reportr" version)) | |
10297 | (sha256 | |
10298 | (base32 | |
10299 | "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) | |
10300 | (build-system r-build-system) | |
10301 | (propagated-inputs `(("r-ore" ,r-ore))) | |
10302 | (home-page "https://github.com/jonclayden/reportr") | |
10303 | (synopsis "General message and error reporting system") | |
10304 | (description | |
10305 | "This package provides a system for reporting messages, which offers | |
10306 | certain useful features over the standard R system, such as the incorporation | |
10307 | of output consolidation, message filtering, assertions, expression | |
10308 | substitution, automatic generation of stack traces for debugging, and | |
10309 | conditional reporting based on the current \"output level\".") | |
10310 | (license license:gpl2))) | |
7eec973e RW |
10311 | |
10312 | (define-public r-tractor-base | |
10313 | (package | |
10314 | (name "r-tractor-base") | |
5cc89654 | 10315 | (version "3.3.2") |
7eec973e RW |
10316 | (source |
10317 | (origin | |
10318 | (method url-fetch) | |
10319 | (uri (cran-uri "tractor.base" version)) | |
10320 | (sha256 | |
10321 | (base32 | |
5cc89654 | 10322 | "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i")))) |
7eec973e RW |
10323 | (properties `((upstream-name . "tractor.base"))) |
10324 | (build-system r-build-system) | |
10325 | (propagated-inputs | |
10326 | `(("r-ore" ,r-ore) | |
10327 | ("r-reportr" ,r-reportr) | |
10328 | ("r-rnifti" ,r-rnifti) | |
10329 | ("r-shades" ,r-shades))) | |
10330 | (home-page "http://www.tractor-mri.org.uk") | |
10331 | (synopsis "Read, manipulate and visualize magnetic resonance images") | |
10332 | (description | |
10333 | "This package provides functions for working with magnetic resonance | |
10334 | images. It supports reading and writing of popular file formats (DICOM, | |
10335 | Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive | |
10336 | visualization; flexible image manipulation; metadata and sparse image | |
10337 | handling.") | |
10338 | (license license:gpl2))) | |
d0eb09a1 RW |
10339 | |
10340 | (define-public r-grimport | |
10341 | (package | |
10342 | (name "r-grimport") | |
e2448b4b | 10343 | (version "0.9-3") |
d0eb09a1 RW |
10344 | (source |
10345 | (origin | |
10346 | (method url-fetch) | |
10347 | (uri (cran-uri "grImport" version)) | |
10348 | (sha256 | |
10349 | (base32 | |
e2448b4b | 10350 | "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd")))) |
d0eb09a1 RW |
10351 | (properties `((upstream-name . "grImport"))) |
10352 | (build-system r-build-system) | |
10353 | (inputs | |
10354 | `(("ghostscript" ,ghostscript))) | |
10355 | (propagated-inputs | |
10356 | `(("r-xml" ,r-xml))) | |
10357 | (home-page "https://cran.r-project.org/web/packages/grImport") | |
10358 | (synopsis "Convert, import, and draw PostScript pictures") | |
10359 | (description | |
10360 | "This package provides functions for converting, importing, and drawing | |
10361 | PostScript pictures in R plots.") | |
10362 | (license license:gpl2+))) | |
78735b9f RW |
10363 | |
10364 | (define-public r-grimport2 | |
10365 | (package | |
10366 | (name "r-grimport2") | |
bb180e8a | 10367 | (version "0.2-0") |
78735b9f RW |
10368 | (source |
10369 | (origin | |
10370 | (method url-fetch) | |
10371 | (uri (cran-uri "grImport2" version)) | |
10372 | (sha256 | |
10373 | (base32 | |
bb180e8a | 10374 | "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1")))) |
78735b9f RW |
10375 | (properties `((upstream-name . "grImport2"))) |
10376 | (build-system r-build-system) | |
10377 | (propagated-inputs | |
10378 | `(("r-base64enc" ,r-base64enc) | |
10379 | ("r-jpeg" ,r-jpeg) | |
10380 | ("r-png" ,r-png) | |
10381 | ("r-xml" ,r-xml))) | |
10382 | (home-page "https://cran.r-project.org/web/packages/grImport2/") | |
10383 | (synopsis "Import SVG graphics") | |
10384 | (description | |
10385 | "This package provides functions for importing external vector images and | |
10386 | drawing them as part of R plots. This package is different from the | |
10387 | @code{grImport} package because, where that package imports PostScript format | |
10388 | images, this package imports SVG format images. Furthermore, this package | |
10389 | imports a specific subset of SVG, so external images must be preprocessed | |
10390 | using a package like @code{rsvg} to produce SVG that this package can import. | |
10391 | SVG features that are not supported by R graphics, such as gradient fills, can | |
10392 | be imported and then exported via the @code{gridSVG} package.") | |
10393 | (license license:gpl2+))) | |
2871b670 RW |
10394 | |
10395 | (define-public r-kohonen | |
10396 | (package | |
10397 | (name "r-kohonen") | |
7dcd8239 | 10398 | (version "3.0.10") |
2871b670 RW |
10399 | (source |
10400 | (origin | |
10401 | (method url-fetch) | |
10402 | (uri (cran-uri "kohonen" version)) | |
10403 | (sha256 | |
10404 | (base32 | |
7dcd8239 | 10405 | "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr")))) |
2871b670 RW |
10406 | (build-system r-build-system) |
10407 | (propagated-inputs | |
7dcd8239 | 10408 | `(("r-rcpp" ,r-rcpp))) |
2871b670 RW |
10409 | (home-page "https://cran.r-project.org/web/packages/kohonen") |
10410 | (synopsis "Supervised and unsupervised self-organising maps") | |
10411 | (description | |
10412 | "This package provides functions to train @dfn{self-organising | |
10413 | maps} (SOMs). Also interrogation of the maps and prediction using trained | |
10414 | maps are supported. The name of the package refers to Teuvo Kohonen, the | |
10415 | inventor of the SOM.") | |
10416 | (license license:gpl2+))) | |
00436e2c RW |
10417 | |
10418 | (define-public r-nnls | |
10419 | (package | |
10420 | (name "r-nnls") | |
10421 | (version "1.4") | |
10422 | (source | |
10423 | (origin | |
10424 | (method url-fetch) | |
10425 | (uri (cran-uri "nnls" version)) | |
10426 | (sha256 | |
10427 | (base32 | |
10428 | "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) | |
10429 | (build-system r-build-system) | |
10430 | (native-inputs `(("gfortran" ,gfortran))) | |
10431 | (home-page "https://cran.r-project.org/web/packages/nnls") | |
10432 | (synopsis "Lawson-Hanson algorithm for non-negative least squares") | |
10433 | (description | |
10434 | "This package provides an R interface to the Lawson-Hanson implementation | |
10435 | of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows | |
10436 | the combination of non-negative and non-positive constraints.") | |
10437 | (license license:gpl2+))) | |
25861356 RW |
10438 | |
10439 | (define-public r-iso | |
10440 | (package | |
10441 | (name "r-iso") | |
85f3ec6a | 10442 | (version "0.0-18") |
25861356 RW |
10443 | (source |
10444 | (origin | |
10445 | (method url-fetch) | |
10446 | (uri (cran-uri "Iso" version)) | |
10447 | (sha256 | |
10448 | (base32 | |
85f3ec6a | 10449 | "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid")))) |
25861356 RW |
10450 | (properties `((upstream-name . "Iso"))) |
10451 | (build-system r-build-system) | |
10452 | (native-inputs `(("gfortran" ,gfortran))) | |
10453 | (home-page "http://www.stat.auckland.ac.nz/~rolf/") | |
10454 | (synopsis "Functions to perform isotonic regression") | |
10455 | (description | |
10456 | "This package provides support for linear order and unimodal | |
10457 | order (univariate) isotonic regression and bivariate isotonic regression with | |
10458 | linear order on both variables.") | |
10459 | (license license:gpl2+))) | |
9401f56b RW |
10460 | |
10461 | (define-public r-chemometricswithr | |
10462 | (package | |
10463 | (name "r-chemometricswithr") | |
e0417402 | 10464 | (version "0.1.13") |
9401f56b RW |
10465 | (source |
10466 | (origin | |
10467 | (method url-fetch) | |
10468 | (uri (cran-uri "ChemometricsWithR" version)) | |
10469 | (sha256 | |
10470 | (base32 | |
e0417402 | 10471 | "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) |
9401f56b RW |
10472 | (properties |
10473 | `((upstream-name . "ChemometricsWithR"))) | |
10474 | (build-system r-build-system) | |
10475 | (propagated-inputs | |
10476 | `(("r-devtools" ,r-devtools) | |
10477 | ("r-kohonen" ,r-kohonen) | |
10478 | ("r-mass" ,r-mass) | |
10479 | ("r-pls" ,r-pls))) | |
10480 | (home-page "https://github.com/rwehrens/CWR") | |
10481 | (synopsis "Chemometrics with R") | |
10482 | (description | |
10483 | "This package provides functions and scripts used in the book | |
10484 | \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and | |
10485 | Life Sciences\" by Ron Wehrens, Springer (2011).") | |
10486 | (license license:gpl2+))) | |
d28be7b7 RW |
10487 | |
10488 | (define-public r-als | |
10489 | (package | |
10490 | (name "r-als") | |
10491 | (version "0.0.6") | |
10492 | (source | |
10493 | (origin | |
10494 | (method url-fetch) | |
10495 | (uri (cran-uri "ALS" version)) | |
10496 | (sha256 | |
10497 | (base32 | |
10498 | "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) | |
10499 | (properties `((upstream-name . "ALS"))) | |
10500 | (build-system r-build-system) | |
10501 | (propagated-inputs | |
10502 | `(("r-iso" ,r-iso) | |
10503 | ("r-nnls" ,r-nnls))) | |
10504 | (home-page "https://cran.r-project.org/web/packages/ALS") | |
10505 | (synopsis "Multivariate curve resolution alternating least squares") | |
10506 | (description | |
10507 | "Alternating least squares is often used to resolve components | |
10508 | contributing to data with a bilinear structure; the basic technique may be | |
10509 | extended to alternating constrained least squares. This package provides an | |
10510 | implementation of @dfn{multivariate curve resolution alternating least | |
10511 | squares} (MCR-ALS). | |
10512 | ||
10513 | Commonly applied constraints include unimodality, non-negativity, and | |
10514 | normalization of components. Several data matrices may be decomposed | |
10515 | simultaneously by assuming that one of the two matrices in the bilinear | |
10516 | decomposition is shared between datasets.") | |
10517 | (license license:gpl2+))) | |
895efece RW |
10518 | |
10519 | (define-public r-strucchange | |
10520 | (package | |
10521 | (name "r-strucchange") | |
f6f76c93 | 10522 | (version "1.5-2") |
895efece RW |
10523 | (source |
10524 | (origin | |
10525 | (method url-fetch) | |
10526 | (uri (cran-uri "strucchange" version)) | |
10527 | (sha256 | |
10528 | (base32 | |
f6f76c93 | 10529 | "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x")))) |
895efece RW |
10530 | (build-system r-build-system) |
10531 | (propagated-inputs | |
10532 | `(("r-sandwich" ,r-sandwich) | |
10533 | ("r-zoo" ,r-zoo))) | |
10534 | (home-page "https://cran.r-project.org/web/packages/strucchange") | |
10535 | (synopsis "Testing, monitoring, and dating structural changes") | |
10536 | (description | |
10537 | "This package provides tools for testing, monitoring and dating | |
10538 | structural changes in (linear) regression models. It features tests/methods | |
10539 | from the generalized fluctuation test framework as well as from the F | |
10540 | test (Chow test) framework. This includes methods to fit, plot and test | |
10541 | fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F | |
10542 | statistics, respectively. It is possible to monitor incoming data online | |
10543 | using fluctuation processes. Finally, the breakpoints in regression models | |
10544 | with structural changes can be estimated together with confidence intervals. | |
10545 | Emphasis is always given to methods for visualizing the data.") | |
10546 | ;; Either of these two GPL versions | |
10547 | (license (list license:gpl2 license:gpl3)))) | |
e7176ac5 RW |
10548 | |
10549 | (define-public r-pixmap | |
10550 | (package | |
10551 | (name "r-pixmap") | |
10552 | (version "0.4-11") | |
10553 | (source | |
10554 | (origin | |
10555 | (method url-fetch) | |
10556 | (uri (cran-uri "pixmap" version)) | |
10557 | (sha256 | |
10558 | (base32 | |
10559 | "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) | |
10560 | (build-system r-build-system) | |
10561 | (home-page "https://cran.r-project.org/web/packages/pixmap") | |
10562 | (synopsis "Tools for bitmap images") | |
10563 | (description | |
10564 | "This package provides functions for importing, exporting, plotting and | |
10565 | other manipulations of bitmapped images.") | |
10566 | (license license:gpl2))) | |
9170eb7f RW |
10567 | |
10568 | (define-public r-rapidjsonr | |
10569 | (package | |
10570 | (name "r-rapidjsonr") | |
10571 | (version "1.1") | |
10572 | (source | |
10573 | (origin | |
10574 | (method url-fetch) | |
10575 | (uri (cran-uri "rapidjsonr" version)) | |
10576 | (sha256 | |
10577 | (base32 | |
10578 | "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd")))) | |
10579 | (build-system r-build-system) | |
10580 | (home-page "https://cran.r-project.org/web/packages/rapidjsonr") | |
10581 | (synopsis "JSON parser") | |
10582 | (description | |
10583 | "This package provides JSON parsing capability through the Rapidjson | |
10584 | library.") | |
10585 | (license license:expat))) | |
ad6fea16 RW |
10586 | |
10587 | (define-public r-ontologyindex | |
10588 | (package | |
10589 | (name "r-ontologyindex") | |
209e504b | 10590 | (version "2.5") |
ad6fea16 RW |
10591 | (source |
10592 | (origin | |
10593 | (method url-fetch) | |
10594 | (uri (cran-uri "ontologyIndex" version)) | |
10595 | (sha256 | |
10596 | (base32 | |
209e504b | 10597 | "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) |
ad6fea16 RW |
10598 | (properties `((upstream-name . "ontologyIndex"))) |
10599 | (build-system r-build-system) | |
10600 | (home-page "https://cran.r-project.org/web/packages/ontologyIndex") | |
10601 | (synopsis "Functions for processing ontologies in R") | |
10602 | (description | |
10603 | "This package provides functions for reading ontologies into R as lists | |
10604 | and manipulating sets of ontological terms.") | |
10605 | (license license:gpl2+))) | |
dfd09f7b | 10606 | |
6275418b RW |
10607 | (define-public r-gargle |
10608 | (package | |
10609 | (name "r-gargle") | |
f817005b | 10610 | (version "0.4.0") |
6275418b RW |
10611 | (source |
10612 | (origin | |
10613 | (method url-fetch) | |
10614 | (uri (cran-uri "gargle" version)) | |
10615 | (sha256 | |
10616 | (base32 | |
f817005b | 10617 | "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx")))) |
6275418b RW |
10618 | (build-system r-build-system) |
10619 | (propagated-inputs | |
10620 | `(("r-fs" ,r-fs) | |
10621 | ("r-glue" ,r-glue) | |
10622 | ("r-httr" ,r-httr) | |
10623 | ("r-jsonlite" ,r-jsonlite) | |
10624 | ("r-rlang" ,r-rlang) | |
10625 | ("r-withr" ,r-withr))) | |
10626 | (home-page "https://gargle.r-lib.org") | |
10627 | (synopsis "Utilities for working with Google APIs") | |
10628 | (description | |
10629 | "This package provides utilities for working with Google APIs. This | |
10630 | includes functions and classes for handling common credential types and for | |
10631 | preparing, executing, and processing HTTP requests.") | |
10632 | (license license:expat))) | |
10633 | ||
dfd09f7b RW |
10634 | (define-public r-bigrquery |
10635 | (package | |
10636 | (name "r-bigrquery") | |
504a5136 | 10637 | (version "1.2.0") |
dfd09f7b RW |
10638 | (source |
10639 | (origin | |
10640 | (method url-fetch) | |
10641 | (uri (cran-uri "bigrquery" version)) | |
10642 | (sha256 | |
10643 | (base32 | |
504a5136 | 10644 | "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb")))) |
dfd09f7b RW |
10645 | (build-system r-build-system) |
10646 | (propagated-inputs | |
10647 | `(("r-assertthat" ,r-assertthat) | |
4bc5d451 | 10648 | ("r-bit64" ,r-bit64) |
dfd09f7b RW |
10649 | ("r-curl" ,r-curl) |
10650 | ("r-dbi" ,r-dbi) | |
504a5136 | 10651 | ("r-gargle" ,r-gargle) |
dfd09f7b RW |
10652 | ("r-glue" ,r-glue) |
10653 | ("r-httr" ,r-httr) | |
10654 | ("r-jsonlite" ,r-jsonlite) | |
10655 | ("r-prettyunits" ,r-prettyunits) | |
10656 | ("r-progress" ,r-progress) | |
10657 | ("r-rapidjsonr" ,r-rapidjsonr) | |
10658 | ("r-rcpp" ,r-rcpp) | |
504a5136 | 10659 | ("r-rlang" ,r-rlang) |
dfd09f7b RW |
10660 | ("r-tibble" ,r-tibble))) |
10661 | (home-page "https://github.com/rstats-db/bigrquery") | |
10662 | (synopsis "R interface to Google's BigQuery API") | |
10663 | (description | |
10664 | "This package provides an R interface to Google's BigQuery database.") | |
10665 | (license license:gpl3))) | |
1ab51604 RW |
10666 | |
10667 | (define-public r-gmp | |
10668 | (package | |
10669 | (name "r-gmp") | |
83bfddd1 | 10670 | (version "0.5-13.5") |
1ab51604 RW |
10671 | (source |
10672 | (origin | |
10673 | (method url-fetch) | |
10674 | (uri (cran-uri "gmp" version)) | |
10675 | (sha256 | |
10676 | (base32 | |
83bfddd1 | 10677 | "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn")))) |
1ab51604 RW |
10678 | (build-system r-build-system) |
10679 | (arguments | |
10680 | '(#:phases | |
10681 | (modify-phases %standard-phases | |
10682 | (add-after 'unpack 'set-CC | |
10683 | (lambda _ (setenv "CC" "gcc") #t))))) | |
10684 | (inputs `(("gmp" ,gmp))) | |
10685 | (home-page "https://cran.r-project.org/web/packages/gmp") | |
10686 | (synopsis "Multiple precision arithmetic") | |
10687 | (description | |
10688 | "This package supports multiple precision arithmetic (big integers and | |
10689 | rationals, prime number tests, matrix computation), \"arithmetic without | |
10690 | limitations\" using the GNU Multiple Precision library.") | |
10691 | ;; Any version of the GPL. | |
10692 | (license license:gpl3+))) | |
a536c7c9 RW |
10693 | |
10694 | (define-public r-rmpfr | |
10695 | (package | |
10696 | (name "r-rmpfr") | |
df00ca25 | 10697 | (version "0.7-2") |
a536c7c9 RW |
10698 | (source |
10699 | (origin | |
10700 | (method url-fetch) | |
10701 | (uri (cran-uri "Rmpfr" version)) | |
10702 | (sha256 | |
10703 | (base32 | |
df00ca25 | 10704 | "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc")))) |
a536c7c9 RW |
10705 | (properties `((upstream-name . "Rmpfr"))) |
10706 | (build-system r-build-system) | |
10707 | (inputs | |
10708 | `(("mpfr" ,mpfr))) | |
10709 | (propagated-inputs | |
10710 | `(("r-gmp" ,r-gmp))) | |
10711 | (home-page "http://rmpfr.r-forge.r-project.org/") | |
10712 | (synopsis "R bindings to the MPFR library") | |
10713 | (description | |
10714 | "This package supports arithmetic (via S4 classes and methods) for | |
10715 | arbitrary precision floating point numbers, including transcendental | |
10716 | functions. To this end, the package interfaces with the @dfn{Multiple | |
10717 | Precision Floating-Point Reliable} (MPFR) library.") | |
10718 | (license license:gpl2+))) | |
8004bb24 RW |
10719 | |
10720 | (define-public r-assertive-base | |
10721 | (package | |
10722 | (name "r-assertive-base") | |
10723 | (version "0.0-7") | |
10724 | (source | |
10725 | (origin | |
10726 | (method url-fetch) | |
10727 | (uri (cran-uri "assertive.base" version)) | |
10728 | (sha256 | |
10729 | (base32 | |
10730 | "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh")))) | |
10731 | (properties | |
10732 | `((upstream-name . "assertive.base"))) | |
10733 | (build-system r-build-system) | |
10734 | (home-page "https://bitbucket.org/richierocks/assertive.base") | |
10735 | (synopsis "Core of the assertive package") | |
10736 | (description | |
10737 | "This package provides a minimal set of predicates and assertions used by | |
10738 | the assertive package. This is mainly for use by other package developers who | |
10739 | want to include run-time testing features in their own packages.") | |
10740 | (license license:gpl3+))) | |
4b2d17ed RW |
10741 | |
10742 | (define-public r-assertive-properties | |
10743 | (package | |
10744 | (name "r-assertive-properties") | |
10745 | (version "0.0-4") | |
10746 | (source | |
10747 | (origin | |
10748 | (method url-fetch) | |
10749 | (uri (cran-uri "assertive.properties" version)) | |
10750 | (sha256 | |
10751 | (base32 | |
10752 | "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw")))) | |
10753 | (properties | |
10754 | `((upstream-name . "assertive.properties"))) | |
10755 | (build-system r-build-system) | |
10756 | (propagated-inputs | |
10757 | `(("r-assertive-base" ,r-assertive-base))) | |
10758 | (home-page "https://bitbucket.org/richierocks/assertive.properties") | |
10759 | (synopsis "Assertions to check properties of variables") | |
10760 | (description | |
10761 | "This package provides a set of predicates and assertions for checking | |
10762 | the properties of variables, such as length, names and attributes. This is | |
10763 | mainly for use by other package developers who want to include run-time | |
10764 | testing features in their own packages.") | |
10765 | (license license:gpl3+))) | |
dac9c1f6 RW |
10766 | |
10767 | (define-public r-assertive-numbers | |
10768 | (package | |
10769 | (name "r-assertive-numbers") | |
10770 | (version "0.0-2") | |
10771 | (source | |
10772 | (origin | |
10773 | (method url-fetch) | |
10774 | (uri (cran-uri "assertive.numbers" version)) | |
10775 | (sha256 | |
10776 | (base32 | |
10777 | "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds")))) | |
10778 | (properties | |
10779 | `((upstream-name . "assertive.numbers"))) | |
10780 | (build-system r-build-system) | |
10781 | (propagated-inputs | |
10782 | `(("r-assertive-base" ,r-assertive-base))) | |
10783 | (home-page "https://bitbucket.org/richierocks/assertive.numbers") | |
10784 | (synopsis "Assertions to check properties of numbers") | |
10785 | (description | |
10786 | "This package provides a set of predicates and assertions for checking | |
10787 | the properties of numbers. This is mainly for use by other package developers | |
10788 | who want to include run-time testing features in their own packages.") | |
10789 | (license license:gpl3+))) | |
2da2d2f6 RW |
10790 | |
10791 | (define-public r-assertive-sets | |
10792 | (package | |
10793 | (name "r-assertive-sets") | |
10794 | (version "0.0-3") | |
10795 | (source | |
10796 | (origin | |
10797 | (method url-fetch) | |
10798 | (uri (cran-uri "assertive.sets" version)) | |
10799 | (sha256 | |
10800 | (base32 | |
10801 | "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7")))) | |
10802 | (properties | |
10803 | `((upstream-name . "assertive.sets"))) | |
10804 | (build-system r-build-system) | |
10805 | (propagated-inputs | |
10806 | `(("r-assertive-base" ,r-assertive-base))) | |
10807 | (home-page "https://bitbucket.org/richierocks/assertive.sets") | |
10808 | (synopsis "Assertions to check properties of sets") | |
10809 | (description | |
10810 | "This package provides a set of predicates and assertions for checking | |
10811 | the properties of sets. This is mainly for use by other package developers | |
10812 | who want to include run-time testing features in their own packages.") | |
10813 | (license license:gpl3+))) | |
905aa46a RW |
10814 | |
10815 | (define-public r-assertive-matrices | |
10816 | (package | |
10817 | (name "r-assertive-matrices") | |
10818 | (version "0.0-2") | |
10819 | (source | |
10820 | (origin | |
10821 | (method url-fetch) | |
10822 | (uri (cran-uri "assertive.matrices" version)) | |
10823 | (sha256 | |
10824 | (base32 | |
10825 | "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil")))) | |
10826 | (properties | |
10827 | `((upstream-name . "assertive.matrices"))) | |
10828 | (build-system r-build-system) | |
10829 | (propagated-inputs | |
10830 | `(("r-assertive-base" ,r-assertive-base))) | |
10831 | (home-page "https://bitbucket.org/richierocks/assertive.matrices") | |
10832 | (synopsis "Assertions to check properties of matrices") | |
10833 | (description | |
10834 | "This package provides a set of predicates and assertions for checking | |
10835 | the properties of matrices. This is mainly for use by other package | |
10836 | developers who want to include run-time testing features in their own | |
10837 | packages.") | |
10838 | (license license:gpl3+))) | |
c358b5d4 RW |
10839 | |
10840 | (define-public r-assertive-models | |
10841 | (package | |
10842 | (name "r-assertive-models") | |
10843 | (version "0.0-2") | |
10844 | (source | |
10845 | (origin | |
10846 | (method url-fetch) | |
10847 | (uri (cran-uri "assertive.models" version)) | |
10848 | (sha256 | |
10849 | (base32 | |
10850 | "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr")))) | |
10851 | (properties | |
10852 | `((upstream-name . "assertive.models"))) | |
10853 | (build-system r-build-system) | |
10854 | (propagated-inputs | |
10855 | `(("r-assertive-base" ,r-assertive-base))) | |
10856 | (home-page "https://bitbucket.org/richierocks/assertive.models") | |
10857 | (synopsis "Assertions to check properties of models") | |
10858 | (description | |
10859 | "This package provides a set of predicates and assertions for checking | |
10860 | the properties of models. This is mainly for use by other package developers | |
10861 | who want to include run-time testing features in their own packages.") | |
10862 | (license license:gpl3+))) | |
dcafcfb4 RW |
10863 | |
10864 | (define-public r-assertive-reflection | |
10865 | (package | |
10866 | (name "r-assertive-reflection") | |
10867 | (version "0.0-4") | |
10868 | (source | |
10869 | (origin | |
10870 | (method url-fetch) | |
10871 | (uri (cran-uri "assertive.reflection" version)) | |
10872 | (sha256 | |
10873 | (base32 | |
10874 | "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj")))) | |
10875 | (properties | |
10876 | `((upstream-name . "assertive.reflection"))) | |
10877 | (build-system r-build-system) | |
10878 | (propagated-inputs | |
10879 | `(("r-assertive-base" ,r-assertive-base))) | |
10880 | (home-page "https://bitbucket.org/richierocks/assertive.reflection") | |
10881 | (synopsis "Assertions for checking the state of R") | |
10882 | (description | |
10883 | "This package provides a set of predicates and assertions for checking | |
10884 | the state and capabilities of R, the operating system it is running on, and | |
10885 | the IDE being used. This is mainly for use by other package developers who | |
10886 | want to include run-time testing features in their own packages.") | |
10887 | (license license:gpl3+))) | |
5e3bd355 RW |
10888 | |
10889 | (define-public r-assertive-types | |
10890 | (package | |
10891 | (name "r-assertive-types") | |
10892 | (version "0.0-3") | |
10893 | (source | |
10894 | (origin | |
10895 | (method url-fetch) | |
10896 | (uri (cran-uri "assertive.types" version)) | |
10897 | (sha256 | |
10898 | (base32 | |
10899 | "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb")))) | |
10900 | (properties | |
10901 | `((upstream-name . "assertive.types"))) | |
10902 | (build-system r-build-system) | |
10903 | (propagated-inputs | |
10904 | `(("r-assertive-base" ,r-assertive-base) | |
10905 | ("r-assertive-properties" ,r-assertive-properties) | |
10906 | ("r-codetools" ,r-codetools))) | |
10907 | (home-page "https://bitbucket.org/richierocks/assertive.types") | |
10908 | (synopsis "Assertions to check types of variables") | |
10909 | (description | |
10910 | "This package provides a set of predicates and assertions for checking | |
10911 | the types of variables. This is mainly for use by other package developers | |
10912 | who want to include run-time testing features in their own packages.") | |
10913 | (license license:gpl3+))) | |
1f0a761a RW |
10914 | |
10915 | (define-public r-assertive-files | |
10916 | (package | |
10917 | (name "r-assertive-files") | |
10918 | (version "0.0-2") | |
10919 | (source | |
10920 | (origin | |
10921 | (method url-fetch) | |
10922 | (uri (cran-uri "assertive.files" version)) | |
10923 | (sha256 | |
10924 | (base32 | |
10925 | "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy")))) | |
10926 | (properties | |
10927 | `((upstream-name . "assertive.files"))) | |
10928 | (build-system r-build-system) | |
10929 | (propagated-inputs | |
10930 | `(("r-assertive-base" ,r-assertive-base) | |
10931 | ("r-assertive-numbers" ,r-assertive-numbers))) | |
10932 | (home-page "https://bitbucket.org/richierocks/assertive.files") | |
10933 | (synopsis "Assertions to check properties of files") | |
10934 | (description | |
10935 | "This package provides a set of predicates and assertions for checking | |
10936 | the properties of files and connections. This is mainly for use by other | |
10937 | package developers who want to include run-time testing features in their own | |
10938 | packages.") | |
10939 | (license license:gpl3+))) | |
50ce8b1e RW |
10940 | |
10941 | (define-public r-assertive-code | |
10942 | (package | |
10943 | (name "r-assertive-code") | |
10944 | (version "0.0-3") | |
10945 | (source | |
10946 | (origin | |
10947 | (method url-fetch) | |
10948 | (uri (cran-uri "assertive.code" version)) | |
10949 | (sha256 | |
10950 | (base32 | |
10951 | "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) | |
10952 | (properties | |
10953 | `((upstream-name . "assertive.code"))) | |
10954 | (build-system r-build-system) | |
10955 | (propagated-inputs | |
10956 | `(("r-assertive-base" ,r-assertive-base) | |
10957 | ("r-assertive-properties" ,r-assertive-properties) | |
10958 | ("r-assertive-types" ,r-assertive-types))) | |
10959 | (home-page "https://bitbucket.org/richierocks/assertive.code") | |
10960 | (synopsis "Assertions to check properties of code") | |
10961 | (description | |
10962 | "This package provides a set of predicates and assertions for checking | |
10963 | the properties of code. This is mainly for use by other package developers | |
10964 | who want to include run-time testing features in their own packages.") | |
10965 | (license license:gpl3+))) | |
29d9a2af RW |
10966 | |
10967 | (define-public r-assertive-datetimes | |
10968 | (package | |
10969 | (name "r-assertive-datetimes") | |
10970 | (version "0.0-2") | |
10971 | (source | |
10972 | (origin | |
10973 | (method url-fetch) | |
10974 | (uri (cran-uri "assertive.datetimes" version)) | |
10975 | (sha256 | |
10976 | (base32 | |
10977 | "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78")))) | |
10978 | (properties | |
10979 | `((upstream-name . "assertive.datetimes"))) | |
10980 | (build-system r-build-system) | |
10981 | (propagated-inputs | |
10982 | `(("r-assertive-base" ,r-assertive-base) | |
10983 | ("r-assertive-types" ,r-assertive-types))) | |
10984 | (home-page "https://bitbucket.org/richierocks/assertive.datetimes") | |
10985 | (synopsis "Assertions to check properties of dates and times") | |
10986 | (description | |
10987 | "This package provides a set of predicates and assertions for checking | |
10988 | the properties of dates and times. This is mainly for use by other package | |
10989 | developers who want to include run-time testing features in their own | |
10990 | packages.") | |
10991 | (license license:gpl3+))) | |
66d0a0a7 RW |
10992 | |
10993 | (define-public r-assertive-strings | |
10994 | (package | |
10995 | (name "r-assertive-strings") | |
10996 | (version "0.0-3") | |
10997 | (source | |
10998 | (origin | |
10999 | (method url-fetch) | |
11000 | (uri (cran-uri "assertive.strings" version)) | |
11001 | (sha256 | |
11002 | (base32 | |
11003 | "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm")))) | |
11004 | (properties | |
11005 | `((upstream-name . "assertive.strings"))) | |
11006 | (build-system r-build-system) | |
11007 | (propagated-inputs | |
11008 | `(("r-assertive-base" ,r-assertive-base) | |
11009 | ("r-assertive-types" ,r-assertive-types) | |
11010 | ("r-stringi" ,r-stringi))) | |
11011 | (home-page "https://bitbucket.org/richierocks/assertive.strings") | |
11012 | (synopsis "Assertions to check properties of strings") | |
11013 | (description | |
11014 | "This package provides a set of predicates and assertions for checking | |
11015 | the properties of strings. This is mainly for use by other package developers | |
11016 | who want to include run-time testing features in their own packages.") | |
11017 | (license license:gpl3+))) | |
6d3702e5 RW |
11018 | |
11019 | (define-public r-assertive-data-us | |
11020 | (package | |
11021 | (name "r-assertive-data-us") | |
11022 | (version "0.0-2") | |
11023 | (source | |
11024 | (origin | |
11025 | (method url-fetch) | |
11026 | (uri (cran-uri "assertive.data.us" version)) | |
11027 | (sha256 | |
11028 | (base32 | |
11029 | "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq")))) | |
11030 | (properties | |
11031 | `((upstream-name . "assertive.data.us"))) | |
11032 | (build-system r-build-system) | |
11033 | (propagated-inputs | |
11034 | `(("r-assertive-base" ,r-assertive-base) | |
11035 | ("r-assertive-strings" ,r-assertive-strings))) | |
11036 | (home-page "https://bitbucket.org/richierocks/assertive.data.us") | |
11037 | (synopsis "Assertions to check properties of strings") | |
11038 | (description | |
11039 | "This package provides a set of predicates and assertions for checking | |
11040 | the properties of US-specific complex data types. This is mainly for use by | |
11041 | other package developers who want to include run-time testing features in | |
11042 | their own packages.") | |
11043 | (license license:gpl3+))) | |
39ef8e09 RW |
11044 | |
11045 | (define-public r-assertive-data-uk | |
11046 | (package | |
11047 | (name "r-assertive-data-uk") | |
11048 | (version "0.0-2") | |
11049 | (source | |
11050 | (origin | |
11051 | (method url-fetch) | |
11052 | (uri (cran-uri "assertive.data.uk" version)) | |
11053 | (sha256 | |
11054 | (base32 | |
11055 | "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b")))) | |
11056 | (properties | |
11057 | `((upstream-name . "assertive.data.uk"))) | |
11058 | (build-system r-build-system) | |
11059 | (propagated-inputs | |
11060 | `(("r-assertive-base" ,r-assertive-base) | |
11061 | ("r-assertive-strings" ,r-assertive-strings))) | |
11062 | (home-page "https://bitbucket.org/richierocks/assertive.data.uk") | |
11063 | (synopsis "Assertions to check properties of strings") | |
11064 | (description | |
11065 | "This package provides a set of predicates and assertions for checking | |
11066 | the properties of UK-specific complex data types. This is mainly for use by | |
11067 | other package developers who want to include run-time testing features in | |
11068 | their own packages.") | |
11069 | (license license:gpl3+))) | |
39231abf RW |
11070 | |
11071 | (define-public r-assertive-data | |
11072 | (package | |
11073 | (name "r-assertive-data") | |
11074 | (version "0.0-3") | |
11075 | (source | |
11076 | (origin | |
11077 | (method url-fetch) | |
11078 | (uri (cran-uri "assertive.data" version)) | |
11079 | (sha256 | |
11080 | (base32 | |
11081 | "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s")))) | |
11082 | (properties | |
11083 | `((upstream-name . "assertive.data"))) | |
11084 | (build-system r-build-system) | |
11085 | (propagated-inputs | |
11086 | `(("r-assertive-base" ,r-assertive-base) | |
11087 | ("r-assertive-strings" ,r-assertive-strings))) | |
11088 | (home-page "https://bitbucket.org/richierocks/assertive.data") | |
11089 | (synopsis "Assertions to check properties of data") | |
11090 | (description | |
11091 | "This package provides a set of predicates and assertions for checking | |
11092 | the properties of (country independent) complex data types. This is mainly | |
11093 | for use by other package developers who want to include run-time testing | |
11094 | features in their own packages.") | |
11095 | (license license:gpl3+))) | |
658b2b62 RW |
11096 | |
11097 | (define-public r-assertive | |
11098 | (package | |
11099 | (name "r-assertive") | |
11100 | (version "0.3-5") | |
11101 | (source | |
11102 | (origin | |
11103 | (method url-fetch) | |
11104 | (uri (cran-uri "assertive" version)) | |
11105 | (sha256 | |
11106 | (base32 | |
11107 | "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3")))) | |
11108 | (build-system r-build-system) | |
11109 | (propagated-inputs | |
11110 | `(("r-assertive-base" ,r-assertive-base) | |
11111 | ("r-assertive-code" ,r-assertive-code) | |
11112 | ("r-assertive-data" ,r-assertive-data) | |
11113 | ("r-assertive-data-uk" ,r-assertive-data-uk) | |
11114 | ("r-assertive-data-us" ,r-assertive-data-us) | |
11115 | ("r-assertive-datetimes" ,r-assertive-datetimes) | |
11116 | ("r-assertive-files" ,r-assertive-files) | |
11117 | ("r-assertive-matrices" ,r-assertive-matrices) | |
11118 | ("r-assertive-models" ,r-assertive-models) | |
11119 | ("r-assertive-numbers" ,r-assertive-numbers) | |
11120 | ("r-assertive-properties" ,r-assertive-properties) | |
11121 | ("r-assertive-reflection" ,r-assertive-reflection) | |
11122 | ("r-assertive-sets" ,r-assertive-sets) | |
11123 | ("r-assertive-strings" ,r-assertive-strings) | |
11124 | ("r-assertive-types" ,r-assertive-types) | |
11125 | ("r-knitr" ,r-knitr))) | |
11126 | (home-page "https://bitbucket.org/richierocks/assertive") | |
11127 | (synopsis "Readable check functions to ensure code integrity") | |
11128 | (description | |
11129 | "This package provides lots of predicates (@code{is_*} functions) to | |
11130 | check the state of your variables, and assertions (@code{assert_*} functions) | |
11131 | to throw errors if they aren't in the right form.") | |
11132 | (license license:gpl3+))) | |
f51dcc27 RW |
11133 | |
11134 | (define-public r-dotcall64 | |
11135 | (package | |
11136 | (name "r-dotcall64") | |
11137 | (version "1.0-0") | |
11138 | (source | |
11139 | (origin | |
11140 | (method url-fetch) | |
11141 | (uri (cran-uri "dotCall64" version)) | |
11142 | (sha256 | |
11143 | (base32 | |
11144 | "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) | |
11145 | (properties `((upstream-name . "dotCall64"))) | |
11146 | (build-system r-build-system) | |
11147 | (native-inputs `(("gfortran" ,gfortran))) | |
11148 | (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") | |
11149 | (synopsis "Enhanced foreign function interface supporting long vectors") | |
11150 | (description | |
11151 | "This package provides @code{.C64()}, an enhanced version of @code{.C()} | |
11152 | and @code{.Fortran()} from the R foreign function interface. @code{.C64()} | |
11153 | supports long vectors, arguments of type 64-bit integer, and provides a | |
11154 | mechanism to avoid unnecessary copies of read-only and write-only arguments. | |
11155 | This makes it a convenient and fast interface to C/C++ and Fortran code.") | |
11156 | (license license:gpl2+))) | |
90104ecd RW |
11157 | |
11158 | (define-public r-spam | |
11159 | (package | |
11160 | (name "r-spam") | |
074c698e | 11161 | (version "2.5-1") |
90104ecd RW |
11162 | (source |
11163 | (origin | |
11164 | (method url-fetch) | |
11165 | (uri (cran-uri "spam" version)) | |
11166 | (sha256 | |
074c698e | 11167 | (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi")))) |
90104ecd RW |
11168 | (build-system r-build-system) |
11169 | (propagated-inputs | |
11170 | `(("r-dotcall64" ,r-dotcall64))) | |
11171 | (native-inputs `(("gfortran" ,gfortran))) | |
11172 | (home-page "https://www.math.uzh.ch/pages/spam/") | |
11173 | (synopsis "Sparse matrix algebra") | |
11174 | (description | |
11175 | "This package provides a set of functions for sparse matrix algebra. | |
11176 | Differences with other sparse matrix packages are: | |
11177 | ||
11178 | @enumerate | |
11179 | @item it only supports (essentially) one sparse matrix format; | |
11180 | @item it is based on transparent and simple structure(s); | |
11181 | @item it is tailored for MCMC calculations within G(M)RF; | |
11182 | @item and it is fast and scalable (with the extension package @code{spam64}). | |
11183 | @end enumerate\n") | |
11184 | ;; Either of these licenses | |
11185 | (license (list license:bsd-3 license:lgpl2.0)))) | |
32725458 RW |
11186 | |
11187 | (define-public r-fields | |
11188 | (package | |
11189 | (name "r-fields") | |
e5a06add | 11190 | (version "10.0") |
32725458 RW |
11191 | (source |
11192 | (origin | |
11193 | (method url-fetch) | |
11194 | (uri (cran-uri "fields" version)) | |
11195 | (sha256 | |
e5a06add | 11196 | (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il")))) |
32725458 RW |
11197 | (build-system r-build-system) |
11198 | (propagated-inputs | |
11199 | `(("r-maps" ,r-maps) | |
11200 | ("r-spam" ,r-spam))) | |
11201 | (native-inputs | |
11202 | `(("gfortran" ,gfortran))) | |
41cc7993 | 11203 | (home-page "https://www.image.ucar.edu/fields") |
32725458 RW |
11204 | (synopsis "Tools for spatial data") |
11205 | (description | |
11206 | "This is a package for curve, surface and function fitting with an | |
11207 | emphasis on splines, spatial data and spatial statistics. The major methods | |
11208 | include cubic, and thin plate splines, Kriging, and compactly supported | |
11209 | covariance functions for large data sets.") | |
11210 | (license license:gpl2+))) | |
99c164a5 RW |
11211 | |
11212 | (define-public r-spatialextremes | |
11213 | (package | |
11214 | (name "r-spatialextremes") | |
ffb97e69 | 11215 | (version "2.0-7.2") |
99c164a5 RW |
11216 | (source |
11217 | (origin | |
11218 | (method url-fetch) | |
11219 | (uri (cran-uri "SpatialExtremes" version)) | |
11220 | (sha256 | |
11221 | (base32 | |
ffb97e69 | 11222 | "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8")))) |
99c164a5 RW |
11223 | (properties |
11224 | `((upstream-name . "SpatialExtremes"))) | |
11225 | (build-system r-build-system) | |
11226 | (propagated-inputs | |
11227 | `(("r-fields" ,r-fields) | |
11228 | ("r-maps" ,r-maps))) | |
11229 | (home-page "http://spatialextremes.r-forge.r-project.org/") | |
11230 | (synopsis "Modelling spatial extremes") | |
11231 | (description | |
11232 | "This package provides tools for the statistical modelling of spatial | |
11233 | extremes using max-stable processes, copula or Bayesian hierarchical models. | |
11234 | More precisely, this package allows (conditional) simulations from various | |
11235 | parametric max-stable models, analysis of the extremal spatial dependence, the | |
11236 | fitting of such processes using composite likelihoods or least square (simple | |
11237 | max-stable processes only), model checking and selection and prediction.") | |
11238 | (license license:gpl2+))) | |
c2d6e866 RW |
11239 | |
11240 | (define-public r-drc | |
11241 | (package | |
11242 | (name "r-drc") | |
11243 | (version "3.0-1") | |
11244 | (source | |
11245 | (origin | |
11246 | (method url-fetch) | |
11247 | (uri (cran-uri "drc" version)) | |
11248 | (sha256 | |
11249 | (base32 | |
11250 | "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) | |
11251 | (build-system r-build-system) | |
11252 | (propagated-inputs | |
11253 | `(("r-car" ,r-car) | |
11254 | ("r-gtools" ,r-gtools) | |
11255 | ("r-mass" ,r-mass) | |
11256 | ("r-multcomp" ,r-multcomp) | |
11257 | ("r-plotrix" ,r-plotrix) | |
11258 | ("r-scales" ,r-scales))) | |
11259 | (home-page "https://cran.r-project.org/web/packages/drc") | |
11260 | (synopsis "Analysis of dose-response curves") | |
11261 | (description | |
11262 | "This package provides a suite of flexible and versatile model fitting | |
11263 | and after-fitting functions for the analysis of dose-response data.") | |
11264 | (license license:gpl2+))) | |
4fcbd7ea RW |
11265 | |
11266 | (define-public r-rmeta | |
11267 | (package | |
11268 | (name "r-rmeta") | |
11269 | (version "3.0") | |
11270 | (source | |
11271 | (origin | |
11272 | (method url-fetch) | |
11273 | (uri (cran-uri "rmeta" version)) | |
11274 | (sha256 | |
11275 | (base32 | |
11276 | "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) | |
11277 | (build-system r-build-system) | |
11278 | (home-page "https://cran.r-project.org/web/packages/rmeta") | |
11279 | (synopsis "Tools for meta-analysis") | |
11280 | (description | |
11281 | "This package provides functions for simple fixed and random effects | |
11282 | meta-analysis for two-sample comparisons and cumulative meta-analyses. It | |
11283 | draws standard summary plots, funnel plots, and computes summaries and tests | |
11284 | for association and heterogeneity.") | |
11285 | (license license:gpl2))) | |
afc0d815 RW |
11286 | |
11287 | (define-public r-bootstrap | |
11288 | (package | |
11289 | (name "r-bootstrap") | |
36ff60f5 | 11290 | (version "2019.6") |
afc0d815 RW |
11291 | (source |
11292 | (origin | |
11293 | (method url-fetch) | |
11294 | (uri (cran-uri "bootstrap" version)) | |
11295 | (sha256 | |
11296 | (base32 | |
36ff60f5 | 11297 | "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj")))) |
afc0d815 RW |
11298 | (build-system r-build-system) |
11299 | (native-inputs `(("gfortran" ,gfortran))) | |
11300 | (home-page "https://cran.r-project.org/web/packages/bootstrap") | |
11301 | (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") | |
11302 | (description | |
11303 | "This package provides software and data for the book \"An Introduction | |
11304 | to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. | |
11305 | This package is primarily provided for projects already based on it, and for | |
11306 | support of the book. New projects should preferentially use the recommended | |
11307 | package \"boot\".") | |
11308 | (license license:bsd-3))) | |
1ea708af RW |
11309 | |
11310 | (define-public r-survivalroc | |
11311 | (package | |
11312 | (name "r-survivalroc") | |
11313 | (version "1.0.3") | |
11314 | (source | |
11315 | (origin | |
11316 | (method url-fetch) | |
11317 | (uri (cran-uri "survivalROC" version)) | |
11318 | (sha256 | |
11319 | (base32 | |
11320 | "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) | |
11321 | (properties `((upstream-name . "survivalROC"))) | |
11322 | (build-system r-build-system) | |
11323 | (home-page "https://cran.r-project.org/web/packages/survivalROC") | |
11324 | (synopsis "Time-dependent ROC curve estimation from censored survival data") | |
11325 | (description | |
11326 | "Compute time-dependent ROC curve from censored survival data using | |
11327 | Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, | |
11328 | Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") | |
11329 | (license license:gpl2+))) | |
6a5bfe09 RW |
11330 | |
11331 | (define-public r-longitudinal | |
11332 | (package | |
11333 | (name "r-longitudinal") | |
11334 | (version "1.1.12") | |
11335 | (source | |
11336 | (origin | |
11337 | (method url-fetch) | |
11338 | (uri (cran-uri "longitudinal" version)) | |
11339 | (sha256 | |
11340 | (base32 | |
11341 | "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l")))) | |
11342 | (build-system r-build-system) | |
11343 | (propagated-inputs `(("r-corpcor" ,r-corpcor))) | |
11344 | (home-page "http://strimmerlab.org/software/longitudinal/") | |
11345 | (synopsis "Analysis of multiple time course data") | |
11346 | (description | |
11347 | "This package contains general data structures and functions for | |
11348 | longitudinal data with multiple variables, repeated measurements, and | |
11349 | irregularly spaced time points. It also implements a shrinkage estimator of | |
11350 | dynamical correlation and dynamical covariance.") | |
11351 | (license license:gpl3+))) | |
e50722c8 RW |
11352 | |
11353 | (define-public r-genenet | |
11354 | (package | |
11355 | (name "r-genenet") | |
11356 | (version "1.2.13") | |
11357 | (source | |
11358 | (origin | |
11359 | (method url-fetch) | |
11360 | (uri (cran-uri "GeneNet" version)) | |
11361 | (sha256 | |
11362 | (base32 | |
11363 | "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p")))) | |
11364 | (properties `((upstream-name . "GeneNet"))) | |
11365 | (build-system r-build-system) | |
11366 | (propagated-inputs | |
11367 | `(("r-corpcor" ,r-corpcor) | |
11368 | ("r-fdrtool" ,r-fdrtool) | |
11369 | ("r-longitudinal" ,r-longitudinal))) | |
11370 | (home-page "http://strimmerlab.org/software/genenet/") | |
11371 | (synopsis "Modeling and inferring gene networks") | |
11372 | (description | |
11373 | "This package analyzes gene expression (time series) data with focus on | |
11374 | the inference of gene networks. In particular, GeneNet implements the methods | |
11375 | of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) | |
11376 | for learning large-scale gene association networks (including assignment of | |
11377 | putative directions).") | |
11378 | (license license:gpl3+))) | |
fe4e9f03 RW |
11379 | |
11380 | (define-public r-rbamtools | |
11381 | (package | |
11382 | (name "r-rbamtools") | |
610f2acc | 11383 | (version "2.16.17") |
fe4e9f03 RW |
11384 | (source |
11385 | (origin | |
11386 | (method url-fetch) | |
11387 | (uri (cran-uri "rbamtools" version)) | |
11388 | (sha256 | |
11389 | (base32 | |
610f2acc | 11390 | "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc")))) |
fe4e9f03 RW |
11391 | (build-system r-build-system) |
11392 | (inputs `(("zlib" ,zlib))) | |
11393 | (propagated-inputs | |
11394 | `(("r-refgenome" ,r-refgenome))) | |
11395 | (home-page "https://cran.r-project.org/web/packages/rbamtools") | |
11396 | (synopsis "Read and write BAM (binary alignment) files") | |
11397 | (description | |
11398 | "This package provides an R interface to functions of the SAMtools | |
11399 | library.") | |
11400 | (license license:artistic2.0))) | |
e3c0e3e3 RW |
11401 | |
11402 | (define-public r-protviz | |
11403 | (package | |
11404 | (name "r-protviz") | |
401cc85e | 11405 | (version "0.5.1") |
e3c0e3e3 RW |
11406 | (source |
11407 | (origin | |
11408 | (method url-fetch) | |
11409 | (uri (cran-uri "protViz" version)) | |
11410 | (sha256 | |
11411 | (base32 | |
401cc85e | 11412 | "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv")))) |
e3c0e3e3 RW |
11413 | (properties `((upstream-name . "protViz"))) |
11414 | (build-system r-build-system) | |
e3c0e3e3 RW |
11415 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) |
11416 | (home-page "https://github.com/protViz/protViz/") | |
11417 | (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") | |
11418 | (description | |
11419 | "This package helps with quality checks, visualizations and analysis of | |
11420 | mass spectrometry data, coming from proteomics experiments. The package is | |
11421 | developed, tested and used at the Functional Genomics Center Zurich, where it | |
11422 | is used mainly for prototyping, teaching, and having fun with proteomics data. | |
11423 | But it can also be used to do data analysis for small scale data sets.") | |
11424 | (license license:gpl3))) | |
7aeec0cf RW |
11425 | |
11426 | (define-public r-cmprsk | |
11427 | (package | |
11428 | (name "r-cmprsk") | |
3d9a6b05 | 11429 | (version "2.2-9") |
7aeec0cf RW |
11430 | (source |
11431 | (origin | |
11432 | (method url-fetch) | |
11433 | (uri (cran-uri "cmprsk" version)) | |
11434 | (sha256 | |
3d9a6b05 | 11435 | (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99")))) |
7aeec0cf RW |
11436 | (build-system r-build-system) |
11437 | (propagated-inputs | |
11438 | `(("r-survival" ,r-survival))) | |
11439 | (native-inputs | |
11440 | `(("gfortran" ,gfortran))) | |
11441 | (home-page "https://cran.r-project.org/web/packages/cmprsk") | |
11442 | (synopsis "Subdistribution analysis of competing risks") | |
11443 | (description | |
11444 | "This package provides tool for estimation, testing and regression | |
11445 | modeling of subdistribution functions in competing risks, as described in | |
11446 | Gray (1988), A class of K-sample tests for comparing the cumulative incidence | |
11447 | of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), | |
11448 | A proportional hazards model for the subdistribution of a competing risk, | |
11449 | JASA, 94:496-509.") | |
11450 | (license license:gpl2+))) | |
728012da RW |
11451 | |
11452 | (define-public r-etm | |
11453 | (package | |
11454 | (name "r-etm") | |
9a749cad | 11455 | (version "1.0.5") |
728012da RW |
11456 | (source |
11457 | (origin | |
11458 | (method url-fetch) | |
11459 | (uri (cran-uri "etm" version)) | |
11460 | (sha256 | |
11461 | (base32 | |
9a749cad | 11462 | "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677")))) |
728012da RW |
11463 | (build-system r-build-system) |
11464 | (propagated-inputs | |
11465 | `(("r-data-table" ,r-data-table) | |
11466 | ("r-lattice" ,r-lattice) | |
11467 | ("r-rcpp" ,r-rcpp) | |
11468 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
11469 | ("r-survival" ,r-survival))) | |
11470 | (home-page "https://cran.r-project.org/web/packages/etm") | |
11471 | (synopsis "Empirical transition matrix") | |
11472 | (description | |
11473 | "The @dfn{empirical transition matrix} (etm) package permits to estimate | |
11474 | the matrix of transition probabilities for any time-inhomogeneous multistate | |
11475 | model with finite state space using the Aalen-Johansen estimator.") | |
11476 | (license license:expat))) | |
17932a0f RW |
11477 | |
11478 | (define-public r-epi | |
11479 | (package | |
11480 | (name "r-epi") | |
0ee5e9fb | 11481 | (version "2.40") |
17932a0f RW |
11482 | (source |
11483 | (origin | |
11484 | (method url-fetch) | |
11485 | (uri (cran-uri "Epi" version)) | |
11486 | (sha256 | |
11487 | (base32 | |
0ee5e9fb | 11488 | "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5")))) |
17932a0f RW |
11489 | (properties `((upstream-name . "Epi"))) |
11490 | (build-system r-build-system) | |
11491 | (propagated-inputs | |
11492 | `(("r-cmprsk" ,r-cmprsk) | |
11493 | ("r-data-table" ,r-data-table) | |
11494 | ("r-etm" ,r-etm) | |
11495 | ("r-mass" ,r-mass) | |
11496 | ("r-matrix" ,r-matrix) | |
11497 | ("r-mgcv" ,r-mgcv) | |
11498 | ("r-numderiv" ,r-numderiv) | |
11499 | ("r-plyr" ,r-plyr) | |
11500 | ("r-survival" ,r-survival) | |
11501 | ("r-zoo" ,r-zoo))) | |
11502 | (home-page "http://BendixCarstensen.com/Epi/") | |
11503 | (synopsis "Statistical analysis in epidemiology") | |
11504 | (description | |
11505 | "This package provides functions for demographic and epidemiological | |
11506 | analysis in the Lexis diagram, i.e. register and cohort follow-up data, in | |
11507 | particular representation, manipulation and simulation of multistate data - | |
11508 | the Lexis suite of functions, which includes interfaces to the @code{mstate}, | |
11509 | @code{etm} and @code{cmprsk} packages. It also contains functions for | |
11510 | Age-Period-Cohort and Lee-Carter modeling and a function for interval censored | |
11511 | data and some useful functions for tabulation and plotting, as well as a | |
11512 | number of epidemiological data sets.") | |
11513 | (license license:gpl2))) | |
879a1520 RW |
11514 | |
11515 | (define-public r-ppls | |
11516 | (package | |
11517 | (name "r-ppls") | |
11518 | (version "1.6-1.1") | |
11519 | (source | |
11520 | (origin | |
11521 | (method url-fetch) | |
11522 | (uri (cran-uri "ppls" version)) | |
11523 | (sha256 | |
11524 | (base32 | |
11525 | "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) | |
11526 | (build-system r-build-system) | |
11527 | (propagated-inputs `(("r-mass" ,r-mass))) | |
11528 | (home-page "https://cran.r-project.org/web/packages/ppls") | |
11529 | (synopsis "Penalized partial least squares") | |
11530 | (description | |
11531 | "This package contains linear and nonlinear regression methods based on | |
11532 | partial least squares and penalization techniques. Model parameters are | |
11533 | selected via cross-validation, and confidence intervals ans tests for the | |
11534 | regression coefficients can be conducted via jackknifing.") | |
11535 | (license license:gpl2+))) | |
0af9616d RW |
11536 | |
11537 | (define-public r-huge | |
11538 | (package | |
11539 | (name "r-huge") | |
5f596112 | 11540 | (version "1.3.4") |
0af9616d RW |
11541 | (source |
11542 | (origin | |
11543 | (method url-fetch) | |
11544 | (uri (cran-uri "huge" version)) | |
11545 | (sha256 | |
5f596112 | 11546 | (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3")))) |
0af9616d RW |
11547 | (build-system r-build-system) |
11548 | (propagated-inputs | |
11549 | `(("r-igraph" ,r-igraph) | |
0af9616d | 11550 | ("r-mass" ,r-mass) |
7706a98c RW |
11551 | ("r-matrix" ,r-matrix) |
11552 | ("r-rcpp" ,r-rcpp) | |
11553 | ("r-rcppeigen" ,r-rcppeigen))) | |
0af9616d RW |
11554 | (home-page "https://cran.r-project.org/web/packages/huge") |
11555 | (synopsis "High-dimensional undirected graph estimation") | |
11556 | (description | |
11557 | "This package provides a general framework for high-dimensional | |
11558 | undirected graph estimation. It integrates data preprocessing, neighborhood | |
11559 | screening, graph estimation, and model selection techniques into a pipeline.") | |
11560 | (license license:gpl2))) | |
39274ab4 RW |
11561 | |
11562 | (define-public r-parcor | |
11563 | (package | |
11564 | (name "r-parcor") | |
11565 | (version "0.2-6") | |
11566 | (source | |
11567 | (origin | |
11568 | (method url-fetch) | |
11569 | (uri (cran-uri "parcor" version)) | |
11570 | (sha256 | |
11571 | (base32 | |
11572 | "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) | |
11573 | (build-system r-build-system) | |
11574 | (propagated-inputs | |
11575 | `(("r-epi" ,r-epi) | |
11576 | ("r-genenet" ,r-genenet) | |
11577 | ("r-glmnet" ,r-glmnet) | |
11578 | ("r-mass" ,r-mass) | |
11579 | ("r-ppls" ,r-ppls))) | |
11580 | (home-page "https://cran.r-project.org/web/packages/parcor") | |
11581 | (synopsis "Regularized estimation of partial correlation matrices") | |
11582 | (description | |
11583 | "This package estimates the matrix of partial correlations based on | |
11584 | different regularized regression methods: lasso, adaptive lasso, PLS, and | |
11585 | Ridge Regression. In addition, the package provides model selection for | |
11586 | lasso, adaptive lasso and Ridge regression based on cross-validation.") | |
11587 | (license license:gpl2+))) | |
cba08f60 RW |
11588 | |
11589 | (define-public r-mcmc | |
11590 | (package | |
11591 | (name "r-mcmc") | |
ae7e6f06 | 11592 | (version "0.9-6") |
cba08f60 RW |
11593 | (source |
11594 | (origin | |
11595 | (method url-fetch) | |
11596 | (uri (cran-uri "mcmc" version)) | |
11597 | (sha256 | |
11598 | (base32 | |
ae7e6f06 | 11599 | "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4")))) |
cba08f60 RW |
11600 | (build-system r-build-system) |
11601 | (home-page "http://www.stat.umn.edu/geyer/mcmc/") | |
11602 | (synopsis "Markov chain Monte Carlo") | |
11603 | (description | |
11604 | "This package simulates continuous distributions of random vectors using | |
11605 | @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R | |
11606 | function that evaluates the log unnormalized density. Algorithms are random | |
11607 | walk Metropolis algorithm (function @code{metrop}), simulated | |
11608 | tempering (function @code{temper}), and morphometric random walk | |
11609 | Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity | |
11610 | by change of variable.") | |
11611 | (license license:expat))) | |
cf4cd8bc RW |
11612 | |
11613 | (define-public r-listenv | |
11614 | (package | |
11615 | (name "r-listenv") | |
bf3ea5ec | 11616 | (version "0.8.0") |
cf4cd8bc RW |
11617 | (source |
11618 | (origin | |
11619 | (method url-fetch) | |
11620 | (uri (cran-uri "listenv" version)) | |
11621 | (sha256 | |
11622 | (base32 | |
bf3ea5ec | 11623 | "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx")))) |
cf4cd8bc RW |
11624 | (build-system r-build-system) |
11625 | (native-inputs | |
11626 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
11627 | (home-page "https://github.com/HenrikBengtsson/listenv") | |
11628 | (synopsis "Environments behaving (almost) as lists") | |
11629 | (description | |
11630 | "This package implements list environments. List environments are | |
11631 | environments that have list-like properties. For instance, the elements of a | |
11632 | list environment are ordered and can be accessed and iterated over using index | |
11633 | subsetting.") | |
11634 | (license license:lgpl2.1+))) | |
226294a4 RW |
11635 | |
11636 | (define-public r-globals | |
11637 | (package | |
11638 | (name "r-globals") | |
88fdfd79 | 11639 | (version "0.12.5") |
226294a4 RW |
11640 | (source |
11641 | (origin | |
11642 | (method url-fetch) | |
11643 | (uri (cran-uri "globals" version)) | |
11644 | (sha256 | |
11645 | (base32 | |
88fdfd79 | 11646 | "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m")))) |
226294a4 RW |
11647 | (build-system r-build-system) |
11648 | (propagated-inputs | |
11649 | `(("r-codetools" ,r-codetools))) | |
11650 | (home-page "https://github.com/HenrikBengtsson/globals") | |
11651 | (synopsis "Identify global objects in R expressions") | |
11652 | (description | |
11653 | "This package provides tools to identify global (\"unknown\" or \"free\") | |
11654 | objects in R expressions by code inspection using various strategies, e.g. | |
11655 | conservative or liberal. The objective of this package is to make it as | |
11656 | simple as possible to identify global objects for the purpose of exporting | |
11657 | them in distributed compute environments.") | |
11658 | (license license:lgpl2.1+))) | |
b3080cdd RW |
11659 | |
11660 | (define-public r-future | |
11661 | (package | |
11662 | (name "r-future") | |
166995af | 11663 | (version "1.15.1") |
b3080cdd RW |
11664 | (source |
11665 | (origin | |
11666 | (method url-fetch) | |
11667 | (uri (cran-uri "future" version)) | |
11668 | (sha256 | |
11669 | (base32 | |
166995af | 11670 | "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd")))) |
b3080cdd RW |
11671 | (build-system r-build-system) |
11672 | (propagated-inputs | |
11673 | `(("r-digest" ,r-digest) | |
11674 | ("r-globals" ,r-globals) | |
11675 | ("r-listenv" ,r-listenv))) | |
11676 | (native-inputs | |
11677 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
11678 | (home-page "https://github.com/HenrikBengtsson/future") | |
11679 | (synopsis "Unified parallel and distributed processing in R") | |
11680 | (description | |
11681 | "The purpose of this package is to provide a lightweight and unified | |
11682 | Future API for sequential and parallel processing of R expression via futures. | |
11683 | This package implements sequential, multicore, multisession, and cluster | |
11684 | futures. With these, R expressions can be evaluated on the local machine, in | |
11685 | parallel a set of local machines, or distributed on a mix of local and remote | |
11686 | machines. Extensions to this package implement additional backends for | |
11687 | processing futures via compute cluster schedulers etc. Because of its unified | |
11688 | API, there is no need to modify any code in order to switch from sequential on | |
11689 | the local machine to, say, distributed processing on a remote compute cluster.") | |
11690 | (license license:lgpl2.1+))) | |
9680047c RW |
11691 | |
11692 | (define-public r-future-apply | |
11693 | (package | |
11694 | (name "r-future-apply") | |
d42fb7d2 | 11695 | (version "1.3.0") |
9680047c RW |
11696 | (source |
11697 | (origin | |
11698 | (method url-fetch) | |
11699 | (uri (cran-uri "future.apply" version)) | |
11700 | (sha256 | |
11701 | (base32 | |
d42fb7d2 | 11702 | "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33")))) |
9680047c RW |
11703 | (properties `((upstream-name . "future.apply"))) |
11704 | (build-system r-build-system) | |
11705 | (propagated-inputs | |
11706 | `(("r-future" ,r-future) | |
11707 | ("r-globals" ,r-globals))) | |
11708 | (native-inputs | |
11709 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
11710 | (home-page "https://github.com/HenrikBengtsson/future.apply") | |
11711 | (synopsis "Apply function to elements in parallel using futures") | |
11712 | (description | |
11713 | "This package provides implementations of @code{apply()}, | |
11714 | @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()}, | |
11715 | @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that | |
11716 | can be resolved using any future-supported backend, e.g. parallel on the local | |
11717 | machine or distributed on a compute cluster.") | |
11718 | (license license:gpl2+))) | |
867e2b1b RW |
11719 | |
11720 | (define-public r-rsvd | |
11721 | (package | |
11722 | (name "r-rsvd") | |
eebd93eb | 11723 | (version "1.0.2") |
867e2b1b RW |
11724 | (source |
11725 | (origin | |
11726 | (method url-fetch) | |
11727 | (uri (cran-uri "rsvd" version)) | |
11728 | (sha256 | |
11729 | (base32 | |
eebd93eb | 11730 | "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8")))) |
867e2b1b RW |
11731 | (build-system r-build-system) |
11732 | (propagated-inputs | |
11733 | `(("r-matrix" ,r-matrix))) | |
11734 | (home-page "https://github.com/erichson/rSVD") | |
11735 | (synopsis "Randomized singular value decomposition") | |
11736 | (description | |
11737 | "Low-rank matrix decompositions are fundamental tools and widely used for | |
11738 | data analysis, dimension reduction, and data compression. Classically, highly | |
11739 | accurate deterministic matrix algorithms are used for this task. However, the | |
11740 | emergence of large-scale data has severely challenged our computational | |
11741 | ability to analyze big data. The concept of randomness has been demonstrated | |
11742 | as an effective strategy to quickly produce approximate answers to familiar | |
11743 | problems such as the @dfn{singular value decomposition} (SVD). This package | |
11744 | provides several randomized matrix algorithms such as the randomized singular | |
11745 | value decomposition (@code{rsvd}), randomized principal component | |
11746 | analysis (@code{rpca}), randomized robust principal component | |
11747 | analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}), | |
11748 | and the randomized CUR decomposition (@code{rcur}). In addition several plot | |
11749 | functions are provided.") | |
11750 | (license license:gpl3+))) | |
14afee3e BG |
11751 | |
11752 | (define-public r-sloop | |
11753 | (package | |
11754 | (name "r-sloop") | |
11755 | (version "1.0.1") | |
11756 | (source | |
11757 | (origin | |
11758 | (method url-fetch) | |
11759 | (uri (cran-uri "sloop" version)) | |
11760 | (sha256 | |
11761 | (base32 | |
11762 | "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j")))) | |
11763 | (build-system r-build-system) | |
11764 | (propagated-inputs | |
11765 | `(("r-codetools" ,r-codetools) | |
11766 | ("r-crayon" ,r-crayon) | |
11767 | ("r-purrr" ,r-purrr) | |
11768 | ("r-rlang" ,r-rlang) | |
11769 | ("r-tibble" ,r-tibble))) | |
11770 | (home-page "https://github.com/r-lib/sloop") | |
11771 | (synopsis "Helpers for object-oriented programming in R") | |
11772 | (description | |
11773 | "This package provides a collection of helper functions designed to | |
11774 | help you to better understand object oriented programming in R, particularly | |
11775 | using @code{S3}.") | |
11776 | (license license:gpl3))) | |
4254b480 RW |
11777 | |
11778 | (define-public r-capushe | |
11779 | (package | |
11780 | (name "r-capushe") | |
11781 | (version "1.1.1") | |
11782 | (source | |
11783 | (origin | |
11784 | (method url-fetch) | |
11785 | (uri (cran-uri "capushe" version)) | |
11786 | (sha256 | |
11787 | (base32 | |
11788 | "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc")))) | |
11789 | (build-system r-build-system) | |
11790 | (propagated-inputs `(("r-mass" ,r-mass))) | |
11791 | (home-page "https://cran.r-project.org/web/packages/capushe/index.html") | |
49369a01 | 11792 | (synopsis "Calibrating penalties using slope heuristics") |
4254b480 RW |
11793 | (description |
11794 | "This package provides tools for the calibration of penalized criteria | |
11795 | for model selection. The calibration methods available are based on the slope | |
11796 | heuristics.") | |
11797 | (license license:gpl2+))) | |
c691c607 RW |
11798 | |
11799 | (define-public r-dorng | |
11800 | (package | |
11801 | (name "r-dorng") | |
11802 | (version "1.7.1") | |
11803 | (source | |
11804 | (origin | |
11805 | (method url-fetch) | |
11806 | (uri (cran-uri "doRNG" version)) | |
11807 | (sha256 | |
11808 | (base32 | |
11809 | "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7")))) | |
11810 | (properties `((upstream-name . "doRNG"))) | |
11811 | (build-system r-build-system) | |
11812 | (propagated-inputs | |
11813 | `(("r-foreach" ,r-foreach) | |
11814 | ("r-iterators" ,r-iterators) | |
11815 | ("r-pkgmaker" ,r-pkgmaker) | |
11816 | ("r-rngtools" ,r-rngtools))) | |
11817 | (home-page "https://renozao.github.io/doRNG/") | |
11818 | (synopsis "Generic reproducible parallel backend for foreach loops") | |
11819 | (description | |
11820 | "This package provides functions to perform reproducible parallel | |
11821 | @code{foreach} loops, using independent random streams as generated by | |
11822 | L'Ecuyer's combined multiple-recursive generator. It enables to easily | |
11823 | convert standard @code{%dopar%} loops into fully reproducible loops, | |
11824 | independently of the number of workers, the task scheduling strategy, or the | |
11825 | chosen parallel environment and associated foreach backend.") | |
11826 | (license license:gpl2+))) | |
f3233bee RW |
11827 | |
11828 | (define-public r-blockmodeling | |
11829 | (package | |
11830 | (name "r-blockmodeling") | |
11831 | (version "0.3.4") | |
11832 | (source | |
11833 | (origin | |
11834 | (method url-fetch) | |
11835 | (uri (cran-uri "blockmodeling" version)) | |
11836 | (sha256 | |
11837 | (base32 | |
11838 | "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2")))) | |
11839 | (build-system r-build-system) | |
11840 | (propagated-inputs | |
11841 | `(("r-doparallel" ,r-doparallel) | |
11842 | ("r-dorng" ,r-dorng) | |
11843 | ("r-foreach" ,r-foreach) | |
11844 | ("r-matrix" ,r-matrix))) | |
11845 | (native-inputs `(("gfortran" ,gfortran))) | |
11846 | (home-page "https://cran.r-project.org/web/packages/blockmodeling") | |
11847 | (synopsis "Generalized and classical blockmodeling of valued networks") | |
11848 | (description | |
11849 | "This package is primarily meant as an implementation of generalized | |
11850 | blockmodeling for valued networks. In addition, measures of similarity or | |
11851 | dissimilarity based on structural equivalence and regular equivalence (REGE | |
11852 | algorithms) can be computed and partitioned matrices can be plotted.") | |
11853 | (license license:gpl2+))) | |
4af186a9 RW |
11854 | |
11855 | (define-public r-upsetr | |
11856 | (package | |
11857 | (name "r-upsetr") | |
20656a02 | 11858 | (version "1.4.0") |
4af186a9 RW |
11859 | (source |
11860 | (origin | |
11861 | (method url-fetch) | |
11862 | (uri (cran-uri "UpSetR" version)) | |
11863 | (sha256 | |
11864 | (base32 | |
20656a02 | 11865 | "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im")))) |
4af186a9 RW |
11866 | (properties `((upstream-name . "UpSetR"))) |
11867 | (build-system r-build-system) | |
11868 | (propagated-inputs | |
11869 | `(("r-ggplot2" ,r-ggplot2) | |
11870 | ("r-gridextra" ,r-gridextra) | |
11871 | ("r-plyr" ,r-plyr) | |
11872 | ("r-scales" ,r-scales))) | |
11873 | (home-page "https://github.com/hms-dbmi/UpSetR") | |
11874 | (synopsis "Visualize intersecting sets") | |
11875 | (description | |
11876 | "This package provides a more scalable alternative to Venn and Euler | |
11877 | diagrams for visualizing intersecting sets. Create visualizations of | |
11878 | intersecting sets using a novel matrix design, along with visualizations of | |
11879 | several common set, element and attribute related tasks.") | |
11880 | (license license:expat))) | |
1901a532 | 11881 | |
849350fb RW |
11882 | ;; This package includes a JavaScript file, which is not minified. When |
11883 | ;; upgrading please check that there are no new minified JavaScript files. | |
11884 | (define-public r-shinybs | |
11885 | (package | |
11886 | (name "r-shinybs") | |
11887 | (version "0.61") | |
11888 | (source | |
11889 | (origin | |
11890 | (method url-fetch) | |
11891 | (uri (cran-uri "shinyBS" version)) | |
11892 | (sha256 | |
11893 | (base32 | |
11894 | "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji")))) | |
11895 | (properties `((upstream-name . "shinyBS"))) | |
11896 | (build-system r-build-system) | |
11897 | ;; The tests spawn Shiny browser apps. They cannot be run | |
11898 | ;; non-interactively. | |
11899 | (arguments '(#:tests? #f)) | |
11900 | (propagated-inputs | |
11901 | `(("r-htmltools" ,r-htmltools) | |
11902 | ("r-shiny" ,r-shiny))) | |
11903 | (home-page "https://ebailey78.github.io/shinyBS/") | |
11904 | (synopsis "Twitter Bootstrap components for Shiny") | |
11905 | (description | |
11906 | "This package adds additional Twitter Bootstrap components to Shiny.") | |
11907 | (license license:gpl3))) | |
11908 | ||
1901a532 RW |
11909 | (define-public r-outliers |
11910 | (package | |
11911 | (name "r-outliers") | |
11912 | (version "0.14") | |
11913 | (source | |
11914 | (origin | |
11915 | (method url-fetch) | |
11916 | (uri (cran-uri "outliers" version)) | |
11917 | (sha256 | |
11918 | (base32 | |
11919 | "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn")))) | |
11920 | (build-system r-build-system) | |
11921 | (home-page "https://cran.r-project.org/web/packages/outliers/index.html") | |
11922 | (synopsis "Tests for outliers") | |
11923 | (description | |
11924 | "This package provides a collection of some tests commonly used for | |
11925 | identifying outliers.") | |
11926 | (license license:gpl2+))) | |
8cd3f49d RW |
11927 | |
11928 | (define-public r-bayesm | |
11929 | (package | |
11930 | (name "r-bayesm") | |
ce756b97 | 11931 | (version "3.1-4") |
8cd3f49d RW |
11932 | (source |
11933 | (origin | |
11934 | (method url-fetch) | |
11935 | (uri (cran-uri "bayesm" version)) | |
11936 | (sha256 | |
ce756b97 | 11937 | (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) |
8cd3f49d RW |
11938 | (build-system r-build-system) |
11939 | (propagated-inputs | |
11940 | `(("r-rcpp" ,r-rcpp) | |
11941 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
11942 | (home-page "http://www.perossi.org/home/bsm-1") | |
11943 | (synopsis "Bayesian inference for marketing/micro-econometrics") | |
11944 | (description | |
11945 | "This package covers many important models used in marketing and | |
11946 | micro-econometrics applications, including Bayes Regression (univariate or | |
11947 | multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and | |
11948 | Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), | |
11949 | Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate | |
11950 | Mixtures of Normals (including clustering), Dirichlet Process Prior Density | |
11951 | Estimation with normal base, Hierarchical Linear Models with normal prior and | |
11952 | covariates, Hierarchical Linear Models with a mixture of normals prior and | |
11953 | covariates, Hierarchical Multinomial Logits with a mixture of normals prior | |
11954 | and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior | |
11955 | and covariates, Hierarchical Negative Binomial Regression Models, Bayesian | |
11956 | analysis of choice-based conjoint data, Bayesian treatment of linear | |
11957 | instrumental variables models, Analysis of Multivariate Ordinal survey data | |
11958 | with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random | |
11959 | Coefficient Logit Models.") | |
11960 | (license license:gpl2+))) | |
262ab4b1 RW |
11961 | |
11962 | (define-public r-tensora | |
11963 | (package | |
11964 | (name "r-tensora") | |
11965 | (version "0.36.1") | |
11966 | (source | |
11967 | (origin | |
11968 | (method url-fetch) | |
11969 | (uri (cran-uri "tensorA" version)) | |
11970 | (sha256 | |
11971 | (base32 | |
11972 | "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7")))) | |
11973 | (properties `((upstream-name . "tensorA"))) | |
11974 | (build-system r-build-system) | |
11975 | (home-page "http://www.stat.boogaart.de/tensorA") | |
11976 | (synopsis "Advanced tensor arithmetic with named indices") | |
11977 | (description | |
11978 | "This package provides convenience functions for advanced linear algebra | |
11979 | with tensors and computation with datasets of tensors on a higher level | |
11980 | abstraction. It includes Einstein and Riemann summing conventions, dragging, | |
11981 | co- and contravariate indices, and parallel computations on sequences of | |
11982 | tensors.") | |
11983 | (license license:gpl2+))) | |
7d779142 RW |
11984 | |
11985 | (define-public r-rarpack | |
11986 | (package | |
11987 | (name "r-rarpack") | |
11988 | (version "0.11-0") | |
11989 | (source | |
11990 | (origin | |
11991 | (method url-fetch) | |
11992 | (uri (cran-uri "rARPACK" version)) | |
11993 | (sha256 | |
11994 | (base32 | |
11995 | "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) | |
11996 | (properties `((upstream-name . "rARPACK"))) | |
11997 | (build-system r-build-system) | |
11998 | (propagated-inputs `(("r-rspectra" ,r-rspectra))) | |
11999 | (home-page "https://github.com/yixuan/rARPACK") | |
12000 | (synopsis "Solvers for large scale eigenvalue and SVD problems") | |
12001 | (description | |
12002 | "This package was previously an R wrapper of the ARPACK library, and now | |
12003 | a shell of the R package RSpectra, an R interface to the Spectra library for | |
12004 | solving large scale eigenvalue/vector problems. The current version of | |
12005 | rARPACK simply imports and exports the functions provided by RSpectra. New | |
12006 | users of rARPACK are advised to switch to the RSpectra package.") | |
12007 | (license license:bsd-3))) | |
5fde35b3 RW |
12008 | |
12009 | (define-public r-compositions | |
12010 | (package | |
12011 | (name "r-compositions") | |
288c9f2b | 12012 | (version "1.40-3") |
5fde35b3 RW |
12013 | (source |
12014 | (origin | |
12015 | (method url-fetch) | |
12016 | (uri (cran-uri "compositions" version)) | |
12017 | (sha256 | |
12018 | (base32 | |
288c9f2b | 12019 | "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4")))) |
5fde35b3 RW |
12020 | (build-system r-build-system) |
12021 | (propagated-inputs | |
12022 | `(("r-bayesm" ,r-bayesm) | |
5fde35b3 RW |
12023 | ("r-robustbase" ,r-robustbase) |
12024 | ("r-tensora" ,r-tensora))) | |
12025 | (home-page "http://www.stat.boogaart.de/compositions") | |
12026 | (synopsis "Compositional data analysis") | |
12027 | (description | |
12028 | "This package provides functions for the consistent analysis of | |
12029 | compositional data (e.g. portions of substances) and positive | |
12030 | numbers (e.g. concentrations).") | |
12031 | (license license:gpl2+))) | |
5f673e2c RW |
12032 | |
12033 | (define-public r-cobs | |
12034 | (package | |
12035 | (name "r-cobs") | |
12036 | (version "1.3-3") | |
12037 | (source | |
12038 | (origin | |
12039 | (method url-fetch) | |
12040 | (uri (cran-uri "cobs" version)) | |
12041 | (sha256 | |
12042 | (base32 | |
12043 | "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb")))) | |
12044 | (build-system r-build-system) | |
12045 | (propagated-inputs | |
12046 | `(("r-quantreg" ,r-quantreg) | |
12047 | ("r-sparsem" ,r-sparsem))) | |
12048 | (home-page "https://cran.r-project.org/web/packages/cobs") | |
12049 | (synopsis "Constrained B-Splines (sparse matrix based)") | |
12050 | (description | |
12051 | "This package provides qualitatively constrained (regression) smoothing | |
12052 | splines via linear programming and sparse matrices.") | |
12053 | (license license:gpl2+))) | |
c60e3e10 RW |
12054 | |
12055 | (define-public r-drimpute | |
12056 | (package | |
12057 | (name "r-drimpute") | |
12058 | (version "1.0") | |
12059 | (source | |
12060 | (origin | |
12061 | (method url-fetch) | |
12062 | (uri (cran-uri "DrImpute" version)) | |
12063 | (sha256 | |
12064 | (base32 | |
12065 | "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b")))) | |
12066 | (properties `((upstream-name . "DrImpute"))) | |
12067 | (build-system r-build-system) | |
12068 | (propagated-inputs | |
12069 | `(("r-rcpp" ,r-rcpp) | |
12070 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
12071 | (home-page "https://github.com/ikwak2/DrImpute") | |
12072 | (synopsis "Imputing dropout events in single-cell RNA-Seq data") | |
12073 | (description | |
12074 | "This is an R package for imputing dropout events. Many statistical | |
12075 | methods in cell type identification, visualization and lineage reconstruction | |
12076 | do not account for dropout events. DrImpute can improve the performance of | |
12077 | such software by imputing dropout events.") | |
12078 | (license license:gpl3))) | |
061a4b68 RW |
12079 | |
12080 | (define-public r-gamlss-dist | |
12081 | (package | |
12082 | (name "r-gamlss-dist") | |
ef10cbb4 | 12083 | (version "5.1-5") |
061a4b68 RW |
12084 | (source |
12085 | (origin | |
12086 | (method url-fetch) | |
12087 | (uri (cran-uri "gamlss.dist" version)) | |
12088 | (sha256 | |
ef10cbb4 | 12089 | (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw")))) |
061a4b68 RW |
12090 | (properties `((upstream-name . "gamlss.dist"))) |
12091 | (build-system r-build-system) | |
12092 | (propagated-inputs `(("r-mass" ,r-mass))) | |
12093 | (home-page "http://www.gamlss.org/") | |
12094 | (synopsis "Distributions for Generalized Additive Models for location scale and shape") | |
12095 | (description | |
12096 | "This package provides a set of distributions which can be used for | |
12097 | modelling the response variables in Generalized Additive Models for Location | |
12098 | Scale and Shape. The distributions can be continuous, discrete or mixed | |
12099 | distributions. Extra distributions can be created, by transforming, any | |
12100 | continuous distribution defined on the real line, to a distribution defined on | |
12101 | ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} | |
12102 | transformation, respectively.") | |
12103 | ;; Either version of the GPL. | |
12104 | (license (list license:gpl2 license:gpl3)))) | |
4fd99443 | 12105 | |
5146a24e RW |
12106 | ;; This package includes JavaScript files, which are not minified. When |
12107 | ;; upgrading please check that there are no new minified JavaScript files. | |
12108 | (define-public r-shinyjs | |
12109 | (package | |
12110 | (name "r-shinyjs") | |
12111 | (version "1.0") | |
12112 | (source | |
12113 | (origin | |
12114 | (method url-fetch) | |
12115 | (uri (cran-uri "shinyjs" version)) | |
12116 | (sha256 | |
12117 | (base32 | |
12118 | "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8")))) | |
12119 | (build-system r-build-system) | |
12120 | (propagated-inputs | |
12121 | `(("r-digest" ,r-digest) | |
12122 | ("r-htmltools" ,r-htmltools) | |
12123 | ("r-jsonlite" ,r-jsonlite) | |
12124 | ("r-shiny" ,r-shiny))) | |
12125 | (home-page "https://deanattali.com/shinyjs") | |
12126 | (synopsis "Improve the user experience of your Shiny apps") | |
12127 | (description | |
12128 | "Perform common useful JavaScript operations in Shiny apps that will | |
12129 | greatly improve your apps without having to know any JavaScript. Examples | |
12130 | include: hiding an element, disabling an input, resetting an input back to its | |
12131 | original value, delaying code execution by a few seconds, and many more useful | |
12132 | functions for both the end user and the developer. Shinyjs can also be used | |
12133 | to easily call your own custom JavaScript functions from R.") | |
12134 | (license license:agpl3+))) | |
12135 | ||
c27927db RW |
12136 | ;; This package includes minified JavaScript files. When upgrading please |
12137 | ;; check that there are no new minified JavaScript files. | |
12138 | (define-public r-colourpicker | |
12139 | (package | |
12140 | (name "r-colourpicker") | |
12141 | (version "1.0") | |
12142 | (source | |
12143 | (origin | |
12144 | (method url-fetch) | |
12145 | (uri (cran-uri "colourpicker" version)) | |
12146 | (sha256 | |
12147 | (base32 | |
12148 | "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi")))) | |
12149 | (build-system r-build-system) | |
12150 | (arguments | |
12151 | `(#:modules ((guix build utils) | |
12152 | (guix build r-build-system) | |
12153 | (srfi srfi-1) | |
12154 | (ice-9 popen)) | |
12155 | #:phases | |
12156 | (modify-phases %standard-phases | |
12157 | (add-after 'unpack 'process-javascript | |
12158 | (lambda* (#:key inputs #:allow-other-keys) | |
12159 | (with-directory-excursion "inst" | |
12160 | (call-with-values | |
12161 | (lambda () | |
12162 | (unzip2 | |
12163 | `((,(assoc-ref inputs "js-salvattore") | |
12164 | "examples/colourInput/www/salvattore.min.js") | |
12165 | (,(assoc-ref inputs "js-jquery") | |
12166 | "htmlwidgets/lib/jquery/jquery.min.js") | |
12167 | ("www/shared/colourpicker/js/colourpicker.js" | |
12168 | "www/shared/colourpicker/js/colourpicker.min.js")))) | |
12169 | (lambda (sources targets) | |
12170 | (for-each (lambda (source target) | |
12171 | (format #t "Processing ~a --> ~a~%" | |
12172 | source target) | |
12173 | (delete-file target) | |
12174 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
12175 | (call-with-output-file target | |
12176 | (lambda (port) | |
12177 | (dump-port minified port))))) | |
12178 | sources targets)))) | |
12179 | #t))))) | |
12180 | (propagated-inputs | |
12181 | `(("r-ggplot2" ,r-ggplot2) | |
12182 | ("r-htmltools" ,r-htmltools) | |
12183 | ("r-htmlwidgets" ,r-htmlwidgets) | |
12184 | ("r-jsonlite" ,r-jsonlite) | |
12185 | ("r-miniui" ,r-miniui) | |
12186 | ("r-shiny" ,r-shiny) | |
12187 | ("r-shinyjs" ,r-shinyjs))) | |
12188 | (native-inputs | |
12189 | `(("uglify-js" ,uglify-js) | |
12190 | ("js-jquery" | |
12191 | ,(origin | |
12192 | (method url-fetch) | |
12193 | (uri "https://code.jquery.com/jquery-3.3.1.js") | |
12194 | (sha256 | |
12195 | (base32 | |
12196 | "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) | |
12197 | ("js-salvattore" | |
12198 | ,(origin | |
12199 | (method url-fetch) | |
12200 | (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js") | |
12201 | (sha256 | |
12202 | (base32 | |
12203 | "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5")))))) | |
12204 | (home-page "https://github.com/daattali/colourpicker") | |
12205 | (synopsis "Color picker tool for Shiny and for selecting colors in plots") | |
12206 | (description | |
12207 | "This package provides a color picker that can be used as an input in | |
12208 | Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, | |
12209 | custom color palettes, and many more options. A plot color helper tool is | |
12210 | available as an RStudio Addin, which helps you pick colors to use in your | |
12211 | plots. A more generic color picker RStudio Addin is also provided to let you | |
12212 | select colors to use in your R code.") | |
12213 | (license license:expat))) | |
12214 | ||
30f53ec8 RW |
12215 | (define-public r-ggextra |
12216 | (package | |
12217 | (name "r-ggextra") | |
e31eb738 | 12218 | (version "0.9") |
30f53ec8 RW |
12219 | (source |
12220 | (origin | |
12221 | (method url-fetch) | |
12222 | (uri (cran-uri "ggExtra" version)) | |
12223 | (sha256 | |
12224 | (base32 | |
e31eb738 | 12225 | "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj")))) |
30f53ec8 RW |
12226 | (properties `((upstream-name . "ggExtra"))) |
12227 | (build-system r-build-system) | |
12228 | (propagated-inputs | |
12229 | `(("r-colourpicker" ,r-colourpicker) | |
12230 | ("r-ggplot2" ,r-ggplot2) | |
12231 | ("r-gtable" ,r-gtable) | |
12232 | ("r-miniui" ,r-miniui) | |
e31eb738 | 12233 | ("r-r6" ,r-r6) |
30f53ec8 RW |
12234 | ("r-scales" ,r-scales) |
12235 | ("r-shiny" ,r-shiny) | |
12236 | ("r-shinyjs" ,r-shinyjs))) | |
12237 | (home-page "https://github.com/daattali/ggExtra") | |
12238 | (synopsis "Marginal histograms for ggplot2 and other enhancements") | |
12239 | (description | |
12240 | "This package is a collection of functions and layers to enhance ggplot2. | |
12241 | The flagship function is @code{ggMarginal()}, which can be used to add | |
12242 | marginal histograms/boxplots/density plots to ggplot2 scatterplots.") | |
12243 | (license license:expat))) | |
12244 | ||
4fd99443 RW |
12245 | (define-public r-minpack-lm |
12246 | (package | |
12247 | (name "r-minpack-lm") | |
12248 | (version "1.2-1") | |
12249 | (source | |
12250 | (origin | |
12251 | (method url-fetch) | |
12252 | (uri (cran-uri "minpack.lm" version)) | |
12253 | (sha256 | |
12254 | (base32 | |
12255 | "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) | |
12256 | (properties `((upstream-name . "minpack.lm"))) | |
12257 | (build-system r-build-system) | |
12258 | (native-inputs `(("gfortran" ,gfortran))) | |
12259 | (home-page "https://cran.r-project.org/web/packages/minpack.lm") | |
12260 | (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") | |
12261 | (description | |
12262 | "The @code{nls.lm} function provides an R interface to @code{lmder} and | |
12263 | @code{lmdif} from the MINPACK library, for solving nonlinear least-squares | |
12264 | problems by a modification of the Levenberg-Marquardt algorithm, with support | |
12265 | for lower and upper parameter bounds. The implementation can be used via | |
2f041a4c | 12266 | @code{nls}-like calls using the @code{nlsLM} function.") |
4fd99443 | 12267 | (license license:gpl3))) |
01fe44cb RW |
12268 | |
12269 | (define-public r-moments | |
12270 | (package | |
12271 | (name "r-moments") | |
12272 | (version "0.14") | |
12273 | (source | |
12274 | (origin | |
12275 | (method url-fetch) | |
12276 | (uri (cran-uri "moments" version)) | |
12277 | (sha256 | |
12278 | (base32 | |
12279 | "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra")))) | |
12280 | (build-system r-build-system) | |
12281 | (home-page "https://cran.r-project.org/web/packages/moments") | |
12282 | (synopsis "Moments, cumulants, skewness, kurtosis and related tests") | |
12283 | (description | |
12284 | "This package provides functions to calculate: moments, Pearson's | |
12285 | kurtosis, Geary's kurtosis and skewness; it also includes tests related to | |
12286 | them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") | |
12287 | (license license:gpl2+))) | |
9e2ff342 RW |
12288 | |
12289 | (define-public r-msir | |
12290 | (package | |
12291 | (name "r-msir") | |
5ccf16c7 | 12292 | (version "1.3.2") |
9e2ff342 RW |
12293 | (source |
12294 | (origin | |
12295 | (method url-fetch) | |
12296 | (uri (cran-uri "msir" version)) | |
12297 | (sha256 | |
12298 | (base32 | |
5ccf16c7 | 12299 | "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb")))) |
9e2ff342 RW |
12300 | (build-system r-build-system) |
12301 | (propagated-inputs | |
5ccf16c7 | 12302 | `(("r-mclust" ,r-mclust))) |
9e2ff342 RW |
12303 | (home-page "https://cran.r-project.org/web/packages/msir") |
12304 | (synopsis "Model-based sliced inverse regression") | |
12305 | (description | |
12306 | "This is an R package for dimension reduction based on finite Gaussian | |
12307 | mixture modeling of inverse regression.") | |
12308 | (license license:gpl2+))) | |
e8be5a00 RW |
12309 | |
12310 | (define-public r-pbivnorm | |
12311 | (package | |
12312 | (name "r-pbivnorm") | |
12313 | (version "0.6.0") | |
12314 | (source | |
12315 | (origin | |
12316 | (method url-fetch) | |
12317 | (uri (cran-uri "pbivnorm" version)) | |
12318 | (sha256 | |
12319 | (base32 | |
12320 | "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) | |
12321 | (build-system r-build-system) | |
12322 | (native-inputs `(("gfortran" ,gfortran))) | |
12323 | (home-page "https://github.com/brentonk/pbivnorm") | |
12324 | (synopsis "Vectorized bivariate normal CDF") | |
12325 | (description | |
12326 | "This package provides a vectorized R function for calculating | |
12327 | probabilities from a standard bivariate normal CDF.") | |
12328 | (license license:gpl2+))) | |
ca3f1370 RW |
12329 | |
12330 | (define-public r-lavaan | |
12331 | (package | |
12332 | (name "r-lavaan") | |
553742fa | 12333 | (version "0.6-5") |
ca3f1370 RW |
12334 | (source |
12335 | (origin | |
12336 | (method url-fetch) | |
12337 | (uri (cran-uri "lavaan" version)) | |
12338 | (sha256 | |
12339 | (base32 | |
553742fa | 12340 | "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy")))) |
ca3f1370 RW |
12341 | (build-system r-build-system) |
12342 | (propagated-inputs | |
12343 | `(("r-mass" ,r-mass) | |
12344 | ("r-mnormt" ,r-mnormt) | |
12345 | ("r-numderiv" ,r-numderiv) | |
12346 | ("r-pbivnorm" ,r-pbivnorm))) | |
12347 | (home-page "http://lavaan.ugent.be") | |
12348 | (synopsis "Latent variable analysis") | |
12349 | (description | |
12350 | "This package provides tools to fit a variety of latent variable models, | |
12351 | including confirmatory factor analysis, structural equation modeling and | |
12352 | latent growth curve models.") | |
12353 | (license license:gpl2+))) | |
4d1f19e0 RW |
12354 | |
12355 | (define-public r-nonnest2 | |
12356 | (package | |
12357 | (name "r-nonnest2") | |
12358 | (version "0.5-2") | |
12359 | (source | |
12360 | (origin | |
12361 | (method url-fetch) | |
12362 | (uri (cran-uri "nonnest2" version)) | |
12363 | (sha256 | |
12364 | (base32 | |
12365 | "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6")))) | |
12366 | (build-system r-build-system) | |
12367 | (propagated-inputs | |
12368 | `(("r-compquadform" ,r-compquadform) | |
12369 | ("r-lavaan" ,r-lavaan) | |
12370 | ("r-mvtnorm" ,r-mvtnorm) | |
12371 | ("r-sandwich" ,r-sandwich))) | |
12372 | (home-page "https://cran.r-project.org/web/packages/nonnest2/") | |
12373 | (synopsis "Tests of non-nested models") | |
12374 | (description | |
12375 | "This package allows for testing of non-nested models. It includes tests | |
12376 | of model distinguishability and of model fit that can be applied to both | |
12377 | nested and non-nested models. The package also includes functionality to | |
12378 | obtain confidence intervals associated with AIC and BIC.") | |
12379 | ;; Either version of the GPL. | |
12380 | (license (list license:gpl2 license:gpl3)))) | |
be0777ba RW |
12381 | |
12382 | (define-public r-penalized | |
12383 | (package | |
12384 | (name "r-penalized") | |
12385 | (version "0.9-51") | |
12386 | (source | |
12387 | (origin | |
12388 | (method url-fetch) | |
12389 | (uri (cran-uri "penalized" version)) | |
12390 | (sha256 | |
12391 | (base32 | |
12392 | "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) | |
12393 | (build-system r-build-system) | |
12394 | (propagated-inputs | |
12395 | `(("r-rcpp" ,r-rcpp) | |
12396 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
12397 | ("r-survival" ,r-survival))) | |
12398 | (home-page "https://cran.r-project.org/web/packages/penalized/") | |
12399 | (synopsis "Penalized estimation in GLMs and in the Cox model") | |
12400 | (description | |
12401 | "This package provides tools for fitting possibly high dimensional | |
12402 | penalized regression models. The penalty structure can be any combination of | |
12403 | an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity | |
12404 | constraint on the regression coefficients. The supported regression models | |
12405 | are linear, logistic and Poisson regression and the Cox Proportional Hazards | |
12406 | model. Cross-validation routines allow optimization of the tuning | |
12407 | parameters.") | |
12408 | (license license:gpl2+))) | |
5570804a RW |
12409 | |
12410 | (define-public r-zim | |
12411 | (package | |
12412 | (name "r-zim") | |
12413 | (version "1.1.0") | |
12414 | (source | |
12415 | (origin | |
12416 | (method url-fetch) | |
12417 | (uri (cran-uri "ZIM" version)) | |
12418 | (sha256 | |
12419 | (base32 | |
12420 | "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) | |
12421 | (properties `((upstream-name . "ZIM"))) | |
12422 | (build-system r-build-system) | |
12423 | (propagated-inputs `(("r-mass" ,r-mass))) | |
12424 | (home-page "https://github.com/biostatstudio/ZIM") | |
12425 | (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") | |
12426 | (description | |
12427 | "Analyze count time series with excess zeros. Two types of statistical | |
12428 | models are supported: Markov regression and state-space models. They are also | |
12429 | known as observation-driven and parameter-driven models respectively in the | |
12430 | time series literature. The functions used for Markov regression or | |
12431 | observation-driven models can also be used to fit ordinary regression models | |
12432 | with independent data under the zero-inflated Poisson (ZIP) or zero-inflated | |
12433 | negative binomial (ZINB) assumption. The package also contains miscellaneous | |
12434 | functions to compute density, distribution, quantile, and generate random | |
12435 | numbers from ZIP and ZINB distributions.") | |
12436 | (license license:gpl3))) | |
026dd77c RW |
12437 | |
12438 | (define-public r-nor1mix | |
12439 | (package | |
12440 | (name "r-nor1mix") | |
776c62d1 | 12441 | (version "1.3-0") |
026dd77c RW |
12442 | (source |
12443 | (origin | |
12444 | (method url-fetch) | |
12445 | (uri (cran-uri "nor1mix" version)) | |
12446 | (sha256 | |
12447 | (base32 | |
776c62d1 | 12448 | "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w")))) |
026dd77c RW |
12449 | (build-system r-build-system) |
12450 | (home-page "https://cran.r-project.org/web/packages/nor1mix/") | |
12451 | (synopsis "Normal (1-d) mixture models") | |
12452 | (description | |
12453 | "This package provides S3 classes and methods for one-dimensional normal | |
12454 | mixture models, for, e.g., density estimation or clustering algorithms | |
12455 | research and teaching; it provides the widely used Marron-Wand densities. It | |
12456 | also provides tools for efficient random number generation and graphics.") | |
12457 | (license license:gpl2+))) | |
648dbd27 RW |
12458 | |
12459 | (define-public r-beanplot | |
12460 | (package | |
12461 | (name "r-beanplot") | |
12462 | (version "1.2") | |
12463 | (source | |
12464 | (origin | |
12465 | (method url-fetch) | |
12466 | (uri (cran-uri "beanplot" version)) | |
12467 | (sha256 | |
12468 | (base32 | |
12469 | "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9")))) | |
12470 | (build-system r-build-system) | |
12471 | (home-page "https://cran.r-project.org/web/packages/beanplot/") | |
12472 | (synopsis "Visualization via beanplots") | |
12473 | (description | |
12474 | "This package provides beanplots, an alternative to | |
12475 | boxplot/stripchart/violin plots. It can be used to plot univariate comparison | |
12476 | graphs.") | |
12477 | (license license:gpl2))) | |
f313baf0 RW |
12478 | |
12479 | (define-public r-pbdzmq | |
12480 | (package | |
12481 | (name "r-pbdzmq") | |
12482 | (version "0.3-3") | |
12483 | (source | |
12484 | (origin | |
12485 | (method url-fetch) | |
12486 | (uri (cran-uri "pbdZMQ" version)) | |
12487 | (sha256 | |
12488 | (base32 | |
12489 | "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf")))) | |
12490 | (properties `((upstream-name . "pbdZMQ"))) | |
12491 | (build-system r-build-system) | |
12492 | (inputs | |
12493 | `(("zeromq" ,zeromq) | |
12494 | ("zlib" ,zlib))) | |
12495 | (native-inputs | |
12496 | `(("pkg-config" ,pkg-config))) | |
12497 | (home-page "https://pbdr.org/") | |
12498 | (synopsis "R interface to ZeroMQ") | |
12499 | (description | |
12500 | "ZeroMQ is a well-known library for high-performance asynchronous | |
12501 | messaging in scalable, distributed applications. This package provides high | |
12502 | level R wrapper functions to easily utilize ZeroMQ. The main focus is on | |
12503 | interactive client/server programming frameworks. A few wrapper functions | |
12504 | compatible with @code{rzmq} are also provided.") | |
12505 | (license license:gpl3))) | |
d17186d6 RW |
12506 | |
12507 | (define-public r-repr | |
12508 | (package | |
12509 | (name "r-repr") | |
5722022f | 12510 | (version "1.0.2") |
d17186d6 RW |
12511 | (source |
12512 | (origin | |
12513 | (method url-fetch) | |
12514 | (uri (cran-uri "repr" version)) | |
12515 | (sha256 | |
12516 | (base32 | |
5722022f | 12517 | "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw")))) |
d17186d6 RW |
12518 | (build-system r-build-system) |
12519 | (propagated-inputs | |
12520 | `(("r-base64enc" ,r-base64enc) | |
12521 | ("r-htmltools" ,r-htmltools) | |
8b96b860 RW |
12522 | ("r-jsonlite" ,r-jsonlite) |
12523 | ("r-pillar" ,r-pillar))) | |
d17186d6 RW |
12524 | (home-page "https://cran.r-project.org/web/packages/repr/") |
12525 | (synopsis "Serializable representations") | |
12526 | (description | |
12527 | "This package provides string and binary representations of objects for | |
12528 | several formats and MIME types.") | |
12529 | (license license:gpl3))) | |
664dedd5 RW |
12530 | |
12531 | (define-public r-irdisplay | |
12532 | (package | |
12533 | (name "r-irdisplay") | |
12534 | (version "0.7.0") | |
12535 | (source | |
12536 | (origin | |
12537 | (method url-fetch) | |
12538 | (uri (cran-uri "IRdisplay" version)) | |
12539 | (sha256 | |
12540 | (base32 | |
12541 | "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli")))) | |
12542 | (properties `((upstream-name . "IRdisplay"))) | |
12543 | (build-system r-build-system) | |
12544 | (propagated-inputs | |
12545 | `(("r-repr" ,r-repr))) | |
12546 | (home-page "https://cran.r-project.org/web/packages/IRdisplay/") | |
12547 | (synopsis "Jupyter display machinery") | |
12548 | (description | |
12549 | "This package provides an interface to the rich display capabilities of | |
12550 | Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a | |
12551 | running IRkernel session.") | |
12552 | (license license:expat))) | |
984a8aa6 RW |
12553 | |
12554 | (define-public r-irkernel | |
12555 | (package | |
12556 | (name "r-irkernel") | |
96fe120b | 12557 | (version "1.1") |
984a8aa6 RW |
12558 | (source |
12559 | (origin | |
12560 | (method url-fetch) | |
12561 | (uri (cran-uri "IRkernel" version)) | |
12562 | (sha256 | |
12563 | (base32 | |
96fe120b | 12564 | "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94")))) |
984a8aa6 RW |
12565 | (properties `((upstream-name . "IRkernel"))) |
12566 | (build-system r-build-system) | |
12567 | (arguments | |
12568 | `(#:phases | |
12569 | (modify-phases %standard-phases | |
12570 | (add-after 'install 'install-kernelspec | |
12571 | (lambda* (#:key outputs #:allow-other-keys) | |
12572 | (let ((out (assoc-ref outputs "out"))) | |
12573 | (setenv "HOME" "/tmp") | |
12574 | (invoke "jupyter" "kernelspec" "install" | |
12575 | "--name" "ir" | |
12576 | "--prefix" out | |
12577 | (string-append out "/site-library/IRkernel/kernelspec")) | |
41bc208e LDB |
12578 | ;; Record the absolute file name of the 'R' executable in |
12579 | ;; 'kernel.json'. | |
12580 | (substitute* (string-append out "/share/jupyter" | |
12581 | "/kernels/ir/kernel.json") | |
12582 | (("\\[\"R\",") | |
12583 | (string-append "[\"" (which "R") "\","))) | |
984a8aa6 RW |
12584 | #t)))))) |
12585 | (inputs | |
12586 | `(("jupyter" ,jupyter))) | |
12587 | (propagated-inputs | |
12588 | `(("r-crayon" ,r-crayon) | |
12589 | ("r-digest" ,r-digest) | |
12590 | ("r-evaluate" ,r-evaluate) | |
12591 | ("r-irdisplay" ,r-irdisplay) | |
12592 | ("r-jsonlite" ,r-jsonlite) | |
41bc208e LDB |
12593 | ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) |
12594 | ("r-minimal" ,r-minimal) | |
984a8aa6 RW |
12595 | ("r-pbdzmq" ,r-pbdzmq) |
12596 | ("r-repr" ,r-repr) | |
12597 | ("r-uuid" ,r-uuid))) | |
12598 | (home-page "https://cran.r-project.org/web/packages/IRkernel/") | |
12599 | (synopsis "Native R kernel for Jupyter") | |
12600 | (description | |
12601 | "The R kernel for the Jupyter environment executes R code which the | |
12602 | front-end (Jupyter Notebook or other front-ends) submits to the kernel via the | |
12603 | network.") | |
12604 | (license license:expat))) | |
51df4340 RW |
12605 | |
12606 | (define-public r-gmodels | |
12607 | (package | |
12608 | (name "r-gmodels") | |
12609 | (version "2.18.1") | |
12610 | (source | |
12611 | (origin | |
12612 | (method url-fetch) | |
12613 | (uri (cran-uri "gmodels" version)) | |
12614 | (sha256 | |
12615 | (base32 | |
12616 | "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) | |
12617 | (build-system r-build-system) | |
12618 | (propagated-inputs | |
12619 | `(("r-gdata" ,r-gdata) | |
12620 | ("r-mass" ,r-mass))) | |
12621 | (home-page "https://cran.r-project.org/web/packages/gmodels/") | |
12622 | (synopsis "Various R programming tools for model fitting") | |
12623 | (description | |
12624 | "This package provides various R programming tools for model fitting.") | |
12625 | (license license:gpl2))) | |
3942bf5e RW |
12626 | |
12627 | (define-public r-apcluster | |
12628 | (package | |
12629 | (name "r-apcluster") | |
53040408 | 12630 | (version "1.4.8") |
3942bf5e RW |
12631 | (source |
12632 | (origin | |
12633 | (method url-fetch) | |
12634 | (uri (cran-uri "apcluster" version)) | |
12635 | (sha256 | |
12636 | (base32 | |
53040408 | 12637 | "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj")))) |
3942bf5e RW |
12638 | (build-system r-build-system) |
12639 | (propagated-inputs | |
12640 | `(("r-matrix" ,r-matrix) | |
12641 | ("r-rcpp" ,r-rcpp))) | |
12642 | (home-page "https://cran.r-project.org/web/packages/apcluster/") | |
12643 | (synopsis "Affinity propagation clustering") | |
12644 | (description | |
12645 | "This package implements affinity propagation clustering introduced by | |
12646 | Frey and Dueck (2007). The package further provides leveraged affinity | |
12647 | propagation and an algorithm for exemplar-based agglomerative clustering that | |
12648 | can also be used to join clusters obtained from affinity propagation. Various | |
12649 | plotting functions are available for analyzing clustering results.") | |
12650 | (license license:gpl2+))) | |
a97796cd RW |
12651 | |
12652 | (define-public r-valr | |
12653 | (package | |
12654 | (name "r-valr") | |
12655 | (version "0.5.0") | |
12656 | (source | |
12657 | (origin | |
12658 | (method url-fetch) | |
12659 | (uri (cran-uri "valr" version)) | |
12660 | (sha256 | |
12661 | (base32 | |
12662 | "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika")))) | |
12663 | (build-system r-build-system) | |
12664 | (propagated-inputs | |
12665 | `(("r-broom" ,r-broom) | |
12666 | ("r-dplyr" ,r-dplyr) | |
12667 | ("r-ggplot2" ,r-ggplot2) | |
12668 | ("r-rcpp" ,r-rcpp) | |
12669 | ("r-readr" ,r-readr) | |
12670 | ("r-rlang" ,r-rlang) | |
12671 | ("r-stringr" ,r-stringr) | |
12672 | ("r-tibble" ,r-tibble))) | |
12673 | (home-page "http://github.com/rnabioco/valr") | |
12674 | (synopsis "Genome interval arithmetic in R") | |
12675 | (description | |
12676 | "This package enables you to read and manipulate genome intervals and | |
12677 | signals. It provides functionality similar to command-line tool suites within | |
12678 | R, enabling interactive analysis and visualization of genome-scale data.") | |
12679 | (license license:expat))) | |
100f5602 NB |
12680 | |
12681 | (define-public r-rematch2 | |
12682 | (package | |
12683 | (name "r-rematch2") | |
8518744e | 12684 | (version "2.1.0") |
100f5602 NB |
12685 | (source |
12686 | (origin | |
12687 | (method url-fetch) | |
12688 | (uri (cran-uri "rematch2" version)) | |
12689 | (sha256 | |
12690 | (base32 | |
8518744e | 12691 | "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq")))) |
100f5602 NB |
12692 | (build-system r-build-system) |
12693 | (propagated-inputs | |
12694 | `(("r-tibble" ,r-tibble))) | |
12695 | (home-page "https://github.com/r-lib/rematch2") | |
12696 | (synopsis "Tidy output from regular expression matching") | |
12697 | (description | |
12698 | "This package provides wrappers on @code{regexpr} and @code{gregexpr} to | |
12699 | return the match results in tidy data frames.") | |
12700 | (license license:expat))) | |
0c02f94f RW |
12701 | |
12702 | (define-public r-picante | |
12703 | (package | |
12704 | (name "r-picante") | |
12705 | (version "1.8") | |
12706 | (source | |
12707 | (origin | |
12708 | (method url-fetch) | |
12709 | (uri (cran-uri "picante" version)) | |
12710 | (sha256 | |
12711 | (base32 | |
12712 | "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1")))) | |
12713 | (build-system r-build-system) | |
12714 | (propagated-inputs | |
12715 | `(("r-ape" ,r-ape) | |
12716 | ("r-nlme" ,r-nlme) | |
12717 | ("r-vegan" ,r-vegan))) | |
12718 | (home-page "https://cran.r-project.org/web/packages/picante/") | |
12719 | (synopsis "Integrating phylogenies and ecology") | |
12720 | (description | |
12721 | "This package provides functions for phylocom integration, community | |
12722 | analyses, null-models, traits and evolution. It implements numerous | |
12723 | ecophylogenetic approaches including measures of community phylogenetic and | |
12724 | trait diversity, phylogenetic signal, estimation of trait values for | |
12725 | unobserved taxa, null models for community and phylogeny randomizations, and | |
12726 | utility functions for data input/output and phylogeny plotting. A full | |
12727 | description of package functionality and methods are provided by Kembel et | |
12728 | al. (2010).") | |
12729 | (license license:gpl2))) | |
93f178b5 RW |
12730 | |
12731 | (define-public r-reinforcelearn | |
12732 | (package | |
12733 | (name "r-reinforcelearn") | |
d1ed092e | 12734 | (version "0.2.1") |
93f178b5 RW |
12735 | (source |
12736 | (origin | |
12737 | (method url-fetch) | |
12738 | (uri (cran-uri "reinforcelearn" version)) | |
12739 | (sha256 | |
12740 | (base32 | |
d1ed092e | 12741 | "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b")))) |
93f178b5 RW |
12742 | (build-system r-build-system) |
12743 | (propagated-inputs | |
12744 | `(("r-checkmate" ,r-checkmate) | |
12745 | ("r-nnet" ,r-nnet) | |
12746 | ("r-purrr" ,r-purrr) | |
12747 | ("r-r6" ,r-r6))) | |
12748 | (home-page "https://markusdumke.github.io/reinforcelearn") | |
12749 | (synopsis "Reinforcement learning") | |
12750 | (description | |
12751 | "This package implements reinforcement learning environments and | |
12752 | algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm | |
12753 | can be used with function approximation, eligibility traces (Singh & Sutton, | |
12754 | 1996) and experience replay (Mnih et al., 2013).") | |
12755 | (license license:expat))) | |
f98d97c6 RW |
12756 | |
12757 | (define-public r-lemon | |
12758 | (package | |
12759 | (name "r-lemon") | |
12760 | (version "0.4.3") | |
12761 | (source | |
12762 | (origin | |
12763 | (method url-fetch) | |
12764 | (uri (cran-uri "lemon" version)) | |
12765 | (sha256 | |
12766 | (base32 | |
12767 | "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw")))) | |
12768 | (build-system r-build-system) | |
12769 | (propagated-inputs | |
12770 | `(("r-ggplot2" ,r-ggplot2) | |
12771 | ("r-gridextra" ,r-gridextra) | |
12772 | ("r-gtable" ,r-gtable) | |
12773 | ("r-knitr" ,r-knitr) | |
12774 | ("r-lattice" ,r-lattice) | |
12775 | ("r-plyr" ,r-plyr) | |
12776 | ("r-scales" ,r-scales))) | |
12777 | (home-page "https://github.com/stefanedwards/lemon") | |
12778 | (synopsis "Freshen up your ggplot2 plots") | |
12779 | (description | |
12780 | "This package provides functions for working with legends and axis lines | |
12781 | of ggplot2, facets that repeat axis lines on all panels, and some knitr | |
12782 | extensions.") | |
12783 | (license license:gpl3))) | |
79db3a1a RW |
12784 | |
12785 | (define-public r-wgaim | |
12786 | (package | |
12787 | (name "r-wgaim") | |
567b223d | 12788 | (version "2.0-1") |
79db3a1a RW |
12789 | (source |
12790 | (origin | |
12791 | (method url-fetch) | |
12792 | (uri (cran-uri "wgaim" version)) | |
12793 | (sha256 | |
567b223d | 12794 | (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4")))) |
79db3a1a RW |
12795 | (build-system r-build-system) |
12796 | (propagated-inputs | |
5feaa775 | 12797 | `(("r-ggplot2" ,r-ggplot2) |
79db3a1a RW |
12798 | ("r-qtl" ,r-qtl))) |
12799 | (home-page "https://cran.r-project.org/web/packages/wgaim") | |
12800 | (synopsis "Whole genome average interval mapping for QTL detection") | |
12801 | (description | |
12802 | "This package integrates sophisticated mixed modelling methods with a | |
12803 | whole genome approach to detecting significant QTL in linkage maps.") | |
12804 | (license license:gpl2+))) | |
f33cb7ab RW |
12805 | |
12806 | (define-public r-bedr | |
12807 | (package | |
12808 | (name "r-bedr") | |
3c18fb13 | 12809 | (version "1.0.7") |
f33cb7ab RW |
12810 | (source |
12811 | (origin | |
12812 | (method url-fetch) | |
12813 | (uri (cran-uri "bedr" version)) | |
12814 | (sha256 | |
12815 | (base32 | |
3c18fb13 | 12816 | "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) |
f33cb7ab RW |
12817 | (build-system r-build-system) |
12818 | (propagated-inputs | |
12819 | `(("r-data-table" ,r-data-table) | |
12820 | ("r-r-utils" ,r-r-utils) | |
12821 | ("r-testthat" ,r-testthat) | |
12822 | ("r-venndiagram" ,r-venndiagram) | |
12823 | ("r-yaml" ,r-yaml) | |
12824 | ("bedops" ,bedops) | |
12825 | ("bedtools" ,bedtools) | |
12826 | ("htslib" ,htslib))) ; for tabix | |
12827 | (native-inputs | |
12828 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
12829 | (home-page "https://cran.r-project.org/web/packages/bedr") | |
12830 | (synopsis "Genomic region processing") | |
12831 | (description | |
12832 | "This package is for genomic regions processing using command line tools | |
12833 | such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient | |
12834 | utilities to perform genome arithmetic e.g indexing, formatting and merging. | |
12835 | The bedr package's API enhances access to these tools as well as offers | |
12836 | additional utilities for genomic regions processing.") | |
12837 | (license license:gpl2))) | |
459dcb95 | 12838 | |
373759ea RW |
12839 | (define-public r-sets |
12840 | (package | |
12841 | (name "r-sets") | |
12842 | (version "1.0-18") | |
12843 | (source | |
12844 | (origin | |
12845 | (method url-fetch) | |
12846 | (uri (cran-uri "sets" version)) | |
12847 | (sha256 | |
12848 | (base32 | |
12849 | "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl")))) | |
12850 | (properties `((upstream-name . "sets"))) | |
12851 | (build-system r-build-system) | |
12852 | (home-page "https://cran.r-project.org/web/packages/sets") | |
12853 | (synopsis "Sets, generalized sets, customizable sets and intervals") | |
12854 | (description | |
12855 | "This package provides data structures and basic operations for ordinary | |
12856 | sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, | |
12857 | customizable sets, and intervals.") | |
12858 | (license license:gpl2))) | |
12859 | ||
459dcb95 RW |
12860 | (define-public r-partitions |
12861 | (package | |
12862 | (name "r-partitions") | |
30aac69f | 12863 | (version "1.9-22") |
459dcb95 RW |
12864 | (source |
12865 | (origin | |
12866 | (method url-fetch) | |
12867 | (uri (cran-uri "partitions" version)) | |
12868 | (sha256 | |
12869 | (base32 | |
30aac69f | 12870 | "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns")))) |
459dcb95 RW |
12871 | (build-system r-build-system) |
12872 | (propagated-inputs | |
12873 | `(("r-gmp" ,r-gmp) | |
30aac69f RW |
12874 | ("r-polynom" ,r-polynom) |
12875 | ("r-sets" ,r-sets))) | |
459dcb95 RW |
12876 | (home-page "https://cran.r-project.org/web/packages/partitions") |
12877 | (synopsis "Additive partitions of integers") | |
12878 | (description | |
12879 | "This package provides tools to enumerates the partitions, unequal | |
12880 | partitions, and restricted partitions of an integer; the three corresponding | |
12881 | partition functions are also given.") | |
12882 | ;; Any version of the GPL | |
12883 | (license license:gpl2+))) | |
761c097f RW |
12884 | |
12885 | (define-public r-brobdingnag | |
12886 | (package | |
12887 | (name "r-brobdingnag") | |
12888 | (version "1.2-6") | |
12889 | (source | |
12890 | (origin | |
12891 | (method url-fetch) | |
12892 | (uri (cran-uri "Brobdingnag" version)) | |
12893 | (sha256 | |
12894 | (base32 | |
12895 | "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r")))) | |
12896 | (properties `((upstream-name . "Brobdingnag"))) | |
12897 | (build-system r-build-system) | |
12898 | (home-page "https://github.com/RobinHankin/Brobdingnag.git") | |
12899 | (synopsis "Very large numbers in R") | |
12900 | (description | |
12901 | "This package handles very large numbers in R. Real numbers are held | |
12902 | using their natural logarithms, plus a logical flag indicating sign. The | |
12903 | package includes a vignette that gives a step-by-step introduction to using S4 | |
12904 | methods.") | |
12905 | ;; Any version of the GPL | |
12906 | (license license:gpl2+))) | |
c30be23a RW |
12907 | |
12908 | (define-public r-untb | |
12909 | (package | |
12910 | (name "r-untb") | |
12911 | (version "1.7-4") | |
12912 | (source | |
12913 | (origin | |
12914 | (method url-fetch) | |
12915 | (uri (cran-uri "untb" version)) | |
12916 | (sha256 | |
12917 | (base32 | |
12918 | "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6")))) | |
12919 | (build-system r-build-system) | |
12920 | (propagated-inputs | |
12921 | `(("r-brobdingnag" ,r-brobdingnag) | |
12922 | ("r-partitions" ,r-partitions) | |
12923 | ("r-polynom" ,r-polynom))) | |
12924 | (home-page "https://github.com/RobinHankin/untb.git") | |
12925 | (synopsis "Ecological drift under the UNTB") | |
12926 | (description | |
12927 | "This package provides numerical simulations, and visualizations, of | |
12928 | Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).") | |
12929 | (license license:gpl2+))) | |
ea87b4e3 RW |
12930 | |
12931 | (define-public r-stepwise | |
12932 | (package | |
12933 | (name "r-stepwise") | |
12934 | (version "0.3") | |
12935 | (source | |
12936 | (origin | |
12937 | (method url-fetch) | |
12938 | (uri (cran-uri "stepwise" version)) | |
12939 | (sha256 | |
12940 | (base32 | |
12941 | "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2")))) | |
12942 | (build-system r-build-system) | |
12943 | (home-page "http://stat.sfu.ca/statgen/research/stepwise.html") | |
12944 | (synopsis "Stepwise detection of recombination breakpoints") | |
12945 | (description | |
12946 | "This package provides a stepwise approach to identifying recombination | |
12947 | breakpoints in a genomic sequence alignment.") | |
12948 | (license license:gpl2+))) | |
2a35bb15 RW |
12949 | |
12950 | (define-public r-snpmaxsel | |
12951 | (package | |
12952 | (name "r-snpmaxsel") | |
12953 | (version "1.0-3") | |
12954 | (source | |
12955 | (origin | |
12956 | (method url-fetch) | |
12957 | (uri (cran-uri "SNPmaxsel" version)) | |
12958 | (sha256 | |
12959 | (base32 | |
12960 | "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z")))) | |
12961 | (properties `((upstream-name . "SNPmaxsel"))) | |
12962 | (build-system r-build-system) | |
12963 | (propagated-inputs | |
12964 | `(("r-combinat" ,r-combinat) | |
12965 | ("r-mvtnorm" ,r-mvtnorm))) | |
12966 | (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") | |
12967 | (synopsis "Maximally selected statistics for SNP data") | |
12968 | (description | |
12969 | "This package implements asymptotic methods related to maximally selected | |
12970 | statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP) | |
12971 | data.") | |
12972 | (license license:gpl2+))) | |
7002c44f | 12973 | |
49a48c49 RW |
12974 | (define-public r-acsnminer |
12975 | (package | |
12976 | (name "r-acsnminer") | |
12977 | (version "0.16.8.25") | |
12978 | (source (origin | |
12979 | (method url-fetch) | |
12980 | (uri (cran-uri "ACSNMineR" version)) | |
12981 | (sha256 | |
12982 | (base32 | |
12983 | "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) | |
12984 | (properties `((upstream-name . "ACSNMineR"))) | |
12985 | (build-system r-build-system) | |
12986 | (propagated-inputs | |
12987 | `(("r-ggplot2" ,r-ggplot2) | |
12988 | ("r-gridextra" ,r-gridextra))) | |
12989 | (home-page "https://cran.r-project.org/web/packages/ACSNMineR") | |
12990 | (synopsis "Gene enrichment analysis") | |
12991 | (description | |
12992 | "This package provides tools to compute and represent gene set enrichment | |
12993 | or depletion from your data based on pre-saved maps from the @dfn{Atlas of | |
12994 | Cancer Signalling Networks} (ACSN) or user imported maps. The gene set | |
12995 | enrichment can be run with hypergeometric test or Fisher exact test, and can | |
12996 | use multiple corrections. Visualization of data can be done either by | |
12997 | barplots or heatmaps.") | |
12998 | (license license:gpl2+))) | |
12999 | ||
c4d521ba RW |
13000 | (define-public r-seqinr |
13001 | (package | |
13002 | (name "r-seqinr") | |
fd399b7a | 13003 | (version "3.6-1") |
c4d521ba RW |
13004 | (source |
13005 | (origin | |
13006 | (method url-fetch) | |
13007 | (uri (cran-uri "seqinr" version)) | |
13008 | (sha256 | |
13009 | (base32 | |
fd399b7a | 13010 | "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4")))) |
c4d521ba RW |
13011 | (build-system r-build-system) |
13012 | (propagated-inputs | |
13013 | `(("r-ade4" ,r-ade4) | |
13014 | ("r-segmented" ,r-segmented))) | |
13015 | (inputs | |
13016 | `(("zlib" ,zlib))) | |
13017 | (home-page "http://seqinr.r-forge.r-project.org/") | |
13018 | (synopsis "Biological sequences retrieval and analysis") | |
13019 | (description | |
13020 | "This package provides tools for exploratory data analysis and data | |
13021 | visualization of biological sequence (DNA and protein) data. It also includes | |
13022 | utilities for sequence data management under the ACNUC system.") | |
13023 | (license license:gpl2+))) | |
13024 | ||
7002c44f RW |
13025 | (define-public r-units |
13026 | (package | |
13027 | (name "r-units") | |
f9598c04 | 13028 | (version "0.6-5") |
7002c44f RW |
13029 | (source |
13030 | (origin | |
13031 | (method url-fetch) | |
13032 | (uri (cran-uri "units" version)) | |
13033 | (sha256 | |
13034 | (base32 | |
f9598c04 | 13035 | "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh")))) |
7002c44f RW |
13036 | (build-system r-build-system) |
13037 | (inputs | |
13038 | `(("udunits" ,udunits))) | |
13039 | (propagated-inputs | |
13040 | `(("r-rcpp" ,r-rcpp))) | |
13041 | (home-page "https://github.com/r-quantities/units/") | |
13042 | (synopsis "Measurement Units for R Vectors") | |
13043 | (description | |
13044 | "This package provides support for measurement units in R vectors, | |
13045 | matrices and arrays: automatic propagation, conversion, derivation and | |
13046 | simplification of units; raising errors in case of unit incompatibility. It | |
13047 | is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} | |
13048 | classes.") | |
13049 | (license license:gpl2))) | |
518c1dea RW |
13050 | |
13051 | (define-public r-classint | |
13052 | (package | |
13053 | (name "r-classint") | |
970eab39 | 13054 | (version "0.4-2") |
518c1dea RW |
13055 | (source |
13056 | (origin | |
13057 | (method url-fetch) | |
13058 | (uri (cran-uri "classInt" version)) | |
13059 | (sha256 | |
13060 | (base32 | |
970eab39 | 13061 | "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv")))) |
518c1dea RW |
13062 | (properties `((upstream-name . "classInt"))) |
13063 | (build-system r-build-system) | |
13064 | (propagated-inputs | |
13065 | `(("r-class" ,r-class) | |
1bbfca18 RW |
13066 | ("r-e1071" ,r-e1071) |
13067 | ("r-kernsmooth" ,r-kernsmooth))) | |
518c1dea RW |
13068 | (native-inputs `(("gfortran" ,gfortran))) |
13069 | (home-page "https://github.com/r-spatial/classInt/") | |
13070 | (synopsis "Choose univariate class intervals") | |
13071 | (description | |
13072 | "This package provides selected commonly used methods for choosing | |
13073 | univariate class intervals for mapping or other graphics purposes.") | |
13074 | (license license:gpl2+))) | |
66c08ff4 RW |
13075 | |
13076 | (define-public r-spdata | |
13077 | (package | |
13078 | (name "r-spdata") | |
b9d9bc66 | 13079 | (version "0.3.2") |
66c08ff4 RW |
13080 | (source |
13081 | (origin | |
13082 | (method url-fetch) | |
13083 | (uri (cran-uri "spData" version)) | |
13084 | (sha256 | |
13085 | (base32 | |
b9d9bc66 | 13086 | "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw")))) |
66c08ff4 RW |
13087 | (properties `((upstream-name . "spData"))) |
13088 | (build-system r-build-system) | |
13089 | (home-page "https://github.com/Nowosad/spData") | |
13090 | (synopsis "Datasets for spatial analysis") | |
13091 | (description | |
13092 | "This a package containing diverse spatial datasets for demonstrating, | |
13093 | benchmarking and teaching spatial data analysis. It includes R data of class | |
13094 | @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a | |
13095 | range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some | |
13096 | of the datasets are designed to illustrate specific analysis techniques. | |
13097 | @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to | |
13098 | illustrate point pattern analysis techniques.") | |
13099 | (license license:cc0))) | |
e5228273 RW |
13100 | |
13101 | (define-public r-learnbayes | |
13102 | (package | |
13103 | (name "r-learnbayes") | |
13104 | (version "2.15.1") | |
13105 | (source | |
13106 | (origin | |
13107 | (method url-fetch) | |
13108 | (uri (cran-uri "LearnBayes" version)) | |
13109 | (sha256 | |
13110 | (base32 | |
13111 | "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv")))) | |
13112 | (properties `((upstream-name . "LearnBayes"))) | |
13113 | (build-system r-build-system) | |
13114 | (home-page "https://cran.r-project.org/web/packages/LearnBayes") | |
13115 | (synopsis "Functions for learning Bayesian inference") | |
13116 | (description | |
13117 | "This package provides a collection of functions helpful in learning the | |
13118 | basic tenets of Bayesian statistical inference. It contains functions for | |
13119 | summarizing basic one and two parameter posterior distributions and predictive | |
13120 | distributions. It contains MCMC algorithms for summarizing posterior | |
13121 | distributions defined by the user. It also contains functions for regression | |
13122 | models, hierarchical models, Bayesian tests, and illustrations of Gibbs | |
13123 | sampling.") | |
13124 | (license license:gpl2+))) | |
dcc50286 RW |
13125 | |
13126 | (define-public r-deldir | |
13127 | (package | |
13128 | (name "r-deldir") | |
4eed03ea | 13129 | (version "0.1-23") |
dcc50286 RW |
13130 | (source |
13131 | (origin | |
13132 | (method url-fetch) | |
13133 | (uri (cran-uri "deldir" version)) | |
13134 | (sha256 | |
13135 | (base32 | |
4eed03ea | 13136 | "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0")))) |
dcc50286 RW |
13137 | (build-system r-build-system) |
13138 | (native-inputs `(("gfortran" ,gfortran))) | |
13139 | (home-page "https://cran.r-project.org/web/packages/deldir") | |
13140 | (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") | |
13141 | (description | |
13142 | "This package provides tools for calculating the Delaunay triangulation | |
13143 | and the Dirichlet or Voronoi tessellation (with respect to the entire plane) | |
13144 | of a planar point set. It plots triangulations and tessellations in various | |
13145 | ways, clips tessellations to sub-windows, calculates perimeters of | |
13146 | tessellations, and summarizes information about the tiles of the | |
13147 | tessellation.") | |
13148 | (license license:gpl2+))) | |
d884e407 RW |
13149 | |
13150 | (define-public r-sf | |
13151 | (package | |
13152 | (name "r-sf") | |
bc9a839f | 13153 | (version "0.8-0") |
d884e407 RW |
13154 | (source |
13155 | (origin | |
13156 | (method url-fetch) | |
13157 | (uri (cran-uri "sf" version)) | |
13158 | (sha256 | |
13159 | (base32 | |
bc9a839f | 13160 | "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf")))) |
d884e407 RW |
13161 | (build-system r-build-system) |
13162 | (inputs | |
13163 | `(("gdal" ,gdal) | |
13164 | ("geos" ,geos) | |
13165 | ("proj" ,proj.4) | |
13166 | ("zlib" ,zlib))) | |
13167 | (propagated-inputs | |
13168 | `(("r-classint" ,r-classint) | |
13169 | ("r-dbi" ,r-dbi) | |
13170 | ("r-magrittr" ,r-magrittr) | |
13171 | ("r-rcpp" ,r-rcpp) | |
13172 | ("r-units" ,r-units))) | |
13173 | (native-inputs `(("pkg-config" ,pkg-config))) | |
13174 | (home-page "https://github.com/r-spatial/sf/") | |
13175 | (synopsis "Simple features for R") | |
13176 | (description | |
13177 | "This package provides support for simple features, a standardized way to | |
13178 | encode spatial vector data. It binds to GDAL for reading and writing data, to | |
13179 | GEOS for geometrical operations, and to PROJ for projection conversions and | |
13180 | datum transformations.") | |
13181 | ;; Either of these licenses | |
13182 | (license (list license:gpl2 license:expat)))) | |
e371e534 RW |
13183 | |
13184 | (define-public r-spdep | |
13185 | (package | |
13186 | (name "r-spdep") | |
4978222a | 13187 | (version "1.1-3") |
e371e534 RW |
13188 | (source |
13189 | (origin | |
13190 | (method url-fetch) | |
13191 | (uri (cran-uri "spdep" version)) | |
13192 | (sha256 | |
13193 | (base32 | |
4978222a | 13194 | "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk")))) |
e371e534 RW |
13195 | (build-system r-build-system) |
13196 | (propagated-inputs | |
13197 | `(("r-boot" ,r-boot) | |
13198 | ("r-coda" ,r-coda) | |
13199 | ("r-deldir" ,r-deldir) | |
13200 | ("r-expm" ,r-expm) | |
13201 | ("r-gmodels" ,r-gmodels) | |
13202 | ("r-learnbayes" ,r-learnbayes) | |
13203 | ("r-mass" ,r-mass) | |
13204 | ("r-matrix" ,r-matrix) | |
13205 | ("r-nlme" ,r-nlme) | |
13206 | ("r-sf" ,r-sf) | |
13207 | ("r-sp" ,r-sp) | |
13208 | ("r-spdata" ,r-spdata))) | |
13209 | (home-page "https://github.com/r-spatial/spdep/") | |
13210 | (synopsis "Spatial dependence: weighting schemes, statistics and models") | |
13211 | (description | |
13212 | "This package provides a collection of functions to create spatial | |
13213 | weights matrix objects from polygon contiguities, from point patterns by | |
13214 | distance and tessellations, for summarizing these objects, and for permitting | |
13215 | their use in spatial data analysis, including regional aggregation by minimum | |
13216 | spanning tree.") | |
13217 | (license license:gpl2+))) | |
91c1fbdf RW |
13218 | |
13219 | (define-public r-adegenet | |
13220 | (package | |
13221 | (name "r-adegenet") | |
13222 | (version "2.1.1") | |
13223 | (source | |
13224 | (origin | |
13225 | (method url-fetch) | |
13226 | (uri (cran-uri "adegenet" version)) | |
13227 | (sha256 | |
13228 | (base32 | |
13229 | "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh")))) | |
13230 | (build-system r-build-system) | |
13231 | (propagated-inputs | |
13232 | `(("r-ade4" ,r-ade4) | |
13233 | ("r-ape" ,r-ape) | |
13234 | ("r-boot" ,r-boot) | |
13235 | ("r-dplyr" ,r-dplyr) | |
13236 | ("r-ggplot2" ,r-ggplot2) | |
13237 | ("r-igraph" ,r-igraph) | |
13238 | ("r-mass" ,r-mass) | |
13239 | ("r-reshape2" ,r-reshape2) | |
13240 | ("r-seqinr" ,r-seqinr) | |
13241 | ("r-shiny" ,r-shiny) | |
13242 | ("r-spdep" ,r-spdep) | |
13243 | ("r-vegan" ,r-vegan))) | |
13244 | (home-page "https://github.com/thibautjombart/adegenet") | |
13245 | (synopsis "Exploratory analysis of genetic and genomic data") | |
13246 | (description | |
13247 | "This package provides a toolset for the exploration of genetic and | |
13248 | genomic data. Adegenet provides formal (S4) classes for storing and handling | |
13249 | various genetic data, including genetic markers with varying ploidy and | |
13250 | hierarchical population structure (@code{genind} class), alleles counts by | |
13251 | populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It | |
13252 | also implements original multivariate methods (DAPC, sPCA), graphics, | |
13253 | statistical tests, simulation tools, distance and similarity measures, and | |
13254 | several spatial methods. A range of both empirical and simulated datasets is | |
13255 | also provided to illustrate various methods.") | |
13256 | (license license:gpl2+))) | |
3d2bc817 RW |
13257 | |
13258 | (define-public r-pegas | |
13259 | (package | |
13260 | (name "r-pegas") | |
44805ca5 | 13261 | (version "0.12") |
3d2bc817 RW |
13262 | (source |
13263 | (origin | |
13264 | (method url-fetch) | |
13265 | (uri (cran-uri "pegas" version)) | |
13266 | (sha256 | |
44805ca5 | 13267 | (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p")))) |
3d2bc817 RW |
13268 | (build-system r-build-system) |
13269 | (propagated-inputs | |
13270 | `(("r-adegenet" ,r-adegenet) | |
13271 | ("r-ape" ,r-ape))) | |
13272 | (home-page "http://ape-package.ird.fr/pegas.html") | |
13273 | (synopsis "Population and evolutionary genetics analysis system") | |
13274 | (description | |
13275 | "This package provides functions for reading, writing, plotting, | |
13276 | analysing, and manipulating allelic and haplotypic data, including from VCF | |
13277 | files, and for the analysis of population nucleotide sequences and | |
13278 | micro-satellites including coalescent analyses, linkage disequilibrium, | |
13279 | population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, | |
13280 | minimum spanning tree and network, and median-joining networks.") | |
13281 | (license license:gpl2+))) | |
cd977b35 RW |
13282 | |
13283 | (define-public r-rmetasim | |
13284 | (package | |
13285 | (name "r-rmetasim") | |
13286 | (version "3.1.7") | |
13287 | (source | |
13288 | (origin | |
13289 | (method url-fetch) | |
13290 | (uri (cran-uri "rmetasim" version)) | |
13291 | (sha256 | |
13292 | (base32 | |
13293 | "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r")))) | |
13294 | (build-system r-build-system) | |
13295 | (propagated-inputs | |
13296 | `(("r-ade4" ,r-ade4) | |
13297 | ("r-adegenet" ,r-adegenet) | |
13298 | ("r-gtools" ,r-gtools) | |
13299 | ("r-pegas" ,r-pegas))) | |
13300 | (home-page "https://cran.r-project.org/web/packages/rmetasim") | |
13301 | (synopsis "Individual-based population genetic simulation environment") | |
13302 | (description | |
13303 | "This package provides an interface between R and the metasim simulation | |
13304 | engine. The simulation environment is documented in: Strand, A.(2002), | |
13305 | Metasim 1.0: an individual-based environment for simulating population | |
13306 | genetics of complex population dynamics.") | |
13307 | ;; Any GPL version | |
13308 | (license license:gpl2+))) | |
601ddf02 RW |
13309 | |
13310 | (define-public r-genetics | |
13311 | (package | |
13312 | (name "r-genetics") | |
f1c1bbc1 | 13313 | (version "1.3.8.1.2") |
601ddf02 RW |
13314 | (source |
13315 | (origin | |
13316 | (method url-fetch) | |
13317 | (uri (cran-uri "genetics" version)) | |
13318 | (sha256 | |
13319 | (base32 | |
f1c1bbc1 | 13320 | "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh")))) |
601ddf02 RW |
13321 | (build-system r-build-system) |
13322 | (propagated-inputs | |
13323 | `(("r-combinat" ,r-combinat) | |
13324 | ("r-gdata" ,r-gdata) | |
13325 | ("r-gtools" ,r-gtools) | |
13326 | ("r-mass" ,r-mass) | |
13327 | ("r-mvtnorm" ,r-mvtnorm))) | |
13328 | (home-page "https://cran.r-project.org/web/packages/genetics/") | |
13329 | (synopsis "Population genetics") | |
13330 | (description | |
13331 | "This package provides classes and methods for handling genetic data. | |
13332 | It includes classes to represent genotypes and haplotypes at single markers up | |
13333 | to multiple markers on multiple chromosomes. Function include allele | |
13334 | frequencies, flagging homo/heterozygotes, flagging carriers of certain | |
13335 | alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating | |
13336 | and testing for linkage disequilibrium, ...") | |
13337 | ;; Any GPL version. | |
13338 | (license license:gpl2+))) | |
5ef7d057 RW |
13339 | |
13340 | (define-public r-snp-plotter | |
13341 | (package | |
13342 | (name "r-snp-plotter") | |
13343 | (version "0.5.1") | |
13344 | (source | |
13345 | (origin | |
13346 | (method url-fetch) | |
13347 | (uri (cran-uri "snp.plotter" version)) | |
13348 | (sha256 | |
13349 | (base32 | |
13350 | "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) | |
13351 | (properties `((upstream-name . "snp.plotter"))) | |
13352 | (build-system r-build-system) | |
13353 | (propagated-inputs `(("r-genetics" ,r-genetics))) | |
13354 | (home-page "https://cran.r-project.org/web/packages/snp.plotter/") | |
13355 | (synopsis "Plot p-values using single SNP and/or haplotype data") | |
13356 | (description | |
13357 | "This package helps you create plots of p-values using single SNP and/or | |
13358 | haplotype data. Main features of the package include options to display a | |
13359 | @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple | |
13360 | datasets simultaneously. Plots can be created using global and/or individual | |
13361 | haplotype p-values along with single SNP p-values. Images are created as | |
13362 | either PDF/EPS files.") | |
13363 | (license license:gpl2+))) | |
6a472af3 RW |
13364 | |
13365 | (define-public r-polspline | |
13366 | (package | |
13367 | (name "r-polspline") | |
2777e06f | 13368 | (version "1.1.17") |
6a472af3 RW |
13369 | (source |
13370 | (origin | |
13371 | (method url-fetch) | |
13372 | (uri (cran-uri "polspline" version)) | |
13373 | (sha256 | |
2777e06f | 13374 | (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn")))) |
6a472af3 RW |
13375 | (build-system r-build-system) |
13376 | (native-inputs `(("gfortran" ,gfortran))) | |
13377 | (home-page "https://cran.r-project.org/web/packages/polspline/") | |
13378 | (synopsis "Polynomial spline routines") | |
13379 | (description | |
13380 | "This package provides routines for the polynomial spline fitting | |
13381 | routines hazard regression, hazard estimation with flexible tails, logspline, | |
13382 | lspec, polyclass, and polymars.") | |
13383 | (license license:gpl2+))) | |
a8c965cf RW |
13384 | |
13385 | (define-public r-rms | |
13386 | (package | |
13387 | (name "r-rms") | |
0645e72f | 13388 | (version "5.1-4") |
a8c965cf RW |
13389 | (source |
13390 | (origin | |
13391 | (method url-fetch) | |
13392 | (uri (cran-uri "rms" version)) | |
13393 | (sha256 | |
0645e72f | 13394 | (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q")))) |
a8c965cf RW |
13395 | (build-system r-build-system) |
13396 | (propagated-inputs | |
13397 | `(("r-ggplot2" ,r-ggplot2) | |
13398 | ("r-hmisc" ,r-hmisc) | |
13399 | ("r-htmltable" ,r-htmltable) | |
13400 | ("r-htmltools" ,r-htmltools) | |
13401 | ("r-lattice" ,r-lattice) | |
13402 | ("r-multcomp" ,r-multcomp) | |
13403 | ("r-nlme" ,r-nlme) | |
13404 | ("r-polspline" ,r-polspline) | |
13405 | ("r-quantreg" ,r-quantreg) | |
13406 | ("r-rpart" ,r-rpart) | |
13407 | ("r-sparsem" ,r-sparsem) | |
13408 | ("r-survival" ,r-survival))) | |
13409 | (native-inputs `(("gfortran" ,gfortran))) | |
13410 | (home-page "http://biostat.mc.vanderbilt.edu/rms") | |
13411 | (synopsis "Regression modeling strategies") | |
13412 | (description | |
13413 | "This is a package for regression modeling, testing, estimation, | |
13414 | validation, graphics, prediction, and typesetting by storing enhanced model | |
13415 | design attributes in the fit. The rms package is a collection of functions | |
13416 | that assist with and streamline modeling. It also contains functions for | |
13417 | binary and ordinal logistic regression models, ordinal models for continuous Y | |
13418 | with a variety of distribution families, and the Buckley-James multiple | |
13419 | regression model for right-censored responses, and implements penalized | |
13420 | maximum likelihood estimation for logistic and ordinary linear models. The | |
13421 | package works with almost any regression model, but it was especially written | |
13422 | to work with binary or ordinal regression models, Cox regression, accelerated | |
13423 | failure time models, ordinary linear models, the Buckley-James model, | |
13424 | generalized least squares for serially or spatially correlated observations, | |
13425 | generalized linear models, and quantile regression.") | |
13426 | (license license:gpl2+))) | |
cd47dcf6 RW |
13427 | |
13428 | (define-public r-haplo-stats | |
13429 | (package | |
13430 | (name "r-haplo-stats") | |
13431 | (version "1.7.9") | |
13432 | (source | |
13433 | (origin | |
13434 | (method url-fetch) | |
13435 | (uri (cran-uri "haplo.stats" version)) | |
13436 | (sha256 | |
13437 | (base32 | |
13438 | "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx")))) | |
13439 | (properties `((upstream-name . "haplo.stats"))) | |
13440 | (build-system r-build-system) | |
13441 | (propagated-inputs | |
13442 | `(("r-rms" ,r-rms))) | |
13443 | (native-inputs | |
13444 | `(("r-r-rsp" ,r-r-rsp))) ; for vignettes | |
13445 | (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") | |
13446 | (synopsis "Analysis of haplotypes when linkage phase is ambiguous") | |
13447 | (description | |
13448 | "This package provides routines for the analysis of indirectly measured | |
13449 | haplotypes. The statistical methods assume that all subjects are unrelated | |
13450 | and that haplotypes are ambiguous (due to unknown linkage phase of the genetic | |
13451 | markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()}, | |
13452 | @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed | |
13453 | examples in the vignette.") | |
13454 | (license license:gpl2+))) | |
bffb5826 RW |
13455 | |
13456 | (define-public r-bqtl | |
13457 | (package | |
13458 | (name "r-bqtl") | |
13459 | (version "1.0-32") | |
13460 | (source | |
13461 | (origin | |
13462 | (method url-fetch) | |
13463 | (uri (cran-uri "bqtl" version)) | |
13464 | (sha256 | |
13465 | (base32 | |
13466 | "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci")))) | |
13467 | (build-system r-build-system) | |
13468 | (native-inputs `(("gfortran" ,gfortran))) | |
13469 | (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") | |
13470 | (synopsis "Bayesian QTL mapping toolkit") | |
13471 | (description | |
13472 | "This is a QTL mapping toolkit for inbred crosses and recombinant inbred | |
13473 | lines. It includes maximum likelihood and Bayesian tools.") | |
13474 | (license license:gpl2+))) | |
73fcd222 RW |
13475 | |
13476 | (define-public r-ibdreg | |
13477 | (package | |
13478 | (name "r-ibdreg") | |
13479 | (version "0.2.5") | |
13480 | (source | |
13481 | (origin | |
13482 | (method url-fetch) | |
13483 | (uri (cran-uri "ibdreg" version)) | |
13484 | (sha256 | |
13485 | (base32 | |
13486 | "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g")))) | |
13487 | (build-system r-build-system) | |
13488 | (home-page "https://www.mayo.edu/research/labs/\ | |
13489 | statistical-genetics-genetic-epidemiology/software") | |
13490 | (synopsis "Regression methods for IBD linkage with covariates") | |
13491 | (description | |
13492 | "This package provides a method to test genetic linkage with covariates | |
13493 | by regression methods with response IBD sharing for relative pairs. Account | |
13494 | for correlations of IBD statistics and covariates for relative pairs within | |
13495 | the same pedigree.") | |
13496 | (license license:gpl2+))) | |
d4a255a4 RW |
13497 | |
13498 | (define-public r-dlmap | |
13499 | (package | |
13500 | (name "r-dlmap") | |
13501 | (version "1.13") | |
13502 | (source | |
13503 | (origin | |
13504 | (method url-fetch) | |
13505 | (uri (cran-uri "dlmap" version)) | |
13506 | (sha256 | |
13507 | (base32 | |
13508 | "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) | |
13509 | (build-system r-build-system) | |
13510 | (propagated-inputs | |
13511 | `(("r-ibdreg" ,r-ibdreg) | |
13512 | ("r-mgcv" ,r-mgcv) | |
13513 | ("r-nlme" ,r-nlme) | |
13514 | ("r-qtl" ,r-qtl) | |
13515 | ("r-wgaim" ,r-wgaim))) | |
13516 | (home-page "https://cran.r-project.org/web/packages/dlmap/") | |
13517 | (synopsis "Detection localization mapping for QTL") | |
13518 | (description | |
13519 | "This is package for QTL mapping in a mixed model framework with separate | |
13520 | detection and localization stages. The first stage detects the number of QTL | |
13521 | on each chromosome based on the genetic variation due to grouped markers on | |
13522 | the chromosome; the second stage uses this information to determine the most | |
13523 | likely QTL positions. The mixed model can accommodate general fixed and | |
13524 | random effects, including spatial effects in field trials and pedigree | |
13525 | effects. It is applicable to backcrosses, doubled haploids, recombinant | |
13526 | inbred lines, F2 intercrosses, and association mapping populations.") | |
13527 | (license license:gpl2))) | |
1cdd9f0e RW |
13528 | |
13529 | (define-public r-ldheatmap | |
13530 | (package | |
13531 | (name "r-ldheatmap") | |
1a88de18 | 13532 | (version "0.99-7") |
1cdd9f0e RW |
13533 | (source |
13534 | (origin | |
13535 | (method url-fetch) | |
13536 | (uri (cran-uri "LDheatmap" version)) | |
13537 | (sha256 | |
13538 | (base32 | |
1a88de18 | 13539 | "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc")))) |
1cdd9f0e RW |
13540 | (properties `((upstream-name . "LDheatmap"))) |
13541 | (build-system r-build-system) | |
13542 | (propagated-inputs | |
13543 | `(("r-genetics" ,r-genetics) | |
1a88de18 | 13544 | ("r-rcpp" ,r-rcpp) |
1cdd9f0e RW |
13545 | ("r-snpstats" ,r-snpstats))) |
13546 | (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html") | |
13547 | (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") | |
13548 | (description | |
13549 | "This package provides tools to produce a graphical display, as a heat | |
13550 | map, of measures of pairwise linkage disequilibria between SNPs. Users may | |
13551 | optionally include the physical locations or genetic map distances of each SNP | |
13552 | on the plot.") | |
13553 | (license license:gpl3))) | |
b8fea3c8 RW |
13554 | |
13555 | (define-public r-hwde | |
13556 | (package | |
13557 | (name "r-hwde") | |
13558 | (version "0.67") | |
13559 | (source | |
13560 | (origin | |
13561 | (method url-fetch) | |
13562 | (uri (cran-uri "hwde" version)) | |
13563 | (sha256 | |
13564 | (base32 | |
13565 | "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy")))) | |
13566 | (build-system r-build-system) | |
13567 | (home-page "https://cran.r-project.org/web/packages/hwde/") | |
13568 | (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium") | |
13569 | (description | |
13570 | "This package fits models for genotypic disequilibria, as described in | |
13571 | Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast | |
13572 | terms are available that account for first order interactions between loci. | |
13573 | It also implements, for a single locus in a single population, a conditional | |
13574 | exact test for Hardy-Weinberg equilibrium.") | |
13575 | (license license:gpl2+))) | |
7cd4ff2f RW |
13576 | |
13577 | (define-public r-tdthap | |
13578 | (package | |
13579 | (name "r-tdthap") | |
87b43815 | 13580 | (version "1.1-11") |
7cd4ff2f RW |
13581 | (source |
13582 | (origin | |
13583 | (method url-fetch) | |
13584 | (uri (cran-uri "tdthap" version)) | |
13585 | (sha256 | |
13586 | (base32 | |
87b43815 | 13587 | "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k")))) |
7cd4ff2f RW |
13588 | (build-system r-build-system) |
13589 | (home-page "https://cran.r-project.org/web/packages/tdthap/") | |
13590 | (synopsis "TDT tests for extended haplotypes") | |
13591 | (description | |
13592 | "Functions and examples are provided for transmission/disequilibrium | |
13593 | tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) | |
13594 | \"Transmission/disequilibrium tests for extended marker haplotypes\".") | |
13595 | (license license:artistic2.0))) | |
469fb438 RW |
13596 | |
13597 | (define-public r-sparql | |
13598 | (package | |
13599 | (name "r-sparql") | |
13600 | (version "1.16") | |
13601 | (source (origin | |
13602 | (method url-fetch) | |
13603 | (uri (cran-uri "SPARQL" version)) | |
13604 | (sha256 | |
13605 | (base32 | |
13606 | "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) | |
13607 | (properties `((upstream-name . "SPARQL"))) | |
13608 | (build-system r-build-system) | |
13609 | (propagated-inputs | |
13610 | `(("r-rcurl" ,r-rcurl) | |
13611 | ("r-xml" ,r-xml))) | |
13612 | (home-page "https://cran.r-project.org/web/packages/SPARQL") | |
13613 | (synopsis "SPARQL client for R") | |
13614 | (description "This package provides an interface to use SPARQL to pose | |
13615 | SELECT or UPDATE queries to an end-point.") | |
13616 | ;; The only license indication is found in the DESCRIPTION file, | |
13617 | ;; which states GPL-3. So we cannot assume GPLv3+. | |
13618 | (license license:gpl3))) | |
0ef062b3 RW |
13619 | |
13620 | (define-public r-bookdown | |
13621 | (package | |
13622 | (name "r-bookdown") | |
19600e08 | 13623 | (version "0.16") |
0ef062b3 RW |
13624 | (source (origin |
13625 | (method url-fetch) | |
13626 | (uri (cran-uri "bookdown" version)) | |
13627 | (sha256 | |
13628 | (base32 | |
19600e08 | 13629 | "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1")))) |
0ef062b3 RW |
13630 | (build-system r-build-system) |
13631 | (propagated-inputs | |
13632 | `(("r-htmltools" ,r-htmltools) | |
13633 | ("r-knitr" ,r-knitr) | |
13634 | ("r-rmarkdown" ,r-rmarkdown) | |
13635 | ("r-tinytex" ,r-tinytex) | |
650e8def RW |
13636 | ("r-xfun" ,r-xfun) |
13637 | ("pandoc" ,ghc-pandoc))) | |
0ef062b3 RW |
13638 | (home-page "https://github.com/rstudio/bookdown") |
13639 | (synopsis "Authoring books and technical documents with R markdown") | |
13640 | (description "This package provides output formats and utilities for | |
13641 | authoring books and technical documents with R Markdown.") | |
13642 | (license license:gpl3))) | |
72a216a9 RW |
13643 | |
13644 | (define-public r-optparse | |
13645 | (package | |
13646 | (name "r-optparse") | |
cbe42da2 | 13647 | (version "1.6.4") |
72a216a9 RW |
13648 | (source |
13649 | (origin | |
13650 | (method url-fetch) | |
13651 | (uri (cran-uri "optparse" version)) | |
13652 | (sha256 | |
13653 | (base32 | |
cbe42da2 | 13654 | "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d")))) |
72a216a9 RW |
13655 | (build-system r-build-system) |
13656 | (propagated-inputs | |
13657 | `(("r-getopt" ,r-getopt))) | |
13658 | (home-page "https://github.com/trevorld/optparse") | |
13659 | (synopsis "Command line option parser") | |
13660 | (description | |
13661 | "This package provides a command line parser inspired by Python's | |
13662 | @code{optparse} library to be used with Rscript to write shebang scripts | |
13663 | that accept short and long options.") | |
13664 | (license license:gpl2+))) | |
c5a2b518 RW |
13665 | |
13666 | (define-public r-wgcna | |
13667 | (package | |
13668 | (name "r-wgcna") | |
7a857771 | 13669 | (version "1.68") |
c5a2b518 RW |
13670 | (source |
13671 | (origin | |
13672 | (method url-fetch) | |
13673 | (uri (cran-uri "WGCNA" version)) | |
13674 | (sha256 | |
13675 | (base32 | |
7a857771 | 13676 | "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a")))) |
c5a2b518 RW |
13677 | (properties `((upstream-name . "WGCNA"))) |
13678 | (build-system r-build-system) | |
13679 | (propagated-inputs | |
13680 | `(("r-annotationdbi" ,r-annotationdbi) | |
13681 | ("r-doparallel" ,r-doparallel) | |
13682 | ("r-dynamictreecut" ,r-dynamictreecut) | |
13683 | ("r-fastcluster" ,r-fastcluster) | |
13684 | ("r-foreach" ,r-foreach) | |
13685 | ("r-go-db" ,r-go-db) | |
13686 | ("r-hmisc" ,r-hmisc) | |
13687 | ("r-impute" ,r-impute) | |
13688 | ("r-rcpp" ,r-rcpp) | |
13689 | ("r-robust" ,r-robust) | |
13690 | ("r-survival" ,r-survival) | |
13691 | ("r-matrixstats" ,r-matrixstats) | |
13692 | ("r-preprocesscore" ,r-preprocesscore))) | |
13693 | (home-page | |
13694 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
13695 | (synopsis "Weighted correlation network analysis") | |
13696 | (description | |
13697 | "This package provides functions necessary to perform Weighted | |
13698 | Correlation Network Analysis on high-dimensional data. It includes functions | |
13699 | for rudimentary data cleaning, construction and summarization of correlation | |
13700 | networks, module identification and functions for relating both variables and | |
13701 | modules to sample traits. It also includes a number of utility functions for | |
13702 | data manipulation and visualization.") | |
13703 | (license license:gpl2+))) | |
bac0ca32 RW |
13704 | |
13705 | (define-public r-kernlab | |
13706 | (package | |
13707 | (name "r-kernlab") | |
17c5b6fc | 13708 | (version "0.9-29") |
bac0ca32 RW |
13709 | (source |
13710 | (origin | |
13711 | (method url-fetch) | |
13712 | (uri (cran-uri "kernlab" version)) | |
13713 | (sha256 | |
17c5b6fc | 13714 | (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3")))) |
bac0ca32 RW |
13715 | (build-system r-build-system) |
13716 | (home-page "https://cran.r-project.org/web/packages/kernlab") | |
13717 | (synopsis "Kernel-based machine learning tools") | |
13718 | (description | |
13719 | "This package provides kernel-based machine learning methods for | |
13720 | classification, regression, clustering, novelty detection, quantile regression | |
13721 | and dimensionality reduction. Among other methods @code{kernlab} includes | |
13722 | Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes | |
13723 | and a QP solver.") | |
13724 | (license license:gpl2))) | |
a0583c0d RW |
13725 | |
13726 | (define-public r-hierfstat | |
13727 | (package | |
13728 | (name "r-hierfstat") | |
13729 | (version "0.04-22") | |
13730 | (source | |
13731 | (origin | |
13732 | (method url-fetch) | |
13733 | (uri (cran-uri "hierfstat" version)) | |
13734 | (sha256 | |
13735 | (base32 | |
13736 | "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx")))) | |
13737 | (build-system r-build-system) | |
13738 | (propagated-inputs | |
13739 | `(("r-ade4" ,r-ade4) | |
13740 | ("r-adegenet" ,r-adegenet) | |
13741 | ("r-gtools" ,r-gtools))) | |
13742 | (home-page "https://cran.r-project.org/web/packages/hierfstat/") | |
13743 | (synopsis "Estimation and tests of hierarchical F-statistics") | |
13744 | (description | |
13745 | "This package allows the estimation of hierarchical F-statistics from | |
13746 | haploid or diploid genetic data with any numbers of levels in the hierarchy, | |
13747 | following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions | |
13748 | are also given to test via randomisations the significance of each F and | |
13749 | variance components, using the likelihood-ratio statistics G.") | |
13750 | (license license:gpl2+))) | |
3080b81a RW |
13751 | |
13752 | (define-public r-hapassoc | |
13753 | (package | |
13754 | (name "r-hapassoc") | |
13755 | (version "1.2-8") | |
13756 | (source | |
13757 | (origin | |
13758 | (method url-fetch) | |
13759 | (uri (cran-uri "hapassoc" version)) | |
13760 | (sha256 | |
13761 | (base32 | |
13762 | "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s")))) | |
13763 | (build-system r-build-system) | |
13764 | (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html") | |
13765 | (synopsis "Inference of trait associations with SNP haplotypes") | |
13766 | (description | |
13767 | "Hapassoc performs likelihood inference of trait associations with | |
13768 | haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The | |
13769 | functions are developed primarily for data collected in cohort or | |
13770 | cross-sectional studies. They can accommodate uncertain haplotype phase and | |
13771 | handle missing genotypes at some SNPs.") | |
13772 | (license license:gpl2))) | |
7166b77a RW |
13773 | |
13774 | (define-public r-sampling | |
13775 | (package | |
13776 | (name "r-sampling") | |
13777 | (version "2.8") | |
13778 | (source | |
13779 | (origin | |
13780 | (method url-fetch) | |
13781 | (uri (cran-uri "sampling" version)) | |
13782 | (sha256 | |
13783 | (base32 | |
13784 | "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m")))) | |
13785 | (build-system r-build-system) | |
13786 | (propagated-inputs | |
13787 | `(("r-lpsolve" ,r-lpsolve) | |
13788 | ("r-mass" ,r-mass))) | |
13789 | (home-page "https://cran.r-project.org/web/packages/sampling/") | |
13790 | (synopsis "Survey sampling") | |
13791 | (description | |
13792 | "This package provides functions for drawing and calibrating samples.") | |
13793 | (license license:gpl2+))) | |
4f8b1fb3 RW |
13794 | |
13795 | (define-public r-r2html | |
13796 | (package | |
13797 | (name "r-r2html") | |
13798 | (version "2.3.2") | |
13799 | (source | |
13800 | (origin | |
13801 | (method url-fetch) | |
13802 | (uri (cran-uri "R2HTML" version)) | |
13803 | (sha256 | |
13804 | (base32 | |
13805 | "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9")))) | |
13806 | (properties `((upstream-name . "R2HTML"))) | |
13807 | (build-system r-build-system) | |
13808 | (home-page "https://github.com/nalimilan/R2HTML") | |
13809 | (synopsis "HTML export for R objects") | |
13810 | (description | |
13811 | "This package includes HTML functions and methods to write in an HTML | |
13812 | file. Thus, making HTML reports is easy. It includes a function that allows | |
13813 | redirection on the fly, which appears to be very useful for teaching purposes, | |
13814 | as the student can keep a copy of the produced output to keep all that they | |
13815 | did during the course. The package comes with a vignette describing how to | |
13816 | write HTML reports for statistical analysis. Finally, a driver for Sweave | |
13817 | allows to parse HTML flat files containing R code and to automatically write | |
13818 | the corresponding outputs (tables and graphs).") | |
13819 | (license license:gpl2+))) | |
3f6e6e98 RW |
13820 | |
13821 | (define-public r-rjava | |
13822 | (package | |
13823 | (name "r-rjava") | |
f2f89e9a | 13824 | (version "0.9-11") |
3f6e6e98 RW |
13825 | (source |
13826 | (origin | |
13827 | (method url-fetch) | |
13828 | (uri (cran-uri "rJava" version)) | |
13829 | (sha256 | |
13830 | (base32 | |
f2f89e9a | 13831 | "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2")))) |
3f6e6e98 RW |
13832 | (properties `((upstream-name . "rJava"))) |
13833 | (build-system r-build-system) | |
13834 | (arguments | |
13835 | `(#:modules ((guix build utils) | |
13836 | (guix build r-build-system) | |
13837 | (ice-9 match)) | |
13838 | #:phases | |
13839 | (modify-phases %standard-phases | |
13840 | (add-after 'unpack 'set-JAVA_HOME | |
13841 | (lambda* (#:key inputs #:allow-other-keys) | |
13842 | (let ((jdk (assoc-ref inputs "jdk"))) | |
13843 | (setenv "JAVA_HOME" jdk) | |
13844 | (setenv "JAVA" (which "java")) | |
13845 | (setenv "JAR" (which "jar")) | |
13846 | (setenv "JAVAC" (which "javac")) | |
13847 | (setenv "JAVAH" (which "javah")) | |
13848 | (setenv "JAVA_CPPFLAGS" | |
13849 | (string-append "-I" jdk "/include " | |
13850 | "-I" jdk "/include/linux")) | |
13851 | (match (find-files (string-append jdk "/jre/lib/") "libjvm.so") | |
13852 | ((lib) (setenv "JAVA_LIBS" lib)) | |
13853 | (_ (error "Could not find libjvm.so")))) | |
13854 | #t))))) | |
13855 | (inputs | |
13856 | `(("icu4c" ,icu4c) | |
13857 | ("jdk" ,icedtea-8 "jdk") | |
13858 | ("pcre" ,pcre) | |
13859 | ("zlib" ,zlib))) | |
13860 | (home-page "http://www.rforge.net/rJava/") | |
13861 | (synopsis "Low-Level R to Java interface") | |
13862 | (description | |
13863 | "This package provides a low-level interface to the Java VM very much | |
13864 | like .C/.Call and friends. It allows the creation of objects, calling methods | |
13865 | and accessing fields.") | |
13866 | (license license:gpl2))) | |
b9b177b3 RW |
13867 | |
13868 | (define-public r-svmisc | |
13869 | (package | |
13870 | (name "r-svmisc") | |
13871 | (version "1.1.0") | |
13872 | (source | |
13873 | (origin | |
13874 | (method url-fetch) | |
13875 | (uri (cran-uri "svMisc" version)) | |
13876 | (sha256 | |
13877 | (base32 | |
13878 | "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2")))) | |
13879 | (properties `((upstream-name . "svMisc"))) | |
13880 | (build-system r-build-system) | |
13881 | (home-page "https://github.com/SciViews/svMisc") | |
13882 | (synopsis "Miscellaneous functions for SciViews") | |
13883 | (description | |
13884 | "This package provides miscellaneous functions for SciViews or general | |
13885 | use, including tools to manage a temporary environment attached to the search | |
13886 | path for temporary variables you do not want to @code{save()} or | |
13887 | @code{load()}; test the current platform; showing progress bars, etc.") | |
13888 | (license license:gpl2))) | |
18c51cf3 RW |
13889 | |
13890 | (define-public r-xyz | |
13891 | (package | |
13892 | (name "r-xyz") | |
13893 | (version "0.2") | |
13894 | (source | |
13895 | (origin | |
13896 | (method url-fetch) | |
13897 | (uri (cran-uri "xyz" version)) | |
13898 | (sha256 | |
13899 | (base32 | |
13900 | "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) | |
13901 | (build-system r-build-system) | |
13902 | (propagated-inputs | |
13903 | `(("r-rcpp" ,r-rcpp))) | |
13904 | (home-page "https://cran.r-project.org/web/packages/xyz/") | |
13905 | (synopsis "Algorithm for fast interaction search in high-dimensional data") | |
13906 | (description | |
13907 | "High dimensional interaction search by brute force requires a quadratic | |
13908 | computational cost in the number of variables. The xyz algorithm provably | |
13909 | finds strong interactions in almost linear time. For details of the algorithm | |
13910 | see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast | |
13911 | interaction search in high-dimensional data.") | |
13912 | ;; Any version of the GPL. | |
13913 | (license license:gpl2+))) | |
81df4e1e RW |
13914 | |
13915 | (define-public r-rttf2pt1 | |
13916 | (package | |
13917 | (name "r-rttf2pt1") | |
13918 | (version "1.3.7") | |
13919 | (source | |
13920 | (origin | |
13921 | (method url-fetch) | |
13922 | (uri (cran-uri "Rttf2pt1" version)) | |
13923 | (sha256 | |
13924 | (base32 | |
13925 | "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja")))) | |
13926 | (properties `((upstream-name . "Rttf2pt1"))) | |
13927 | (build-system r-build-system) | |
13928 | (home-page "https://github.com/wch/Rttf2pt1") | |
13929 | (synopsis "Font conversion utility") | |
13930 | (description | |
13931 | "This package contains the program @code{ttf2pt1}, for use with the | |
13932 | @code{extrafont} package.") | |
13933 | ;; Most of the files are covered under the Expat license. Some files are | |
13934 | ;; covered under BSD-3. Deviations for individual files are recorded in | |
13935 | ;; the LICENSE file. | |
13936 | (license (list license:bsd-3 license:expat | |
13937 | (license:non-copyleft "file://LICENSE"))))) | |
b6933ea6 RW |
13938 | |
13939 | (define-public r-extrafontdb | |
13940 | (package | |
13941 | (name "r-extrafontdb") | |
13942 | (version "1.0") | |
13943 | (source | |
13944 | (origin | |
13945 | (method url-fetch) | |
13946 | (uri (cran-uri "extrafontdb" version)) | |
13947 | (sha256 | |
13948 | (base32 | |
13949 | "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs")))) | |
13950 | (build-system r-build-system) | |
13951 | (home-page "https://github.com/wch/extrafontdb") | |
13952 | (synopsis "Database for the extrafont package") | |
13953 | (description | |
13954 | "This package holds the database for the @code{extrafont} package.") | |
13955 | (license license:gpl2))) | |
2331bf2a RW |
13956 | |
13957 | (define-public r-extrafont | |
13958 | (package | |
13959 | (name "r-extrafont") | |
13960 | (version "0.17") | |
13961 | (source | |
13962 | (origin | |
13963 | (method url-fetch) | |
13964 | (uri (cran-uri "extrafont" version)) | |
13965 | (sha256 | |
13966 | (base32 | |
13967 | "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g")))) | |
13968 | (build-system r-build-system) | |
13969 | (propagated-inputs | |
13970 | `(("r-extrafontdb" ,r-extrafontdb) | |
13971 | ("r-rttf2pt1" ,r-rttf2pt1))) | |
13972 | (home-page "https://github.com/wch/extrafont") | |
13973 | (synopsis "Tools for using fonts in R") | |
13974 | (description | |
13975 | "The extrafont package makes it easier to use fonts other than the basic | |
13976 | PostScript fonts that R uses. Fonts that are imported into extrafont can be | |
13977 | used with PDF or PostScript output files. There are two hurdles for using | |
13978 | fonts in PDF (or Postscript) output files: | |
13979 | ||
13980 | @enumerate | |
13981 | @item Making R aware of the font and the dimensions of the characters. | |
13982 | @item Embedding the fonts in the PDF file so that the PDF can be displayed | |
13983 | properly on a device that doesn't have the font. This is usually needed if | |
13984 | you want to print the PDF file or share it with others. | |
13985 | @end enumerate | |
13986 | ||
13987 | The extrafont package makes both of these things easier.") | |
13988 | (license license:gpl2))) | |
2d704608 RW |
13989 | |
13990 | (define-public r-xkcd | |
13991 | (package | |
13992 | (name "r-xkcd") | |
13993 | (version "0.0.6") | |
13994 | (source | |
13995 | (origin | |
13996 | (method url-fetch) | |
13997 | (uri (cran-uri "xkcd" version)) | |
13998 | (sha256 | |
13999 | (base32 | |
14000 | "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) | |
14001 | (build-system r-build-system) | |
14002 | (propagated-inputs | |
14003 | `(("r-extrafont" ,r-extrafont) | |
14004 | ("r-ggplot2" ,r-ggplot2) | |
14005 | ("r-hmisc" ,r-hmisc))) | |
14006 | (home-page "https://cran.r-project.org/web/packages/xkcd/") | |
14007 | (synopsis "Plot ggplot2 graphics in the XKCD style") | |
14008 | (description | |
14009 | "This package provides the means to plot ggplot2 graphs in the style of | |
14010 | the XKCD web comic.") | |
14011 | (license license:gpl3))) | |
0d50d0df RW |
14012 | |
14013 | (define-public r-msigdbr | |
14014 | (package | |
14015 | (name "r-msigdbr") | |
995a20e8 | 14016 | (version "7.0.1") |
0d50d0df RW |
14017 | (source |
14018 | (origin | |
14019 | (method url-fetch) | |
14020 | (uri (cran-uri "msigdbr" version)) | |
14021 | (sha256 | |
14022 | (base32 | |
995a20e8 | 14023 | "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd")))) |
0d50d0df RW |
14024 | (build-system r-build-system) |
14025 | (propagated-inputs | |
14026 | `(("r-dplyr" ,r-dplyr) | |
14027 | ("r-magrittr" ,r-magrittr) | |
14028 | ("r-rlang" ,r-rlang) | |
14029 | ("r-tibble" ,r-tibble))) | |
14030 | (home-page "https://github.com/igordot/msigdbr") | |
14031 | (synopsis "MSigDB gene sets for multiple organisms") | |
14032 | (description | |
14033 | "This package provides the @dfn{Molecular Signatures Database} (MSigDB) | |
14034 | gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA) | |
14035 | software in a standard R data frame with key-value pairs. Included are the | |
14036 | original human gene symbols and Entrez IDs as well as the equivalents for | |
14037 | various frequently studied model organisms such as mouse, rat, pig, fly, and | |
14038 | yeast.") | |
14039 | ;; The package is covered under the Expat license, but the upstream MSigDB | |
14040 | ;; files are made available under the Creative Commons Attribution 4.0 | |
14041 | ;; International license. | |
14042 | (license (list license:expat license:cc-by4.0)))) | |
585d5ae0 RW |
14043 | |
14044 | (define-public r-gridgraphics | |
14045 | (package | |
14046 | (name "r-gridgraphics") | |
b985cc35 | 14047 | (version "0.4-1") |
585d5ae0 RW |
14048 | (source |
14049 | (origin | |
14050 | (method url-fetch) | |
14051 | (uri (cran-uri "gridGraphics" version)) | |
14052 | (sha256 | |
14053 | (base32 | |
b985cc35 | 14054 | "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p")))) |
585d5ae0 RW |
14055 | (properties `((upstream-name . "gridGraphics"))) |
14056 | (build-system r-build-system) | |
14057 | (home-page "https://github.com/pmur002/gridgraphics") | |
14058 | (synopsis "Redraw base graphics using @code{grid} graphics") | |
14059 | (description | |
14060 | "This package provides functions to convert a page of plots drawn with | |
14061 | the @code{graphics} package into identical output drawn with the @code{grid} | |
14062 | package. The result looks like the original @code{graphics}-based plot, but | |
14063 | consists of @code{grid} grobs and viewports that can then be manipulated with | |
14064 | @code{grid} functions (e.g., edit grobs and revisit viewports).") | |
14065 | (license license:gpl2+))) | |
1c59ec70 RW |
14066 | |
14067 | (define-public r-farver | |
14068 | (package | |
14069 | (name "r-farver") | |
f4061505 | 14070 | (version "2.0.1") |
1c59ec70 RW |
14071 | (source |
14072 | (origin | |
14073 | (method url-fetch) | |
14074 | (uri (cran-uri "farver" version)) | |
14075 | (sha256 | |
14076 | (base32 | |
f4061505 | 14077 | "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn")))) |
1c59ec70 | 14078 | (build-system r-build-system) |
1c59ec70 RW |
14079 | (home-page "https://github.com/thomasp85/farver") |
14080 | (synopsis "Vectorized color conversion and comparison") | |
14081 | (description | |
14082 | "The encoding of color can be handled in many different ways, using | |
14083 | different color spaces. As different color spaces have different uses, | |
14084 | efficient conversion between these representations are important. This | |
14085 | package provides a set of functions that gives access to very fast color space | |
14086 | conversion and comparisons implemented in C++, and offers 100-fold speed | |
14087 | improvements over the @code{convertColor} function in the @code{grDevices} | |
14088 | package.") | |
14089 | (license license:expat))) | |
e2582883 RW |
14090 | |
14091 | (define-public r-ggplotify | |
14092 | (package | |
14093 | (name "r-ggplotify") | |
f2758945 | 14094 | (version "0.0.4") |
e2582883 RW |
14095 | (source |
14096 | (origin | |
14097 | (method url-fetch) | |
14098 | (uri (cran-uri "ggplotify" version)) | |
14099 | (sha256 | |
14100 | (base32 | |
f2758945 | 14101 | "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg")))) |
e2582883 RW |
14102 | (build-system r-build-system) |
14103 | (propagated-inputs | |
14104 | `(("r-ggplot2" ,r-ggplot2) | |
14105 | ("r-gridgraphics" ,r-gridgraphics) | |
14106 | ("r-rvcheck" ,r-rvcheck))) | |
14107 | (home-page "https://github.com/GuangchuangYu/ggplotify") | |
14108 | (synopsis "Convert plots to @code{grob} or @code{ggplot} object") | |
14109 | (description | |
14110 | "This package provides tools to convert plot function calls (using | |
14111 | expression or formula) to @code{grob} or @code{ggplot} objects that are | |
14112 | compatible with the @code{grid} and @code{ggplot2} environment. With this | |
14113 | package, we are able to e.g. use @code{cowplot} to align plots produced by | |
14114 | @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by | |
14115 | converting them to @code{ggplot} objects.") | |
14116 | (license license:artistic2.0))) | |
85431ca3 RW |
14117 | |
14118 | (define-public r-triebeard | |
14119 | (package | |
14120 | (name "r-triebeard") | |
14121 | (version "0.3.0") | |
14122 | (source | |
14123 | (origin | |
14124 | (method url-fetch) | |
14125 | (uri (cran-uri "triebeard" version)) | |
14126 | (sha256 | |
14127 | (base32 | |
14128 | "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) | |
14129 | (build-system r-build-system) | |
14130 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
14131 | (home-page "https://github.com/Ironholds/triebeard/") | |
14132 | (synopsis "Radix trees in Rcpp") | |
14133 | (description | |
14134 | "Radix trees, or tries, are key-value data structures optimized for | |
14135 | efficient lookups, similar in purpose to hash tables. This package provides | |
14136 | an implementation of radix trees for use in R programming and in developing | |
14137 | packages with Rcpp.") | |
14138 | (license license:expat))) | |
91e06bed RW |
14139 | |
14140 | (define-public r-tweenr | |
14141 | (package | |
14142 | (name "r-tweenr") | |
14143 | (version "1.0.1") | |
14144 | (source | |
14145 | (origin | |
14146 | (method url-fetch) | |
14147 | (uri (cran-uri "tweenr" version)) | |
14148 | (sha256 | |
14149 | (base32 | |
14150 | "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg")))) | |
14151 | (build-system r-build-system) | |
14152 | (propagated-inputs | |
14153 | `(("r-farver" ,r-farver) | |
14154 | ("r-magrittr" ,r-magrittr) | |
14155 | ("r-rcpp" ,r-rcpp) | |
14156 | ("r-rlang" ,r-rlang))) | |
14157 | (home-page "https://github.com/thomasp85/tweenr") | |
14158 | (synopsis "Interpolate data for smooth animations") | |
14159 | (description | |
14160 | "In order to create smooth animation between states of data, tweening is | |
14161 | necessary. This package provides a range of functions for creating tweened | |
14162 | data that can be used as basis for animation. Furthermore it adds a number of | |
14163 | vectorized interpolaters for common R data types such as numeric, date and | |
14164 | color.") | |
14165 | (license license:expat))) | |
09dde7fb RW |
14166 | |
14167 | (define-public r-polyclip | |
14168 | (package | |
14169 | (name "r-polyclip") | |
14170 | (version "1.10-0") | |
14171 | (source | |
14172 | (origin | |
14173 | (method url-fetch) | |
14174 | (uri (cran-uri "polyclip" version)) | |
14175 | (sha256 | |
14176 | (base32 | |
14177 | "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl")))) | |
14178 | (build-system r-build-system) | |
14179 | (native-inputs `(("pkg-config" ,pkg-config))) | |
14180 | (home-page "http://www.angusj.com/delphi/clipper.php") | |
14181 | (synopsis "Polygon clipping") | |
14182 | (description | |
14183 | "This package provides an R port of the library Clipper. It performs | |
14184 | polygon clipping operations (intersection, union, set minus, set difference) | |
14185 | for polygonal regions of arbitrary complexity, including holes. It computes | |
14186 | offset polygons (spatial buffer zones, morphological dilations, Minkowski | |
14187 | dilations) for polygonal regions and polygonal lines. It computes the | |
14188 | Minkowski Sum of general polygons. There is a function for removing | |
14189 | self-intersections from polygon data.") | |
14190 | (license license:boost1.0))) | |
d4ff09af RW |
14191 | |
14192 | (define-public r-urltools | |
14193 | (package | |
14194 | (name "r-urltools") | |
7015ae68 | 14195 | (version "1.7.3") |
d4ff09af RW |
14196 | (source |
14197 | (origin | |
14198 | (method url-fetch) | |
14199 | (uri (cran-uri "urltools" version)) | |
14200 | (sha256 | |
14201 | (base32 | |
7015ae68 | 14202 | "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830")))) |
d4ff09af RW |
14203 | (build-system r-build-system) |
14204 | (propagated-inputs | |
14205 | `(("r-rcpp" ,r-rcpp) | |
14206 | ("r-triebeard" ,r-triebeard))) | |
14207 | (home-page "https://github.com/Ironholds/urltools/") | |
14208 | (synopsis "Vectorized tools for URL handling and parsing") | |
14209 | (description | |
14210 | "This package provides a toolkit for all URL-handling needs, including | |
14211 | encoding and decoding, parsing, parameter extraction and modification. All | |
14212 | functions are designed to be both fast and entirely vectorized. It is | |
14213 | intended to be useful for people dealing with web-related datasets, such as | |
14214 | server-side logs, although may be useful for other situations involving large | |
14215 | sets of URLs.") | |
14216 | (license license:expat))) | |
83f43284 RW |
14217 | |
14218 | (define-public r-ggforce | |
14219 | (package | |
14220 | (name "r-ggforce") | |
466e68b4 | 14221 | (version "0.3.1") |
83f43284 RW |
14222 | (source |
14223 | (origin | |
14224 | (method url-fetch) | |
14225 | (uri (cran-uri "ggforce" version)) | |
14226 | (sha256 | |
14227 | (base32 | |
466e68b4 | 14228 | "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0")))) |
83f43284 RW |
14229 | (build-system r-build-system) |
14230 | (propagated-inputs | |
14231 | `(("r-ggplot2" ,r-ggplot2) | |
14232 | ("r-gtable" ,r-gtable) | |
14233 | ("r-mass" ,r-mass) | |
14234 | ("r-polyclip" ,r-polyclip) | |
14235 | ("r-rcpp" ,r-rcpp) | |
14236 | ("r-rcppeigen" ,r-rcppeigen) | |
14237 | ("r-rlang" ,r-rlang) | |
14238 | ("r-scales" ,r-scales) | |
3ea54829 RW |
14239 | ("r-tidyselect" ,r-tidyselect) |
14240 | ("r-tweenr" ,r-tweenr) | |
14241 | ("r-withr" ,r-withr))) | |
83f43284 RW |
14242 | (home-page "https://ggforce.data-imaginist.com") |
14243 | (synopsis "Accelerating ggplot2") | |
14244 | (description | |
14245 | "The aim of the ggplot2 package is to aid in visual data investigations. | |
14246 | This focus has led to a lack of facilities for composing specialized plots. | |
14247 | Thi package aims to be a collection of mainly new statistics and geometries | |
14248 | that fills this gap.") | |
14249 | (license license:expat))) | |
b5b0a2ff RW |
14250 | |
14251 | (define-public r-europepmc | |
14252 | (package | |
14253 | (name "r-europepmc") | |
14254 | (version "0.3") | |
14255 | (source | |
14256 | (origin | |
14257 | (method url-fetch) | |
14258 | (uri (cran-uri "europepmc" version)) | |
14259 | (sha256 | |
14260 | (base32 | |
14261 | "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h")))) | |
14262 | (build-system r-build-system) | |
14263 | (propagated-inputs | |
14264 | `(("r-dplyr" ,r-dplyr) | |
14265 | ("r-httr" ,r-httr) | |
14266 | ("r-jsonlite" ,r-jsonlite) | |
14267 | ("r-plyr" ,r-plyr) | |
14268 | ("r-progress" ,r-progress) | |
14269 | ("r-purrr" ,r-purrr) | |
14270 | ("r-urltools" ,r-urltools) | |
14271 | ("r-xml2" ,r-xml2))) | |
14272 | (home-page "https://github.com/ropensci/europepmc/") | |
14273 | (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") | |
14274 | (description | |
14275 | "This package provides an R Client for the | |
14276 | @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web | |
14277 | Service}. It gives access to both metadata on life science literature and | |
14278 | open access full texts. Europe PMC indexes all PubMed content and other | |
14279 | literature sources including Agricola, a bibliographic database of citations | |
14280 | to the agricultural literature, or Biological Patents. In addition to | |
14281 | bibliographic metadata, the client allows users to fetch citations and | |
14282 | reference lists. Links between life-science literature and other EBI | |
14283 | databases, including ENA, PDB or ChEMBL are also accessible.") | |
14284 | (license license:gpl3))) | |
11f226e1 RW |
14285 | |
14286 | (define-public r-ggraph | |
14287 | (package | |
14288 | (name "r-ggraph") | |
801dc98f | 14289 | (version "2.0.0") |
11f226e1 RW |
14290 | (source |
14291 | (origin | |
14292 | (method url-fetch) | |
14293 | (uri (cran-uri "ggraph" version)) | |
14294 | (sha256 | |
14295 | (base32 | |
801dc98f | 14296 | "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3")))) |
11f226e1 RW |
14297 | (build-system r-build-system) |
14298 | (propagated-inputs | |
14299 | `(("r-digest" ,r-digest) | |
14300 | ("r-dplyr" ,r-dplyr) | |
14301 | ("r-ggforce" ,r-ggforce) | |
14302 | ("r-ggplot2" ,r-ggplot2) | |
14303 | ("r-ggrepel" ,r-ggrepel) | |
801dc98f | 14304 | ("r-graphlayouts" ,r-graphlayouts) |
11f226e1 RW |
14305 | ("r-gtable" ,r-gtable) |
14306 | ("r-igraph" ,r-igraph) | |
14307 | ("r-mass" ,r-mass) | |
11f226e1 | 14308 | ("r-rcpp" ,r-rcpp) |
801dc98f | 14309 | ("r-rlang" ,r-rlang) |
11f226e1 | 14310 | ("r-scales" ,r-scales) |
801dc98f | 14311 | ("r-tidygraph" ,r-tidygraph) |
11f226e1 RW |
14312 | ("r-viridis" ,r-viridis))) |
14313 | (home-page "https://cran.r-project.org/web/packages/ggraph/") | |
14314 | (synopsis "Implementation of grammar of graphics for graphs and networks") | |
14315 | (description | |
14316 | "The grammar of graphics as implemented in ggplot2 is a poor fit for | |
14317 | graph and network visualizations due to its reliance on tabular data input. | |
14318 | The ggraph package is an extension of the ggplot2 API tailored to graph | |
14319 | visualizations and provides the same flexible approach to building up plots | |
14320 | layer by layer.") | |
14321 | (license license:gpl3))) | |
1c0c4b54 RW |
14322 | |
14323 | (define-public r-varselrf | |
14324 | (package | |
14325 | (name "r-varselrf") | |
14326 | (version "0.7-8") | |
14327 | (source | |
14328 | (origin | |
14329 | (method url-fetch) | |
14330 | (uri (cran-uri "varSelRF" version)) | |
14331 | (sha256 | |
14332 | (base32 | |
14333 | "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i")))) | |
14334 | (properties `((upstream-name . "varSelRF"))) | |
14335 | (build-system r-build-system) | |
14336 | (propagated-inputs | |
14337 | `(("r-randomforest" ,r-randomforest))) | |
14338 | (home-page "http://ligarto.org/rdiaz/Software/Software.html") | |
14339 | (synopsis "Variable selection using random forests") | |
14340 | (description | |
14341 | "This package provides tools for the variable selection from random | |
14342 | forests using both backwards variable elimination (for the selection of small | |
14343 | sets of non-redundant variables) and selection based on the importance | |
14344 | spectrum (somewhat similar to scree plots; for the selection of large, | |
14345 | potentially highly-correlated variables). The main applications are in | |
14346 | high-dimensional data (e.g., microarray data, and other genomics and | |
14347 | proteomics applications).") | |
14348 | (license license:gpl2+))) | |
aae0b86d RW |
14349 | |
14350 | (define-public r-pamr | |
14351 | (package | |
14352 | (name "r-pamr") | |
8fc6188e | 14353 | (version "1.56.1") |
aae0b86d RW |
14354 | (source |
14355 | (origin | |
14356 | (method url-fetch) | |
14357 | (uri (cran-uri "pamr" version)) | |
14358 | (sha256 | |
14359 | (base32 | |
8fc6188e | 14360 | "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) |
aae0b86d RW |
14361 | (build-system r-build-system) |
14362 | (propagated-inputs | |
14363 | `(("r-cluster" ,r-cluster) | |
14364 | ("r-survival" ,r-survival))) | |
14365 | (native-inputs `(("gfortran" ,gfortran))) | |
14366 | (home-page "https://cran.r-project.org/web/packages/pamr/") | |
14367 | (synopsis "Prediction Analysis for Microarrays") | |
14368 | (description | |
14369 | "This package provides some functions for sample classification in | |
14370 | microarrays.") | |
14371 | (license license:gpl2))) | |
fe3fb4e7 RW |
14372 | |
14373 | (define-public r-rda | |
14374 | (package | |
14375 | (name "r-rda") | |
14376 | (version "1.0.2-2.1") | |
14377 | (source | |
14378 | (origin | |
14379 | (method url-fetch) | |
14380 | (uri (cran-uri "rda" version)) | |
14381 | (sha256 | |
14382 | (base32 | |
14383 | "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639")))) | |
14384 | (build-system r-build-system) | |
14385 | (home-page "https://cran.r-project.org/web/packages/rda/") | |
14386 | (synopsis "Shrunken centroids regularized discriminant analysis") | |
14387 | (description | |
14388 | "This package provides tools for shrunken centroids regularized | |
14389 | discriminant analysis for the purpose of classifying high dimensional data.") | |
14390 | (license license:gpl2+))) | |
8473597f RW |
14391 | |
14392 | (define-public r-ggvis | |
14393 | (package | |
14394 | (name "r-ggvis") | |
04eb73ee | 14395 | (version "0.4.5") |
8473597f RW |
14396 | (source |
14397 | (origin | |
14398 | (method url-fetch) | |
14399 | (uri (cran-uri "ggvis" version)) | |
14400 | (sha256 | |
14401 | (base32 | |
04eb73ee | 14402 | "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2")))) |
8473597f RW |
14403 | (build-system r-build-system) |
14404 | (propagated-inputs | |
14405 | `(("r-assertthat" ,r-assertthat) | |
14406 | ("r-dplyr" ,r-dplyr) | |
14407 | ("r-htmltools" ,r-htmltools) | |
14408 | ("r-jsonlite" ,r-jsonlite) | |
14409 | ("r-lazyeval" ,r-lazyeval) | |
14410 | ("r-magrittr" ,r-magrittr) | |
14411 | ("r-shiny" ,r-shiny))) | |
14412 | (home-page "https://ggvis.rstudio.com/") | |
14413 | (synopsis "Interactive grammar of graphics") | |
14414 | (description | |
14415 | "This package is a data visualization package for R providing an | |
14416 | implementation of an interactive grammar of graphics, taking the best parts of | |
14417 | ggplot2, combining them with the reactive framework of Shiny and drawing web | |
14418 | graphics using Vega.") | |
14419 | (license license:gpl2))) | |
d59df334 RW |
14420 | |
14421 | (define-public r-gbm | |
14422 | (package | |
14423 | (name "r-gbm") | |
14424 | (version "2.1.5") | |
14425 | (source | |
14426 | (origin | |
14427 | (method url-fetch) | |
14428 | (uri (cran-uri "gbm" version)) | |
14429 | (sha256 | |
14430 | (base32 | |
14431 | "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6")))) | |
14432 | (build-system r-build-system) | |
14433 | (propagated-inputs | |
14434 | `(("r-gridextra" ,r-gridextra) | |
14435 | ("r-lattice" ,r-lattice) | |
14436 | ("r-survival" ,r-survival))) | |
14437 | (home-page "https://github.com/gbm-developers/gbm") | |
14438 | (synopsis "Generalized boosted regression models") | |
14439 | (description | |
14440 | "This package is an implementation of extensions to Freund and Schapire's | |
14441 | AdaBoost algorithm and Friedman's gradient boosting machine. It includes | |
14442 | regression methods for least squares, absolute loss, t-distribution loss, | |
14443 | quantile regression, logistic, multinomial logistic, Poisson, Cox proportional | |
14444 | hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, | |
14445 | and Learning to Rank measures (LambdaMart).") | |
14446 | (license license:gpl2+))) | |
efba5613 RW |
14447 | |
14448 | (define-public r-threejs | |
14449 | (package | |
14450 | (name "r-threejs") | |
14451 | (version "0.3.1") | |
14452 | (source | |
14453 | (origin | |
14454 | (method url-fetch) | |
14455 | (uri (cran-uri "threejs" version)) | |
14456 | (sha256 | |
14457 | (base32 | |
14458 | "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi")))) | |
14459 | (build-system r-build-system) | |
14460 | (arguments | |
14461 | `(#:modules ((guix build utils) | |
14462 | (guix build r-build-system) | |
14463 | (srfi srfi-1) | |
14464 | (ice-9 popen)) | |
14465 | #:phases | |
14466 | (modify-phases %standard-phases | |
14467 | (add-after 'unpack 'process-javascript | |
14468 | (lambda* (#:key inputs #:allow-other-keys) | |
14469 | (with-directory-excursion "inst" | |
14470 | (call-with-values | |
14471 | (lambda () | |
14472 | (unzip2 | |
14473 | `((,(assoc-ref inputs "js-jquery") | |
14474 | "htmlwidgets/lib/jquery/jquery.min.js") | |
14475 | (,(assoc-ref inputs "js-threejs-85") | |
14476 | "htmlwidgets/lib/threejs-85/three.min.js")))) | |
14477 | (lambda (sources targets) | |
14478 | (for-each (lambda (source target) | |
14479 | (format #t "Processing ~a --> ~a~%" | |
14480 | source target) | |
14481 | (delete-file target) | |
14482 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
14483 | (call-with-output-file target | |
14484 | (lambda (port) | |
14485 | (dump-port minified port))))) | |
14486 | sources targets)))) | |
14487 | #t))))) | |
14488 | (propagated-inputs | |
14489 | `(("r-base64enc" ,r-base64enc) | |
14490 | ("r-crosstalk" ,r-crosstalk) | |
14491 | ("r-htmlwidgets" ,r-htmlwidgets) | |
14492 | ("r-igraph" ,r-igraph))) | |
14493 | (native-inputs | |
14494 | `(("uglify-js" ,uglify-js) | |
14495 | ("js-jquery" | |
14496 | ,(origin | |
14497 | (method url-fetch) | |
14498 | (uri "https://code.jquery.com/jquery-3.3.1.js") | |
14499 | (sha256 | |
14500 | (base32 | |
14501 | "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) | |
14502 | ("js-threejs-85" | |
14503 | ,(origin | |
14504 | (method url-fetch) | |
14505 | (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js") | |
14506 | (sha256 | |
14507 | (base32 | |
14508 | "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl")))))) | |
14509 | (home-page "https://bwlewis.github.io/rthreejs") | |
14510 | (synopsis "Interactive 3D scatter plots, networks and globes") | |
14511 | (description | |
14512 | "Create interactive 3D scatter plots, network plots, and globes in R | |
14513 | using the three.js visualization library.") | |
14514 | (license license:expat))) | |
74cada8e RW |
14515 | |
14516 | (define-public r-mlbench | |
14517 | (package | |
14518 | (name "r-mlbench") | |
14519 | (version "2.1-1") | |
14520 | (source | |
14521 | (origin | |
14522 | (method url-fetch) | |
14523 | (uri (cran-uri "mlbench" version)) | |
14524 | (sha256 | |
14525 | (base32 | |
14526 | "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl")))) | |
14527 | (build-system r-build-system) | |
14528 | (home-page "https://cran.r-project.org/web/packages/mlbench/") | |
14529 | (synopsis "Machine learning benchmark problems") | |
14530 | (description | |
14531 | "This package provides a collection of artificial and real-world machine | |
14532 | learning benchmark problems, including, e.g., several data sets from the UCI | |
14533 | repository.") | |
14534 | (license license:gpl2))) | |
409a13fe RW |
14535 | |
14536 | (define-public r-mpm | |
14537 | (package | |
14538 | (name "r-mpm") | |
14539 | (version "1.0-22") | |
14540 | (source | |
14541 | (origin | |
14542 | (method url-fetch) | |
14543 | (uri (cran-uri "mpm" version)) | |
14544 | (sha256 | |
14545 | (base32 | |
14546 | "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk")))) | |
14547 | (build-system r-build-system) | |
14548 | (propagated-inputs | |
14549 | `(("r-kernsmooth" ,r-kernsmooth) | |
14550 | ("r-mass" ,r-mass))) | |
14551 | (home-page "http://mpm.r-forge.r-project.org") | |
14552 | (synopsis "Multivariate projection methods") | |
14553 | (description | |
14554 | "This is a package for exploratory graphical analysis of multivariate | |
14555 | data, specifically gene expression data with different projection methods: | |
14556 | principal component analysis, correspondence analysis, spectral map | |
14557 | analysis.") | |
14558 | (license license:gpl2+))) | |
d8a28332 | 14559 | |
d2aa2d24 RW |
14560 | (define-public r-png |
14561 | (package | |
14562 | (name "r-png") | |
14563 | (version "0.1-7") | |
14564 | (source (origin | |
14565 | (method url-fetch) | |
14566 | (uri (cran-uri "png" version)) | |
14567 | (sha256 | |
14568 | (base32 | |
14569 | "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) | |
14570 | (build-system r-build-system) | |
14571 | (inputs | |
14572 | `(("libpng" ,libpng) | |
14573 | ("zlib" ,zlib))) | |
14574 | (home-page "http://www.rforge.net/png/") | |
14575 | (synopsis "Read and write PNG images") | |
14576 | (description | |
14577 | "This package provides an easy and simple way to read, write and display | |
14578 | bitmap images stored in the PNG format. It can read and write both files and | |
14579 | in-memory raw vectors.") | |
14580 | ;; Any of these GPL versions. | |
14581 | (license (list license:gpl2 license:gpl3)))) | |
14582 | ||
d8a28332 RW |
14583 | (define-public r-ggcorrplot |
14584 | (package | |
14585 | (name "r-ggcorrplot") | |
e9c526be | 14586 | (version "0.1.3") |
d8a28332 RW |
14587 | (source |
14588 | (origin | |
14589 | (method url-fetch) | |
14590 | (uri (cran-uri "ggcorrplot" version)) | |
14591 | (sha256 | |
14592 | (base32 | |
e9c526be | 14593 | "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b")))) |
d8a28332 RW |
14594 | (build-system r-build-system) |
14595 | (propagated-inputs | |
14596 | `(("r-ggplot2" ,r-ggplot2) | |
14597 | ("r-reshape2" ,r-reshape2))) | |
14598 | (home-page "http://www.sthda.com/english/wiki/ggcorrplot") | |
14599 | (synopsis "Visualization of a correlation matrix using ggplot2") | |
14600 | (description | |
14601 | "The ggcorrplot package can be used to visualize easily a correlation | |
14602 | matrix using ggplot2. It provides a solution for reordering the correlation | |
14603 | matrix and displays the significance level on the plot. It also includes a | |
14604 | function for computing a matrix of correlation p-values.") | |
14605 | (license license:gpl2))) | |
f084e41e RW |
14606 | |
14607 | (define-public r-flexdashboard | |
14608 | (package | |
14609 | (name "r-flexdashboard") | |
14610 | (version "0.5.1.1") | |
14611 | (source | |
14612 | (origin | |
14613 | (method url-fetch) | |
14614 | (uri (cran-uri "flexdashboard" version)) | |
14615 | (sha256 | |
14616 | (base32 | |
14617 | "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x")))) | |
14618 | (build-system r-build-system) | |
14619 | (arguments | |
14620 | `(#:modules ((guix build utils) | |
14621 | (guix build r-build-system) | |
14622 | (srfi srfi-1) | |
14623 | (srfi srfi-26) | |
14624 | (ice-9 popen) | |
14625 | (ice-9 textual-ports)) | |
14626 | #:phases | |
14627 | (modify-phases %standard-phases | |
14628 | (add-after 'unpack 'process-javascript | |
14629 | (lambda* (#:key inputs #:allow-other-keys) | |
14630 | (with-directory-excursion "inst" | |
14631 | ;; Concatenate all components of prism.js | |
14632 | (let ((contents (string-join | |
14633 | (map (lambda (name) | |
14634 | (call-with-input-file | |
14635 | (assoc-ref inputs name) | |
14636 | get-string-all)) | |
14637 | (list "js-prism" | |
14638 | "js-prism-r" | |
14639 | "js-prism-line-numbers")) | |
14640 | "\n"))) | |
14641 | (call-with-output-file "prism-src.js" | |
14642 | (cut display contents <>))) | |
14643 | (call-with-values | |
14644 | (lambda () | |
14645 | (unzip2 | |
14646 | `(("www/stickytableheaders/jquery.stickytableheaders.js" | |
14647 | "www/stickytableheaders/jquery.stickytableheaders.min.js") | |
14648 | ("www/sly/sly.js" | |
14649 | "www/sly/sly.min.js") | |
14650 | ("prism-src.js" | |
14651 | "www/prism/prism.js") | |
14652 | (,(assoc-ref inputs "js-raphael") | |
14653 | "htmlwidgets/lib/raphael/raphael-2.1.4.min.js") | |
14654 | (,(assoc-ref inputs "js-featherlight") | |
14655 | "www/featherlight/featherlight.min.js")))) | |
14656 | (lambda (sources targets) | |
14657 | (for-each (lambda (source target) | |
14658 | (format #t "Processing ~a --> ~a~%" | |
14659 | source target) | |
14660 | (delete-file target) | |
14661 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
14662 | (call-with-output-file target | |
14663 | (lambda (port) | |
14664 | (dump-port minified port))))) | |
14665 | sources targets)))) | |
14666 | #t))))) | |
14667 | (propagated-inputs | |
14668 | `(("r-htmltools" ,r-htmltools) | |
14669 | ("r-htmlwidgets" ,r-htmlwidgets) | |
14670 | ("r-jsonlite" ,r-jsonlite) | |
14671 | ("r-knitr" ,r-knitr) | |
14672 | ("r-rmarkdown" ,r-rmarkdown) | |
14673 | ("r-shiny" ,r-shiny))) | |
14674 | (native-inputs | |
14675 | `(("uglify-js" ,uglify-js) | |
14676 | ("js-raphael" | |
14677 | ,(origin | |
14678 | (method url-fetch) | |
14679 | (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js") | |
14680 | (sha256 | |
14681 | (base32 | |
14682 | "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x")))) | |
14683 | ("js-prism" | |
14684 | ,(origin | |
14685 | (method url-fetch) | |
14686 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js") | |
14687 | (sha256 | |
14688 | (base32 | |
14689 | "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c")))) | |
14690 | ("js-prism-r" | |
14691 | ,(origin | |
14692 | (method url-fetch) | |
14693 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js") | |
14694 | (sha256 | |
14695 | (base32 | |
14696 | "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki")))) | |
14697 | ("js-prism-line-numbers" | |
14698 | ,(origin | |
14699 | (method url-fetch) | |
14700 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js") | |
14701 | (sha256 | |
14702 | (base32 | |
14703 | "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991")))) | |
14704 | ("js-featherlight" | |
14705 | ,(origin | |
14706 | (method url-fetch) | |
14707 | (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js") | |
14708 | (sha256 | |
14709 | (base32 | |
14710 | "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb")))))) | |
14711 | (home-page "https://rmarkdown.rstudio.com/flexdashboard") | |
14712 | (synopsis "R Markdown format for flexible dashboards") | |
14713 | (description | |
14714 | "This package provides an R Markdown format for converting an R Markdown | |
14715 | document to a grid-oriented dashboard. The dashboard flexibly adapts the size | |
14716 | of its components to the containing web page.") | |
14717 | (license license:expat))) | |
c54ab337 RW |
14718 | |
14719 | (define-public r-preseqr | |
14720 | (package | |
14721 | (name "r-preseqr") | |
14722 | (version "4.0.0") | |
14723 | (source | |
14724 | (origin | |
14725 | (method url-fetch) | |
14726 | (uri (cran-uri "preseqR" version)) | |
14727 | (sha256 | |
14728 | (base32 | |
14729 | "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1")))) | |
14730 | (properties `((upstream-name . "preseqR"))) | |
14731 | (build-system r-build-system) | |
14732 | (propagated-inputs | |
14733 | `(("r-polynom" ,r-polynom))) | |
14734 | (home-page "https://cran.r-project.org/web/packages/preseqR/") | |
14735 | (synopsis "Predicting species accumulation curves") | |
14736 | (description | |
14737 | "This package can be used to predict the r-species accumulation | |
14738 | curve (r-SAC), which is the number of species represented at least r times as | |
14739 | a function of the sampling effort. When r = 1, the curve is known as the | |
14740 | species accumulation curve, or the library complexity curve in high-throughput | |
14741 | genomic sequencing. The package includes both parametric and nonparametric | |
14742 | methods, as described by Deng C, et al. (2018).") | |
14743 | (license license:gpl3))) | |
1fab2cf8 RW |
14744 | |
14745 | (define-public r-mapplots | |
14746 | (package | |
14747 | (name "r-mapplots") | |
14748 | (version "1.5.1") | |
14749 | (source | |
14750 | (origin | |
14751 | (method url-fetch) | |
14752 | (uri (cran-uri "mapplots" version)) | |
14753 | (sha256 | |
14754 | (base32 | |
14755 | "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p")))) | |
14756 | (build-system r-build-system) | |
14757 | (home-page "https://cran.r-project.org/web/packages/mapplots/") | |
14758 | (synopsis "Data visualization on maps") | |
14759 | (description | |
14760 | "This package helps you create simple maps; add sub-plots like pie plots | |
14761 | to a map or any other plot; format, plot and export gridded data. The package | |
14762 | was developed for displaying fisheries data but most functions can be used for | |
14763 | more generic data visualisation.") | |
14764 | (license license:gpl2+))) | |
9563dd55 RW |
14765 | |
14766 | (define-public r-pmcmr | |
14767 | (package | |
14768 | (name "r-pmcmr") | |
14769 | (version "4.3") | |
14770 | (source | |
14771 | (origin | |
14772 | (method url-fetch) | |
14773 | (uri (cran-uri "PMCMR" version)) | |
14774 | (sha256 | |
14775 | (base32 | |
14776 | "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij")))) | |
14777 | (properties `((upstream-name . "PMCMR"))) | |
14778 | (build-system r-build-system) | |
14779 | (home-page "https://cran.r-project.org/web/packages/PMCMR/") | |
14780 | (synopsis "Calculate pairwise multiple comparisons of mean rank sums") | |
14781 | (description | |
14782 | "This is a deprecated package for calculating pairwise multiple | |
14783 | comparisons of mean rank sums. This package is superseded by the novel | |
14784 | PMCMRplus package. The PMCMR package is no longer maintained, but kept for | |
c8ae38d3 | 14785 | compatibility of dependent packages for some time.") |
9563dd55 | 14786 | (license license:gpl3+))) |
8d1990d4 RW |
14787 | |
14788 | (define-public r-downloader | |
14789 | (package | |
14790 | (name "r-downloader") | |
14791 | (version "0.4") | |
14792 | (source | |
14793 | (origin | |
14794 | (method url-fetch) | |
14795 | (uri (cran-uri "downloader" version)) | |
14796 | (sha256 | |
14797 | (base32 | |
14798 | "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q")))) | |
14799 | (build-system r-build-system) | |
14800 | (propagated-inputs | |
14801 | `(("r-digest" ,r-digest))) | |
14802 | (home-page "https://github.com/wch/downloader") | |
14803 | (synopsis "Download files over HTTP and HTTPS") | |
14804 | (description | |
14805 | "This package provides a wrapper for the @code{download.file} function, | |
14806 | making it possible to download files over HTTPS across platforms. The | |
14807 | @code{RCurl} package provides this functionality (and much more) but has | |
14808 | external dependencies. This package has is implemented purely in R.") | |
14809 | (license license:gpl2))) | |
296ea15c NB |
14810 | |
14811 | (define-public r-rex | |
14812 | (package | |
14813 | (name "r-rex") | |
14814 | (version "1.1.2") | |
14815 | (source | |
14816 | (origin | |
14817 | (method url-fetch) | |
14818 | (uri (cran-uri "rex" version)) | |
14819 | (sha256 | |
14820 | (base32 | |
14821 | "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x")))) | |
14822 | (build-system r-build-system) | |
14823 | (propagated-inputs | |
14824 | `(("r-lazyeval" ,r-lazyeval) | |
14825 | ("r-magrittr" ,r-magrittr))) | |
14826 | (home-page "https://github.com/kevinushey/rex") | |
14827 | (synopsis "Friendly regular expressions") | |
14828 | (description | |
14829 | "This package provides a friendly interface for the construction of | |
14830 | regular expressions. Regular expressions are a very powerful feature, however | |
14831 | they are often difficult to interpret. Rex allows you to build complex | |
14832 | regular expressions from human readable expressions") | |
14833 | (license license:expat))) | |
9b86fea0 | 14834 | |
f00da074 NB |
14835 | (define-public r-xmlparsedata |
14836 | (package | |
14837 | (name "r-xmlparsedata") | |
14838 | (version "1.0.3") | |
14839 | (source | |
14840 | (origin | |
14841 | (method url-fetch) | |
14842 | (uri (cran-uri "xmlparsedata" version)) | |
14843 | (sha256 | |
14844 | (base32 | |
14845 | "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh")))) | |
14846 | (properties `((upstream-name . "xmlparsedata"))) | |
14847 | (build-system r-build-system) | |
14848 | (home-page "https://github.com/r-lib/xmlparsedata#readme") | |
14849 | (synopsis "Parse data of @code{R} code as an @code{XML} tree") | |
14850 | (description | |
14851 | "This package provides tools to convert the output of | |
14852 | @code{utils::getParseData()} to an @code{XML} tree, that one can search via | |
14853 | @code{XPath}, and is easier to manipulate in general.") | |
14854 | (license license:expat))) | |
14855 | ||
bd538a03 NB |
14856 | (define-public r-cyclocomp |
14857 | (package | |
14858 | (name "r-cyclocomp") | |
14859 | (version "1.1.0") | |
14860 | (source | |
14861 | (origin | |
14862 | (method url-fetch) | |
14863 | (uri (cran-uri "cyclocomp" version)) | |
14864 | (sha256 | |
14865 | (base32 | |
14866 | "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd")))) | |
14867 | (properties `((upstream-name . "cyclocomp"))) | |
14868 | (build-system r-build-system) | |
14869 | (propagated-inputs | |
14870 | `(("r-callr" ,r-callr) | |
14871 | ("r-crayon" ,r-crayon) | |
14872 | ("r-desc" ,r-desc) | |
14873 | ("r-remotes" ,r-remotes) | |
14874 | ("r-withr" ,r-withr))) | |
14875 | (home-page "https://github.com/MangoTheCat/cyclocomp") | |
14876 | (synopsis "Cyclomatic complexity of R code") | |
14877 | (description | |
14878 | "Cyclomatic complexity is a software metric, used to indicate the | |
14879 | complexity of a program. It is a quantitative measure of the number of | |
14880 | linearly independent paths through a program's source code. This package | |
14881 | provides tools to compute this metric.") | |
14882 | (license license:expat))) | |
14883 | ||
6c3021a8 NB |
14884 | (define-public r-lintr |
14885 | (package | |
14886 | (name "r-lintr") | |
14887 | (version "2.0.0") | |
14888 | (source | |
14889 | (origin | |
14890 | (method url-fetch) | |
14891 | (uri (cran-uri "lintr" version)) | |
14892 | (sha256 | |
14893 | (base32 | |
14894 | "09gbci4v5n4gsfzminly8332fw7faxdi1kkyvpa10dydx02sjcwb")))) | |
14895 | (properties `((upstream-name . "lintr"))) | |
14896 | (build-system r-build-system) | |
14897 | (propagated-inputs | |
14898 | `(("r-codetools" ,r-codetools) | |
14899 | ("r-crayon" ,r-crayon) | |
14900 | ("r-cyclocomp" ,r-cyclocomp) | |
14901 | ("r-digest" ,r-digest) | |
14902 | ("r-httr" ,r-httr) | |
14903 | ("r-jsonlite" ,r-jsonlite) | |
14904 | ("r-knitr" ,r-knitr) | |
14905 | ("r-rex" ,r-rex) | |
14906 | ("r-rstudioapi" ,r-rstudioapi) | |
14907 | ("r-stringdist" ,r-stringdist) | |
14908 | ("r-testthat" ,r-testthat) | |
14909 | ("r-xml2" ,r-xml2) | |
14910 | ("r-xmlparsedata" ,r-xmlparsedata))) | |
14911 | (home-page "https://github.com/jimhester/lintr") | |
14912 | (synopsis "Linter for R code") | |
14913 | (description "This package checks adherence to a given style, syntax | |
14914 | errors and possible semantic issues. It supports on the fly checking of R | |
14915 | code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") | |
14916 | (license license:expat))) | |
14917 | ||
9b86fea0 RW |
14918 | (define-public r-sctransform |
14919 | (package | |
14920 | (name "r-sctransform") | |
20622ad1 | 14921 | (version "0.2.1") |
9b86fea0 RW |
14922 | (source |
14923 | (origin | |
14924 | (method url-fetch) | |
14925 | (uri (cran-uri "sctransform" version)) | |
14926 | (sha256 | |
14927 | (base32 | |
20622ad1 | 14928 | "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn")))) |
9b86fea0 RW |
14929 | (build-system r-build-system) |
14930 | (propagated-inputs | |
20622ad1 | 14931 | `(("r-future-apply" ,r-future-apply) |
9b86fea0 RW |
14932 | ("r-ggplot2" ,r-ggplot2) |
14933 | ("r-gridextra" ,r-gridextra) | |
14934 | ("r-mass" ,r-mass) | |
14935 | ("r-matrix" ,r-matrix) | |
14936 | ("r-rcpp" ,r-rcpp) | |
14937 | ("r-rcppeigen" ,r-rcppeigen) | |
14938 | ("r-reshape2" ,r-reshape2))) | |
14939 | (home-page "https://github.com/ChristophH/sctransform") | |
14940 | (synopsis "Variance stabilizing transformations for Single Cell UMI Data") | |
14941 | (description | |
14942 | "This package provides a normalization method for single-cell UMI count | |
14943 | data using a variance stabilizing transformation. The transformation is based | |
14944 | on a negative binomial regression model with regularized parameters. As part | |
14945 | of the same regression framework, this package also provides functions for | |
14946 | batch correction, and data correction.") | |
14947 | (license license:gpl3))) | |
107850b3 NB |
14948 | |
14949 | (define-public r-styler | |
14950 | (package | |
14951 | (name "r-styler") | |
67b7a379 | 14952 | (version "1.2.0") |
107850b3 NB |
14953 | (source |
14954 | (origin | |
14955 | (method url-fetch) | |
14956 | (uri (cran-uri "styler" version)) | |
14957 | (sha256 | |
14958 | (base32 | |
67b7a379 | 14959 | "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9")))) |
107850b3 NB |
14960 | (build-system r-build-system) |
14961 | (propagated-inputs | |
14962 | `(("r-backports" ,r-backports) | |
14963 | ("r-cli" ,r-cli) | |
14964 | ("r-magrittr" ,r-magrittr) | |
14965 | ("r-purrr" ,r-purrr) | |
14966 | ("r-rematch2" ,r-rematch2) | |
14967 | ("r-rlang" ,r-rlang) | |
14968 | ("r-rprojroot" ,r-rprojroot) | |
14969 | ("r-tibble" ,r-tibble) | |
14970 | ("r-withr" ,r-withr) | |
14971 | ("r-xfun" ,r-xfun))) | |
14972 | (home-page "https://github.com/r-lib/styler") | |
14973 | (synopsis "Non-invasive pretty printing of R code") | |
14974 | (description | |
14975 | "This is a package for pretty-printing R code without changing the user's | |
14976 | formatting intent.") | |
14977 | (license license:gpl3))) | |
2b9d4f58 RW |
14978 | |
14979 | (define-public r-scrime | |
14980 | (package | |
14981 | (name "r-scrime") | |
14982 | (version "1.3.5") | |
14983 | (source | |
14984 | (origin | |
14985 | (method url-fetch) | |
14986 | (uri (cran-uri "scrime" version)) | |
14987 | (sha256 | |
14988 | (base32 | |
14989 | "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx")))) | |
14990 | (build-system r-build-system) | |
14991 | (home-page "https://cran.r-project.org/web/packages/scrime/") | |
14992 | (synopsis "Analysis of high-dimensional categorical data such as SNP data") | |
14993 | (description | |
14994 | "This package provides tools for the analysis of high-dimensional data | |
14995 | developed/implemented at the group \"Statistical Complexity Reduction In | |
14996 | Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of | |
14997 | the functions can also be applied to other types of categorical data.") | |
14998 | (license license:gpl2))) | |
04bf86ba | 14999 | |
3e63f078 RW |
15000 | (define-public r-pbmcapply |
15001 | (package | |
15002 | (name "r-pbmcapply") | |
15003 | (version "1.5.0") | |
15004 | (source | |
15005 | (origin | |
15006 | (method url-fetch) | |
15007 | (uri (cran-uri "pbmcapply" version)) | |
15008 | (sha256 | |
15009 | (base32 | |
15010 | "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz")))) | |
15011 | (build-system r-build-system) | |
15012 | (home-page "https://github.com/kvnkuang/pbmcapply") | |
15013 | (synopsis "Track the progress of apply procedures with a progress bar") | |
15014 | (description | |
15015 | "This light-weight package helps you track and visualize the progress of | |
15016 | parallel versions of vectorized R functions of the @code{mc*apply} family.") | |
15017 | (license license:expat))) | |
15018 | ||
04bf86ba RW |
15019 | (define-public r-blme |
15020 | (package | |
15021 | (name "r-blme") | |
15022 | (version "1.0-4") | |
15023 | (source | |
15024 | (origin | |
15025 | (method url-fetch) | |
15026 | (uri (cran-uri "blme" version)) | |
15027 | (sha256 | |
15028 | (base32 | |
15029 | "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2")))) | |
15030 | (build-system r-build-system) | |
15031 | (propagated-inputs `(("r-lme4" ,r-lme4))) | |
15032 | (home-page "https://github.com/vdorie/blme") | |
15033 | (synopsis "Bayesian linear mixed-effects models") | |
15034 | (description | |
15035 | "This package provides tools for maximum a posteriori estimation for | |
15036 | linear and generalized linear mixed-effects models in a Bayesian setting. It | |
15037 | extends the lme4 package.") | |
15038 | (license license:gpl2+))) | |
be23c491 RW |
15039 | |
15040 | (define-public r-batchtools | |
15041 | (package | |
15042 | (name "r-batchtools") | |
15043 | (version "0.9.11") | |
15044 | (source | |
15045 | (origin | |
15046 | (method url-fetch) | |
15047 | (uri (cran-uri "batchtools" version)) | |
15048 | (sha256 | |
15049 | (base32 | |
15050 | "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v")))) | |
15051 | (build-system r-build-system) | |
15052 | (propagated-inputs | |
15053 | `(("r-backports" ,r-backports) | |
15054 | ("r-base64url" ,r-base64url) | |
15055 | ("r-brew" ,r-brew) | |
15056 | ("r-checkmate" ,r-checkmate) | |
15057 | ("r-data-table" ,r-data-table) | |
15058 | ("r-digest" ,r-digest) | |
15059 | ("r-fs" ,r-fs) | |
15060 | ("r-progress" ,r-progress) | |
15061 | ("r-r6" ,r-r6) | |
15062 | ("r-rappdirs" ,r-rappdirs) | |
15063 | ("r-stringi" ,r-stringi) | |
15064 | ("r-withr" ,r-withr))) | |
15065 | (home-page "https://github.com/mllg/batchtools") | |
15066 | (synopsis "Tools for computation on batch systems") | |
15067 | (description | |
15068 | "As a successor of the packages BatchJobs and BatchExperiments, this | |
15069 | package provides a parallel implementation of the Map function for high | |
15070 | performance computing systems managed by various schedulers. A multicore and | |
15071 | socket mode allow the parallelization on a local machines, and multiple | |
15072 | machines can be hooked up via SSH to create a makeshift cluster. Moreover, | |
15073 | the package provides an abstraction mechanism to define large-scale computer | |
15074 | experiments in a well-organized and reproducible way.") | |
15075 | (license license:lgpl3))) | |
0c8960df RW |
15076 | |
15077 | (define-public r-clue | |
15078 | (package | |
15079 | (name "r-clue") | |
15080 | (version "0.3-57") | |
15081 | (source | |
15082 | (origin | |
15083 | (method url-fetch) | |
15084 | (uri (cran-uri "clue" version)) | |
15085 | (sha256 | |
15086 | (base32 | |
15087 | "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf")))) | |
15088 | (build-system r-build-system) | |
15089 | (propagated-inputs `(("r-cluster" ,r-cluster))) | |
15090 | (home-page "https://cran.r-project.org/web/packages/clue/") | |
15091 | (synopsis "Tools for analyzing cluster ensembles") | |
15092 | (description "Cluster ensembles are collections of individual solutions to | |
15093 | a given clustering problem which are useful or necessary to consider in a wide | |
15094 | range of applications. This R package provides an extensible computational | |
15095 | environment for creating and analyzing cluster ensembles, with basic data | |
15096 | structures for representing partitions and hierarchies, and facilities for | |
15097 | computing on them, including methods for measuring proximity and obtaining | |
15098 | consensus and secondary clusterings.") | |
15099 | (license license:gpl2))) | |
b8d6dffb RW |
15100 | |
15101 | (define-public r-sitmo | |
15102 | (package | |
15103 | (name "r-sitmo") | |
15104 | (version "2.0.1") | |
15105 | (source | |
15106 | (origin | |
15107 | (method url-fetch) | |
15108 | (uri (cran-uri "sitmo" version)) | |
15109 | (sha256 | |
15110 | (base32 | |
15111 | "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c")))) | |
15112 | (build-system r-build-system) | |
15113 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
15114 | (home-page "https://github.com/coatless/sitmo/") | |
15115 | (synopsis "Parallel pseudo random number generator header files") | |
15116 | (description | |
15117 | "This package provides two high quality and fast PPRNGs that may be used | |
15118 | in an OpenMP parallel environment. In addition, there is a generator for one | |
15119 | dimensional low-discrepancy sequence.") | |
15120 | (license license:expat))) | |
3961b3b9 RW |
15121 | |
15122 | (define-public r-dqrng | |
15123 | (package | |
15124 | (name "r-dqrng") | |
12242ffb | 15125 | (version "0.2.1") |
3961b3b9 RW |
15126 | (source |
15127 | (origin | |
15128 | (method url-fetch) | |
15129 | (uri (cran-uri "dqrng" version)) | |
15130 | (sha256 | |
15131 | (base32 | |
12242ffb | 15132 | "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1")))) |
3961b3b9 RW |
15133 | (build-system r-build-system) |
15134 | (propagated-inputs | |
15135 | `(("r-bh" ,r-bh) | |
15136 | ("r-rcpp" ,r-rcpp) | |
15137 | ("r-sitmo" ,r-sitmo))) | |
15138 | (home-page "https://www.daqana.org/dqrng") | |
15139 | (synopsis "Fast pseudo random number generators") | |
15140 | (description | |
15141 | "Several fast random number generators are provided as C++ header-only | |
15142 | libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+. | |
15143 | Additionally, fast functions for generating random numbers according to a | |
15144 | uniform, normal and exponential distribution are included. The latter two use | |
15145 | the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These | |
15146 | functions are exported to R and as a C++ interface and are enabled for use | |
15147 | with the default 64 bit generator from the PCG family, Xoroshiro128+ and | |
15148 | Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry | |
15149 | engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") | |
15150 | ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a | |
15151 | ;; whole is distributed under the terms of the AGPL 3. | |
15152 | (license license:agpl3))) | |
5bea832f RW |
15153 | |
15154 | (define-public r-dalex | |
15155 | (package | |
15156 | (name "r-dalex") | |
0eed4fde | 15157 | (version "0.4.9") |
5bea832f RW |
15158 | (source |
15159 | (origin | |
15160 | (method url-fetch) | |
15161 | (uri (cran-uri "DALEX" version)) | |
15162 | (sha256 | |
15163 | (base32 | |
0eed4fde | 15164 | "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421")))) |
5bea832f RW |
15165 | (properties `((upstream-name . "DALEX"))) |
15166 | (build-system r-build-system) | |
15167 | (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) | |
15168 | (home-page "https://pbiecek.github.io/DALEX/") | |
15169 | (synopsis "Descriptive machine learning explanations") | |
15170 | (description | |
15171 | "Machine Learning models are widely used and have various applications in | |
15172 | classification or regression. Models created with boosting, bagging, stacking | |
15173 | or similar techniques are often used due to their high performance, but such | |
15174 | black-box models usually lack interpretability. The DALEX package contains | |
15175 | various explainers that help to understand the link between input variables | |
15176 | and model output.") | |
15177 | ;; Any version of the GPL | |
15178 | (license license:gpl3+))) | |
70debac5 RW |
15179 | |
15180 | (define-public r-enrichr | |
15181 | (package | |
15182 | (name "r-enrichr") | |
7a90573f | 15183 | (version "2.1") |
70debac5 RW |
15184 | (source |
15185 | (origin | |
15186 | (method url-fetch) | |
15187 | (uri (cran-uri "enrichR" version)) | |
15188 | (sha256 | |
15189 | (base32 | |
7a90573f | 15190 | "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1")))) |
70debac5 RW |
15191 | (properties `((upstream-name . "enrichR"))) |
15192 | (build-system r-build-system) | |
15193 | (propagated-inputs | |
15194 | `(("r-httr" ,r-httr) | |
15195 | ("r-rjson" ,r-rjson))) | |
15196 | (home-page "https://cran.r-project.org/web/packages/enrichR/") | |
15197 | (synopsis "R Interface to Enrichr database for analyzing gene sets") | |
15198 | (description | |
15199 | "This package provides an R interface to all Enrichr databases, a | |
15200 | web-based tool for analyzing gene sets and returns any enrichment of common | |
15201 | annotated biological functions.") | |
15202 | (license license:gpl2+))) | |
c9487dfa RW |
15203 | |
15204 | (define-public r-plot3d | |
15205 | (package | |
15206 | (name "r-plot3d") | |
db904d5c | 15207 | (version "1.3") |
c9487dfa RW |
15208 | (source |
15209 | (origin | |
15210 | (method url-fetch) | |
15211 | (uri (cran-uri "plot3D" version)) | |
15212 | (sha256 | |
15213 | (base32 | |
db904d5c | 15214 | "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r")))) |
c9487dfa RW |
15215 | (properties `((upstream-name . "plot3D"))) |
15216 | (build-system r-build-system) | |
15217 | (propagated-inputs `(("r-misc3d" ,r-misc3d))) | |
15218 | (home-page "https://cran.r-project.org/web/packages/plot3D") | |
15219 | (synopsis "Plot multi-dimensional data") | |
15220 | (description | |
15221 | "This package provides functions for viewing 2D and 3D data, including | |
15222 | perspective plots, slice plots, surface plots, scatter plots, etc. It | |
15223 | includes data sets from oceanography.") | |
15224 | (license license:gpl3+))) | |
85625cae RW |
15225 | |
15226 | (define-public r-ggfortify | |
15227 | (package | |
15228 | (name "r-ggfortify") | |
a6412edf | 15229 | (version "0.4.8") |
85625cae RW |
15230 | (source |
15231 | (origin | |
15232 | (method url-fetch) | |
15233 | (uri (cran-uri "ggfortify" version)) | |
15234 | (sha256 | |
15235 | (base32 | |
a6412edf | 15236 | "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3")))) |
85625cae RW |
15237 | (build-system r-build-system) |
15238 | (propagated-inputs | |
15239 | `(("r-dplyr" ,r-dplyr) | |
15240 | ("r-ggplot2" ,r-ggplot2) | |
15241 | ("r-gridextra" ,r-gridextra) | |
15242 | ("r-scales" ,r-scales) | |
15243 | ("r-stringr" ,r-stringr) | |
15244 | ("r-tibble" ,r-tibble) | |
15245 | ("r-tidyr" ,r-tidyr))) | |
15246 | (home-page "https://github.com/sinhrks/ggfortify") | |
15247 | (synopsis "Data visualization tools for statistical analysis results") | |
15248 | (description | |
15249 | "This package provides unified plotting tools for statistics commonly | |
15250 | used, such as GLM, time series, PCA families, clustering and survival | |
15251 | analysis. The package offers a single plotting interface for these analysis | |
15252 | results and plots in a unified style using the @code{ggplot2} package.") | |
15253 | (license license:gpl2))) | |
afc4370d RW |
15254 | |
15255 | (define-public r-refmanager | |
15256 | (package | |
15257 | (name "r-refmanager") | |
15258 | (version "1.2.12") | |
15259 | (source | |
15260 | (origin | |
15261 | (method url-fetch) | |
15262 | (uri (cran-uri "RefManageR" version)) | |
15263 | (sha256 | |
15264 | (base32 | |
15265 | "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp")))) | |
15266 | (properties `((upstream-name . "RefManageR"))) | |
15267 | (build-system r-build-system) | |
15268 | (propagated-inputs | |
15269 | `(("r-bibtex" ,r-bibtex) | |
15270 | ("r-httr" ,r-httr) | |
15271 | ("r-jsonlite" ,r-jsonlite) | |
15272 | ("r-lubridate" ,r-lubridate) | |
15273 | ("r-plyr" ,r-plyr) | |
15274 | ("r-stringr" ,r-stringr) | |
15275 | ("r-xml2" ,r-xml2))) | |
15276 | (home-page "https://github.com/ropensci/RefManageR/") | |
15277 | (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") | |
15278 | (description | |
15279 | "This package provides tools for importing and working with bibliographic | |
15280 | references. It greatly enhances the @code{bibentry} class by providing a | |
15281 | class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports | |
15282 | UTF-8 encoding, and can be easily searched by any field, by date ranges, and | |
15283 | by various formats for name lists (author by last names, translator by full | |
15284 | names, etc.). Entries can be updated, combined, sorted, printed in a number | |
15285 | of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read | |
15286 | into R and converted to @code{BibEntry} objects.") | |
15287 | ;; Any of these licenses may be picked. | |
15288 | (license (list license:gpl2 license:gpl3 license:bsd-3)))) | |
29591ca6 RW |
15289 | |
15290 | (define-public r-citr | |
15291 | (package | |
15292 | (name "r-citr") | |
6b28386d | 15293 | (version "0.3.2") |
29591ca6 RW |
15294 | (source |
15295 | (origin | |
15296 | (method url-fetch) | |
15297 | (uri (cran-uri "citr" version)) | |
15298 | (sha256 | |
15299 | (base32 | |
6b28386d | 15300 | "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las")))) |
29591ca6 RW |
15301 | (build-system r-build-system) |
15302 | (propagated-inputs | |
15303 | `(("r-assertthat" ,r-assertthat) | |
29591ca6 RW |
15304 | ("r-curl" ,r-curl) |
15305 | ("r-httr" ,r-httr) | |
15306 | ("r-miniui" ,r-miniui) | |
15307 | ("r-refmanager" ,r-refmanager) | |
15308 | ("r-rstudioapi" ,r-rstudioapi) | |
15309 | ("r-shiny" ,r-shiny) | |
15310 | ("r-shinyjs" ,r-shinyjs) | |
15311 | ("r-yaml" ,r-yaml))) | |
15312 | (home-page "https://github.com/crsh/citr") | |
15313 | (synopsis "RStudio add-in to insert Markdown citations") | |
15314 | (description | |
15315 | "This package provides functions and an RStudio add-in that search a | |
15316 | BibTeX or BibLaTeX file to create and insert formatted Markdown citations into | |
15317 | the current document.") | |
15318 | (license license:expat))) | |
30f1029f RW |
15319 | |
15320 | (define-public r-xgboost | |
15321 | (package | |
15322 | (name "r-xgboost") | |
00300de5 | 15323 | (version "0.90.0.2") |
30f1029f RW |
15324 | (source |
15325 | (origin | |
15326 | (method url-fetch) | |
15327 | (uri (cran-uri "xgboost" version)) | |
15328 | (sha256 | |
15329 | (base32 | |
00300de5 | 15330 | "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194")))) |
30f1029f RW |
15331 | (build-system r-build-system) |
15332 | (propagated-inputs | |
15333 | `(("r-data-table" ,r-data-table) | |
15334 | ("r-magrittr" ,r-magrittr) | |
15335 | ("r-matrix" ,r-matrix) | |
15336 | ("r-stringi" ,r-stringi))) | |
15337 | (home-page "https://github.com/dmlc/xgboost") | |
15338 | (synopsis "Extreme gradient boosting") | |
15339 | (description | |
15340 | "This package provides an R interface to Extreme Gradient Boosting, which | |
15341 | is an efficient implementation of the gradient boosting framework from Chen | |
15342 | and Guestrin (2016). The package includes efficient linear model solver and | |
15343 | tree learning algorithms. The package can automatically do parallel | |
15344 | computation on a single machine. It supports various objective functions, | |
15345 | including regression, classification and ranking. The package is made to be | |
15346 | extensible, so that users are also allowed to define their own objectives | |
15347 | easily.") | |
15348 | (license license:asl2.0))) | |
1c0b2e74 | 15349 | |
15350 | (define-public r-umap | |
15351 | (package | |
15352 | (name "r-umap") | |
ca0b3401 | 15353 | (version "0.2.4.0") |
1c0b2e74 | 15354 | (source |
15355 | (origin | |
15356 | (method url-fetch) | |
15357 | (uri (cran-uri "umap" version)) | |
15358 | (sha256 | |
15359 | (base32 | |
ca0b3401 | 15360 | "1dzbwq96k5vqr64wk6s26ks4311h570xg6gf0prr4vnn033pqnch")))) |
1c0b2e74 | 15361 | (build-system r-build-system) |
15362 | (propagated-inputs | |
8bcd6c95 RW |
15363 | `(("r-openssl" ,r-openssl) |
15364 | ("r-rcpp" ,r-rcpp) | |
1c0b2e74 | 15365 | ("r-reticulate" ,r-reticulate) |
15366 | ("r-rspectra" ,r-rspectra))) | |
15367 | (home-page "https://github.com/tkonopka/umap") | |
15368 | (synopsis "Uniform manifold approximation and projection") | |
15369 | (description | |
15370 | "Uniform manifold approximation and projection is a technique for | |
15371 | dimension reduction. This package provides an interface to the UMAP algorithm | |
15372 | in R, including a translation of the original algorithm into R.") | |
15373 | (license license:expat))) | |
6deb08a3 | 15374 | |
86c46d71 RW |
15375 | (define-public r-uwot |
15376 | (package | |
15377 | (name "r-uwot") | |
d8d60630 | 15378 | (version "0.1.5") |
86c46d71 RW |
15379 | (source |
15380 | (origin | |
15381 | (method url-fetch) | |
15382 | (uri (cran-uri "uwot" version)) | |
15383 | (sha256 | |
15384 | (base32 | |
d8d60630 | 15385 | "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj")))) |
86c46d71 RW |
15386 | (build-system r-build-system) |
15387 | (propagated-inputs | |
15388 | `(("r-dqrng" ,r-dqrng) | |
15389 | ("r-fnn" ,r-fnn) | |
15390 | ("r-irlba" ,r-irlba) | |
15391 | ("r-matrix" ,r-matrix) | |
15392 | ("r-rcpp" ,r-rcpp) | |
15393 | ("r-rcppannoy" ,r-rcppannoy) | |
15394 | ("r-rcppparallel" ,r-rcppparallel) | |
15395 | ("r-rcppprogress" ,r-rcppprogress) | |
15396 | ("r-rspectra" ,r-rspectra))) | |
15397 | (home-page "https://github.com/jlmelville/uwot") | |
15398 | (synopsis "Uniform manifold approximation and projection") | |
15399 | (description | |
15400 | "This package provides an implementation of the Uniform Manifold | |
15401 | Approximation and Projection dimensionality reduction by McInnes et | |
15402 | al. (2018). It also provides means to transform new data and to carry out | |
15403 | supervised dimensionality reduction. An implementation of the related | |
15404 | LargeVis method of Tang et al. (2016) is also provided.") | |
15405 | (license license:gpl3))) | |
15406 | ||
6deb08a3 | 15407 | (define-public r-kableextra |
15408 | (package | |
15409 | (name "r-kableextra") | |
15410 | (version "1.1.0") | |
15411 | (source | |
15412 | (origin | |
15413 | (method url-fetch) | |
15414 | (uri (cran-uri "kableExtra" version)) | |
15415 | (sha256 | |
15416 | (base32 | |
15417 | "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i")))) | |
15418 | (properties `((upstream-name . "kableExtra"))) | |
15419 | (build-system r-build-system) | |
15420 | (propagated-inputs | |
15421 | `(("r-digest" ,r-digest) | |
15422 | ("r-glue" ,r-glue) | |
15423 | ("r-htmltools" ,r-htmltools) | |
15424 | ("r-knitr" ,r-knitr) | |
15425 | ("r-magrittr" ,r-magrittr) | |
15426 | ("r-readr" ,r-readr) | |
15427 | ("r-rmarkdown" ,r-rmarkdown) | |
15428 | ("r-rstudioapi" ,r-rstudioapi) | |
15429 | ("r-rvest" ,r-rvest) | |
15430 | ("r-scales" ,r-scales) | |
15431 | ("r-stringr" ,r-stringr) | |
15432 | ("r-viridislite" ,r-viridislite) | |
15433 | ("r-webshot" ,r-webshot) | |
15434 | ("r-xml2" ,r-xml2))) | |
15435 | (home-page "https://haozhu233.github.io/kableExtra/") | |
15436 | (synopsis "Construct complex tables with pipe syntax") | |
15437 | (description | |
15438 | "Build complex HTML or LaTeX tables using @code{kable()} from | |
15439 | @code{knitr} and the piping syntax from @code{magrittr}. The function | |
15440 | @code{kable()} is a light weight table generator coming from @code{knitr}. | |
15441 | This package simplifies the way to manipulate the HTML or LaTeX codes | |
15442 | generated by @code{kable()} and allows users to construct complex tables and | |
15443 | customize styles using a readable syntax.") | |
15444 | (license license:expat))) | |
79f04920 RW |
15445 | |
15446 | (define-public r-glasso | |
15447 | (package | |
15448 | (name "r-glasso") | |
afbc3a87 | 15449 | (version "1.11") |
79f04920 RW |
15450 | (source |
15451 | (origin | |
15452 | (method url-fetch) | |
15453 | (uri (cran-uri "glasso" version)) | |
15454 | (sha256 | |
afbc3a87 | 15455 | (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc")))) |
79f04920 RW |
15456 | (build-system r-build-system) |
15457 | (native-inputs `(("gfortran" ,gfortran))) | |
15458 | (home-page "http://www-stat.stanford.edu/~tibs/glasso") | |
15459 | (synopsis "Graphical Lasso: estimation of Gaussian graphical models") | |
15460 | (description | |
15461 | "This is a package for estimation of a sparse inverse covariance matrix | |
15462 | using a lasso (L1) penalty. Facilities are provided for estimates along a | |
15463 | path of values for the regularization parameter.") | |
15464 | (license license:gpl2))) | |
37120e7a RW |
15465 | |
15466 | (define-public r-rhpcblasctl | |
15467 | (package | |
15468 | (name "r-rhpcblasctl") | |
15469 | (version "0.18-205") | |
15470 | (source | |
15471 | (origin | |
15472 | (method url-fetch) | |
15473 | (uri (cran-uri "RhpcBLASctl" version)) | |
15474 | (sha256 | |
15475 | (base32 | |
15476 | "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp")))) | |
15477 | (properties `((upstream-name . "RhpcBLASctl"))) | |
15478 | (build-system r-build-system) | |
15479 | (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/") | |
15480 | (synopsis "Control the number of threads on BLAS") | |
15481 | (description | |
15482 | "This package allows you to control the number of threads the BLAS | |
15483 | library uses. It is also possible to control the number of threads in | |
15484 | OpenMP.") | |
15485 | (license license:agpl3+))) | |
6e7553ff | 15486 | |
19f1aac0 RW |
15487 | (define-public r-lda |
15488 | (package | |
15489 | (name "r-lda") | |
15490 | (version "1.4.2") | |
15491 | (source | |
15492 | (origin | |
15493 | (method url-fetch) | |
15494 | (uri (cran-uri "lda" version)) | |
15495 | (sha256 | |
15496 | (base32 | |
15497 | "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn")))) | |
15498 | (build-system r-build-system) | |
15499 | (home-page "https://cran.r-project.org/web/packages/lda/") | |
15500 | (synopsis "Collapsed Gibbs sampling methods for topic models") | |
15501 | (description | |
15502 | "This package implements @dfn{latent Dirichlet allocation} (LDA) and | |
15503 | related models. This includes (but is not limited to) sLDA, corrLDA, and the | |
15504 | mixed-membership stochastic blockmodel. Inference for all of these models is | |
15505 | implemented via a fast collapsed Gibbs sampler written in C. Utility | |
15506 | functions for reading/writing data typically used in topic models, as well as | |
15507 | tools for examining posterior distributions are also included.") | |
15508 | ;; Any version of the LGPL | |
15509 | (license license:lgpl3+))) | |
15510 | ||
6e7553ff RW |
15511 | (define-public r-rann-l1 |
15512 | (package | |
15513 | (name "r-rann-l1") | |
15514 | (version "2.5.2") | |
15515 | (source | |
15516 | (origin | |
15517 | (method url-fetch) | |
15518 | (uri (cran-uri "RANN.L1" version)) | |
15519 | (sha256 | |
15520 | (base32 | |
15521 | "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44")))) | |
15522 | (properties `((upstream-name . "RANN.L1"))) | |
15523 | (build-system r-build-system) | |
15524 | (home-page "https://github.com/jefferis/RANN/tree/master-L1") | |
15525 | (synopsis "Fast nearest neighbour search using L1 metric") | |
15526 | (description | |
15527 | "This package provides tools to find the k nearest neighbours for every | |
15528 | point in a given dataset in O(N log N) time using Arya and Mount's ANN | |
15529 | library. There is support for approximate as well as exact searches, fixed | |
15530 | radius searches and @code{bd} as well as @code{kd} trees. The distance is | |
15531 | computed using the L1 (Manhattan, taxicab) metric.") | |
15532 | (license license:gpl3+))) | |
9c3bfea6 | 15533 | |
8e28535d RW |
15534 | (define-public r-leiden |
15535 | (package | |
15536 | (name "r-leiden") | |
15537 | (version "0.3.1") | |
15538 | (source | |
15539 | (origin | |
15540 | (method url-fetch) | |
15541 | (uri (cran-uri "leiden" version)) | |
15542 | (sha256 | |
15543 | (base32 | |
15544 | "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp")))) | |
15545 | (properties `((upstream-name . "leiden"))) | |
15546 | (build-system r-build-system) | |
15547 | (propagated-inputs | |
15548 | `(("r-igraph" ,r-igraph) | |
15549 | ("r-matrix" ,r-matrix) | |
15550 | ("r-reticulate" ,r-reticulate))) | |
15551 | (home-page "https://github.com/TomKellyGenetics/leiden") | |
15552 | (synopsis "R implementation of Leiden clustering algorithm") | |
15553 | (description | |
15554 | "This package implements the Python @code{leidenalg} module to be called | |
15555 | in R. It enables clustering using the Leiden algorithm for partitioning a | |
15556 | graph into communities. See also Traag et al (2018) \"From Louvain to Leiden: | |
15557 | guaranteeing well-connected communities.\" <arXiv:1810.08473>.") | |
15558 | (license license:gpl3))) | |
15559 | ||
9c3bfea6 RW |
15560 | (define-public r-patchwork |
15561 | ;; There has been no public release yet. | |
15562 | (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242") | |
15563 | (revision "1")) | |
15564 | (package | |
15565 | (name "r-patchwork") | |
15566 | (version (git-version "0.0.1" revision commit)) | |
15567 | (source | |
15568 | (origin | |
15569 | (method git-fetch) | |
15570 | (uri (git-reference | |
15571 | (url "https://github.com/thomasp85/patchwork.git") | |
15572 | (commit commit))) | |
15573 | (file-name (git-file-name name version)) | |
15574 | (sha256 | |
15575 | (base32 | |
15576 | "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4")))) | |
15577 | (build-system r-build-system) | |
15578 | (propagated-inputs | |
15579 | `(("r-ggplot2" ,r-ggplot2) | |
15580 | ("r-gtable" ,r-gtable))) | |
15581 | (home-page "https://github.com/thomasp85/patchwork") | |
15582 | (synopsis "Compose ggplot2 plots") | |
15583 | (description | |
15584 | "The @code{ggplot2} package provides a strong API for sequentially | |
15585 | building up a plot, but does not concern itself with composition of multiple | |
15586 | plots. Patchwork is a package that expands the API to allow for arbitrarily | |
15587 | complex composition of plots by providing mathmatical operators for combining | |
15588 | multiple plots.") | |
15589 | (license license:expat)))) | |
86d38228 RW |
15590 | |
15591 | (define-public r-liger | |
15592 | (package | |
15593 | (name "r-liger") | |
15594 | (version "0.4.2") | |
15595 | (source | |
15596 | (origin | |
15597 | (method git-fetch) | |
15598 | (uri (git-reference | |
15599 | (url "https://github.com/MacoskoLab/liger.git") | |
15600 | (commit (string-append "v" version)))) | |
15601 | (file-name (git-file-name name version)) | |
15602 | (sha256 | |
15603 | (base32 | |
15604 | "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx")) | |
15605 | (modules '((guix build utils))) | |
15606 | (snippet | |
15607 | '(begin | |
15608 | (delete-file "inst/java/ModularityOptimizer.jar") | |
15609 | #t)))) | |
15610 | (build-system r-build-system) | |
15611 | (arguments | |
15612 | `(#:phases | |
15613 | (modify-phases %standard-phases | |
15614 | (add-after 'unpack 'build-java-part | |
15615 | (lambda* (#:key inputs #:allow-other-keys) | |
15616 | (invoke "unzip" (assoc-ref inputs "optimizer-src")) | |
15617 | (for-each (lambda (file) (invoke "javac" file)) | |
15618 | (find-files "." "\\.java$")) | |
15619 | (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar" | |
15620 | (find-files "." "\\.class$")) | |
15621 | #t))))) | |
15622 | (propagated-inputs | |
15623 | `(("r-cowplot" ,r-cowplot) | |
15624 | ("r-dosnow" ,r-dosnow) | |
15625 | ("r-dplyr" ,r-dplyr) | |
15626 | ("r-fnn" ,r-fnn) | |
15627 | ("r-foreach" ,r-foreach) | |
15628 | ("r-ggplot2" ,r-ggplot2) | |
15629 | ("r-ggrepel" ,r-ggrepel) | |
15630 | ("r-hmisc" ,r-hmisc) | |
15631 | ("r-ica" ,r-ica) | |
15632 | ("r-irlba" ,r-irlba) | |
15633 | ("r-matrix" ,r-matrix) | |
15634 | ("r-mclust" ,r-mclust) | |
15635 | ("r-patchwork" ,r-patchwork) | |
15636 | ("r-plyr" ,r-plyr) | |
15637 | ("r-rann-l1" ,r-rann-l1) | |
15638 | ("r-rcpp" ,r-rcpp) | |
15639 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
15640 | ("r-riverplot" ,r-riverplot) | |
15641 | ("r-rtsne" ,r-rtsne) | |
15642 | ("r-snow" ,r-snow))) | |
15643 | (native-inputs | |
15644 | `(("jdk" ,icedtea "jdk") | |
15645 | ;; See https://github.com/MacoskoLab/liger/issues/96 | |
15646 | ;; The optimizer is released under the Expat license. | |
15647 | ("optimizer-src" | |
15648 | ,(origin | |
15649 | (method url-fetch) | |
15650 | (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip") | |
15651 | (sha256 | |
15652 | (base32 | |
15653 | "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18")))) | |
15654 | ("unzip" ,unzip) | |
15655 | ("r-knitr" ,r-knitr))) ; for vignettes | |
15656 | (home-page "https://github.com/MacoskoLab/liger") | |
15657 | (synopsis "Integrate and analyze multiple single-cell datasets") | |
15658 | (description | |
15659 | "LIGER is a package for integrating and analyzing multiple single-cell | |
15660 | datasets, developed and maintained by the Macosko lab. It relies on | |
15661 | integrative non-negative matrix factorization to identify shared and | |
15662 | dataset-specific factors.") | |
15663 | (license license:gpl3))) | |
711cec9d RW |
15664 | |
15665 | (define-public r-harmony | |
15666 | ;; There are no tagged commits | |
15667 | (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a") | |
15668 | (revision "1")) | |
15669 | (package | |
15670 | (name "r-harmony") | |
15671 | (version (git-version "1.0" revision commit)) | |
15672 | (source | |
15673 | (origin | |
15674 | (method git-fetch) | |
15675 | (uri (git-reference | |
15676 | (url "https://github.com/immunogenomics/harmony") | |
15677 | (commit commit))) | |
15678 | (file-name (git-file-name name version)) | |
15679 | (sha256 | |
15680 | (base32 | |
15681 | "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85")))) | |
15682 | (build-system r-build-system) | |
15683 | (propagated-inputs | |
15684 | `(("r-cowplot" ,r-cowplot) | |
15685 | ("r-dplyr" ,r-dplyr) | |
15686 | ("r-ggplot2" ,r-ggplot2) | |
15687 | ("r-irlba" ,r-irlba) | |
15688 | ("r-matrix" ,r-matrix) | |
15689 | ("r-rcpp" ,r-rcpp) | |
15690 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
15691 | ("r-rcppprogress" ,r-rcppprogress) | |
15692 | ("r-rlang" ,r-rlang) | |
15693 | ("r-tibble" ,r-tibble) | |
15694 | ("r-tidyr" ,r-tidyr))) | |
15695 | (home-page "https://github.com/immunogenomics/harmony") | |
15696 | (synopsis "Integration of single cell sequencing data") | |
15697 | (description | |
15698 | "This package provides an implementation of the Harmony algorithm for | |
15699 | single cell integration, described in Korsunsky et al | |
15700 | @url{doi.org/10.1101/461954}. The package includes a standalone Harmony | |
15701 | function and interfaces to external frameworks.") | |
15702 | (license license:gpl3)))) | |
7a5ed348 RW |
15703 | |
15704 | (define-public r-covr | |
15705 | (package | |
15706 | (name "r-covr") | |
7b18e6d0 | 15707 | (version "3.4.0") |
7a5ed348 RW |
15708 | (source |
15709 | (origin | |
15710 | (method url-fetch) | |
15711 | (uri (cran-uri "covr" version)) | |
15712 | (sha256 | |
7b18e6d0 | 15713 | (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5")))) |
7a5ed348 RW |
15714 | (properties `((upstream-name . "covr"))) |
15715 | (build-system r-build-system) | |
15716 | (propagated-inputs | |
15717 | `(("r-crayon" ,r-crayon) | |
15718 | ("r-digest" ,r-digest) | |
15719 | ("r-httr" ,r-httr) | |
15720 | ("r-jsonlite" ,r-jsonlite) | |
15721 | ("r-rex" ,r-rex) | |
15722 | ("r-withr" ,r-withr) | |
15723 | ("r-yaml" ,r-yaml))) | |
15724 | (home-page "https://github.com/r-lib/covr") | |
15725 | (synopsis "Test coverage for R packages") | |
15726 | (description | |
15727 | "Thisp package enables you to track and report code coverage for your | |
15728 | package and (optionally) upload the results to a coverage service. Code | |
15729 | coverage is a measure of the amount of code being exercised by a set of tests. | |
15730 | It is an indirect measure of test quality and completeness. This package is | |
15731 | compatible with any testing methodology or framework and tracks coverage of | |
15732 | both R code and compiled C/C++/FORTRAN code.") | |
15733 | (license license:gpl3))) | |
6983178b RW |
15734 | |
15735 | (define-public r-systemfonts | |
15736 | (package | |
15737 | (name "r-systemfonts") | |
15738 | (version "0.1.1") | |
15739 | (source | |
15740 | (origin | |
15741 | (method url-fetch) | |
15742 | (uri (cran-uri "systemfonts" version)) | |
15743 | (sha256 | |
15744 | (base32 | |
15745 | "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z")))) | |
15746 | (properties `((upstream-name . "systemfonts"))) | |
15747 | (build-system r-build-system) | |
15748 | (inputs | |
15749 | `(("fontconfig" ,fontconfig) | |
15750 | ("freetype" ,freetype) | |
15751 | ("zlib" ,zlib))) | |
15752 | (native-inputs | |
15753 | `(("pkg-config" ,pkg-config))) | |
15754 | (home-page "https://github.com/r-lib/systemfonts") | |
15755 | (synopsis "System native font finding") | |
15756 | (description | |
15757 | "This package provides system native access to the font catalogue. As | |
15758 | font handling varies between systems it is difficult to correctly locate | |
15759 | installed fonts across different operating systems. The 'systemfonts' package | |
15760 | provides bindings to the native libraries for finding font files that can then | |
15761 | be used further by e.g. graphic devices.") | |
15762 | (license license:expat))) | |
93903009 RW |
15763 | |
15764 | (define-public r-graphlayouts | |
15765 | (package | |
15766 | (name "r-graphlayouts") | |
15767 | (version "0.5.0") | |
15768 | (source | |
15769 | (origin | |
15770 | (method url-fetch) | |
15771 | (uri (cran-uri "graphlayouts" version)) | |
15772 | (sha256 | |
15773 | (base32 | |
15774 | "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3")))) | |
15775 | (properties `((upstream-name . "graphlayouts"))) | |
15776 | (build-system r-build-system) | |
15777 | (propagated-inputs | |
15778 | `(("r-igraph" ,r-igraph) | |
15779 | ("r-rcpp" ,r-rcpp) | |
15780 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
15781 | (home-page "https://github.com/schochastics/graphlayouts") | |
15782 | (synopsis "Additional layout algorithms for network visualizations") | |
15783 | (description | |
15784 | "This package provides several layout algorithms to visualize networks | |
15785 | which are not part of the igraph library. Most are based on the concept of | |
15786 | stress majorization by Gansner et al. (2004) | |
15787 | <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to | |
15788 | emphasize hidden group structures in networks or focus on specific nodes.") | |
15789 | (license license:expat))) | |
9567bd8d RW |
15790 | |
15791 | (define-public r-tidygraph | |
15792 | (package | |
15793 | (name "r-tidygraph") | |
15794 | (version "1.1.2") | |
15795 | (source | |
15796 | (origin | |
15797 | (method url-fetch) | |
15798 | (uri (cran-uri "tidygraph" version)) | |
15799 | (sha256 | |
15800 | (base32 | |
15801 | "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn")))) | |
15802 | (properties `((upstream-name . "tidygraph"))) | |
15803 | (build-system r-build-system) | |
15804 | (propagated-inputs | |
15805 | `(("r-dplyr" ,r-dplyr) | |
15806 | ("r-igraph" ,r-igraph) | |
15807 | ("r-magrittr" ,r-magrittr) | |
15808 | ("r-pillar" ,r-pillar) | |
15809 | ("r-r6" ,r-r6) | |
15810 | ("r-rcpp" ,r-rcpp) | |
15811 | ("r-rlang" ,r-rlang) | |
15812 | ("r-tibble" ,r-tibble) | |
15813 | ("r-tidyr" ,r-tidyr))) | |
15814 | (home-page "https://github.com/thomasp85/tidygraph") | |
15815 | (synopsis "Tidy API for graph manipulation") | |
15816 | (description | |
15817 | "This package provides a graph implementation that can be thought of as | |
15818 | two tidy data frames describing node and edge data respectively. It provides | |
15819 | an approach to manipulate these two virtual data frames using the API defined | |
15820 | in the @code{dplyr} package, and it also provides tidy interfaces to a lot of | |
15821 | common graph algorithms.") | |
15822 | (license license:expat))) | |
3a341e82 RW |
15823 | |
15824 | (define-public r-soupx | |
15825 | (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8") | |
15826 | (revision "1")) | |
15827 | (package | |
15828 | (name "r-soupx") | |
15829 | (version (git-version "0.3.1" revision commit)) | |
15830 | (source | |
15831 | (origin | |
15832 | (method git-fetch) | |
15833 | (uri (git-reference | |
15834 | (url "https://github.com/constantAmateur/SoupX") | |
15835 | (commit commit))) | |
15836 | (file-name (git-file-name name version)) | |
15837 | (sha256 | |
15838 | (base32 | |
15839 | "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99")))) | |
15840 | (properties `((upstream-name . "SoupX"))) | |
15841 | (build-system r-build-system) | |
15842 | (propagated-inputs | |
15843 | `(("r-ggplot2" ,r-ggplot2) | |
15844 | ("r-matrix" ,r-matrix) | |
15845 | ("r-seurat" ,r-seurat))) | |
15846 | (home-page "https://github.com/constantAmateur/SoupX") | |
15847 | (synopsis "Single cell mRNA Soup eXterminator") | |
15848 | (description | |
15849 | "This package provides a package for quantifying, profiling and | |
15850 | removing cell free mRNA contamination (the \"soup\") from droplet based single | |
15851 | cell RNA-seq experiments.") | |
15852 | (license license:gpl2)))) | |
16fddf17 WŻ |
15853 | |
15854 | (define-public r-assertr | |
15855 | (package | |
15856 | (name "r-assertr") | |
15857 | (version "2.6") | |
15858 | (source | |
15859 | (origin | |
15860 | (method url-fetch) | |
15861 | (uri (cran-uri "assertr" version)) | |
15862 | (sha256 | |
15863 | (base32 | |
15864 | "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj")))) | |
15865 | (build-system r-build-system) | |
15866 | (propagated-inputs | |
15867 | `(("r-dplyr" ,r-dplyr) | |
15868 | ("r-mass" ,r-mass) | |
15869 | ("r-rlang" ,r-rlang))) | |
15870 | (native-inputs | |
15871 | `(("r-knitr" ,r-knitr))) ; needed for vignette | |
15872 | (home-page "https://github.com/ropensci/assertr") | |
15873 | (synopsis "Assertive programming for R analysis pipelines") | |
15874 | (description | |
15875 | "This package provides functionality to assert conditions that have to be | |
15876 | met so that errors in data used in analysis pipelines can fail quickly. It is | |
15877 | similar to @code{stopifnot()} but more powerful, friendly, and easier for use | |
15878 | in pipelines.") | |
15879 | (license license:expat))) | |
a5a79dd0 RW |
15880 | |
15881 | (define-public r-parameters | |
15882 | (package | |
15883 | (name "r-parameters") | |
eb6aad88 | 15884 | (version "0.3.0") |
a5a79dd0 RW |
15885 | (source |
15886 | (origin | |
15887 | (method url-fetch) | |
15888 | (uri (cran-uri "parameters" version)) | |
15889 | (sha256 | |
15890 | (base32 | |
eb6aad88 | 15891 | "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv")))) |
a5a79dd0 RW |
15892 | (properties `((upstream-name . "parameters"))) |
15893 | (build-system r-build-system) | |
15894 | (propagated-inputs | |
15895 | `(("r-bayestestr" ,r-bayestestr) | |
15896 | ("r-insight" ,r-insight))) | |
15897 | (home-page "https://cran.r-project.org/web/packages/parameters") | |
15898 | (synopsis "Processing of model parameters") | |
15899 | (description | |
15900 | "This package provides utilities for processing the parameters of various | |
15901 | statistical models. Beyond computing p values, CIs, and other indices for a | |
15902 | wide variety of models, this package implements features like standardization | |
15903 | or bootstrapping of parameters and models, feature reduction (feature | |
15904 | extraction and variable selection) as well as conversion between indices of | |
15905 | effect size.") | |
15906 | (license license:gpl3))) | |
a0244ef0 RW |
15907 | |
15908 | (define-public r-rgdal | |
15909 | (package | |
15910 | (name "r-rgdal") | |
28d94096 | 15911 | (version "1.4-8") |
a0244ef0 RW |
15912 | (source |
15913 | (origin | |
15914 | (method url-fetch) | |
15915 | (uri (cran-uri "rgdal" version)) | |
15916 | (sha256 | |
28d94096 | 15917 | (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as")))) |
a0244ef0 RW |
15918 | (properties `((upstream-name . "rgdal"))) |
15919 | (build-system r-build-system) | |
15920 | (inputs | |
15921 | `(("gdal" ,gdal) | |
15922 | ("proj.4" ,proj.4) | |
15923 | ("zlib" ,zlib))) | |
15924 | (propagated-inputs | |
15925 | `(("r-sp" ,r-sp))) | |
15926 | (native-inputs | |
15927 | `(("pkg-config" ,pkg-config))) | |
15928 | (home-page "http://rgdal.r-forge.r-project.org") | |
15929 | (synopsis "Bindings for the Geospatial Data Abstraction Library") | |
15930 | (description | |
15931 | "This package provides bindings to the Geospatial Data Abstraction | |
15932 | Library (GDAL) and access to projection/transformation operations from the | |
15933 | PROJ.4 library.") | |
15934 | (license license:gpl2+))) | |
5ad9da9a RW |
15935 | |
15936 | (define-public r-insol | |
15937 | (package | |
15938 | (name "r-insol") | |
126a7b44 | 15939 | (version "1.2.1") |
5ad9da9a RW |
15940 | (source |
15941 | (origin | |
15942 | (method url-fetch) | |
15943 | (uri (cran-uri "insol" version)) | |
15944 | (sha256 | |
15945 | (base32 | |
126a7b44 | 15946 | "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1")))) |
5ad9da9a RW |
15947 | (properties `((upstream-name . "insol"))) |
15948 | (build-system r-build-system) | |
15949 | (propagated-inputs | |
126a7b44 | 15950 | `(("r-raster" ,r-raster))) |
5ad9da9a RW |
15951 | (native-inputs |
15952 | `(("gfortran" ,gfortran))) | |
15953 | (home-page "https://meteoexploration.com/R/insol/index.html") | |
15954 | (synopsis "Tools for calculating solar radiation") | |
15955 | (description | |
15956 | "This package provides functions to compute insolation on tilted | |
15957 | surfaces, computes atmospheric transmittance and related parameters such as: | |
15958 | Earth radius vector, declination, sunset and sunrise, daylength, equation of | |
15959 | time, vector in the direction of the sun, vector normal to surface, and some | |
15960 | atmospheric physics.") | |
15961 | (license license:gpl2+))) | |
f5b1354f RW |
15962 | |
15963 | (define-public r-lifecycle | |
15964 | (package | |
15965 | (name "r-lifecycle") | |
15966 | (version "0.1.0") | |
15967 | (source | |
15968 | (origin | |
15969 | (method url-fetch) | |
15970 | (uri (cran-uri "lifecycle" version)) | |
15971 | (sha256 | |
15972 | (base32 | |
15973 | "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n")))) | |
15974 | (properties `((upstream-name . "lifecycle"))) | |
15975 | (build-system r-build-system) | |
15976 | (propagated-inputs | |
15977 | `(("r-glue" ,r-glue) | |
15978 | ("r-rlang" ,r-rlang))) | |
15979 | (home-page "https://github.com/r-lib/lifecycle") | |
15980 | (synopsis "Manage the life cycle of your package functions") | |
15981 | (description | |
15982 | "Manage the life cycle of your exported functions with shared | |
15983 | conventions, documentation badges, and non-invasive deprecation warnings. The | |
15984 | lifecycle package defines four development stages (experimental, maturing, | |
15985 | stable, and questioning) and three deprecation stages (soft-deprecated, | |
15986 | deprecated, and defunct). It makes it easy to insert badges corresponding to | |
15987 | these stages in your documentation. Usage of deprecated functions are | |
15988 | signalled with increasing levels of non-invasive verbosity.") | |
15989 | (license license:gpl3))) | |
195854a5 WŻ |
15990 | |
15991 | (define-public r-assertable | |
15992 | (package | |
15993 | (name "r-assertable") | |
b1a112f4 | 15994 | (version "0.2.7") |
195854a5 WŻ |
15995 | (source |
15996 | (origin | |
15997 | (method url-fetch) | |
15998 | (uri (cran-uri "assertable" version)) | |
15999 | (sha256 | |
16000 | (base32 | |
b1a112f4 | 16001 | "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk")))) |
195854a5 WŻ |
16002 | (build-system r-build-system) |
16003 | (propagated-inputs | |
16004 | `(("r-data-table" ,r-data-table))) | |
16005 | (home-page "https://cran.r-project.org/web/packages/assertable/") | |
16006 | (synopsis "Verbose assertions for tabular data (data.frames and data.tables)") | |
16007 | (description "This package provides simple, flexible assertions on | |
16008 | data.frame or data.table objects with verbose output for vetting. While other | |
16009 | assertion packages apply towards more general use-cases, @code{assertable} is | |
16010 | tailored towards tabular data. It includes functions to check variable names | |
16011 | and values, whether the dataset contains all combinations of a given set of | |
16012 | unique identifiers, and whether it is a certain length. In addition, | |
16013 | @code{assertable} includes utility functions to check the existence of target | |
16014 | files and to efficiently import multiple tabular data files into one | |
16015 | data.table.") | |
16016 | (license license:gpl3))) | |
0eb59d9e | 16017 | |
16018 | (define-public r-quadprog | |
16019 | (package | |
16020 | (name "r-quadprog") | |
16021 | (version "1.5-8") | |
16022 | (source | |
16023 | (origin | |
16024 | (method url-fetch) | |
16025 | (uri (cran-uri "quadprog" version)) | |
16026 | (sha256 | |
16027 | (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) | |
16028 | (build-system r-build-system) | |
16029 | (native-inputs | |
16030 | `(("gfortran" ,gfortran))) | |
16031 | (home-page "https://cran.r-project.org/web/packages/quadprog") | |
16032 | (synopsis "Functions to solve quadratic programming problems") | |
16033 | (description | |
16034 | "This package contains routines and documentation for solving quadratic | |
16035 | programming problems.") | |
16036 | (license license:gpl3+))) | |
9bd56b1a | 16037 | |
16038 | (define-public r-desolve | |
16039 | (package | |
16040 | (name "r-desolve") | |
046fecdc | 16041 | (version "1.27") |
9bd56b1a | 16042 | (source |
16043 | (origin | |
16044 | (method url-fetch) | |
16045 | (uri (cran-uri "deSolve" version)) | |
16046 | (sha256 | |
046fecdc | 16047 | (base32 "1qhjq4vxlxd9qmhf6i26x1k7bzhldlxzbby1zgcplicdvlqk951d")))) |
9bd56b1a | 16048 | (properties `((upstream-name . "deSolve"))) |
16049 | (build-system r-build-system) | |
16050 | (native-inputs | |
16051 | `(("gfortran" ,gfortran))) | |
16052 | (home-page "https://desolve.r-forge.r-project.org/") | |
16053 | (synopsis "Solvers for initial value problems of differential equations") | |
ba4fcea4 RW |
16054 | (description "This package provides functions that solve initial value |
16055 | problems of a system of first-order @dfn{ordinary differential | |
16056 | equations} (ODE), of @dfn{partial differential equations} (PDE), of | |
16057 | @dfn{differential algebraic equations} (DAE), and of delay differential | |
16058 | equations. The functions provide an interface to the FORTRAN functions | |
16059 | @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK | |
16060 | collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a | |
16061 | C-implementation of solvers of the Runge-Kutta family with fixed or variable | |
16062 | time steps. The package contains routines designed for solving ODEs resulting | |
16063 | from 1-D, 2-D and 3-D partial differential equations that have been converted | |
16064 | to ODEs by numerical differencing.") | |
9bd56b1a | 16065 | (license license:gpl2+))) |
682768de | 16066 | |
16067 | (define-public r-pracma | |
16068 | (package | |
16069 | (name "r-pracma") | |
aaa74ee5 | 16070 | (version "2.2.9") |
682768de | 16071 | (source (origin |
16072 | (method url-fetch) | |
16073 | (uri (cran-uri "pracma" version)) | |
16074 | (sha256 | |
aaa74ee5 | 16075 | (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc")))) |
682768de | 16076 | (build-system r-build-system) |
16077 | (home-page "https://cran.r-project.org/web/packages/pracma/") | |
16078 | (synopsis "Practical numerical math functions") | |
16079 | (description "This package provides functions for numerical analysis and | |
16080 | linear algebra, numerical optimization, differential equations, plus some | |
16081 | special functions. It uses Matlab function names where appropriate to simplify | |
16082 | porting.") | |
16083 | (license license:gpl3+))) | |
ef7944b9 | 16084 | |
16085 | (define-public r-subplex | |
16086 | (package | |
16087 | (name "r-subplex") | |
16088 | (version "1.5-4") | |
16089 | (source | |
16090 | (origin | |
16091 | (method url-fetch) | |
16092 | (uri (cran-uri "subplex" version)) | |
16093 | (sha256 | |
16094 | (base32 | |
16095 | "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z")))) | |
16096 | (build-system r-build-system) | |
16097 | (native-inputs | |
16098 | `(("gfortran" ,gfortran))) | |
16099 | (home-page "https://cran.r-project.org/web/packages/subplex") | |
16100 | (synopsis "Unconstrained optimization using the subplex algorithm") | |
16101 | (description | |
16102 | "This package implements the Subplex optimization algorithm. | |
16103 | It solves unconstrained optimization problems using a simplex method on | |
16104 | subspaces. The method is well suited for optimizing objective functions that | |
16105 | are noisy or are discontinuous at the solution.") | |
16106 | (license license:gpl3+))) | |
dcc7fad0 RW |
16107 | |
16108 | (define-public r-txtplot | |
16109 | (package | |
16110 | (name "r-txtplot") | |
16111 | (version "1.0-3") | |
16112 | (source | |
16113 | (origin | |
16114 | (method url-fetch) | |
16115 | (uri (cran-uri "txtplot" version)) | |
16116 | (sha256 | |
16117 | (base32 | |
16118 | "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h")))) | |
16119 | (build-system r-build-system) | |
16120 | (home-page "https://cran.r-project.org/web/packages/txtplot/") | |
16121 | (synopsis "Text-based plotting") | |
16122 | (description "This package provides functions to produce rudimentary ASCII | |
16123 | graphics directly in the terminal window. This package provides a basic | |
16124 | plotting function (and equivalents of curve, density, acf and barplot) as well | |
16125 | as a boxplot function.") | |
16126 | (license license:lgpl3+))) | |
e44c4cd7 RW |
16127 | |
16128 | (define-public r-bio3d | |
16129 | (package | |
16130 | (name "r-bio3d") | |
16131 | (version "2.4-0") | |
16132 | (source | |
16133 | (origin | |
16134 | (method url-fetch) | |
16135 | (uri (cran-uri "bio3d" version)) | |
16136 | (sha256 | |
16137 | (base32 | |
16138 | "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s")))) | |
16139 | (properties `((upstream-name . "bio3d"))) | |
16140 | (build-system r-build-system) | |
16141 | (inputs `(("zlib" ,zlib))) | |
16142 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
16143 | (home-page "http://thegrantlab.org/bio3d/") | |
16144 | (synopsis "Biological structure analysis") | |
16145 | (description | |
16146 | "This package provides utilities to process, organize and explore protein | |
16147 | structure, sequence and dynamics data. Features include the ability to read | |
16148 | and write structure, sequence and dynamic trajectory data, perform sequence | |
16149 | and structure database searches, data summaries, atom selection, alignment, | |
16150 | superposition, rigid core identification, clustering, torsion analysis, | |
16151 | distance matrix analysis, structure and sequence conservation analysis, normal | |
16152 | mode analysis, principal component analysis of heterogeneous structure data, | |
16153 | and correlation network analysis from normal mode and molecular dynamics data. | |
16154 | In addition, various utility functions are provided to enable the statistical | |
16155 | and graphical power of the R environment to work with biological sequence and | |
16156 | structural data.") | |
16157 | (license license:gpl2+))) | |
db07641a RW |
16158 | |
16159 | (define-public r-bios2cor | |
16160 | (package | |
16161 | (name "r-bios2cor") | |
16162 | (version "2.0") | |
16163 | (source | |
16164 | (origin | |
16165 | (method url-fetch) | |
16166 | (uri (cran-uri "Bios2cor" version)) | |
16167 | (sha256 | |
16168 | (base32 | |
16169 | "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n")))) | |
16170 | (properties `((upstream-name . "Bios2cor"))) | |
16171 | (build-system r-build-system) | |
16172 | (propagated-inputs | |
16173 | `(("r-bigmemory" ,r-bigmemory) | |
16174 | ("r-bio3d" ,r-bio3d) | |
16175 | ("r-circular" ,r-circular) | |
16176 | ("r-igraph" ,r-igraph))) | |
16177 | (home-page "https://cran.r-project.org/web/packages/Bios2cor/") | |
16178 | (synopsis "From biological sequences and simulations to correlation analysis") | |
16179 | (description | |
16180 | "This package provides utilities for computation and analysis of | |
16181 | correlation/covariation in multiple sequence alignments and in side chain | |
16182 | motions during molecular dynamics simulations. Features include the | |
16183 | computation of correlation/covariation scores using a variety of scoring | |
16184 | functions between either sequence positions in alignments or side chain | |
16185 | dihedral angles in molecular dynamics simulations and utilities to analyze the | |
16186 | correlation/covariation matrix through a variety of tools including network | |
16187 | representation and principal components analysis. In addition, several | |
16188 | utility functions are based on the R graphical environment to provide friendly | |
16189 | tools for help in data interpretation.") | |
16190 | (license license:gpl2+))) | |
59beb0d2 RW |
16191 | |
16192 | ;; This package includes minified JavaScript files. When upgrading please | |
16193 | ;; check that there are no new minified JavaScript files. | |
16194 | (define-public r-networkd3 | |
16195 | (package | |
16196 | (name "r-networkd3") | |
16197 | (version "0.4") | |
16198 | (source | |
16199 | (origin | |
16200 | (method url-fetch) | |
16201 | (uri (cran-uri "networkD3" version)) | |
16202 | (sha256 | |
16203 | (base32 | |
16204 | "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k")) | |
16205 | (snippet | |
16206 | '(begin | |
16207 | (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js") | |
16208 | #t)))) | |
16209 | (properties `((upstream-name . "networkD3"))) | |
16210 | (build-system r-build-system) | |
16211 | (arguments | |
16212 | `(#:modules ((guix build utils) | |
16213 | (guix build r-build-system) | |
16214 | (srfi srfi-1) | |
16215 | (ice-9 popen)) | |
16216 | #:phases | |
16217 | (modify-phases %standard-phases | |
16218 | (add-after 'unpack 'process-javascript | |
16219 | (lambda* (#:key inputs #:allow-other-keys) | |
16220 | (with-directory-excursion "inst/htmlwidgets/lib/" | |
16221 | (call-with-values | |
16222 | (lambda () | |
16223 | (unzip2 | |
16224 | `((,(assoc-ref inputs "d3.v4.js") | |
16225 | "d3-4.5.0/d3.min.js")))) | |
16226 | (lambda (sources targets) | |
16227 | (for-each (lambda (source target) | |
16228 | (format #t "Processing ~a --> ~a~%" | |
16229 | source target) | |
16230 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
16231 | (call-with-output-file target | |
16232 | (lambda (port) | |
16233 | (dump-port minified port))))) | |
16234 | sources targets)))) | |
16235 | #t))))) | |
16236 | (native-inputs | |
16237 | `(("uglify-js" ,uglify-js) | |
16238 | ;; NOTE: Make sure that this version of d3 is still valid when | |
16239 | ;; upgrading the package. | |
16240 | ("d3.v4.js" | |
16241 | ,(origin | |
16242 | (method url-fetch) | |
16243 | (uri "https://d3js.org/d3.v4.js") | |
16244 | (sha256 | |
16245 | (base32 | |
16246 | "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) | |
16247 | (propagated-inputs | |
16248 | `(("r-htmlwidgets" ,r-htmlwidgets) | |
16249 | ("r-igraph" ,r-igraph) | |
16250 | ("r-magrittr" ,r-magrittr))) | |
16251 | (home-page "https://cran.r-project.org/package=networkD3") | |
16252 | (synopsis "D3 JavaScript network graphs from R") | |
16253 | (description | |
16254 | "This package creates D3 JavaScript network, tree, dendrogram, and Sankey | |
16255 | graphs from R.") | |
16256 | (license license:gpl3+))) | |
303c7d1d RW |
16257 | |
16258 | (define-public r-aasea | |
16259 | (package | |
16260 | (name "r-aasea") | |
16261 | (version "1.1.0") | |
16262 | (source | |
16263 | (origin | |
16264 | (method url-fetch) | |
16265 | (uri (cran-uri "aaSEA" version)) | |
16266 | (sha256 | |
16267 | (base32 | |
16268 | "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h")))) | |
16269 | (properties `((upstream-name . "aaSEA"))) | |
16270 | (build-system r-build-system) | |
16271 | (propagated-inputs | |
16272 | `(("r-bios2cor" ,r-bios2cor) | |
16273 | ("r-dt" ,r-dt) | |
16274 | ("r-hmisc" ,r-hmisc) | |
16275 | ("r-magrittr" ,r-magrittr) | |
16276 | ("r-networkd3" ,r-networkd3) | |
16277 | ("r-plotly" ,r-plotly) | |
16278 | ("r-seqinr" ,r-seqinr) | |
16279 | ("r-shiny" ,r-shiny) | |
16280 | ("r-shinydashboard" ,r-shinydashboard))) | |
16281 | (home-page "https://cran.r-project.org/web/packages/aaSEA/") | |
16282 | (synopsis "Amino acid substitution effect analyzer") | |
16283 | (description | |
16284 | "Given a protein multiple sequence alignment, it is a daunting task to | |
16285 | assess the effects of substitutions along sequence length. The aaSEA package | |
16286 | is intended to help researchers to rapidly analyze property changes caused by | |
16287 | single, multiple and correlated amino acid substitutions in proteins.") | |
16288 | (license license:gpl3))) | |
595d9502 RW |
16289 | |
16290 | (define-public r-abacus | |
16291 | (package | |
16292 | (name "r-abacus") | |
16293 | (version "1.0.0") | |
16294 | (source | |
16295 | (origin | |
16296 | (method url-fetch) | |
16297 | (uri (cran-uri "ABACUS" version)) | |
16298 | (sha256 | |
16299 | (base32 | |
16300 | "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i")))) | |
16301 | (properties `((upstream-name . "ABACUS"))) | |
16302 | (build-system r-build-system) | |
16303 | (propagated-inputs | |
16304 | `(("r-ggplot2" ,r-ggplot2) | |
16305 | ("r-shiny" ,r-shiny))) | |
16306 | (home-page "https://shiny.abdn.ac.uk/Stats/apps/") | |
16307 | (synopsis "Apps-based activities for communicating and understanding statistics") | |
16308 | (description | |
16309 | "This package provides a set of Shiny apps for effective communication | |
16310 | and understanding in statistics. The current version includes properties of | |
16311 | normal distribution, properties of sampling distribution, one-sample z and t | |
16312 | tests, two samples independent (unpaired) t test and analysis of variance.") | |
16313 | (license license:gpl3))) | |
8fed766a RW |
16314 | |
16315 | (define-public r-abc-rap | |
16316 | (package | |
16317 | (name "r-abc-rap") | |
16318 | (version "0.9.0") | |
16319 | (source | |
16320 | (origin | |
16321 | (method url-fetch) | |
16322 | (uri (cran-uri "ABC.RAP" version)) | |
16323 | (sha256 | |
16324 | (base32 | |
16325 | "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk")))) | |
16326 | (properties `((upstream-name . "ABC.RAP"))) | |
16327 | (build-system r-build-system) | |
16328 | (home-page "https://cran.r-project.org/web/packages/ABC.RAP/") | |
16329 | (synopsis "Array-based CpG region analysis pipeline") | |
16330 | (description | |
16331 | "This package aims to identify candidate genes that are differentially | |
16332 | methylated between cases and controls. It applies Student's t-test and delta | |
16333 | beta analysis to identify candidate genes containing multiple CpG sites.") | |
16334 | (license license:gpl3))) | |
647ff4a9 RW |
16335 | |
16336 | (define-public r-abcadm | |
16337 | (package | |
16338 | (name "r-abcadm") | |
16339 | (version "1.0") | |
16340 | (source | |
16341 | (origin | |
16342 | (method url-fetch) | |
16343 | (uri (cran-uri "abcADM" version)) | |
16344 | (sha256 | |
16345 | (base32 | |
16346 | "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10")))) | |
16347 | (properties `((upstream-name . "abcADM"))) | |
16348 | (build-system r-build-system) | |
16349 | (propagated-inputs | |
16350 | `(("r-bh" ,r-bh) | |
16351 | ("r-rcpp" ,r-rcpp))) | |
16352 | (home-page "https://cran.r-project.org/web/packages/abcADM/") | |
16353 | (synopsis "Fit accumulated damage models and estimate reliability using ABC") | |
16354 | (description | |
16355 | "This package provides tools to estimate parameters of accumulated | |
16356 | damage (load duration) models based on failure time data under a Bayesian | |
16357 | framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess | |
16358 | long-term reliability under stochastic load profiles.") | |
16359 | (license license:gpl3))) | |
72e5c6e9 RW |
16360 | |
16361 | (define-public r-rglpk | |
16362 | (package | |
16363 | (name "r-rglpk") | |
16364 | (version "0.6-4") | |
16365 | (source | |
16366 | (origin | |
16367 | (method url-fetch) | |
16368 | (uri (cran-uri "Rglpk" version)) | |
16369 | (sha256 | |
16370 | (base32 | |
16371 | "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2")))) | |
16372 | (properties `((upstream-name . "Rglpk"))) | |
16373 | (build-system r-build-system) | |
16374 | (propagated-inputs | |
16375 | `(("r-slam" ,r-slam))) | |
16376 | (inputs | |
16377 | `(("glpk" ,glpk))) | |
16378 | (home-page "http://R-Forge.R-project.org/projects/rglp/") | |
16379 | (synopsis "R interface to the GNU Linear Programming Kit") | |
16380 | (description | |
16381 | "This package provides an R interface to the GNU Linear Programming Kit, | |
16382 | software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed | |
16383 | integer linear programming} (MILP) and other related problems.") | |
16384 | ;; Either license | |
16385 | (license (list license:gpl2 license:gpl3)))) | |
84822497 RW |
16386 | |
16387 | (define-public r-abcdefba | |
16388 | (package | |
16389 | (name "r-abcdefba") | |
16390 | (version "0.4") | |
16391 | (source | |
16392 | (origin | |
16393 | (method url-fetch) | |
16394 | (uri (cran-uri "abcdeFBA" version)) | |
16395 | (sha256 | |
16396 | (base32 | |
16397 | "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4")))) | |
16398 | (properties `((upstream-name . "abcdeFBA"))) | |
16399 | (build-system r-build-system) | |
16400 | (propagated-inputs | |
16401 | `(("r-corrplot" ,r-corrplot) | |
16402 | ("r-lattice" ,r-lattice) | |
16403 | ("r-rgl" ,r-rgl) | |
16404 | ("r-rglpk" ,r-rglpk))) | |
16405 | (home-page "https://cran.r-project.org/web/packages/abcdeFBA/") | |
16406 | (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package") | |
16407 | (description | |
16408 | "This package provides functions for Constraint Based Simulation using | |
16409 | Flux Balance Analysis and informative analysis of the data generated during | |
16410 | simulation.") | |
16411 | (license license:gpl2))) | |
ae07172c RW |
16412 | |
16413 | (define-public r-abcrlda | |
16414 | (package | |
16415 | (name "r-abcrlda") | |
16416 | (version "1.0.1") | |
16417 | (source | |
16418 | (origin | |
16419 | (method url-fetch) | |
16420 | (uri (cran-uri "abcrlda" version)) | |
16421 | (sha256 | |
16422 | (base32 | |
16423 | "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85")))) | |
16424 | (properties `((upstream-name . "abcrlda"))) | |
16425 | (build-system r-build-system) | |
16426 | (home-page "https://ieeexplore.ieee.org/document/8720003/") | |
16427 | (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis") | |
16428 | (description | |
16429 | "This package offers methods to perform @dfn{asymptotically | |
16430 | bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for | |
16431 | cost-sensitive binary classification. The bias-correction is an estimate of | |
16432 | the bias term added to regularized discriminant analysis that minimizes the | |
16433 | overall risk.") | |
16434 | (license license:gpl3))) | |
3e333777 RW |
16435 | |
16436 | (define-public r-abemus | |
16437 | (package | |
16438 | (name "r-abemus") | |
16439 | (version "1.0.1") | |
16440 | (source | |
16441 | (origin | |
16442 | (method url-fetch) | |
16443 | (uri (cran-uri "abemus" version)) | |
16444 | (sha256 | |
16445 | (base32 | |
16446 | "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb")))) | |
16447 | (properties `((upstream-name . "abemus"))) | |
16448 | (build-system r-build-system) | |
16449 | (propagated-inputs | |
16450 | `(("r-data-table" ,r-data-table))) | |
16451 | (home-page "https://cran.r-project.org/web/packages/abemus/") | |
16452 | (synopsis "Adaptive base error model in ultra-deep sequencing data") | |
16453 | (description | |
16454 | "This package provides an implementation of @dfn{Adaptive Base Error | |
16455 | Model in Ultra-deep Sequencing data} (ABEMUS), which combines | |
16456 | platform-specific genetic knowledge and empirical signal to readily detect and | |
16457 | quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating | |
16458 | cell free DNA} (cfDNA).") | |
16459 | (license license:gpl3))) | |
8990fc15 RW |
16460 | |
16461 | ;; This package includes minified JavaScript files. When upgrading please | |
16462 | ;; check that there are no new minified JavaScript files. | |
16463 | (define-public r-rintrojs | |
16464 | (package | |
16465 | (name "r-rintrojs") | |
16466 | (version "0.2.2") | |
16467 | (source | |
16468 | (origin | |
16469 | (method url-fetch) | |
16470 | (uri (cran-uri "rintrojs" version)) | |
16471 | (sha256 | |
16472 | (base32 | |
16473 | "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427")))) | |
16474 | (properties `((upstream-name . "rintrojs"))) | |
16475 | (build-system r-build-system) | |
16476 | (arguments | |
16477 | `(#:modules ((guix build utils) | |
16478 | (guix build r-build-system) | |
16479 | (srfi srfi-1) | |
16480 | (ice-9 popen)) | |
16481 | #:phases | |
16482 | (modify-phases %standard-phases | |
16483 | (add-after 'unpack 'process-javascript | |
16484 | (lambda* (#:key inputs #:allow-other-keys) | |
16485 | (with-directory-excursion "inst/javascript/introjs/" | |
16486 | (call-with-values | |
16487 | (lambda () | |
16488 | (unzip2 | |
16489 | `((,(assoc-ref inputs "intro.js") | |
16490 | "intro.min.js")))) | |
16491 | (lambda (sources targets) | |
16492 | (for-each (lambda (source target) | |
16493 | (format #t "Processing ~a --> ~a~%" | |
16494 | source target) | |
16495 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
16496 | (call-with-output-file target | |
16497 | (lambda (port) | |
16498 | (dump-port minified port))))) | |
16499 | sources targets)))) | |
16500 | #t))))) | |
16501 | (native-inputs | |
16502 | `(("uglify-js" ,uglify-js) | |
16503 | ("intro.js" | |
16504 | ,(origin | |
16505 | (method url-fetch) | |
16506 | (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js") | |
16507 | (sha256 | |
16508 | (base32 | |
16509 | "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8")))))) | |
16510 | (propagated-inputs | |
16511 | `(("r-jsonlite" ,r-jsonlite) | |
16512 | ("r-shiny" ,r-shiny))) | |
16513 | (home-page "https://github.com/carlganz/rintrojs") | |
16514 | (synopsis "Wrapper for the Intro.js library") | |
16515 | (description | |
16516 | "This package provides a wrapper for the @url{http://www.introjs.com, | |
16517 | Intro.js} library. This package makes it easy to include step-by-step | |
16518 | introductions, and clickable hints in a Shiny application. It supports both | |
16519 | static introductions in the UI, and programmatic introductions from the | |
16520 | server-side.") | |
16521 | (license license:agpl3+))) | |
322e8d85 RW |
16522 | |
16523 | (define-public r-sysfonts | |
16524 | (package | |
16525 | (name "r-sysfonts") | |
16526 | (version "0.8") | |
16527 | (source | |
16528 | (origin | |
16529 | (method url-fetch) | |
16530 | (uri (cran-uri "sysfonts" version)) | |
16531 | (sha256 | |
16532 | (base32 | |
16533 | "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43")))) | |
16534 | (properties `((upstream-name . "sysfonts"))) | |
16535 | (build-system r-build-system) | |
16536 | (inputs | |
16537 | `(("freetype" ,freetype) | |
16538 | ("libpng" ,libpng) | |
16539 | ("zlib" ,zlib))) | |
16540 | (native-inputs | |
16541 | `(("pkg-config" ,pkg-config))) | |
16542 | (home-page "https://github.com/yixuan/sysfonts") | |
16543 | (synopsis "Loading fonts into R") | |
16544 | (description | |
16545 | "This is a package to simplify loading of system fonts and Google Fonts | |
16546 | into R, in order to support other packages.") | |
16547 | (license license:gpl2))) | |
369e1bb6 RW |
16548 | |
16549 | (define-public r-showtextdb | |
16550 | (package | |
16551 | (name "r-showtextdb") | |
16552 | (version "2.0") | |
16553 | (source | |
16554 | (origin | |
16555 | (method url-fetch) | |
16556 | (uri (cran-uri "showtextdb" version)) | |
16557 | (sha256 | |
16558 | (base32 | |
16559 | "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh")))) | |
16560 | (properties `((upstream-name . "showtextdb"))) | |
16561 | (build-system r-build-system) | |
16562 | (propagated-inputs | |
16563 | `(("r-sysfonts" ,r-sysfonts))) | |
16564 | (home-page "https://cran.r-project.org/web/packages/showtextdb/") | |
16565 | (synopsis "Font files for the 'showtext' package") | |
16566 | (description | |
16567 | "This package provides font files that can be used by the @code{showtext} | |
16568 | package.") | |
16569 | (license license:asl2.0))) | |
d7937243 RW |
16570 | |
16571 | (define-public r-showtext | |
16572 | (package | |
16573 | (name "r-showtext") | |
16574 | (version "0.7") | |
16575 | (source | |
16576 | (origin | |
16577 | (method url-fetch) | |
16578 | (uri (cran-uri "showtext" version)) | |
16579 | (sha256 | |
16580 | (base32 | |
16581 | "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73")))) | |
16582 | (properties `((upstream-name . "showtext"))) | |
16583 | (build-system r-build-system) | |
16584 | (inputs | |
16585 | `(("freetype" ,freetype) | |
16586 | ("libpng" ,libpng) | |
16587 | ("zlib" ,zlib))) | |
16588 | (propagated-inputs | |
16589 | `(("r-showtextdb" ,r-showtextdb) | |
16590 | ("r-sysfonts" ,r-sysfonts))) | |
16591 | (native-inputs `(("pkg-config" ,pkg-config))) | |
16592 | (home-page "https://github.com/yixuan/showtext") | |
16593 | (synopsis "Using fonts more easily in R graphs") | |
16594 | (description | |
16595 | "This package aims to make it easy to use various types of | |
16596 | fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports | |
16597 | most output formats of R graphics including PNG, PDF and SVG. Text glyphs | |
16598 | will be converted into polygons or raster images, hence after the plot has | |
16599 | been created, it no longer relies on the font files. No external software | |
16600 | such as Ghostscript is needed to use this package.") | |
16601 | (license license:asl2.0))) | |
2ecd4e3b RW |
16602 | |
16603 | (define-public r-emojifont | |
16604 | (package | |
16605 | (name "r-emojifont") | |
16606 | (version "0.5.3") | |
16607 | (source | |
16608 | (origin | |
16609 | (method url-fetch) | |
16610 | (uri (cran-uri "emojifont" version)) | |
16611 | (sha256 | |
16612 | (base32 | |
16613 | "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k")))) | |
16614 | (properties `((upstream-name . "emojifont"))) | |
16615 | (build-system r-build-system) | |
16616 | (propagated-inputs | |
16617 | `(("r-ggplot2" ,r-ggplot2) | |
16618 | ("r-proto" ,r-proto) | |
16619 | ("r-showtext" ,r-showtext) | |
16620 | ("r-sysfonts" ,r-sysfonts))) | |
16621 | (home-page "https://guangchuangyu.github.io/emojifont") | |
16622 | (synopsis "Emoji and Font Awesome in R graphics") | |
16623 | (description | |
16624 | "This package enables the use of emoji and the Font Awesome glyphs in | |
16625 | both base and ggplot2 graphics.") | |
16626 | (license license:artistic2.0))) | |
a99c4c75 RW |
16627 | |
16628 | (define-public r-abstractr | |
16629 | (package | |
16630 | (name "r-abstractr") | |
16631 | (version "0.1.0") | |
16632 | (source | |
16633 | (origin | |
16634 | (method url-fetch) | |
16635 | (uri (cran-uri "abstractr" version)) | |
16636 | (sha256 | |
16637 | (base32 | |
16638 | "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig")))) | |
16639 | (properties `((upstream-name . "abstractr"))) | |
16640 | (build-system r-build-system) | |
16641 | (propagated-inputs | |
16642 | `(("r-colourpicker" ,r-colourpicker) | |
16643 | ("r-emojifont" ,r-emojifont) | |
16644 | ("r-ggplot2" ,r-ggplot2) | |
16645 | ("r-gridextra" ,r-gridextra) | |
16646 | ("r-rintrojs" ,r-rintrojs) | |
16647 | ("r-shiny" ,r-shiny) | |
16648 | ("r-shinythemes" ,r-shinythemes))) | |
16649 | (home-page "https://matt-kumar.shinyapps.io/portfolio") | |
16650 | (synopsis "R-Shiny application for creating visual abstracts") | |
16651 | (description | |
16652 | "This package provides an R Shiny application to create visual abstracts | |
16653 | for original research. A variety of user defined options and formatting are | |
16654 | included.") | |
16655 | (license license:gpl3))) | |
bd74d7e6 RW |
16656 | |
16657 | (define-public r-abtest | |
16658 | (package | |
16659 | (name "r-abtest") | |
16660 | (version "0.2.0") | |
16661 | (source | |
16662 | (origin | |
16663 | (method url-fetch) | |
16664 | (uri (cran-uri "abtest" version)) | |
16665 | (sha256 | |
16666 | (base32 | |
16667 | "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws")))) | |
16668 | (properties `((upstream-name . "abtest"))) | |
16669 | (build-system r-build-system) | |
16670 | (propagated-inputs | |
16671 | `(("r-matrix" ,r-matrix) | |
16672 | ("r-mvtnorm" ,r-mvtnorm) | |
16673 | ("r-plotrix" ,r-plotrix) | |
16674 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
16675 | ("r-rcpp" ,r-rcpp) | |
16676 | ("r-sn" ,r-sn) | |
16677 | ("r-truncnorm" ,r-truncnorm) | |
16678 | ("r-vgam" ,r-vgam))) | |
16679 | (home-page "https://cran.r-project.org/web/packages/abtest/") | |
16680 | (synopsis "Bayesian A/B testing") | |
16681 | (description | |
16682 | "This package provides functions for Bayesian A/B testing including prior | |
16683 | elicitation options based on Kass and Vaidyanathan (1992) | |
16684 | @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.") | |
16685 | (license license:gpl2+))) | |
0379a167 RW |
16686 | |
16687 | (define-public r-accept | |
16688 | (package | |
16689 | (name "r-accept") | |
16690 | (version "0.7.0") | |
16691 | (source | |
16692 | (origin | |
16693 | (method url-fetch) | |
16694 | (uri (cran-uri "accept" version)) | |
16695 | (sha256 | |
16696 | (base32 | |
16697 | "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx")))) | |
16698 | (properties `((upstream-name . "accept"))) | |
16699 | (build-system r-build-system) | |
16700 | (propagated-inputs | |
16701 | `(("r-dplyr" ,r-dplyr) | |
16702 | ("r-extrafont" ,r-extrafont) | |
16703 | ("r-mass" ,r-mass) | |
16704 | ("r-plotly" ,r-plotly) | |
16705 | ("r-stringr" ,r-stringr) | |
16706 | ("r-viridis" ,r-viridis))) | |
16707 | (home-page "https://cran.r-project.org/web/packages/accept/") | |
16708 | (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") | |
16709 | (description | |
16710 | "This package allows clinicians to predict the rate and severity of | |
16711 | future acute exacerbation in @dfn{Chronic Obstructive Pulmonary | |
16712 | Disease} (COPD) patients, based on the clinical prediction model published in | |
16713 | Adibi et al. (2019) @url{doi:10.1101/651901}.") | |
16714 | (license license:gpl3))) | |
bba4ec62 RW |
16715 | |
16716 | (define-public r-smpracticals | |
16717 | (package | |
16718 | (name "r-smpracticals") | |
16719 | (version "1.4-3") | |
16720 | (source | |
16721 | (origin | |
16722 | (method url-fetch) | |
16723 | (uri (cran-uri "SMPracticals" version)) | |
16724 | (sha256 | |
16725 | (base32 | |
16726 | "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf")))) | |
16727 | (properties `((upstream-name . "SMPracticals"))) | |
16728 | (build-system r-build-system) | |
16729 | (propagated-inputs | |
16730 | `(("r-ellipse" ,r-ellipse) | |
16731 | ("r-mass" ,r-mass) | |
16732 | ("r-nlme" ,r-nlme) | |
16733 | ("r-survival" ,r-survival))) | |
16734 | (home-page "http://statwww.epfl.ch/davison/SM/") | |
16735 | (synopsis "Practicals for use with Davison (2003) Statistical Models") | |
16736 | (description | |
16737 | "This package contains the datasets and a few functions for use with the | |
16738 | practicals outlined in Appendix A of the book Statistical Models (Davison, | |
16739 | 2003, Cambridge University Press). The practicals themselves can be found at | |
16740 | @url{http://statwww.epfl.ch/davison/SM/}.") | |
16741 | (license license:gpl2+))) | |
5a5431e4 RW |
16742 | |
16743 | (define-public r-fgui | |
16744 | (package | |
16745 | (name "r-fgui") | |
16746 | (version "1.0-8") | |
16747 | (source | |
16748 | (origin | |
16749 | (method url-fetch) | |
16750 | (uri (cran-uri "fgui" version)) | |
16751 | (sha256 | |
16752 | (base32 | |
16753 | "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv")))) | |
16754 | (properties `((upstream-name . "fgui"))) | |
16755 | (build-system r-build-system) | |
16756 | (home-page | |
16757 | "https://sites.google.com/site/thomashoffmannproject/software/fgui") | |
16758 | (synopsis "Create GUI for R functions") | |
16759 | (description | |
16760 | "Rapidly create a GUI for a function you created by automatically | |
16761 | creating widgets for arguments of the function. This package automatically | |
16762 | parses help routines for context-sensitive help to these arguments. The | |
16763 | interface is essentially a wrapper to some Tcl/Tk routines to both simplify | |
16764 | and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be | |
16765 | incorporated into the interface for greater customization for the more | |
16766 | experienced.") | |
16767 | ;; Any version of the GPL. | |
16768 | (license (list license:gpl2+ license:gpl3+)))) | |
f9d9c831 RW |
16769 | |
16770 | (define-public r-tcltk2 | |
16771 | (package | |
16772 | (name "r-tcltk2") | |
16773 | (version "1.2-11") | |
16774 | (source | |
16775 | (origin | |
16776 | (method url-fetch) | |
16777 | (uri (cran-uri "tcltk2" version)) | |
16778 | (sha256 | |
16779 | (base32 | |
16780 | "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d")))) | |
16781 | (properties `((upstream-name . "tcltk2"))) | |
16782 | (build-system r-build-system) | |
16783 | (inputs | |
16784 | `(("tcl" ,tcl) | |
16785 | ("tk" ,tk))) | |
16786 | (home-page "http://www.sciviews.org/SciViews-R") | |
16787 | (synopsis "Tcl/Tk additions") | |
16788 | (description | |
16789 | "This package provides a series of additional Tcl commands and Tk widgets | |
16790 | with style and various functions to supplement the tcltk package") | |
16791 | (license license:lgpl3))) | |
c5b86d3a RW |
16792 | |
16793 | (define-public r-accrual | |
16794 | (package | |
16795 | (name "r-accrual") | |
16796 | (version "1.3") | |
16797 | (source | |
16798 | (origin | |
16799 | (method url-fetch) | |
16800 | (uri (cran-uri "accrual" version)) | |
16801 | (sha256 | |
16802 | (base32 | |
16803 | "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z")))) | |
16804 | (properties `((upstream-name . "accrual"))) | |
16805 | (build-system r-build-system) | |
16806 | (propagated-inputs | |
16807 | `(("r-fgui" ,r-fgui) | |
16808 | ("r-smpracticals" ,r-smpracticals) | |
16809 | ("r-tcltk2" ,r-tcltk2))) | |
16810 | (home-page "https://cran.r-project.org/web/packages/accrual/") | |
16811 | (synopsis "Bayesian accrual prediction") | |
16812 | (description | |
16813 | "Subject recruitment for medical research is challenging. Slow patient | |
16814 | accrual leads to delay in research. Accrual monitoring during the process of | |
16815 | recruitment is critical. Researchers need reliable tools to manage the | |
16816 | accrual rate. This package provides an implementation of a Bayesian method | |
16817 | that integrates researcher's experience on previous trials and data from the | |
16818 | current study, providing reliable prediction on accrual rate for clinical | |
16819 | studies. It provides functions for Bayesian accrual prediction which can be | |
16820 | easily used by statisticians and clinical researchers.") | |
16821 | (license license:gpl2))) | |
592d423c RW |
16822 | |
16823 | (define-public r-accrued | |
16824 | (package | |
16825 | (name "r-accrued") | |
16826 | (version "1.4.1") | |
16827 | (source | |
16828 | (origin | |
16829 | (method url-fetch) | |
16830 | (uri (cran-uri "accrued" version)) | |
16831 | (sha256 | |
16832 | (base32 | |
16833 | "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5")))) | |
16834 | (properties `((upstream-name . "accrued"))) | |
16835 | (build-system r-build-system) | |
16836 | (home-page "https://cran.r-project.org/web/packages/accrued/") | |
16837 | (synopsis "Data quality visualization tools for partially accruing data") | |
16838 | (description | |
16839 | "This is a package for visualizing data quality of partially accruing | |
16840 | data.") | |
16841 | (license license:gpl3))) | |
7e2e46cb RW |
16842 | |
16843 | (define-public r-mda | |
16844 | (package | |
16845 | (name "r-mda") | |
16846 | (version "0.4-10") | |
16847 | (source | |
16848 | (origin | |
16849 | (method url-fetch) | |
16850 | (uri (cran-uri "mda" version)) | |
16851 | (sha256 | |
16852 | (base32 | |
16853 | "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh")))) | |
16854 | (properties `((upstream-name . "mda"))) | |
16855 | (build-system r-build-system) | |
16856 | (propagated-inputs `(("r-class" ,r-class))) | |
16857 | (native-inputs `(("gfortran" ,gfortran))) | |
16858 | (home-page "https://cran.r-project.org/web/packages/mda/") | |
16859 | (synopsis "Mixture and flexible discriminant analysis") | |
16860 | (description | |
16861 | "This is a package for mixture and flexible discriminant analysis, | |
16862 | @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.") | |
16863 | (license license:gpl2))) | |
c909b710 RW |
16864 | |
16865 | (define-public r-elasticnet | |
16866 | (package | |
16867 | (name "r-elasticnet") | |
16868 | (version "1.1.1") | |
16869 | (source | |
16870 | (origin | |
16871 | (method url-fetch) | |
16872 | (uri (cran-uri "elasticnet" version)) | |
16873 | (sha256 | |
16874 | (base32 | |
16875 | "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb")))) | |
16876 | (properties `((upstream-name . "elasticnet"))) | |
16877 | (build-system r-build-system) | |
16878 | (propagated-inputs | |
16879 | `(("r-lars" ,r-lars))) | |
16880 | (home-page "http://www.stat.umn.edu/~hzou") | |
16881 | (synopsis "Elastic-Net for sparse estimation and sparse PCA") | |
16882 | (description | |
16883 | "This package provides functions for fitting the entire solution path of | |
16884 | the Elastic-Net and also provides functions for estimating sparse Principal | |
16885 | Components. The Lasso solution paths can be computed by the same function.") | |
16886 | (license license:gpl2+))) | |
7199d2a5 RW |
16887 | |
16888 | (define-public r-sparselda | |
16889 | (package | |
16890 | (name "r-sparselda") | |
16891 | (version "0.1-9") | |
16892 | (source | |
16893 | (origin | |
16894 | (method url-fetch) | |
16895 | (uri (cran-uri "sparseLDA" version)) | |
16896 | (sha256 | |
16897 | (base32 | |
16898 | "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb")))) | |
16899 | (properties `((upstream-name . "sparseLDA"))) | |
16900 | (build-system r-build-system) | |
16901 | (propagated-inputs | |
16902 | `(("r-elasticnet" ,r-elasticnet) | |
16903 | ("r-mass" ,r-mass) | |
16904 | ("r-mda" ,r-mda))) | |
16905 | (home-page "http://www.imm.dtu.dk/~lhc") | |
16906 | (synopsis "Sparse discriminant analysis") | |
16907 | (description | |
16908 | "This package performs sparse linear discriminant analysis for Gaussians | |
16909 | and mixture of Gaussian models.") | |
16910 | (license license:gpl2+))) | |
b8d52fe2 RW |
16911 | |
16912 | (define-public r-accsda | |
16913 | (package | |
16914 | (name "r-accsda") | |
16915 | (version "1.0.0") | |
16916 | (source | |
16917 | (origin | |
16918 | (method url-fetch) | |
16919 | (uri (cran-uri "accSDA" version)) | |
16920 | (sha256 | |
16921 | (base32 | |
16922 | "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61")))) | |
16923 | (properties `((upstream-name . "accSDA"))) | |
16924 | (build-system r-build-system) | |
16925 | (propagated-inputs | |
16926 | `(("r-ggplot2" ,r-ggplot2) | |
16927 | ("r-ggthemes" ,r-ggthemes) | |
16928 | ("r-gridextra" ,r-gridextra) | |
16929 | ("r-mass" ,r-mass) | |
16930 | ("r-rarpack" ,r-rarpack) | |
16931 | ("r-sparselda" ,r-sparselda))) | |
16932 | (home-page "https://github.com/gumeo/accSDA/wiki") | |
16933 | (synopsis "Accelerated sparse discriminant analysis") | |
16934 | (description | |
16935 | "This package provides an implementation of sparse linear discriminant | |
16936 | analysis, which is a supervised classification method for multiple classes. | |
16937 | Various novel optimization approaches to this problem are implemented | |
16938 | including @dfn{alternating direction method of multipliers} (ADMM), | |
16939 | @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG). | |
16940 | Functions for performing cross validation are also supplied along with basic | |
16941 | prediction and plotting functions. @dfn{Sparse zero variance | |
16942 | discriminant} (SZVD) analysis is also included in the package.") | |
16943 | (license license:gpl2+))) | |
b441dac7 RW |
16944 | |
16945 | (define-public r-ace2fastq | |
16946 | (package | |
16947 | (name "r-ace2fastq") | |
16948 | (version "0.6.0") | |
16949 | (source | |
16950 | (origin | |
16951 | (method url-fetch) | |
16952 | (uri (cran-uri "ace2fastq" version)) | |
16953 | (sha256 | |
16954 | (base32 | |
16955 | "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic")))) | |
16956 | (properties `((upstream-name . "ace2fastq"))) | |
16957 | (build-system r-build-system) | |
16958 | (propagated-inputs | |
16959 | `(("r-stringr" ,r-stringr))) | |
16960 | (home-page "https://github.com/c5sire/ace2fastq") | |
16961 | (synopsis "ACE file to FASTQ converter") | |
16962 | (description | |
16963 | "The ACE file format is used in genomics to store contigs from sequencing | |
16964 | machines. This tools converts it into FASTQ format. Both formats contain the | |
16965 | sequence characters and their corresponding quality information. Unlike the | |
16966 | FASTQ file, the ACE file stores the quality values numerically. The | |
16967 | conversion algorithm uses the standard Sanger formula. The package | |
16968 | facilitates insertion into pipelines, and content inspection.") | |
16969 | (license license:gpl3))) | |
ca1bc50c RW |
16970 | |
16971 | (define-public r-rngwell | |
16972 | (package | |
16973 | (name "r-rngwell") | |
16974 | (version "0.10-5") | |
16975 | (source | |
16976 | (origin | |
16977 | (method url-fetch) | |
16978 | (uri (cran-uri "rngWELL" version)) | |
16979 | (sha256 | |
16980 | (base32 | |
16981 | "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb")))) | |
16982 | (properties `((upstream-name . "rngWELL"))) | |
16983 | (build-system r-build-system) | |
16984 | (home-page "https://cran.r-project.org/web/packages/rngWELL/") | |
16985 | (synopsis "Toolbox for WELL random number generators") | |
16986 | (description | |
16987 | "This is a dedicated package to WELL pseudo random generators, which were | |
16988 | introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based | |
16989 | on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") | |
16990 | (license license:bsd-3))) | |
e6bf1472 RW |
16991 | |
16992 | (define-public r-randtoolbox | |
16993 | (package | |
16994 | (name "r-randtoolbox") | |
16995 | (version "1.30.0") | |
16996 | (source | |
16997 | (origin | |
16998 | (method url-fetch) | |
16999 | (uri (cran-uri "randtoolbox" version)) | |
17000 | (sha256 | |
17001 | (base32 | |
17002 | "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd")))) | |
17003 | (properties `((upstream-name . "randtoolbox"))) | |
17004 | (build-system r-build-system) | |
17005 | (propagated-inputs | |
17006 | `(("r-rngwell" ,r-rngwell))) | |
17007 | (native-inputs | |
17008 | `(("gfortran" ,gfortran))) | |
17009 | (home-page "https://cran.r-project.org/web/packages/randtoolbox/") | |
17010 | (synopsis "Toolbox for pseudo and quasi random number generation") | |
17011 | (description | |
17012 | "This package provides | |
17013 | ||
17014 | @enumerate | |
17015 | @item pseudo random generators, such as general linear | |
17016 | congruential generators, multiple recursive generators and generalized | |
17017 | feedback shift register (SF-Mersenne Twister algorithm and WELL | |
17018 | generators) | |
17019 | ||
17020 | @item quasi random generators, such as the Torus algorithm, the Sobol | |
17021 | sequence, the Halton sequence (including the Van der Corput sequence), and | |
17022 | ||
17023 | @item some generator tests: the gap test, the serial test, the poker test. | |
17024 | @end enumerate | |
17025 | ||
17026 | See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") | |
17027 | (license license:bsd-3))) | |
390bc872 RW |
17028 | |
17029 | (define-public r-lhs | |
17030 | (package | |
17031 | (name "r-lhs") | |
17032 | (version "1.0.1") | |
17033 | (source | |
17034 | (origin | |
17035 | (method url-fetch) | |
17036 | (uri (cran-uri "lhs" version)) | |
17037 | (sha256 | |
17038 | (base32 | |
17039 | "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4")))) | |
17040 | (properties `((upstream-name . "lhs"))) | |
17041 | (build-system r-build-system) | |
17042 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
17043 | (home-page "https://github.com/bertcarnell/lhs") | |
17044 | (synopsis "Latin Hypercube Samples") | |
17045 | (description | |
17046 | "This package provides a number of methods for creating and augmenting | |
17047 | Latin Hypercube Samples.") | |
17048 | (license license:gpl3))) | |
1442ca73 RW |
17049 | |
17050 | (define-public r-acebayes | |
17051 | (package | |
17052 | (name "r-acebayes") | |
17053 | (version "1.8") | |
17054 | (source | |
17055 | (origin | |
17056 | (method url-fetch) | |
17057 | (uri (cran-uri "acebayes" version)) | |
17058 | (sha256 | |
17059 | (base32 | |
17060 | "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln")))) | |
17061 | (properties `((upstream-name . "acebayes"))) | |
17062 | (build-system r-build-system) | |
17063 | (propagated-inputs | |
17064 | `(("r-compare" ,r-compare) | |
17065 | ("r-lhs" ,r-lhs) | |
17066 | ("r-randtoolbox" ,r-randtoolbox) | |
17067 | ("r-rcpp" ,r-rcpp) | |
17068 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
17069 | (home-page "https://cran.r-project.org/web/packages/acebayes/") | |
17070 | (synopsis "Optimal Bayesian experimental design using the ACE algorithm") | |
17071 | (description | |
17072 | "Finding an optimal Bayesian experimental design involves maximizing an | |
17073 | objective function given by the expectation of some appropriately chosen | |
17074 | utility function with respect to the joint distribution of unknown | |
17075 | quantities (including responses). This objective function is usually not | |
17076 | available in closed form and the design space can be continuous and of high | |
17077 | dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE) | |
17078 | to maximise an approximation to the expectation of the utility function.") | |
17079 | (license license:gpl2))) | |
43a70edc RW |
17080 | |
17081 | (define-public r-acet | |
17082 | (package | |
17083 | (name "r-acet") | |
17084 | (version "1.8.0") | |
17085 | (source | |
17086 | (origin | |
17087 | (method url-fetch) | |
17088 | (uri (cran-uri "ACEt" version)) | |
17089 | (sha256 | |
17090 | (base32 | |
17091 | "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq")))) | |
17092 | (properties `((upstream-name . "ACEt"))) | |
17093 | (build-system r-build-system) | |
17094 | (propagated-inputs | |
17095 | `(("r-bh" ,r-bh) | |
17096 | ("r-mass" ,r-mass) | |
17097 | ("r-rcpp" ,r-rcpp) | |
17098 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
17099 | (home-page "https://cran.r-project.org/web/packages/ACEt/") | |
17100 | (synopsis "Estimating dynamic heritability and twin model comparison") | |
17101 | (description | |
17102 | "This package supports twin models that are able to estimate the dynamic | |
17103 | behaviour of the variance components in the classical twin models with respect | |
17104 | to age using B-splines and P-splines.") | |
17105 | (license license:gpl2+))) | |
a8a7ba9a RW |
17106 | |
17107 | (define-public r-acfmperiod | |
17108 | (package | |
17109 | (name "r-acfmperiod") | |
17110 | (version "1.0.0") | |
17111 | (source | |
17112 | (origin | |
17113 | (method url-fetch) | |
17114 | (uri (cran-uri "acfMPeriod" version)) | |
17115 | (sha256 | |
17116 | (base32 | |
17117 | "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5")))) | |
17118 | (properties `((upstream-name . "acfMPeriod"))) | |
17119 | (build-system r-build-system) | |
17120 | (propagated-inputs | |
17121 | `(("r-mass" ,r-mass))) | |
17122 | (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") | |
17123 | (synopsis "Estimation of the ACF from the M-periodogram") | |
17124 | (description | |
17125 | "This package support non-robust and robust computations of the sample | |
17126 | autocovariance (ACOVF) and sample autocorrelation functions (ACF) of | |
17127 | univariate and multivariate processes. The methodology consists in reversing | |
17128 | the diagonalization procedure involving the periodogram or the | |
17129 | cross-periodogram and the Fourier transform vectors, and, thus, obtaining the | |
17130 | ACOVF or the ACF as discussed in Fuller (1995) | |
17131 | @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting | |
17132 | robust M-regressors to obtain the M-periodogram or M-cross-periodogram as | |
17133 | discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") | |
17134 | (license license:gpl2+))) | |
3b89a8af RW |
17135 | |
17136 | (define-public r-gamlss-data | |
17137 | (package | |
17138 | (name "r-gamlss-data") | |
17139 | (version "5.1-4") | |
17140 | (source | |
17141 | (origin | |
17142 | (method url-fetch) | |
17143 | (uri (cran-uri "gamlss.data" version)) | |
17144 | (sha256 | |
17145 | (base32 | |
17146 | "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd")))) | |
17147 | (properties `((upstream-name . "gamlss.data"))) | |
17148 | (build-system r-build-system) | |
17149 | (home-page "http://www.gamlss.org/") | |
17150 | (synopsis "GAMLSS data") | |
17151 | (description | |
17152 | "This package provides data used as examples to demonstrate GAMLSS | |
17153 | models.") | |
17154 | ;; Either version of the license | |
17155 | (license (list license:gpl2 license:gpl3)))) | |
6cc356c3 RW |
17156 | |
17157 | (define-public r-gamlss | |
17158 | (package | |
17159 | (name "r-gamlss") | |
17160 | (version "5.1-5") | |
17161 | (source | |
17162 | (origin | |
17163 | (method url-fetch) | |
17164 | (uri (cran-uri "gamlss" version)) | |
17165 | (sha256 | |
17166 | (base32 | |
17167 | "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc")))) | |
17168 | (properties `((upstream-name . "gamlss"))) | |
17169 | (build-system r-build-system) | |
17170 | (propagated-inputs | |
17171 | `(("r-gamlss-data" ,r-gamlss-data) | |
17172 | ("r-gamlss-dist" ,r-gamlss-dist) | |
17173 | ("r-mass" ,r-mass) | |
17174 | ("r-nlme" ,r-nlme) | |
17175 | ("r-survival" ,r-survival))) | |
17176 | (home-page "http://www.gamlss.org/") | |
17177 | (synopsis "Generalized additive models for location scale and shape") | |
17178 | (description | |
17179 | "This package provides functions for fitting the generalized additive | |
17180 | models for location scale and shape introduced by Rigby and | |
17181 | Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models | |
17182 | use a distributional regression approach where all the parameters of the | |
17183 | conditional distribution of the response variable are modelled using | |
17184 | explanatory variables.") | |
17185 | ;; Either version of the license | |
17186 | (license (list license:gpl2 license:gpl3)))) | |
220557a7 RW |
17187 | |
17188 | (define-public r-acid | |
17189 | (package | |
17190 | (name "r-acid") | |
17191 | (version "1.1") | |
17192 | (source | |
17193 | (origin | |
17194 | (method url-fetch) | |
17195 | (uri (cran-uri "acid" version)) | |
17196 | (sha256 | |
17197 | (base32 | |
17198 | "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd")))) | |
17199 | (properties `((upstream-name . "acid"))) | |
17200 | (build-system r-build-system) | |
17201 | (propagated-inputs | |
17202 | `(("r-gamlss" ,r-gamlss) | |
17203 | ("r-gamlss-dist" ,r-gamlss-dist) | |
17204 | ("r-hmisc" ,r-hmisc))) | |
17205 | (home-page "https://cran.r-project.org/web/packages/acid/") | |
17206 | (synopsis "Analysing conditional income distributions") | |
17207 | (description | |
17208 | "This package provides functions for the analysis of income distributions | |
17209 | for subgroups of the population as defined by a set of variables like age, | |
17210 | gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture | |
17211 | distribution as well as functions for moments, inequality measures, entropy | |
17212 | measures and polarisation measures of income distributions. This package thus | |
17213 | aides the analysis of income inequality by offering tools for the exploratory | |
17214 | analysis of income distributions at the disaggregated level.") | |
17215 | (license license:gpl3))) | |
542590c5 RW |
17216 | |
17217 | (define-public r-acm4r | |
17218 | (package | |
17219 | (name "r-acm4r") | |
17220 | (version "1.0") | |
17221 | (source | |
17222 | (origin | |
17223 | (method url-fetch) | |
17224 | (uri (cran-uri "acm4r" version)) | |
17225 | (sha256 | |
17226 | (base32 | |
17227 | "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) | |
17228 | (properties `((upstream-name . "acm4r"))) | |
17229 | (build-system r-build-system) | |
17230 | (propagated-inputs `(("r-mass" ,r-mass))) | |
17231 | (home-page "https://cran.r-project.org/web/packages/acm4r/") | |
17232 | (synopsis "Align-and-count method comparisons of RFLP data") | |
17233 | (description | |
17234 | "This is a package to compare sequence fragment lengths or molecular | |
17235 | weights from pairs of lanes. The number of matching bands in the | |
17236 | @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using | |
17237 | the align-and-count method.") | |
17238 | ;; Any version of the GPL | |
17239 | (license (list license:gpl2+ license:gpl3+)))) | |
fa82997f RW |
17240 | |
17241 | (define-public r-filematrix | |
17242 | (package | |
17243 | (name "r-filematrix") | |
17244 | (version "1.3") | |
17245 | (source | |
17246 | (origin | |
17247 | (method url-fetch) | |
17248 | (uri (cran-uri "filematrix" version)) | |
17249 | (sha256 | |
17250 | (base32 | |
17251 | "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b")))) | |
17252 | (properties `((upstream-name . "filematrix"))) | |
17253 | (build-system r-build-system) | |
17254 | ;; These inputs are needed for vignettes | |
17255 | (native-inputs | |
17256 | `(("r-knitr" ,r-knitr) | |
17257 | ("r-rmarkdown" ,r-rmarkdown) | |
17258 | ("pandoc-citeproc" ,ghc-pandoc-citeproc))) | |
17259 | (home-page "https://github.com/andreyshabalin/filematrix") | |
17260 | (synopsis "File-backed matrix class with convenient read and write access") | |
17261 | (description | |
17262 | "This package provides an interface for working with large matrices | |
17263 | stored in files, not in computer memory. It supports multiple non-character | |
17264 | data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 | |
17265 | byte real values). Access to parts of the matrix is done by indexing, exactly | |
17266 | as with usual R matrices. It supports very large matrices; the package has | |
17267 | been tested on multi-terabyte matrices. It allows for more than 2^32 rows or | |
17268 | columns, ad allows for quick addition of extra columns to a filematrix.") | |
17269 | (license license:lgpl3))) | |
73f055df RW |
17270 | |
17271 | (define-public r-acmeeqtl | |
17272 | (package | |
17273 | (name "r-acmeeqtl") | |
17274 | (version "1.6") | |
17275 | (source | |
17276 | (origin | |
17277 | (method url-fetch) | |
17278 | (uri (cran-uri "ACMEeqtl" version)) | |
17279 | (sha256 | |
17280 | (base32 | |
17281 | "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz")))) | |
17282 | (properties `((upstream-name . "ACMEeqtl"))) | |
17283 | (build-system r-build-system) | |
17284 | (propagated-inputs | |
17285 | `(("r-filematrix" ,r-filematrix))) | |
17286 | (home-page "https://github.com/andreyshabalin/ACMEeqtl") | |
17287 | (synopsis "Estimation of interpretable eQTL effect sizes") | |
17288 | (description | |
17289 | "This package provides a non-linear model, termed ACME, that reflects a | |
17290 | parsimonious biological model for allelic contributions of cis-acting eQTLs. | |
17291 | With non-linear least-squares algorithm the maximum likelihood parameters can | |
17292 | be estimated. The ACME model provides interpretable effect size estimates and | |
17293 | p-values with well controlled Type-I error.") | |
17294 | (license license:lgpl3))) | |
2dc8723a RW |
17295 | |
17296 | (define-public r-acmer | |
17297 | (package | |
17298 | (name "r-acmer") | |
17299 | (version "1.1.0") | |
17300 | (source | |
17301 | (origin | |
17302 | (method url-fetch) | |
17303 | (uri (cran-uri "acmeR" version)) | |
17304 | (sha256 | |
17305 | (base32 | |
17306 | "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) | |
17307 | (properties `((upstream-name . "acmeR"))) | |
17308 | (build-system r-build-system) | |
17309 | (propagated-inputs `(("r-foreign" ,r-foreign))) | |
17310 | (home-page "https://cran.r-project.org/web/packages/acmeR/") | |
17311 | (synopsis "ACME estimator of bird and bat mortality by wind turbines") | |
17312 | (description | |
17313 | "This package provides an implementation of the ACME estimator, described | |
17314 | in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran | |
17315 | Mortality at Wind Turbines. Unlike most other models, this estimator supports | |
17316 | decreasing-hazard Weibull model for persistence; decreasing search proficiency | |
17317 | as carcasses age; variable bleed-through at successive searches; and interval | |
17318 | mortality estimates. The package provides, based on search data, functions | |
17319 | for estimating the mortality inflation factor in Frequentist and Bayesian | |
17320 | settings.") | |
17321 | (license license:expat))) | |
1c2e3d7d RW |
17322 | |
17323 | (define-public r-r-huge | |
17324 | (package | |
17325 | (name "r-r-huge") | |
17326 | (version "0.9.0") | |
17327 | (source | |
17328 | (origin | |
17329 | (method url-fetch) | |
17330 | (uri (cran-uri "R.huge" version)) | |
17331 | (sha256 | |
17332 | (base32 | |
17333 | "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi")))) | |
17334 | (properties `((upstream-name . "R.huge"))) | |
17335 | (build-system r-build-system) | |
17336 | (propagated-inputs | |
17337 | `(("r-r-methodss3" ,r-r-methodss3) | |
17338 | ("r-r-oo" ,r-r-oo) | |
17339 | ("r-r-utils" ,r-r-utils))) | |
17340 | (home-page "https://github.com/HenrikBengtsson/R.huge") | |
17341 | (synopsis "Methods for accessing huge amounts of data") | |
17342 | (description | |
17343 | "This is a deprecated package for accessing huge amounts of data. | |
17344 | Cross-platform alternatives are the following packages: bigmemory (CRAN), | |
17345 | ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside | |
17346 | the @code{aroma.affymetrix} package.") | |
17347 | (license license:lgpl2.1+))) | |
2fe1e66c RW |
17348 | |
17349 | (define-public r-r-filesets | |
17350 | (package | |
17351 | (name "r-r-filesets") | |
17352 | (version "2.13.0") | |
17353 | (source | |
17354 | (origin | |
17355 | (method url-fetch) | |
17356 | (uri (cran-uri "R.filesets" version)) | |
17357 | (sha256 | |
17358 | (base32 | |
17359 | "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg")))) | |
17360 | (properties `((upstream-name . "R.filesets"))) | |
17361 | (build-system r-build-system) | |
17362 | (propagated-inputs | |
17363 | `(("r-digest" ,r-digest) | |
17364 | ("r-r-cache" ,r-r-cache) | |
17365 | ("r-r-methodss3" ,r-r-methodss3) | |
17366 | ("r-r-oo" ,r-r-oo) | |
17367 | ("r-r-utils" ,r-r-utils))) | |
17368 | (home-page "https://github.com/HenrikBengtsson/R.filesets") | |
17369 | (synopsis "Easy handling of and access to files") | |
17370 | (description | |
17371 | "This package provides classes and methods to locate, setup, subset, | |
17372 | navigate and iterate file sets, i.e. sets of files located in one or more | |
17373 | directories on the file system. The API is designed such that these classes | |
17374 | can be extended via inheritance to provide a richer API for special file | |
17375 | formats. Moreover, a specific name format is defined such that filenames and | |
17376 | directories can be considered to have full names which consists of a name | |
17377 | followed by comma-separated tags. This adds additional flexibility to | |
17378 | identify file sets and individual files.") | |
17379 | (license license:lgpl2.1+))) | |
217cd2e3 RW |
17380 | |
17381 | (define-public r-r-devices | |
17382 | (package | |
17383 | (name "r-r-devices") | |
17384 | (version "2.16.1") | |
17385 | (source | |
17386 | (origin | |
17387 | (method url-fetch) | |
17388 | (uri (cran-uri "R.devices" version)) | |
17389 | (sha256 | |
17390 | (base32 | |
17391 | "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd")))) | |
17392 | (properties `((upstream-name . "R.devices"))) | |
17393 | (build-system r-build-system) | |
17394 | (propagated-inputs | |
17395 | `(("r-base64enc" ,r-base64enc) | |
17396 | ("r-r-methodss3" ,r-r-methodss3) | |
17397 | ("r-r-oo" ,r-r-oo) | |
17398 | ("r-r-utils" ,r-r-utils))) | |
17399 | (home-page "https://github.com/HenrikBengtsson/R.devices") | |
17400 | (synopsis "Unified handling of graphics devices") | |
17401 | (description | |
17402 | "This package provides functions for creating plots and image files in a | |
17403 | unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). | |
17404 | Default device options as well as scales and aspect ratios are controlled in a | |
17405 | uniform way across all device types. Switching output format requires minimal | |
17406 | changes in code. This package is ideal for large-scale batch processing, | |
17407 | because it will never leave open graphics devices or incomplete image files | |
17408 | behind, even on errors or user interrupts.") | |
17409 | (license license:lgpl2.1+))) | |
eff3e8a4 RW |
17410 | |
17411 | (define-public r-acnr | |
17412 | (package | |
17413 | (name "r-acnr") | |
17414 | (version "1.0.0") | |
17415 | (source | |
17416 | (origin | |
17417 | (method url-fetch) | |
17418 | (uri (cran-uri "acnr" version)) | |
17419 | (sha256 | |
17420 | (base32 | |
17421 | "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym")))) | |
17422 | (properties `((upstream-name . "acnr"))) | |
17423 | (build-system r-build-system) | |
17424 | (home-page "https://github.com/mpierrejean/acnr") | |
17425 | (synopsis "Annotated copy-number regions") | |
17426 | (description | |
17427 | "This package provides SNP array data from different types of copy-number | |
17428 | regions. These regions were identified manually by the authors of the package | |
17429 | and may be used to generate realistic data sets with known truth.") | |
17430 | (license license:lgpl2.1+))) | |
5d887a03 RW |
17431 | |
17432 | (define-public r-acopula | |
17433 | (package | |
17434 | (name "r-acopula") | |
17435 | (version "0.9.3") | |
17436 | (source | |
17437 | (origin | |
17438 | (method url-fetch) | |
17439 | (uri (cran-uri "acopula" version)) | |
17440 | (sha256 | |
17441 | (base32 | |
17442 | "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln")))) | |
17443 | (properties `((upstream-name . "acopula"))) | |
17444 | (build-system r-build-system) | |
17445 | (home-page "https://cran.r-project.org/web/packages/acopula/") | |
17446 | (synopsis "Modelling dependence with multivariate Archimax copulas") | |
17447 | (description | |
17448 | "Archimax copulas are a mixture of Archimedean and EV copulas. This | |
17449 | package provides definitions of several parametric families of generator and | |
17450 | dependence function, computes CDF and PDF, estimates parameters, tests for | |
17451 | goodness of fit, generates random sample and checks copula properties for | |
17452 | custom constructs. In the 2-dimensional case explicit formulas for density | |
17453 | are used, contrary to higher dimensions when all derivatives are linearly | |
17454 | approximated. Several non-archimax families (normal, FGM, Plackett) are | |
17455 | provided as well.") | |
17456 | (license license:gpl2))) | |
cb350053 RW |
17457 | |
17458 | (define-public r-tuner | |
17459 | (package | |
17460 | (name "r-tuner") | |
17461 | (version "1.3.3") | |
17462 | (source | |
17463 | (origin | |
17464 | (method url-fetch) | |
17465 | (uri (cran-uri "tuneR" version)) | |
17466 | (sha256 | |
17467 | (base32 | |
17468 | "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx")))) | |
17469 | (properties `((upstream-name . "tuneR"))) | |
17470 | (build-system r-build-system) | |
17471 | (propagated-inputs `(("r-signal" ,r-signal))) | |
17472 | (home-page "https://cran.r-project.org/web/packages/tuneR/") | |
17473 | (synopsis "Analysis of music and speech") | |
17474 | (description | |
17475 | "This is a package for the analysis of music and speech. Analyze music | |
17476 | and speech, extract features like MFCCs, handle wave files and their | |
17477 | representation in various ways, read MP3, read MIDI, perform steps of a | |
17478 | transcription, ...") | |
17479 | ;; Either of these versions. | |
17480 | (license (list license:gpl2 license:gpl3)))) | |
19172e12 RW |
17481 | |
17482 | (define-public r-seewave | |
17483 | (package | |
17484 | (name "r-seewave") | |
17485 | (version "2.1.5") | |
17486 | (source | |
17487 | (origin | |
17488 | (method url-fetch) | |
17489 | (uri (cran-uri "seewave" version)) | |
17490 | (sha256 | |
17491 | (base32 | |
17492 | "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi")))) | |
17493 | (properties `((upstream-name . "seewave"))) | |
17494 | (build-system r-build-system) | |
17495 | (propagated-inputs | |
17496 | `(("r-tuner" ,r-tuner))) | |
17497 | (home-page "http://rug.mnhn.fr/seewave") | |
17498 | (synopsis "Sound analysis and synthesis") | |
17499 | (description | |
17500 | "This package provides functions for analysing, manipulating, displaying, | |
17501 | editing and synthesizing time waves (particularly sound). This package | |
17502 | processes time analysis (oscillograms and envelopes), spectral content, | |
17503 | resonance quality factor, entropy, cross correlation and autocorrelation, | |
17504 | zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D | |
17505 | and 3D spectrograms and many other analyses.") | |
17506 | (license license:gpl2+))) | |
c12227d9 RW |
17507 | |
17508 | (define-public r-acousticndlcoder | |
17509 | (package | |
17510 | (name "r-acousticndlcoder") | |
17511 | (version "1.0.2") | |
17512 | (source | |
17513 | (origin | |
17514 | (method url-fetch) | |
17515 | (uri (cran-uri "AcousticNDLCodeR" version)) | |
17516 | (sha256 | |
17517 | (base32 | |
17518 | "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb")))) | |
17519 | (properties | |
17520 | `((upstream-name . "AcousticNDLCodeR"))) | |
17521 | (build-system r-build-system) | |
17522 | (propagated-inputs | |
17523 | `(("r-seewave" ,r-seewave) | |
17524 | ("r-tuner" ,r-tuner) | |
17525 | ("r-zoo" ,r-zoo))) | |
17526 | (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") | |
17527 | (synopsis "Coding sound files for use with NDL") | |
17528 | (description | |
17529 | "Make acoustic cues to use with the R package @code{ndl}. | |
17530 | The package implements functions used in the PLoS ONE paper \"Words from | |
17531 | spontaneous conversational speech can be recognized with human-like accuracy | |
17532 | by an error-driven learning algorithm that discriminates between meanings | |
17533 | straight from smart acoustic features, bypassing the phoneme as recognition | |
17534 | unit.\" @url{doi:10.1371/journal.pone.0174623}") | |
17535 | (license license:gpl2+))) | |
56cba940 RW |
17536 | |
17537 | (define-public r-acp | |
17538 | (package | |
17539 | (name "r-acp") | |
17540 | (version "2.1") | |
17541 | (source | |
17542 | (origin | |
17543 | (method url-fetch) | |
17544 | (uri (cran-uri "acp" version)) | |
17545 | (sha256 | |
17546 | (base32 | |
17547 | "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn")))) | |
17548 | (properties `((upstream-name . "acp"))) | |
17549 | (build-system r-build-system) | |
17550 | (propagated-inputs | |
17551 | `(("r-quantmod" ,r-quantmod) | |
17552 | ("r-tseries" ,r-tseries))) | |
17553 | (home-page "https://cran.r-project.org/web/packages/acp/") | |
17554 | (synopsis "Autoregressive conditional Poisson") | |
17555 | (description | |
17556 | "This package supports the analysis of count data exhibiting | |
17557 | autoregressive properties, using the @dfn{Autoregressive Conditional Poisson} | |
17558 | model (ACP(p,q)) proposed by Heinen (2003).") | |
17559 | (license license:gpl2))) | |
f18c0544 RW |
17560 | |
17561 | (define-public r-ada | |
17562 | (package | |
17563 | (name "r-ada") | |
17564 | (version "2.0-5") | |
17565 | (source | |
17566 | (origin | |
17567 | (method url-fetch) | |
17568 | (uri (cran-uri "ada" version)) | |
17569 | (sha256 | |
17570 | (base32 | |
17571 | "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) | |
17572 | (properties `((upstream-name . "ada"))) | |
17573 | (build-system r-build-system) | |
17574 | (propagated-inputs `(("r-rpart" ,r-rpart))) | |
17575 | (home-page "https://cran.r-project.org/web/packages/ada/") | |
17576 | (synopsis "Stochastic boosting") | |
17577 | (description | |
17578 | "This package provides a straightforward, well-documented, and broad | |
17579 | boosting routine for classification, ideally suited for small to | |
17580 | moderate-sized data sets. It performs discrete, real, and gentle boost under | |
17581 | both exponential and logistic loss on a given data set.") | |
17582 | ;; Any version of the GPL. | |
17583 | (license (list license:gpl2+ license:gpl3+)))) | |
270529f6 RW |
17584 | |
17585 | (define-public r-genalg | |
17586 | (package | |
17587 | (name "r-genalg") | |
17588 | (version "0.2.0") | |
17589 | (source | |
17590 | (origin | |
17591 | (method url-fetch) | |
17592 | (uri (cran-uri "genalg" version)) | |
17593 | (sha256 | |
17594 | (base32 | |
17595 | "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s")))) | |
17596 | (properties `((upstream-name . "genalg"))) | |
17597 | (build-system r-build-system) | |
17598 | (home-page "https://github.com/egonw/genalg") | |
17599 | (synopsis "R based genetic algorithm") | |
17600 | (description | |
17601 | "This package provides an R based genetic algorithm for binary and | |
17602 | floating point chromosomes.") | |
17603 | (license license:gpl2))) | |
6afc037e RW |
17604 | |
17605 | (define-public r-kernelfactory | |
17606 | (package | |
17607 | (name "r-kernelfactory") | |
17608 | (version "0.3.0") | |
17609 | (source | |
17610 | (origin | |
17611 | (method url-fetch) | |
17612 | (uri (cran-uri "kernelFactory" version)) | |
17613 | (sha256 | |
17614 | (base32 | |
17615 | "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j")))) | |
17616 | (properties `((upstream-name . "kernelFactory"))) | |
17617 | (build-system r-build-system) | |
17618 | (propagated-inputs | |
17619 | `(("r-auc" ,r-auc) | |
17620 | ("r-genalg" ,r-genalg) | |
17621 | ("r-kernlab" ,r-kernlab) | |
17622 | ("r-randomforest" ,r-randomforest))) | |
17623 | (home-page "https://cran.r-project.org/web/packages/kernelFactory/") | |
17624 | (synopsis "Ensemble of kernel machines") | |
17625 | (description | |
17626 | "Kernel factory is an ensemble method where each base classifier (random | |
17627 | forest) is fit on the kernel matrix of a subset of the training data.") | |
17628 | (license license:gpl2+))) | |
6c2dcba9 RW |
17629 | |
17630 | (define-public r-dummies | |
17631 | (package | |
17632 | (name "r-dummies") | |
17633 | (version "1.5.6") | |
17634 | (source | |
17635 | (origin | |
17636 | (method url-fetch) | |
17637 | (uri (cran-uri "dummies" version)) | |
17638 | (sha256 | |
17639 | (base32 | |
17640 | "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm")))) | |
17641 | (properties `((upstream-name . "dummies"))) | |
17642 | (build-system r-build-system) | |
17643 | (home-page "http://www.decisionpatterns.com") | |
17644 | (synopsis "Create dummy/indicator variables flexibly and efficiently") | |
17645 | (description | |
17646 | "This package lets you expand factors, characters and other eligible | |
17647 | classes into dummy/indicator variables.") | |
17648 | (license license:gpl2+))) | |
3bc2c210 RW |
17649 | |
17650 | (define-public r-acrm | |
17651 | (package | |
17652 | (name "r-acrm") | |
17653 | (version "0.1.1") | |
17654 | (source | |
17655 | (origin | |
17656 | (method url-fetch) | |
17657 | (uri (cran-uri "aCRM" version)) | |
17658 | (sha256 | |
17659 | (base32 | |
17660 | "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v")))) | |
17661 | (properties `((upstream-name . "aCRM"))) | |
17662 | (build-system r-build-system) | |
17663 | (propagated-inputs | |
17664 | `(("r-ada" ,r-ada) | |
17665 | ("r-dummies" ,r-dummies) | |
17666 | ("r-kernelfactory" ,r-kernelfactory) | |
17667 | ("r-randomforest" ,r-randomforest))) | |
17668 | (home-page "https://cran.r-project.org/web/packages/aCRM/") | |
17669 | (synopsis "Convenience functions for analytical customer relationship management") | |
17670 | (description | |
17671 | "This package provides convenience functions for data preparation and | |
17672 | modeling often used in @dfn{analytical customer relationship | |
17673 | management} (aCRM).") | |
17674 | (license license:gpl2+))) | |
c3f5989c RW |
17675 | |
17676 | (define-public r-treeclust | |
17677 | (package | |
17678 | (name "r-treeclust") | |
17679 | (version "1.1-7") | |
17680 | (source | |
17681 | (origin | |
17682 | (method url-fetch) | |
17683 | (uri (cran-uri "treeClust" version)) | |
17684 | (sha256 | |
17685 | (base32 | |
17686 | "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z")))) | |
17687 | (properties `((upstream-name . "treeClust"))) | |
17688 | (build-system r-build-system) | |
17689 | (propagated-inputs | |
17690 | `(("r-cluster" ,r-cluster) | |
17691 | ("r-rpart" ,r-rpart))) | |
17692 | (home-page "https://cran.r-project.org/web/packages/treeClust/") | |
17693 | (synopsis "Cluster distances through trees") | |
17694 | (description | |
17695 | "This package provides tools to create a measure of inter-point | |
17696 | dissimilarity useful for clustering mixed data, and, optionally, perform the | |
17697 | clustering.") | |
17698 | (license license:gpl2+))) | |
4b44bfb6 RW |
17699 | |
17700 | (define-public r-acrosstic | |
17701 | (package | |
17702 | (name "r-acrosstic") | |
17703 | (version "1.0-3") | |
17704 | (source | |
17705 | (origin | |
17706 | (method url-fetch) | |
17707 | (uri (cran-uri "AcrossTic" version)) | |
17708 | (sha256 | |
17709 | (base32 | |
17710 | "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0")))) | |
17711 | (properties `((upstream-name . "AcrossTic"))) | |
17712 | (build-system r-build-system) | |
17713 | (propagated-inputs | |
17714 | `(("r-lpsolve" ,r-lpsolve) | |
17715 | ("r-treeclust" ,r-treeclust))) | |
17716 | (home-page "https://cran.r-project.org/web/packages/AcrossTic/") | |
17717 | (synopsis "Cost-minimal regular spanning subgraph with TreeClust") | |
17718 | (description | |
17719 | "This is a package for constructing minimum-cost regular spanning | |
17720 | subgraph as part of a non-parametric two-sample test for equality of | |
17721 | distribution.") | |
17722 | (license license:gpl2+))) | |
d015db6f RW |
17723 | |
17724 | (define-public r-acrt | |
17725 | (package | |
17726 | (name "r-acrt") | |
17727 | (version "1.0.1") | |
17728 | (source | |
17729 | (origin | |
17730 | (method url-fetch) | |
17731 | (uri (cran-uri "acrt" version)) | |
17732 | (sha256 | |
17733 | (base32 | |
17734 | "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s")))) | |
17735 | (properties `((upstream-name . "acrt"))) | |
17736 | (build-system r-build-system) | |
17737 | (propagated-inputs | |
17738 | `(("r-rcpp" ,r-rcpp) | |
17739 | ("r-rcppeigen" ,r-rcppeigen) | |
17740 | ("r-sandwich" ,r-sandwich))) | |
17741 | (home-page "https://cran.r-project.org/web/packages/acrt/") | |
17742 | (synopsis "Autocorrelation robust testing") | |
17743 | (description | |
17744 | "This package provides functions for testing affine hypotheses on the | |
17745 | regression coefficient vector in regression models with autocorrelated | |
17746 | errors.") | |
17747 | (license license:gpl2))) | |
49e9a9ae RW |
17748 | |
17749 | (define-public r-acs | |
17750 | (package | |
17751 | (name "r-acs") | |
17752 | (version "2.1.4") | |
17753 | (source | |
17754 | (origin | |
17755 | (method url-fetch) | |
17756 | (uri (cran-uri "acs" version)) | |
17757 | (sha256 | |
17758 | (base32 | |
17759 | "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5")))) | |
17760 | (properties `((upstream-name . "acs"))) | |
17761 | (build-system r-build-system) | |
17762 | (propagated-inputs | |
17763 | `(("r-httr" ,r-httr) | |
17764 | ("r-plyr" ,r-plyr) | |
17765 | ("r-rcpp" ,r-rcpp) | |
17766 | ("r-stringr" ,r-stringr) | |
17767 | ("r-xml" ,r-xml))) | |
17768 | (home-page "http://dusp.mit.edu/faculty/ezra-glenn") | |
17769 | (synopsis "Work with data from the US Census") | |
17770 | (description | |
17771 | "This package provides a general toolkit for downloading, managing, | |
17772 | analyzing, and presenting data from the | |
17773 | @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census}, | |
17774 | including SF1 (Decennial short-form), SF3 (Decennial long-form), and the | |
17775 | American Community Survey (ACS). Confidence intervals provided with ACS data | |
17776 | are converted to standard errors to be bundled with estimates in complex | |
17777 | @code{acs} objects. The package provides new methods to conduct standard | |
17778 | operations on @code{acs} objects and present/plot data in statistically | |
17779 | appropriate ways.") | |
17780 | (license license:gpl3))) | |
07d958fe RW |
17781 | |
17782 | (define-public r-acss-data | |
17783 | (package | |
17784 | (name "r-acss-data") | |
17785 | (version "1.0") | |
17786 | (source | |
17787 | (origin | |
17788 | (method url-fetch) | |
17789 | (uri (cran-uri "acss.data" version)) | |
17790 | (sha256 | |
17791 | (base32 | |
17792 | "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv")))) | |
17793 | (properties `((upstream-name . "acss.data"))) | |
17794 | (build-system r-build-system) | |
17795 | (home-page "http://complexitycalculator.com/methodology.html") | |
17796 | (synopsis "Data for algorithmic complexity of short strings") | |
17797 | (description | |
17798 | "This is a data only package providing the algorithmic complexity of | |
17799 | short strings, computed using the coding theorem method. For a given set of | |
17800 | symbols in a string, all possible or a large number of random samples of | |
17801 | Turing machines with a given number of states (e.g., 5) and number of symbols | |
17802 | corresponding to the number of symbols in the strings were simulated until | |
17803 | they reached a halting state or failed to end. This package contains data on | |
17804 | 4.5 million strings from length 1 to 12 simulated on Turing machines with 2, | |
17805 | 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the | |
17806 | distribution of the halting states.") | |
17807 | (license license:gpl2+))) | |
0ea0b2dd RW |
17808 | |
17809 | (define-public r-acss | |
17810 | (package | |
17811 | (name "r-acss") | |
17812 | (version "0.2-5") | |
17813 | (source | |
17814 | (origin | |
17815 | (method url-fetch) | |
17816 | (uri (cran-uri "acss" version)) | |
17817 | (sha256 | |
17818 | (base32 | |
17819 | "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk")))) | |
17820 | (properties `((upstream-name . "acss"))) | |
17821 | (build-system r-build-system) | |
17822 | (propagated-inputs | |
17823 | `(("r-acss-data" ,r-acss-data) | |
17824 | ("r-zoo" ,r-zoo))) | |
17825 | (home-page "http://complexitycalculator.com/methodology.html") | |
17826 | (synopsis "Algorithmic complexity for short strings") | |
17827 | (description | |
17828 | "The main purpose of this package is to provide the algorithmic | |
17829 | complexity for short strings, an approximation of the Kolmogorov Complexity of | |
17830 | a short string using the coding theorem method. While the database containing | |
17831 | the complexity is provided in the data only package @code{acss.data}, this | |
17832 | package provides functions accessing the data such as @code{prob_random} | |
17833 | returning the posterior probability that a given string was produced by a | |
17834 | random process. In addition, two traditional (but problematic) measures of | |
17835 | complexity are also provided: entropy and change complexity.") | |
17836 | (license license:gpl2+))) | |
ffecbcbf RW |
17837 | |
17838 | (define-public r-acswr | |
17839 | (package | |
17840 | (name "r-acswr") | |
17841 | (version "1.0") | |
17842 | (source | |
17843 | (origin | |
17844 | (method url-fetch) | |
17845 | (uri (cran-uri "ACSWR" version)) | |
17846 | (sha256 | |
17847 | (base32 | |
17848 | "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n")))) | |
17849 | (properties `((upstream-name . "ACSWR"))) | |
17850 | (build-system r-build-system) | |
17851 | (propagated-inputs | |
17852 | `(("r-mass" ,r-mass))) | |
17853 | (home-page "https://cran.r-project.org/web/packages/ACSWR/") | |
17854 | (synopsis "Companion package for the book \"A Course in Statistics with R\"") | |
17855 | (description | |
17856 | "This is a companion package for the book \"A Course in Statistics with | |
17857 | R\" (ISBN 978-1-119-15272-9.)") | |
17858 | (license license:gpl2))) | |
6f0a5ab0 RW |
17859 | |
17860 | (define-public r-alabama | |
17861 | (package | |
17862 | (name "r-alabama") | |
17863 | (version "2015.3-1") | |
17864 | (source | |
17865 | (origin | |
17866 | (method url-fetch) | |
17867 | (uri (cran-uri "alabama" version)) | |
17868 | (sha256 | |
17869 | (base32 | |
17870 | "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036")))) | |
17871 | (properties `((upstream-name . "alabama"))) | |
17872 | (build-system r-build-system) | |
17873 | (propagated-inputs `(("r-numderiv" ,r-numderiv))) | |
17874 | (home-page "https://cran.r-project.org/web/packages/alabama/") | |
17875 | (synopsis "Constrained nonlinear optimization") | |
17876 | (description | |
17877 | "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization | |
17878 | Algorithm; it is used for optimizing smooth nonlinear objective functions with | |
17879 | constraints. Linear or nonlinear equality and inequality constraints are | |
17880 | allowed.") | |
17881 | (license license:gpl2+))) | |
70c0dbe7 RW |
17882 | |
17883 | (define-public r-gdina | |
17884 | (package | |
17885 | (name "r-gdina") | |
17886 | (version "2.7.3") | |
17887 | (source | |
17888 | (origin | |
17889 | (method url-fetch) | |
17890 | (uri (cran-uri "GDINA" version)) | |
17891 | (sha256 | |
17892 | (base32 | |
17893 | "0875xfbm36gqzr0116xzlbm8rlff85rybr4s4hjzfflfvjdhgvfx")))) | |
17894 | (properties `((upstream-name . "GDINA"))) | |
17895 | (build-system r-build-system) | |
17896 | (propagated-inputs | |
17897 | `(("r-alabama" ,r-alabama) | |
17898 | ("r-ggplot2" ,r-ggplot2) | |
17899 | ("r-mass" ,r-mass) | |
17900 | ("r-nloptr" ,r-nloptr) | |
17901 | ("r-numderiv" ,r-numderiv) | |
17902 | ("r-rcpp" ,r-rcpp) | |
17903 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
17904 | ("r-rsolnp" ,r-rsolnp) | |
17905 | ("r-shiny" ,r-shiny) | |
17906 | ("r-shinydashboard" ,r-shinydashboard))) | |
17907 | (home-page "https://github.com/Wenchao-Ma/GDINA") | |
17908 | (synopsis "Generalized DINA model framework") | |
17909 | (description | |
17910 | "This package provides a set of psychometric tools for cognitive | |
17911 | diagnosis modeling based on the generalized deterministic inputs, noisy and | |
17912 | gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7} | |
17913 | and its extensions, including the sequential G-DINA model by Ma and de la | |
17914 | Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the | |
17915 | polytomous G-DINA model by Chen and de la Torre | |
17916 | @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute | |
17917 | distribution can be independent, saturated, higher-order, loglinear smoothed | |
17918 | or structured. Q-matrix validation, item and model fit statistics, model | |
17919 | comparison at test and item level and differential item functioning can also | |
17920 | be conducted. A graphical user interface is also provided.") | |
17921 | (license license:gpl3))) | |
d024207e RW |
17922 | |
17923 | (define-public r-actcd | |
17924 | (package | |
17925 | (name "r-actcd") | |
17926 | (version "1.2-0") | |
17927 | (source | |
17928 | (origin | |
17929 | (method url-fetch) | |
17930 | (uri (cran-uri "ACTCD" version)) | |
17931 | (sha256 | |
17932 | (base32 | |
17933 | "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p")))) | |
17934 | (properties `((upstream-name . "ACTCD"))) | |
17935 | (build-system r-build-system) | |
17936 | (propagated-inputs | |
17937 | `(("r-gdina" ,r-gdina) | |
17938 | ("r-r-methodss3" ,r-r-methodss3))) | |
17939 | (native-inputs | |
17940 | `(("gfortran" ,gfortran))) | |
17941 | (home-page "https://cran.r-project.org/web/packages/ACTCD/") | |
17942 | (synopsis "Asymptotic classification theory for cognitive diagnosis") | |
17943 | (description | |
17944 | "This is a package supporting cluster analysis for cognitive diagnosis | |
17945 | based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; | |
17946 | @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of | |
17947 | sum-scores, cluster analysis techniques can be used to classify examinees into | |
17948 | latent classes based on their attribute patterns. In addition to the | |
17949 | algorithms used to classify data, three labeling approaches are proposed to | |
17950 | label clusters so that examinees' attribute profiles can be obtained.") | |
17951 | (license license:gpl2+))) | |
6790adf3 RW |
17952 | |
17953 | (define-public r-ineq | |
17954 | (package | |
17955 | (name "r-ineq") | |
17956 | (version "0.2-13") | |
17957 | (source | |
17958 | (origin | |
17959 | (method url-fetch) | |
17960 | (uri (cran-uri "ineq" version)) | |
17961 | (sha256 | |
17962 | (base32 | |
17963 | "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0")))) | |
17964 | (properties `((upstream-name . "ineq"))) | |
17965 | (build-system r-build-system) | |
17966 | (home-page "https://cran.r-project.org/web/packages/ineq/") | |
17967 | (synopsis "Measuring inequality, concentration, and poverty") | |
17968 | (description | |
17969 | "This package provides tools for measuring inequality, concentration, and | |
17970 | poverty measures. It provides both empirical and theoretical Lorenz curves.") | |
17971 | ;; Either of these two versions. | |
17972 | (license (list license:gpl2 license:gpl3)))) | |
c090b997 RW |
17973 | |
17974 | (define-public r-actfrag | |
17975 | (package | |
17976 | (name "r-actfrag") | |
17977 | (version "0.1.0") | |
17978 | (source | |
17979 | (origin | |
17980 | (method url-fetch) | |
17981 | (uri (cran-uri "ActFrag" version)) | |
17982 | (sha256 | |
17983 | (base32 | |
17984 | "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d")))) | |
17985 | (properties `((upstream-name . "ActFrag"))) | |
17986 | (build-system r-build-system) | |
17987 | (propagated-inputs | |
17988 | `(("r-accelerometry" ,r-accelerometry) | |
17989 | ("r-dplyr" ,r-dplyr) | |
17990 | ("r-ineq" ,r-ineq) | |
17991 | ("r-survival" ,r-survival) | |
17992 | ("r-tidyr" ,r-tidyr))) | |
17993 | (home-page "https://github.com/junruidi/ActFrag") | |
17994 | (synopsis "Activity fragmentation metrics extraction") | |
17995 | (description | |
17996 | "This package provides functions to extract commonly used fragmentation | |
17997 | metrics to quantify time accumulation strategies based on minute level | |
17998 | actigraphy-measured activity counts data.") | |
17999 | (license license:gpl3))) | |
77a5bf93 RW |
18000 | |
18001 | (define-public r-fda | |
18002 | (package | |
18003 | (name "r-fda") | |
18004 | (version "2.4.8") | |
18005 | (source | |
18006 | (origin | |
18007 | (method url-fetch) | |
18008 | (uri (cran-uri "fda" version)) | |
18009 | (sha256 | |
18010 | (base32 | |
18011 | "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2")))) | |
18012 | (properties `((upstream-name . "fda"))) | |
18013 | (build-system r-build-system) | |
18014 | (propagated-inputs | |
18015 | `(("r-matrix" ,r-matrix))) | |
18016 | (home-page "http://www.functionaldata.org") | |
18017 | (synopsis "Functional data analysis") | |
18018 | (description | |
18019 | "These functions were developed to support functional data analysis as | |
18020 | described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data | |
18021 | Analysis. The package includes data sets and script files working many | |
18022 | examples.") | |
18023 | (license license:gpl2+))) | |
402dae07 RW |
18024 | |
18025 | (define-public r-actigraphy | |
18026 | (package | |
18027 | (name "r-actigraphy") | |
18028 | (version "1.3.2") | |
18029 | (source | |
18030 | (origin | |
18031 | (method url-fetch) | |
18032 | (uri (cran-uri "Actigraphy" version)) | |
18033 | (sha256 | |
18034 | (base32 | |
18035 | "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574")))) | |
18036 | (properties `((upstream-name . "Actigraphy"))) | |
18037 | (build-system r-build-system) | |
18038 | (propagated-inputs | |
18039 | `(("r-fda" ,r-fda) | |
18040 | ("r-sdmtools" ,r-sdmtools))) | |
18041 | (home-page "https://cran.r-project.org/web/packages/Actigraphy/") | |
18042 | (synopsis "Actigraphy data analysis") | |
18043 | (description | |
18044 | "This package provides tools for functional linear modeling and analysis | |
18045 | of actigraphy data.") | |
18046 | (license license:asl2.0))) | |
7f960d81 RW |
18047 | |
18048 | (define-public r-activedriver | |
18049 | (package | |
18050 | (name "r-activedriver") | |
18051 | (version "1.0.0") | |
18052 | (source | |
18053 | (origin | |
18054 | (method url-fetch) | |
18055 | (uri (cran-uri "ActiveDriver" version)) | |
18056 | (sha256 | |
18057 | (base32 | |
18058 | "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa")))) | |
18059 | (properties `((upstream-name . "ActiveDriver"))) | |
18060 | (build-system r-build-system) | |
18061 | (propagated-inputs | |
18062 | `(("r-mass" ,r-mass))) | |
18063 | (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") | |
18064 | (synopsis "Tools for finding cancer driver proteins") | |
18065 | (description | |
18066 | "This package provides a mutation analysis tool that discovers cancer | |
18067 | driver genes with frequent mutations in protein signalling sites such as | |
18068 | post-translational modifications (phosphorylation, ubiquitination, etc). The | |
18069 | Poisson generalized linear regression model identifies genes where cancer | |
18070 | mutations in signalling sites are more frequent than expected from the | |
18071 | sequence of the entire gene. Integration of mutations with signalling | |
18072 | information helps find new driver genes and propose candidate mechanisms to | |
18073 | known drivers.") | |
18074 | (license license:gpl2+))) | |
89d4f154 RW |
18075 | |
18076 | (define-public r-activitycounts | |
18077 | (package | |
18078 | (name "r-activitycounts") | |
18079 | (version "0.1.2") | |
18080 | (source | |
18081 | (origin | |
18082 | (method url-fetch) | |
18083 | (uri (cran-uri "activityCounts" version)) | |
18084 | (sha256 | |
18085 | (base32 | |
18086 | "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz")))) | |
18087 | (properties | |
18088 | `((upstream-name . "activityCounts"))) | |
18089 | (build-system r-build-system) | |
18090 | (propagated-inputs | |
18091 | `(("r-lubridate" ,r-lubridate) | |
18092 | ("r-magrittr" ,r-magrittr) | |
18093 | ("r-seewave" ,r-seewave) | |
18094 | ("r-signal" ,r-signal) | |
18095 | ("r-tibble" ,r-tibble))) | |
18096 | (home-page "https://github.com/walkabillylab/activityCounts") | |
18097 | (synopsis "Generate ActiLife counts") | |
18098 | (description | |
18099 | "ActiLife generates activity counts from data collected by Actigraph | |
18100 | accelerometers. Actigraph is one of the most common research-grade | |
18101 | accelerometers. There is considerable research validating and developing | |
18102 | algorithms for human activity using ActiLife counts. Unfortunately, ActiLife | |
18103 | counts are proprietary and difficult to implement if researchers use different | |
18104 | accelerometer brands. The code creates ActiLife counts from raw acceleration | |
18105 | data for different accelerometer brands.") | |
18106 | (license license:gpl3))) | |
6f94a3e5 RW |
18107 | |
18108 | (define-public r-activityindex | |
18109 | (package | |
18110 | (name "r-activityindex") | |
18111 | (version "0.3.6") | |
18112 | (source | |
18113 | (origin | |
18114 | (method url-fetch) | |
18115 | (uri (cran-uri "ActivityIndex" version)) | |
18116 | (sha256 | |
18117 | (base32 | |
18118 | "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk")))) | |
18119 | (properties `((upstream-name . "ActivityIndex"))) | |
18120 | (build-system r-build-system) | |
18121 | (propagated-inputs | |
18122 | `(("r-data-table" ,r-data-table) | |
18123 | ("r-matrixstats" ,r-matrixstats) | |
18124 | ("r-r-utils" ,r-r-utils))) | |
18125 | (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") | |
18126 | (synopsis "Activity Index calculation using raw accelerometry data") | |
18127 | (description | |
18128 | "This is a package to read raw accelerometry from GT3X+ accelerometry | |
18129 | data and plain table data to calculate the Activity Index from Bai et | |
18130 | al. (2016) @url{doi:10.1371/journal.pone.0160644}.") | |
18131 | (license license:gpl3))) | |
bbaab253 RW |
18132 | |
18133 | (define-public r-activpal | |
18134 | (package | |
18135 | (name "r-activpal") | |
18136 | (version "0.1.3") | |
18137 | (source | |
18138 | (origin | |
18139 | (method url-fetch) | |
18140 | (uri (cran-uri "activPAL" version)) | |
18141 | (sha256 | |
18142 | (base32 | |
18143 | "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na")))) | |
18144 | (properties `((upstream-name . "activPAL"))) | |
18145 | (build-system r-build-system) | |
18146 | (propagated-inputs | |
18147 | `(("r-devtools" ,r-devtools) | |
18148 | ("r-dplyr" ,r-dplyr) | |
18149 | ("r-ggplot2" ,r-ggplot2) | |
18150 | ("r-lubridate" ,r-lubridate) | |
18151 | ("r-magrittr" ,r-magrittr) | |
18152 | ("r-tidyr" ,r-tidyr))) | |
18153 | (home-page "https://cran.r-project.org/web/packages/activPAL") | |
18154 | (synopsis "Processing and chart generation from activPAL events files") | |
18155 | (description | |
18156 | "This package contains functions to generate pre-defined summary | |
18157 | statistics from activPAL events files. The package also contains functions to | |
18158 | produce informative graphics that visualize physical activity behaviour and | |
18159 | trends. This includes generating graphs that align physical activity | |
18160 | behaviour with additional time based observations described by other data | |
18161 | sets, such as sleep diaries and continuous glucose monitoring data.") | |
18162 | (license license:gpl3))) | |
a5d4dc7e RW |
18163 | |
18164 | (define-public r-activpalprocessing | |
18165 | (package | |
18166 | (name "r-activpalprocessing") | |
18167 | (version "1.0.2") | |
18168 | (source | |
18169 | (origin | |
18170 | (method url-fetch) | |
18171 | (uri (cran-uri "activpalProcessing" version)) | |
18172 | (sha256 | |
18173 | (base32 | |
18174 | "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1")))) | |
18175 | (properties | |
18176 | `((upstream-name . "activpalProcessing"))) | |
18177 | (build-system r-build-system) | |
18178 | (propagated-inputs | |
18179 | `(("r-chron" ,r-chron))) | |
18180 | (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") | |
18181 | (synopsis "Process activPAL events files") | |
18182 | (description | |
18183 | "This package performs estimation of physical activity and sedentary | |
18184 | behavior variables from activPAL events files.") | |
18185 | ;; Either version of the GPL. | |
18186 | (license (list license:gpl2 license:gpl3)))) | |
5f08fa64 RW |
18187 | |
18188 | (define-public r-actogrammr | |
18189 | (package | |
18190 | (name "r-actogrammr") | |
18191 | (version "0.2.3") | |
18192 | (source | |
18193 | (origin | |
18194 | (method url-fetch) | |
18195 | (uri (cran-uri "actogrammr" version)) | |
18196 | (sha256 | |
18197 | (base32 | |
18198 | "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa")))) | |
18199 | (properties `((upstream-name . "actogrammr"))) | |
18200 | (build-system r-build-system) | |
18201 | (propagated-inputs | |
18202 | `(("r-dplyr" ,r-dplyr) | |
18203 | ("r-ggplot2" ,r-ggplot2) | |
18204 | ("r-lubridate" ,r-lubridate) | |
18205 | ("r-readr" ,r-readr) | |
18206 | ("r-tidyr" ,r-tidyr))) | |
18207 | (home-page "https://cran.r-project.org/web/packages/actogrammr/") | |
18208 | (synopsis "Read in activity data and plot actograms") | |
18209 | (description | |
18210 | "Read in activity measurements from standard file formats used by | |
18211 | circadian rhythm researchers, currently only ClockLab format, and process and | |
18212 | plot the data. The central type of plot is the actogram, as first described | |
18213 | in \"Activity and distribution of certain wild mice in relation to biotic | |
18214 | communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") | |
18215 | (license license:gpl3))) | |
1830e038 RW |
18216 | |
18217 | (define-public r-expint | |
18218 | (package | |
18219 | (name "r-expint") | |
18220 | (version "0.1-6") | |
18221 | (source | |
18222 | (origin | |
18223 | (method url-fetch) | |
18224 | (uri (cran-uri "expint" version)) | |
18225 | (sha256 | |
18226 | (base32 | |
18227 | "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7")))) | |
18228 | (properties `((upstream-name . "expint"))) | |
18229 | (build-system r-build-system) | |
18230 | (home-page "https://gitlab.com/vigou3/expint") | |
18231 | (synopsis "Exponential integral and incomplete Gamma function") | |
18232 | (description | |
18233 | "This package provides the exponential integrals @code{E_1(x)}, | |
18234 | @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma | |
18235 | function @code{G(a, x)} defined for negative values of its first argument. | |
18236 | The package also gives easy access to the underlying C routines through an | |
18237 | API; see the package vignette for details.") | |
18238 | (license license:gpl2+))) | |
7faa0537 RW |
18239 | |
18240 | (define-public r-actuar | |
18241 | (package | |
18242 | (name "r-actuar") | |
18243 | (version "2.3-3") | |
18244 | (source | |
18245 | (origin | |
18246 | (method url-fetch) | |
18247 | (uri (cran-uri "actuar" version)) | |
18248 | (sha256 | |
18249 | (base32 | |
18250 | "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih")))) | |
18251 | (properties `((upstream-name . "actuar"))) | |
18252 | (build-system r-build-system) | |
18253 | (propagated-inputs `(("r-expint" ,r-expint))) | |
18254 | (home-page "https://gitlab.com/vigou3/actuar") | |
18255 | (synopsis "Actuarial functions and heavy tailed distributions") | |
18256 | (description | |
18257 | "This package provides functions and data sets for actuarial science: | |
18258 | modeling of loss distributions; risk theory and ruin theory; simulation of | |
18259 | compound models, discrete mixtures and compound hierarchical models; | |
18260 | credibility theory. It boasts support for many additional probability | |
18261 | distributions to model insurance loss amounts and loss frequency: 19 | |
18262 | continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete | |
18263 | distribution; zero-truncated and zero-modified extensions of the standard | |
18264 | discrete distributions. It also supports phase-type distributions commonly | |
18265 | used to compute ruin probabilities.") | |
18266 | (license license:gpl2+))) | |
6968aa2f RW |
18267 | |
18268 | (define-public r-bmp | |
18269 | (package | |
18270 | (name "r-bmp") | |
18271 | (version "0.3") | |
18272 | (source | |
18273 | (origin | |
18274 | (method url-fetch) | |
18275 | (uri (cran-uri "bmp" version)) | |
18276 | (sha256 | |
18277 | (base32 | |
18278 | "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx")))) | |
18279 | (properties `((upstream-name . "bmp"))) | |
18280 | (build-system r-build-system) | |
18281 | (home-page "https://cran.r-project.org/web/packages/bmp/") | |
18282 | (synopsis "Read Bitmap (BMP) images") | |
18283 | (description | |
18284 | "This package provides pure R tools to read BMP format images. It is | |
18285 | currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") | |
18286 | (license license:gpl2+))) | |
7dd1fbf9 RW |
18287 | |
18288 | (define-public r-readbitmap | |
18289 | (package | |
18290 | (name "r-readbitmap") | |
18291 | (version "0.1.5") | |
18292 | (source | |
18293 | (origin | |
18294 | (method url-fetch) | |
18295 | (uri (cran-uri "readbitmap" version)) | |
18296 | (sha256 | |
18297 | (base32 | |
18298 | "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk")))) | |
18299 | (properties `((upstream-name . "readbitmap"))) | |
18300 | (build-system r-build-system) | |
18301 | (inputs | |
18302 | `(("libjpeg" ,libjpeg) | |
18303 | ("libpng" ,libpng))) | |
18304 | (propagated-inputs | |
18305 | `(("r-bmp" ,r-bmp) | |
18306 | ("r-jpeg" ,r-jpeg) | |
18307 | ("r-png" ,r-png) | |
18308 | ("r-tiff" ,r-tiff))) | |
18309 | (home-page "https://github.com/jefferis/readbitmap") | |
18310 | (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") | |
18311 | (description | |
18312 | "This package provides tools to identify and read BMP, JPEG, PNG, and | |
18313 | TIFF format bitmap images. Identification defaults to the use of the magic | |
18314 | number embedded in the file rather than the file extension.") | |
18315 | (license license:gpl2+))) | |
5e2ad376 RW |
18316 | |
18317 | (define-public r-imager | |
18318 | (package | |
18319 | (name "r-imager") | |
18320 | (version "0.41.2") | |
18321 | (source | |
18322 | (origin | |
18323 | (method url-fetch) | |
18324 | (uri (cran-uri "imager" version)) | |
18325 | (sha256 | |
18326 | (base32 | |
18327 | "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v")))) | |
18328 | (properties `((upstream-name . "imager"))) | |
18329 | (build-system r-build-system) | |
18330 | (inputs | |
18331 | `(("fftw" ,fftw) | |
18332 | ("libtiff" ,libtiff) | |
18333 | ("libx11" ,libx11) | |
18334 | ("zlib" ,zlib))) | |
18335 | (propagated-inputs | |
18336 | `(("r-cairo" ,r-cairo) | |
18337 | ("r-downloader" ,r-downloader) | |
18338 | ("r-igraph" ,r-igraph) | |
18339 | ("r-jpeg" ,r-jpeg) | |
18340 | ("r-magrittr" ,r-magrittr) | |
18341 | ("r-plyr" ,r-plyr) | |
18342 | ("r-png" ,r-png) | |
18343 | ("r-purrr" ,r-purrr) | |
18344 | ("r-rcpp" ,r-rcpp) | |
18345 | ("r-readbitmap" ,r-readbitmap) | |
18346 | ("r-stringr" ,r-stringr))) | |
18347 | (native-inputs `(("pkg-config" ,pkg-config))) | |
18348 | (home-page "http://dahtah.github.io/imager") | |
18349 | (synopsis "Image processing library") | |
18350 | (description | |
18351 | "This is a package for fast image processing for images in up to 4 | |
18352 | dimensions (two spatial dimensions, one time/depth dimension, one color | |
18353 | dimension). It provides most traditional image processing tools (filtering, | |
18354 | morphology, transformations, etc.) as well as various functions for easily | |
18355 | analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a | |
18356 | simple, modern C++ library for image processing.") | |
18357 | (license license:lgpl3))) | |
154555e4 RW |
18358 | |
18359 | (define-public r-acuityview | |
18360 | (package | |
18361 | (name "r-acuityview") | |
18362 | (version "0.1") | |
18363 | (source | |
18364 | (origin | |
18365 | (method url-fetch) | |
18366 | (uri (cran-uri "AcuityView" version)) | |
18367 | (sha256 | |
18368 | (base32 | |
18369 | "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l")))) | |
18370 | (properties `((upstream-name . "AcuityView"))) | |
18371 | (build-system r-build-system) | |
18372 | (propagated-inputs | |
18373 | `(("r-fftwtools" ,r-fftwtools) | |
18374 | ("r-imager" ,r-imager) | |
18375 | ("r-plotrix" ,r-plotrix))) | |
18376 | (home-page "https://cran.r-project.org/web/packages/AcuityView/") | |
18377 | (synopsis "Display scenes as seen by an animal with less acute vision") | |
18378 | (description | |
18379 | "This package provides a simple method for representing a visual scene as | |
18380 | it may be seen by an animal with less acute vision.") | |
18381 | (license license:gpl2+))) | |
2a1fd518 RW |
18382 | |
18383 | (define-public r-adabag | |
18384 | (package | |
18385 | (name "r-adabag") | |
18386 | (version "4.2") | |
18387 | (source | |
18388 | (origin | |
18389 | (method url-fetch) | |
18390 | (uri (cran-uri "adabag" version)) | |
18391 | (sha256 | |
18392 | (base32 | |
18393 | "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7")))) | |
18394 | (properties `((upstream-name . "adabag"))) | |
18395 | (build-system r-build-system) | |
18396 | (propagated-inputs | |
18397 | `(("r-caret" ,r-caret) | |
18398 | ("r-doparallel" ,r-doparallel) | |
18399 | ("r-foreach" ,r-foreach) | |
18400 | ("r-rpart" ,r-rpart))) | |
18401 | (home-page "https://cran.r-project.org/web/packages/adabag/") | |
18402 | (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") | |
18403 | (description | |
18404 | "This package implements Freund and Schapire's Adaboost.M1 algorithm and | |
18405 | Breiman's Bagging algorithm using classification trees as individual | |
18406 | classifiers. Once these classifiers have been trained, they can be used to | |
18407 | predict on new data. Also, cross validation estimation of the error can be | |
18408 | done.") | |
18409 | (license license:gpl2+))) | |
0b13a757 RW |
18410 | |
18411 | (define-public r-adagio | |
18412 | (package | |
18413 | (name "r-adagio") | |
18414 | (version "0.7.1") | |
18415 | (source | |
18416 | (origin | |
18417 | (method url-fetch) | |
18418 | (uri (cran-uri "adagio" version)) | |
18419 | (sha256 | |
18420 | (base32 | |
18421 | "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k")))) | |
18422 | (properties `((upstream-name . "adagio"))) | |
18423 | (build-system r-build-system) | |
18424 | (native-inputs `(("gfortran" ,gfortran))) | |
18425 | (home-page "https://cran.r-project.org/web/packages/adagio/") | |
18426 | (synopsis "Discrete and global optimization routines") | |
18427 | (description | |
18428 | "This package provides methods and algorithms for discrete optimization, | |
18429 | e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and | |
18430 | Hooke-Jeeves minimization, and some (evolutionary) global optimization | |
18431 | functions.") | |
18432 | (license license:gpl3+))) | |
09e9ad33 RW |
18433 | |
18434 | (define-public r-univoutl | |
18435 | (package | |
18436 | (name "r-univoutl") | |
18437 | (version "0.1-5") | |
18438 | (source | |
18439 | (origin | |
18440 | (method url-fetch) | |
18441 | (uri (cran-uri "univOutl" version)) | |
18442 | (sha256 | |
18443 | (base32 | |
18444 | "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi")))) | |
18445 | (properties `((upstream-name . "univOutl"))) | |
18446 | (build-system r-build-system) | |
18447 | (propagated-inputs | |
18448 | `(("r-hmisc" ,r-hmisc) | |
18449 | ("r-robustbase" ,r-robustbase))) | |
18450 | (home-page "https://github.com/marcellodo/univOutl") | |
18451 | (synopsis "Detection of univariate outliers") | |
18452 | (description | |
18453 | "This package provides well-known outlier detection techniques in the | |
18454 | univariate case. Methods to deal with skewed distribution are included too. | |
18455 | The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of | |
18456 | historical data is implemented as well. When available, survey weights can be | |
18457 | used in outliers detection.") | |
18458 | (license license:gpl2+))) | |
5458490e RW |
18459 | |
18460 | (define-public r-tolerance | |
18461 | (package | |
18462 | (name "r-tolerance") | |
18463 | (version "1.3.0") | |
18464 | (source | |
18465 | (origin | |
18466 | (method url-fetch) | |
18467 | (uri (cran-uri "tolerance" version)) | |
18468 | (sha256 | |
18469 | (base32 | |
18470 | "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86")))) | |
18471 | (properties `((upstream-name . "tolerance"))) | |
18472 | (build-system r-build-system) | |
18473 | (propagated-inputs | |
18474 | `(("r-rgl" ,r-rgl))) | |
18475 | (home-page "https://cran.r-project.org/web/packages/tolerance/") | |
18476 | (synopsis "Statistical tolerance intervals and regions") | |
18477 | (description | |
18478 | "This package provides functions for estimating tolerance | |
18479 | limits (intervals) for various univariate distributions (binomial, Cauchy, | |
18480 | discrete Pareto, exponential, two-parameter exponential, extreme value, | |
18481 | hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, | |
18482 | normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), | |
18483 | Bayesian normal tolerance limits, multivariate normal tolerance regions, | |
18484 | nonparametric tolerance intervals, tolerance bands for regression | |
18485 | settings (linear regression, nonlinear regression, nonparametric regression, | |
18486 | and multivariate regression), and analysis of variance tolerance intervals. | |
18487 | Visualizations are also available for most of these settings.") | |
18488 | (license license:gpl2+))) | |
94ecf713 RW |
18489 | |
18490 | (define-public r-additivitytests | |
18491 | (package | |
18492 | (name "r-additivitytests") | |
18493 | (version "1.1-4") | |
18494 | (source | |
18495 | (origin | |
18496 | (method url-fetch) | |
18497 | (uri (cran-uri "additivityTests" version)) | |
18498 | (sha256 | |
18499 | (base32 | |
18500 | "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw")))) | |
18501 | (properties | |
18502 | `((upstream-name . "additivityTests"))) | |
18503 | (build-system r-build-system) | |
18504 | (home-page "https://github.com/simecek/additivityTests") | |
18505 | (synopsis "Additivity tests in the two way Anova with single sub-class numbers") | |
18506 | (description | |
18507 | "This package provides an implementation of the Tukey, Mandel, | |
18508 | Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") | |
18509 | (license license:gpl3))) | |
9906cb80 RW |
18510 | |
18511 | (define-public r-flexclust | |
18512 | (package | |
18513 | (name "r-flexclust") | |
18514 | (version "1.4-0") | |
18515 | (source | |
18516 | (origin | |
18517 | (method url-fetch) | |
18518 | (uri (cran-uri "flexclust" version)) | |
18519 | (sha256 | |
18520 | (base32 | |
18521 | "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2")))) | |
18522 | (properties `((upstream-name . "flexclust"))) | |
18523 | (build-system r-build-system) | |
18524 | (propagated-inputs | |
18525 | `(("r-class" ,r-class) | |
18526 | ("r-lattice" ,r-lattice) | |
18527 | ("r-modeltools" ,r-modeltools))) | |
18528 | (home-page "https://cran.r-project.org/web/packages/flexclust/") | |
18529 | (synopsis "Flexible cluster algorithms") | |
18530 | (description | |
18531 | "The main function @code{kcca} implements a general framework for | |
18532 | k-centroids cluster analysis supporting arbitrary distance measures and | |
18533 | centroid computation. Further cluster methods include hard competitive | |
18534 | learning, neural gas, and QT clustering. There are numerous visualization | |
18535 | methods for cluster results (neighborhood graphs, convex cluster hulls, | |
18536 | barcharts of centroids, ...), and bootstrap methods for the analysis of | |
18537 | cluster stability.") | |
18538 | (license license:gpl2))) | |
86a760cc RW |
18539 | |
18540 | (define-public r-biclust | |
18541 | (package | |
18542 | (name "r-biclust") | |
18543 | (version "2.0.1") | |
18544 | (source | |
18545 | (origin | |
18546 | (method url-fetch) | |
18547 | (uri (cran-uri "biclust" version)) | |
18548 | (sha256 | |
18549 | (base32 | |
18550 | "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0")))) | |
18551 | (properties `((upstream-name . "biclust"))) | |
18552 | (build-system r-build-system) | |
18553 | (propagated-inputs | |
18554 | `(("r-additivitytests" ,r-additivitytests) | |
18555 | ("r-colorspace" ,r-colorspace) | |
18556 | ("r-flexclust" ,r-flexclust) | |
18557 | ("r-ggplot2" ,r-ggplot2) | |
18558 | ("r-lattice" ,r-lattice) | |
18559 | ("r-mass" ,r-mass) | |
18560 | ("r-tidyr" ,r-tidyr))) | |
18561 | (home-page "https://cran.r-project.org/web/packages/biclust/") | |
18562 | (synopsis "BiCluster algorithms") | |
18563 | (description | |
18564 | "The main function @code{biclust()} provides several algorithms to find | |
18565 | biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax. | |
18566 | In addition, the package provides methods for data | |
18567 | preprocessing (normalization and discretization), visualization, and | |
18568 | validation of bicluster solutions.") | |
18569 | (license license:gpl3))) | |
9cd3ae86 RW |
18570 | |
18571 | (define-public r-icge | |
18572 | (package | |
18573 | (name "r-icge") | |
18574 | (version "0.3") | |
18575 | (source | |
18576 | (origin | |
18577 | (method url-fetch) | |
18578 | (uri (cran-uri "ICGE" version)) | |
18579 | (sha256 | |
18580 | (base32 | |
18581 | "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa")))) | |
18582 | (properties `((upstream-name . "ICGE"))) | |
18583 | (build-system r-build-system) | |
18584 | (propagated-inputs | |
18585 | `(("r-cluster" ,r-cluster) | |
18586 | ("r-mass" ,r-mass))) | |
18587 | (home-page "https://cran.r-project.org/web/packages/ICGE/") | |
18588 | (synopsis "Cluster estimation and identification of atypical units") | |
18589 | (description | |
18590 | "ICGE is a package that helps to estimate the number of real clusters in | |
18591 | data as well as to identify atypical units. The underlying methods are based | |
18592 | on distances rather than on unit x variables.") | |
18593 | (license license:gpl2+))) | |
9fd2d4fd RW |
18594 | |
18595 | (define-public r-depth | |
18596 | (package | |
18597 | (name "r-depth") | |
18598 | (version "2.1-1.1") | |
18599 | (source | |
18600 | (origin | |
18601 | (method url-fetch) | |
18602 | (uri (cran-uri "depth" version)) | |
18603 | (sha256 | |
18604 | (base32 | |
18605 | "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m")))) | |
18606 | (properties `((upstream-name . "depth"))) | |
18607 | (build-system r-build-system) | |
18608 | (propagated-inputs | |
18609 | `(("r-abind" ,r-abind) | |
18610 | ("r-circular" ,r-circular) | |
18611 | ("r-rgl" ,r-rgl))) | |
18612 | (native-inputs | |
18613 | `(("gfortran" ,gfortran))) | |
18614 | (home-page "https://cran.r-project.org/web/packages/depth/") | |
18615 | (synopsis "Nonparametric depth functions for multivariate analysis") | |
18616 | (description | |
18617 | "This package provides tools for depth functions methodology applied to | |
18618 | multivariate analysis. Besides allowing calculation of depth values and | |
18619 | depth-based location estimators, the package includes functions or drawing | |
18620 | contour plots and perspective plots of depth functions. Euclidian and | |
18621 | spherical depths are supported.") | |
18622 | (license license:gpl2))) | |
ccc2c19b RW |
18623 | |
18624 | (define-public r-archetypes | |
18625 | (package | |
18626 | (name "r-archetypes") | |
18627 | (version "2.2-0.1") | |
18628 | (source | |
18629 | (origin | |
18630 | (method url-fetch) | |
18631 | (uri (cran-uri "archetypes" version)) | |
18632 | (sha256 | |
18633 | (base32 | |
18634 | "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0")))) | |
18635 | (properties `((upstream-name . "archetypes"))) | |
18636 | (build-system r-build-system) | |
18637 | (propagated-inputs | |
18638 | `(("r-modeltools" ,r-modeltools) | |
18639 | ("r-nnls" ,r-nnls))) | |
18640 | (home-page "https://cran.r-project.org/web/packages/archetypes") | |
18641 | (synopsis "Archetypal analysis") | |
18642 | (description | |
18643 | "The main function @code{archetypes} implements a framework for | |
18644 | archetypal analysis supporting arbitrary problem solving mechanisms for the | |
18645 | different conceptual parts of the algorithm.") | |
18646 | (license license:gpl2+))) | |
c7172465 RW |
18647 | |
18648 | (define-public r-shapes | |
18649 | (package | |
18650 | (name "r-shapes") | |
18651 | (version "1.2.5") | |
18652 | (source | |
18653 | (origin | |
18654 | (method url-fetch) | |
18655 | (uri (cran-uri "shapes" version)) | |
18656 | (sha256 | |
18657 | (base32 | |
18658 | "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s")))) | |
18659 | (properties `((upstream-name . "shapes"))) | |
18660 | (build-system r-build-system) | |
18661 | (propagated-inputs | |
18662 | `(("r-mass" ,r-mass) | |
18663 | ("r-minpack-lm" ,r-minpack-lm) | |
18664 | ("r-rgl" ,r-rgl) | |
18665 | ("r-scatterplot3d" ,r-scatterplot3d))) | |
18666 | (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes") | |
18667 | (synopsis "Statistical shape analysis") | |
18668 | (description | |
18669 | "This package provides routines for the statistical analysis of landmark | |
18670 | shapes, including Procrustes analysis, graphical displays, principal | |
18671 | components analysis, permutation and bootstrap tests, thin-plate spline | |
18672 | transformation grids and comparing covariance matrices. See Dryden, I.L. and | |
18673 | Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd | |
18674 | Edition), John Wiley and Sons.") | |
18675 | (license license:gpl2))) | |
c6750807 RW |
18676 | |
18677 | (define-public r-anthropometry | |
18678 | (package | |
18679 | (name "r-anthropometry") | |
18680 | (version "1.13") | |
18681 | (source | |
18682 | (origin | |
18683 | (method url-fetch) | |
18684 | (uri (cran-uri "Anthropometry" version)) | |
18685 | (sha256 | |
18686 | (base32 | |
18687 | "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8")))) | |
18688 | (properties `((upstream-name . "Anthropometry"))) | |
18689 | (build-system r-build-system) | |
18690 | (propagated-inputs | |
18691 | `(("r-archetypes" ,r-archetypes) | |
18692 | ("r-biclust" ,r-biclust) | |
18693 | ("r-cluster" ,r-cluster) | |
18694 | ("r-depth" ,r-depth) | |
18695 | ("r-fnn" ,r-fnn) | |
18696 | ("r-icge" ,r-icge) | |
18697 | ("r-nnls" ,r-nnls) | |
18698 | ("r-rgl" ,r-rgl) | |
18699 | ("r-shapes" ,r-shapes))) | |
18700 | (home-page "https://cran.r-project.org/web/packages/Anthropometry/") | |
18701 | (synopsis "Statistical methods for anthropometric data") | |
18702 | (description | |
18703 | "This package provides statistical methods especially developed to | |
18704 | analyze anthropometric data. These methods are aimed at providing effective | |
18705 | solutions to some commons problems related to Ergonomics and Anthropometry. | |
18706 | They are based on clustering, the statistical concept of data depth, | |
18707 | statistical shape analysis and archetypal analysis.") | |
18708 | (license license:gpl2+))) | |
5c0b5b8a RW |
18709 | |
18710 | (define-public r-adamethods | |
18711 | (package | |
18712 | (name "r-adamethods") | |
18713 | (version "1.2") | |
18714 | (source | |
18715 | (origin | |
18716 | (method url-fetch) | |
18717 | (uri (cran-uri "adamethods" version)) | |
18718 | (sha256 | |
18719 | (base32 | |
18720 | "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh")))) | |
18721 | (properties `((upstream-name . "adamethods"))) | |
18722 | (build-system r-build-system) | |
18723 | (propagated-inputs | |
18724 | `(("r-anthropometry" ,r-anthropometry) | |
18725 | ("r-archetypes" ,r-archetypes) | |
18726 | ("r-fnn" ,r-fnn) | |
18727 | ("r-foreach" ,r-foreach) | |
18728 | ("r-nnls" ,r-nnls) | |
18729 | ("r-tolerance" ,r-tolerance) | |
18730 | ("r-univoutl" ,r-univoutl))) | |
18731 | (home-page "https://cran.r-project.org/web/packages/adamethods/") | |
18732 | (synopsis "Archetypoid algorithms and anomaly detection") | |
18733 | (description | |
18734 | "This package is a collection of several algorithms to obtain | |
18735 | archetypoids with small and large databases and with both classical | |
18736 | multivariate data and functional data (univariate and multivariate). Some of | |
18737 | these algorithms also allow to detect anomalies (outliers).") | |
18738 | (license license:gpl2+))) | |
b5b6e74e RW |
18739 | |
18740 | (define-public r-idpmisc | |
18741 | (package | |
18742 | (name "r-idpmisc") | |
18743 | (version "1.1.19") | |
18744 | (source | |
18745 | (origin | |
18746 | (method url-fetch) | |
18747 | (uri (cran-uri "IDPmisc" version)) | |
18748 | (sha256 | |
18749 | (base32 | |
18750 | "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd")))) | |
18751 | (properties `((upstream-name . "IDPmisc"))) | |
18752 | (build-system r-build-system) | |
18753 | (propagated-inputs | |
18754 | `(("r-lattice" ,r-lattice))) | |
18755 | (home-page "https://cran.r-project.org/web/packages/IDPmisc/") | |
18756 | (synopsis "Functions for data analyses and visualization") | |
18757 | (description | |
18758 | "This package provides different high-level graphics functions for | |
18759 | displaying large datasets, displaying circular data in a very flexible way, | |
18760 | finding local maxima, brewing color ramps, drawing nice arrows, zooming | |
18761 | 2D-plots, creating figures with differently colored margin and plot region. | |
18762 | In addition, the package contains auxiliary functions for data manipulation | |
18763 | like omitting observations with irregular values or selecting data by logical | |
18764 | vectors, which include NAs. Other functions are especially useful in | |
18765 | spectroscopy and analyses of environmental data: robust baseline fitting, | |
18766 | finding peaks in spectra, converting humidity measures.") | |
18767 | (license license:gpl3+))) | |
eb15df8d RW |
18768 | |
18769 | (define-public r-qqman | |
18770 | (package | |
18771 | (name "r-qqman") | |
18772 | (version "0.1.4") | |
18773 | (source | |
18774 | (origin | |
18775 | (method url-fetch) | |
18776 | (uri (cran-uri "qqman" version)) | |
18777 | (sha256 | |
18778 | (base32 | |
18779 | "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s")))) | |
18780 | (properties `((upstream-name . "qqman"))) | |
18781 | (build-system r-build-system) | |
18782 | (propagated-inputs | |
18783 | `(("r-calibrate" ,r-calibrate))) | |
18784 | (home-page "https://cran.r-project.org/web/packages/qqman/") | |
18785 | (synopsis "Q-Q and Manhattan plots for GWAS data") | |
18786 | (description | |
18787 | "This package allows you to create Q-Q and Manhattan plots for GWAS data | |
18788 | from PLINK results.") | |
18789 | (license license:gpl3))) | |
5aa7e882 RW |
18790 | |
18791 | (define-public r-ggplot-multistats | |
18792 | (package | |
18793 | (name "r-ggplot-multistats") | |
18794 | (version "1.0.0") | |
18795 | (source | |
18796 | (origin | |
18797 | (method url-fetch) | |
18798 | (uri (cran-uri "ggplot.multistats" version)) | |
18799 | (sha256 | |
18800 | (base32 | |
18801 | "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il")))) | |
18802 | (properties | |
18803 | `((upstream-name . "ggplot.multistats"))) | |
18804 | (build-system r-build-system) | |
18805 | (propagated-inputs | |
18806 | `(("r-ggplot2" ,r-ggplot2) | |
18807 | ("r-hexbin" ,r-hexbin) | |
18808 | ("r-rlang" ,r-rlang) | |
18809 | ("r-scales" ,r-scales))) | |
18810 | (home-page "https://github.com/flying-sheep/ggplot.multistats") | |
18811 | (synopsis "Multiple summary statistics for binned stats/geometries") | |
18812 | (description | |
18813 | "This package provides the ggplot binning layer @code{stat_summaries_hex()}, | |
18814 | which functions similar to its singular form, but allows the use of multiple | |
18815 | statistics per bin. Those statistics can be mapped to multiple bin | |
18816 | aesthetics.") | |
18817 | (license license:gpl3))) | |
257b3b81 RW |
18818 | |
18819 | (define-public r-knn-covertree | |
18820 | (package | |
18821 | (name "r-knn-covertree") | |
18822 | (version "1.0") | |
18823 | (source | |
18824 | (origin | |
18825 | (method url-fetch) | |
18826 | (uri (cran-uri "knn.covertree" version)) | |
18827 | (sha256 | |
18828 | (base32 | |
18829 | "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz")))) | |
18830 | (properties `((upstream-name . "knn.covertree"))) | |
18831 | (build-system r-build-system) | |
18832 | (propagated-inputs | |
18833 | `(("r-matrix" ,r-matrix) | |
18834 | ("r-rcpp" ,r-rcpp) | |
18835 | ("r-rcppeigen" ,r-rcppeigen))) | |
18836 | (home-page "https://github.com/flying-sheep/knn.covertree") | |
18837 | (synopsis "Accurate kNN Implementation with multiple distance measures") | |
18838 | (description | |
18839 | "Similarly to the FNN package, this package allows calculation of the k | |
18840 | nearest neighbors (kNN) of a data matrix. The implementation is based on | |
18841 | cover trees introduced by Alina Beygelzimer, Sham Kakade, and John | |
18842 | Langford (2006) @url{doi:10.1145/1143844.1143857}.") | |
18843 | (license license:agpl3+))) | |
5828dd03 RW |
18844 | |
18845 | (define-public r-poibin | |
18846 | (package | |
18847 | (name "r-poibin") | |
18848 | (version "1.4") | |
18849 | (source | |
18850 | (origin | |
18851 | (method url-fetch) | |
18852 | (uri (cran-uri "poibin" version)) | |
18853 | (sha256 | |
18854 | (base32 | |
18855 | "1rllgmk7yanb5amysl33kmi11lx86q5kqblyb8qqb3ckj2w4jhm2")))) | |
18856 | (properties `((upstream-name . "poibin"))) | |
18857 | (build-system r-build-system) | |
18858 | (home-page "https://cran.r-project.org/web/packages/poibin/") | |
18859 | (synopsis "Poisson binomial distribution") | |
18860 | (description | |
18861 | "This package provides an implementation of both the exact and | |
18862 | approximation methods for computing the @dfn{cumulative distribution | |
18863 | function} (CDF) of the Poisson binomial distribution. It also provides the | |
18864 | @dfn{probability mass function} (PMF), quantile function, and random number | |
18865 | generation for the Poisson binomial distribution.") | |
18866 | (license license:gpl2))) | |
c686e53a RW |
18867 | |
18868 | (define-public r-diagram | |
18869 | (package | |
18870 | (name "r-diagram") | |
18871 | (version "1.6.4") | |
18872 | (source | |
18873 | (origin | |
18874 | (method url-fetch) | |
18875 | (uri (cran-uri "diagram" version)) | |
18876 | (sha256 | |
18877 | (base32 | |
18878 | "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw")))) | |
18879 | (properties `((upstream-name . "diagram"))) | |
18880 | (build-system r-build-system) | |
18881 | (propagated-inputs | |
18882 | `(("r-shape" ,r-shape))) | |
18883 | (home-page "https://cran.r-project.org/web/packages/diagram/") | |
18884 | (synopsis "Visualize simple graphs (networks) and plot flow diagrams") | |
18885 | (description | |
18886 | "This package provides tools to visualize simple graphs (networks) based | |
18887 | on a transition matrix, utilities to plot flow diagrams, visualizing webs, | |
18888 | electrical networks, etc. It also includes supporting material for the book | |
18889 | \"A practical guide to ecological modelling - using R as a simulation | |
18890 | platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book | |
18891 | \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and | |
18892 | Francesca Mazzia (2012).") | |
18893 | (license license:gpl2+))) | |
96afb6c6 RW |
18894 | |
18895 | (define-public r-lim | |
18896 | (package | |
18897 | (name "r-lim") | |
18898 | (version "1.4.6") | |
18899 | (source | |
18900 | (origin | |
18901 | (method url-fetch) | |
18902 | (uri (cran-uri "LIM" version)) | |
18903 | (sha256 | |
18904 | (base32 | |
18905 | "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8")))) | |
18906 | (properties `((upstream-name . "LIM"))) | |
18907 | (build-system r-build-system) | |
18908 | (propagated-inputs | |
18909 | `(("r-diagram" ,r-diagram) | |
18910 | ("r-limsolve" ,r-limsolve))) | |
18911 | (home-page "https://cran.r-project.org/web/packages/LIM/") | |
18912 | (synopsis "Linear inverse model examples and solution methods") | |
18913 | (description | |
18914 | "This package provides functions that read and solve linear inverse | |
18915 | problems (food web problems, linear programming problems).") | |
18916 | (license license:gpl2+))) | |
59d485e1 RW |
18917 | |
18918 | (define-public r-shinycssloaders | |
18919 | (package | |
18920 | (name "r-shinycssloaders") | |
18921 | (version "0.2.0") | |
18922 | (source | |
18923 | (origin | |
18924 | (method url-fetch) | |
18925 | (uri (cran-uri "shinycssloaders" version)) | |
18926 | (sha256 | |
18927 | (base32 | |
18928 | "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4")))) | |
18929 | (properties | |
18930 | `((upstream-name . "shinycssloaders"))) | |
18931 | (build-system r-build-system) | |
18932 | (propagated-inputs | |
18933 | `(("r-digest" ,r-digest) | |
18934 | ("r-glue" ,r-glue) | |
18935 | ("r-shiny" ,r-shiny))) | |
18936 | (home-page "https://github.com/andrewsali/shinycssloaders") | |
18937 | (synopsis "Add CSS loading animations to Shiny outputs") | |
18938 | (description | |
18939 | "This package provides tools to create a lightweight Shiny wrapper for | |
18940 | the css-loaders created by Luke Hass | |
18941 | @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will | |
18942 | automatically show a loader when the output is (re)calculating.") | |
18943 | (license license:gpl3))) | |
1028bf0a RW |
18944 | |
18945 | (define-public r-rsvg | |
18946 | (package | |
18947 | (name "r-rsvg") | |
18948 | (version "1.3") | |
18949 | (source | |
18950 | (origin | |
18951 | (method url-fetch) | |
18952 | (uri (cran-uri "rsvg" version)) | |
18953 | (sha256 | |
18954 | (base32 | |
18955 | "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g")))) | |
18956 | (properties `((upstream-name . "rsvg"))) | |
18957 | (build-system r-build-system) | |
18958 | (inputs | |
18959 | `(("librsvg" ,librsvg) | |
18960 | ("zlib" ,zlib))) | |
18961 | (native-inputs | |
18962 | `(("pkg-config" ,pkg-config))) | |
18963 | (home-page "https://github.com/jeroen/rsvg#readme") | |
18964 | (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays") | |
18965 | (description | |
18966 | "This package allows you to render vector-based SVG images into | |
18967 | high-quality custom-size bitmap arrays using the librsvg2 library. The | |
18968 | resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In | |
18969 | addition, the package can convert images directly to various formats such as | |
18970 | PDF or PostScript.") | |
18971 | (license license:expat))) | |
3eacc8fa RW |
18972 | |
18973 | (define-public r-influencer | |
18974 | (package | |
18975 | (name "r-influencer") | |
18976 | (version "0.1.0") | |
18977 | (source | |
18978 | (origin | |
18979 | (method url-fetch) | |
18980 | (uri (cran-uri "influenceR" version)) | |
18981 | (sha256 | |
18982 | (base32 | |
18983 | "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag")))) | |
18984 | (properties `((upstream-name . "influenceR"))) | |
18985 | (build-system r-build-system) | |
18986 | (propagated-inputs | |
18987 | `(("r-igraph" ,r-igraph) | |
18988 | ("r-matrix" ,r-matrix))) | |
18989 | (home-page "https://github.com/rcc-uchicago/influenceR") | |
18990 | (synopsis "Tools to quantify structural importance of nodes in a network") | |
18991 | (description | |
18992 | "This package provides functionality to compute various node centrality | |
18993 | measures on networks. Included are functions to compute betweenness | |
18994 | centrality (by utilizing Madduri and Bader's SNAP library), implementations of | |
18995 | Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's | |
18996 | algorithm to identify key players, and Valente's bridging metric. The | |
18997 | betweenness, Key Players, and bridging implementations are parallelized with | |
18998 | OpenMP.") | |
18999 | (license license:gpl2))) | |
0f5ae473 RW |
19000 | |
19001 | (define-public r-emplik | |
19002 | (package | |
19003 | (name "r-emplik") | |
19004 | (version "1.0-4.3") | |
19005 | (source | |
19006 | (origin | |
19007 | (method url-fetch) | |
19008 | (uri (cran-uri "emplik" version)) | |
19009 | (sha256 | |
19010 | (base32 | |
19011 | "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c")))) | |
19012 | (properties `((upstream-name . "emplik"))) | |
19013 | (build-system r-build-system) | |
19014 | (propagated-inputs | |
19015 | `(("r-quantreg" ,r-quantreg))) | |
19016 | (home-page "http://www.ms.uky.edu/~mai/EmpLik.html") | |
19017 | (synopsis "Empirical likelihood ratio for censored/truncated data") | |
19018 | (description | |
19019 | "This package provides empirical likelihood ratio tests for | |
19020 | means/quantiles/hazards from possibly censored and/or truncated data. It also | |
19021 | does regression.") | |
19022 | (license license:gpl2+))) | |
9eb680b1 RW |
19023 | |
19024 | (define-public r-imputeyn | |
19025 | (package | |
19026 | (name "r-imputeyn") | |
19027 | (version "1.3") | |
19028 | (source | |
19029 | (origin | |
19030 | (method url-fetch) | |
19031 | (uri (cran-uri "imputeYn" version)) | |
19032 | (sha256 | |
19033 | (base32 | |
19034 | "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs")))) | |
19035 | (properties `((upstream-name . "imputeYn"))) | |
19036 | (build-system r-build-system) | |
19037 | (propagated-inputs | |
19038 | `(("r-boot" ,r-boot) | |
19039 | ("r-emplik" ,r-emplik) | |
19040 | ("r-mvtnorm" ,r-mvtnorm) | |
19041 | ("r-quadprog" ,r-quadprog) | |
19042 | ("r-survival" ,r-survival))) | |
19043 | (home-page "https://cran.r-project.org/web/packages/imputeYn/") | |
19044 | (synopsis "Impute last largest censored observation under weighted least squares") | |
19045 | (description | |
19046 | "This package allows for the imputation of the last largest censored | |
19047 | observantions. This method brings less bias and more efficient estimates for | |
19048 | AFT models.") | |
19049 | (license license:gpl2))) | |
69442bd0 RW |
19050 | |
19051 | (define-public r-adapenetclass | |
19052 | (package | |
19053 | (name "r-adapenetclass") | |
19054 | (version "1.2") | |
19055 | (source | |
19056 | (origin | |
19057 | (method url-fetch) | |
19058 | (uri (cran-uri "AdapEnetClass" version)) | |
19059 | (sha256 | |
19060 | (base32 | |
19061 | "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc")))) | |
19062 | (properties `((upstream-name . "AdapEnetClass"))) | |
19063 | (build-system r-build-system) | |
19064 | (propagated-inputs | |
19065 | `(("r-glmnet" ,r-glmnet) | |
19066 | ("r-imputeyn" ,r-imputeyn) | |
19067 | ("r-lars" ,r-lars) | |
19068 | ("r-quadprog" ,r-quadprog))) | |
19069 | (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/") | |
19070 | (synopsis "Class of adaptive elastic net methods for censored data") | |
19071 | (description | |
19072 | "This package provides methods for variable selection for AFT models.") | |
19073 | (license license:gpl2))) | |
be9d0ab2 RW |
19074 | |
19075 | (define-public r-flock | |
19076 | (package | |
19077 | (name "r-flock") | |
19078 | (version "0.7") | |
19079 | (source | |
19080 | (origin | |
19081 | (method url-fetch) | |
19082 | (uri (cran-uri "flock" version)) | |
19083 | (sha256 | |
19084 | (base32 | |
19085 | "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7")))) | |
19086 | (properties `((upstream-name . "flock"))) | |
19087 | (build-system r-build-system) | |
19088 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
19089 | (home-page "https://cran.r-project.org/web/packages/flock/") | |
19090 | (synopsis "Process synchronization using file locks") | |
19091 | (description | |
19092 | "This package implements synchronization between R processes (spawned by | |
19093 | using the @code{parallel} package for instance) using file locks. It supports | |
19094 | both exclusive and shared locking.") | |
19095 | (license license:asl2.0))) | |
1a1ba087 RW |
19096 | |
19097 | (define-public r-archivist | |
19098 | (package | |
19099 | (name "r-archivist") | |
19100 | (version "2.3.4") | |
19101 | (source | |
19102 | (origin | |
19103 | (method url-fetch) | |
19104 | (uri (cran-uri "archivist" version)) | |
19105 | (sha256 | |
19106 | (base32 | |
19107 | "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7")))) | |
19108 | (properties `((upstream-name . "archivist"))) | |
19109 | (build-system r-build-system) | |
19110 | (propagated-inputs | |
19111 | `(("r-dbi" ,r-dbi) | |
19112 | ("r-digest" ,r-digest) | |
19113 | ("r-flock" ,r-flock) | |
19114 | ("r-httr" ,r-httr) | |
19115 | ("r-lubridate" ,r-lubridate) | |
19116 | ("r-magrittr" ,r-magrittr) | |
19117 | ("r-rcurl" ,r-rcurl) | |
19118 | ("r-rsqlite" ,r-rsqlite))) | |
19119 | (home-page "https://pbiecek.github.io/archivist/") | |
19120 | (synopsis "Tools for storing, restoring and searching for R objects") | |
19121 | (description | |
19122 | "Data exploration and modelling is a process in which a lot of data | |
19123 | artifacts are produced. Artifacts like: subsets, data aggregates, plots, | |
19124 | statistical models, different versions of data sets and different versions of | |
19125 | results. Archivist helps to store and manage artifacts created in R. It | |
19126 | allows you to store selected artifacts as binary files together with their | |
19127 | metadata and relations. Archivist allows sharing artifacts with others. It | |
19128 | can look for already created artifacts by using its class, name, date of the | |
19129 | creation or other properties. It also makes it easy to restore such | |
19130 | artifacts.") | |
19131 | (license license:gpl2))) | |
a581caa0 RW |
19132 | |
19133 | (define-public r-versions | |
19134 | (package | |
19135 | (name "r-versions") | |
19136 | (version "0.3") | |
19137 | (source | |
19138 | (origin | |
19139 | (method url-fetch) | |
19140 | (uri (cran-uri "versions" version)) | |
19141 | (sha256 | |
19142 | (base32 | |
19143 | "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd")))) | |
19144 | (properties `((upstream-name . "versions"))) | |
19145 | (build-system r-build-system) | |
19146 | (home-page "https://cran.r-project.org/web/packages/versions/") | |
19147 | (synopsis "Query and install specific versions of CRAN packages") | |
19148 | (description | |
19149 | "This package allows you to install specified versions of R packages | |
19150 | hosted on CRAN and provides functions to list available versions and the | |
19151 | versions of currently installed packages.") | |
19152 | (license license:bsd-3))) | |
7340ae0c RW |
19153 | |
19154 | (define-public r-adapr | |
19155 | (package | |
19156 | (name "r-adapr") | |
19157 | (version "2.0.0") | |
19158 | (source | |
19159 | (origin | |
19160 | (method url-fetch) | |
19161 | (uri (cran-uri "adapr" version)) | |
19162 | (sha256 | |
19163 | (base32 | |
19164 | "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw")))) | |
19165 | (properties `((upstream-name . "adapr"))) | |
19166 | (build-system r-build-system) | |
19167 | (propagated-inputs | |
19168 | `(("r-archivist" ,r-archivist) | |
19169 | ("r-devtools" ,r-devtools) | |
19170 | ("r-digest" ,r-digest) | |
19171 | ("r-doparallel" ,r-doparallel) | |
19172 | ("r-gdata" ,r-gdata) | |
19173 | ("r-ggplot2" ,r-ggplot2) | |
19174 | ("r-git2r" ,r-git2r) | |
19175 | ("r-igraph" ,r-igraph) | |
19176 | ("r-knitr" ,r-knitr) | |
19177 | ("r-plotly" ,r-plotly) | |
19178 | ("r-plyr" ,r-plyr) | |
19179 | ("r-rmarkdown" ,r-rmarkdown) | |
19180 | ("r-shiny" ,r-shiny) | |
19181 | ("r-shinydashboard" ,r-shinydashboard) | |
19182 | ("r-versions" ,r-versions))) | |
19183 | (home-page "https://cran.r-project.org/web/packages/adapr/") | |
19184 | (synopsis "Implementation of an accountable data analysis process") | |
19185 | (description | |
19186 | "This package tracks reading and writing within R scripts that are | |
19187 | organized into a directed acyclic graph. It contains an interactive Shiny | |
19188 | application @code{adaprApp()}. It uses Git and file hashes to track version | |
19189 | histories of inputs and outputs.") | |
19190 | (license license:lgpl2.0))) | |
536a7ca2 RW |
19191 | |
19192 | (define-public r-adapsamp | |
19193 | (package | |
19194 | (name "r-adapsamp") | |
19195 | (version "1.1.1") | |
19196 | (source | |
19197 | (origin | |
19198 | (method url-fetch) | |
19199 | (uri (cran-uri "AdapSamp" version)) | |
19200 | (sha256 | |
19201 | (base32 | |
19202 | "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis")))) | |
19203 | (properties `((upstream-name . "AdapSamp"))) | |
19204 | (build-system r-build-system) | |
19205 | (propagated-inputs `(("r-pracma" ,r-pracma))) | |
19206 | (home-page "https://cran.r-project.org/web/packages/AdapSamp/") | |
19207 | (synopsis "Adaptive sampling algorithms") | |
19208 | (description | |
19209 | "For distributions whose probability density functions are log-concave, | |
19210 | the adaptive rejection sampling algorithm can be used to build envelope | |
19211 | functions for sampling. For others, the modified adaptive rejection sampling | |
19212 | algorithm, the concave-convex adaptive rejection sampling algorithm, and the | |
19213 | adaptive slice sampling algorithm can be used. This R package mainly includes | |
19214 | these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and | |
19215 | @code{rASS()}. These functions can realize sampling based on the algorithms | |
19216 | above.") | |
19217 | (license license:gpl2))) | |
9380968a RW |
19218 | |
19219 | (define-public r-adaptalint | |
19220 | (package | |
19221 | (name "r-adaptalint") | |
19222 | (version "0.2.4") | |
19223 | (source | |
19224 | (origin | |
19225 | (method url-fetch) | |
19226 | (uri (cran-uri "adaptalint" version)) | |
19227 | (sha256 | |
19228 | (base32 | |
19229 | "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf")))) | |
19230 | (properties `((upstream-name . "adaptalint"))) | |
19231 | (build-system r-build-system) | |
19232 | (propagated-inputs | |
19233 | `(("r-dplyr" ,r-dplyr) | |
19234 | ("r-lintr" ,r-lintr) | |
19235 | ("r-purrr" ,r-purrr))) | |
19236 | (home-page "https://cran.r-project.org/web/packages/adaptalint/") | |
19237 | (synopsis "Check R code style") | |
19238 | (description | |
19239 | "This package provides tools to infer the code style (which style rules | |
19240 | are followed and which ones are not) from one package and use it to check | |
19241 | another. This makes it easier to find and correct the most important problems | |
19242 | first.") | |
19243 | (license license:gpl3))) |