Commit | Line | Data |
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056468dc | 1 | ;;; GNU Guix --- Functional package management for GNU |
92ce1883 | 2 | ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
c80fb90f | 3 | ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> |
ddbf2a98 | 4 | ;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org> |
97b44f5e | 5 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
53cc59a1 | 6 | ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> |
109b2f7c | 7 | ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com> |
c56739df | 8 | ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net> |
96e22362 | 9 | ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com> |
d2a507ef | 10 | ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> |
1cde7467 | 11 | ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> |
c994418b | 12 | ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> |
b55697fb | 13 | ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com> |
60a166c6 | 14 | ;;; Copyright © 2018 Leo Famulari <leo@famulari.name> |
d9bec9a8 | 15 | ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> |
34bac6c3 | 16 | ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net> |
100f5602 | 17 | ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> |
16fddf17 | 18 | ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> |
056468dc RW |
19 | ;;; |
20 | ;;; This file is part of GNU Guix. | |
21 | ;;; | |
22 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
23 | ;;; under the terms of the GNU General Public License as published by | |
24 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
25 | ;;; your option) any later version. | |
26 | ;;; | |
27 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
28 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
29 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
30 | ;;; GNU General Public License for more details. | |
31 | ;;; | |
32 | ;;; You should have received a copy of the GNU General Public License | |
33 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
34 | ||
35 | (define-module (gnu packages cran) | |
36 | #:use-module ((guix licenses) #:prefix license:) | |
37 | #:use-module (guix packages) | |
38 | #:use-module (guix download) | |
92ce1883 | 39 | #:use-module (guix git-download) |
056468dc | 40 | #:use-module (guix utils) |
c69d27db | 41 | #:use-module (guix build-system r) |
44b0c5b5 | 42 | #:use-module (gnu packages algebra) |
ff939ef4 | 43 | #:use-module (gnu packages base) |
f33cb7ab | 44 | #:use-module (gnu packages bioinformatics) |
7002c44f | 45 | #:use-module (gnu packages c) |
546fc4aa | 46 | #:use-module (gnu packages compression) |
92ce1883 | 47 | #:use-module (gnu packages curl) |
d9bec9a8 | 48 | #:use-module (gnu packages databases) |
f338e480 | 49 | #:use-module (gnu packages fontutils) |
062b6dbd | 50 | #:use-module (gnu packages gcc) |
d884e407 | 51 | #:use-module (gnu packages geo) |
d0eb09a1 | 52 | #:use-module (gnu packages ghostscript) |
f338e480 | 53 | #:use-module (gnu packages gl) |
01af264d | 54 | #:use-module (gnu packages gnome) |
3d62d98e | 55 | #:use-module (gnu packages graph) |
01af264d | 56 | #:use-module (gnu packages gtk) |
dddbc90c | 57 | #:use-module (gnu packages haskell-xyz) |
3f6e6e98 | 58 | #:use-module (gnu packages icu4c) |
f338e480 | 59 | #:use-module (gnu packages image) |
dab3e92c | 60 | #:use-module (gnu packages imagemagick) |
3f6e6e98 | 61 | #:use-module (gnu packages java) |
92ce1883 RW |
62 | #:use-module (gnu packages javascript) |
63 | #:use-module (gnu packages lisp) | |
f97ce815 | 64 | #:use-module (gnu packages machine-learning) |
521e0703 | 65 | #:use-module (gnu packages maths) |
94989d4b | 66 | #:use-module (gnu packages mpi) |
1ab51604 | 67 | #:use-module (gnu packages multiprecision) |
f313baf0 | 68 | #:use-module (gnu packages networking) |
3f6e6e98 | 69 | #:use-module (gnu packages pcre) |
e0268ff2 | 70 | #:use-module (gnu packages perl) |
e33498b8 | 71 | #:use-module (gnu packages pkg-config) |
9f56ceec | 72 | #:use-module (gnu packages python) |
984a8aa6 | 73 | #:use-module (gnu packages python-xyz) |
e0268ff2 | 74 | #:use-module (gnu packages statistics) |
9944399a | 75 | #:use-module (gnu packages tls) |
f338e480 RW |
76 | #:use-module (gnu packages web) |
77 | #:use-module (gnu packages xorg)) | |
056468dc | 78 | |
88e4ed55 RW |
79 | (define-public r-clipr |
80 | (package | |
81 | (name "r-clipr") | |
710ecc9c | 82 | (version "0.7.0") |
88e4ed55 RW |
83 | (source |
84 | (origin | |
85 | (method url-fetch) | |
86 | (uri (cran-uri "clipr" version)) | |
87 | (sha256 | |
88 | (base32 | |
710ecc9c | 89 | "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903")))) |
88e4ed55 RW |
90 | (build-system r-build-system) |
91 | (home-page "https://github.com/mdlincoln/clipr") | |
92 | (synopsis "Read and write from the system clipboard") | |
93 | (description | |
94 | "This package provides simple utility functions to read from and write to | |
95 | the system clipboards.") | |
96 | (license license:gpl3))) | |
97 | ||
3f22a115 RW |
98 | (define-public r-ellipsis |
99 | (package | |
100 | (name "r-ellipsis") | |
f3575adf | 101 | (version "0.3.0") |
3f22a115 RW |
102 | (source |
103 | (origin | |
104 | (method url-fetch) | |
105 | (uri (cran-uri "ellipsis" version)) | |
106 | (sha256 | |
107 | (base32 | |
f3575adf | 108 | "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b")))) |
3f22a115 | 109 | (build-system r-build-system) |
a4bc73b2 RW |
110 | (propagated-inputs |
111 | `(("r-rlang" ,r-rlang))) | |
3f22a115 RW |
112 | (home-page "https://github.com/hadley/ellipsis") |
113 | (synopsis "Tools for working with additional arguments") | |
114 | (description | |
115 | "In S3 generics, it's useful to take @code{...} so that methods can have | |
116 | additional arguments. But this flexibility comes at a cost: misspelled | |
117 | arguments will be silently ignored. The @code{ellipsis} package is an | |
118 | experiment that allows a generic to warn if any arguments passed in @code{...} | |
119 | are not used.") | |
120 | (license license:gpl3))) | |
121 | ||
0b2883e1 RW |
122 | (define-public r-grr |
123 | (package | |
124 | (name "r-grr") | |
125 | (version "0.9.5") | |
126 | (source | |
127 | (origin | |
128 | (method url-fetch) | |
129 | (uri (cran-uri "grr" version)) | |
130 | (sha256 | |
131 | (base32 | |
132 | "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9")))) | |
133 | (build-system r-build-system) | |
134 | (home-page "https://cran.r-project.org/web/packages/grr") | |
135 | (synopsis "Alternative implementations of base R functions") | |
136 | (description | |
137 | "This package provides alternative implementations of some base R | |
138 | functions, including @code{sort}, @code{order}, and @code{match}. The | |
139 | functions are simplified but can be faster or have other advantages.") | |
140 | (license license:gpl3))) | |
141 | ||
cf51d895 RW |
142 | (define-public r-matrix-utils |
143 | (package | |
144 | (name "r-matrix-utils") | |
145 | (version "0.9.7") | |
146 | (source | |
147 | (origin | |
148 | (method url-fetch) | |
149 | (uri (cran-uri "Matrix.utils" version)) | |
150 | (sha256 | |
151 | (base32 | |
152 | "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va")))) | |
153 | (properties `((upstream-name . "Matrix.utils"))) | |
154 | (build-system r-build-system) | |
155 | (propagated-inputs | |
156 | `(("r-grr" ,r-grr) | |
157 | ("r-matrix" ,r-matrix))) | |
158 | (home-page "https://github.com/cvarrichio/Matrix.utils") | |
159 | (synopsis | |
160 | "Data.frame-Like Operations on Sparse and Dense Matrix Objects") | |
161 | (description | |
162 | "This package implements data manipulation methods such as @code{cast}, | |
163 | @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like | |
164 | objects.") | |
165 | (license license:gpl3))) | |
166 | ||
2b106a8d RW |
167 | (define-public r-sys |
168 | (package | |
169 | (name "r-sys") | |
d9a382ec | 170 | (version "3.3") |
2b106a8d RW |
171 | (source |
172 | (origin | |
173 | (method url-fetch) | |
174 | (uri (cran-uri "sys" version)) | |
175 | (sha256 | |
176 | (base32 | |
d9a382ec | 177 | "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6")))) |
2b106a8d RW |
178 | (build-system r-build-system) |
179 | (home-page "https://github.com/jeroen/sys") | |
180 | (synopsis "Powerful and reliable tools for running system commands in R") | |
181 | (description | |
182 | "This package provides drop-in replacements for the base @code{system2()} | |
183 | function with fine control and consistent behavior across platforms. It | |
184 | supports clean interruption, timeout, background tasks, and streaming STDIN / | |
185 | STDOUT / STDERR over binary or text connections. The package also provides | |
186 | functions for evaluating expressions inside a temporary fork. Such | |
187 | evaluations have no side effects on the main R process, and support reliable | |
188 | interrupts and timeouts. This provides the basis for a sandboxing | |
189 | mechanism.") | |
190 | (license license:expat))) | |
191 | ||
9d3a4672 RW |
192 | (define-public r-askpass |
193 | (package | |
194 | (name "r-askpass") | |
195 | (version "1.1") | |
196 | (source | |
197 | (origin | |
198 | (method url-fetch) | |
199 | (uri (cran-uri "askpass" version)) | |
200 | (sha256 | |
201 | (base32 | |
202 | "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) | |
203 | (build-system r-build-system) | |
204 | (propagated-inputs `(("r-sys" ,r-sys))) | |
205 | (home-page "https://github.com/jeroen/askpass") | |
206 | (synopsis "Safe password entry for R") | |
207 | (description | |
208 | "This package provides cross-platform utilities for prompting the user | |
209 | for credentials or a passphrase, for example to authenticate with a server or | |
210 | read a protected key.") | |
211 | (license license:expat))) | |
212 | ||
c80fb90f RW |
213 | (define-public r-vegan |
214 | (package | |
215 | (name "r-vegan") | |
0ce4b23d | 216 | (version "2.5-6") |
c80fb90f RW |
217 | (source |
218 | (origin | |
219 | (method url-fetch) | |
220 | (uri (cran-uri "vegan" version)) | |
221 | (sha256 | |
222 | (base32 | |
0ce4b23d | 223 | "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k")))) |
c80fb90f RW |
224 | (build-system r-build-system) |
225 | (native-inputs | |
226 | `(("gfortran" ,gfortran))) | |
227 | (propagated-inputs | |
228 | `(("r-cluster" ,r-cluster) | |
229 | ("r-knitr" ,r-knitr) ; needed for vignettes | |
230 | ("r-lattice" ,r-lattice) | |
231 | ("r-mass" ,r-mass) | |
232 | ("r-mgcv" ,r-mgcv) | |
233 | ("r-permute" ,r-permute))) | |
234 | (home-page "https://cran.r-project.org/web/packages/vegan") | |
235 | (synopsis "Functions for community ecology") | |
236 | (description | |
237 | "The vegan package provides tools for descriptive community ecology. It | |
238 | has most basic functions of diversity analysis, community ordination and | |
239 | dissimilarity analysis. Most of its multivariate tools can be used for other | |
240 | data types as well.") | |
241 | (license license:gpl2+))) | |
242 | ||
786d3de2 CR |
243 | (define-public r-tidyverse |
244 | (package | |
245 | (name "r-tidyverse") | |
246 | (version "1.2.1") | |
247 | (source | |
248 | (origin | |
249 | (method url-fetch) | |
250 | (uri (cran-uri "tidyverse" version)) | |
251 | (sha256 | |
252 | (base32 | |
253 | "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd")))) | |
254 | (build-system r-build-system) | |
255 | (propagated-inputs | |
256 | `(("r-broom" ,r-broom) | |
257 | ("r-cli" ,r-cli) | |
258 | ("r-crayon" ,r-crayon) | |
259 | ("r-dbplyr" ,r-dbplyr) | |
260 | ("r-dplyr" ,r-dplyr) | |
261 | ("r-forcats" ,r-forcats) | |
262 | ("r-ggplot2" ,r-ggplot2) | |
263 | ("r-haven" ,r-haven) | |
264 | ("r-hms" ,r-hms) | |
265 | ("r-httr" ,r-httr) | |
266 | ("r-jsonlite" ,r-jsonlite) | |
267 | ("r-lubridate" ,r-lubridate) | |
268 | ("r-magrittr" ,r-magrittr) | |
269 | ("r-modelr" ,r-modelr) | |
270 | ("r-purrr" ,r-purrr) | |
271 | ("r-readr" ,r-readr) | |
272 | ("r-readxl" ,r-readxl) | |
273 | ("r-reprex" ,r-reprex) | |
274 | ("r-rlang" ,r-rlang) | |
275 | ("r-rstudioapi" ,r-rstudioapi) | |
276 | ("r-rvest" ,r-rvest) | |
277 | ("r-stringr" ,r-stringr) | |
278 | ("r-tibble" ,r-tibble) | |
279 | ("r-tidyr" ,r-tidyr) | |
280 | ("r-xml2" ,r-xml2))) | |
281 | (home-page "https://tidyverse.tidyverse.org") | |
282 | (synopsis "Install and load packages from the \"Tidyverse\"") | |
283 | (description | |
284 | "The @code{tidyverse} is a set of packages that work in harmony because | |
285 | they share common data representations and API design. This package is | |
286 | designed to make it easy to install and load multiple tidyverse packages in a | |
287 | single step.") | |
288 | (license license:gpl3))) | |
289 | ||
8a1ef6ac CR |
290 | (define-public r-rvest |
291 | (package | |
292 | (name "r-rvest") | |
8bfc6dc5 | 293 | (version "0.3.4") |
8a1ef6ac CR |
294 | (source |
295 | (origin | |
296 | (method url-fetch) | |
297 | (uri (cran-uri "rvest" version)) | |
298 | (sha256 | |
299 | (base32 | |
8bfc6dc5 | 300 | "0ji5lk8g1gbv4d9c4jg1fg6rgsqrrwkm05j1id7drdw9kqdifgj1")))) |
8a1ef6ac CR |
301 | (build-system r-build-system) |
302 | (propagated-inputs | |
303 | `(("r-httr" ,r-httr) | |
304 | ("r-magrittr" ,r-magrittr) | |
305 | ("r-selectr" ,r-selectr) | |
306 | ("r-xml2" ,r-xml2))) | |
307 | (home-page "https://github.com/hadley/rvest") | |
308 | (synopsis "Simple web scraping for R") | |
309 | (description | |
310 | "@code{r-rvest} helps you scrape information from web pages. It is | |
311 | designed to work with @code{magrittr} to make it easy to express common web | |
312 | scraping tasks, inspired by libraries like @code{BeautifulSoup}.") | |
313 | (license license:gpl3))) | |
314 | ||
81a9d4a4 CR |
315 | (define-public r-selectr |
316 | (package | |
317 | (name "r-selectr") | |
41e8bd77 | 318 | (version "0.4-1") |
81a9d4a4 CR |
319 | (source |
320 | (origin | |
321 | (method url-fetch) | |
322 | (uri (cran-uri "selectr" version)) | |
323 | (sha256 | |
324 | (base32 | |
41e8bd77 | 325 | "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b")))) |
81a9d4a4 | 326 | (build-system r-build-system) |
41e8bd77 RW |
327 | (propagated-inputs |
328 | `(("r-stringr" ,r-stringr) | |
329 | ("r-r6" ,r-r6))) | |
81a9d4a4 CR |
330 | (home-page "https://sjp.co.nz/projects/selectr/") |
331 | (synopsis "Translate CSS selectors to XPath expressions") | |
332 | (description | |
333 | "@code{r-selectr} translates a CSS3 selector into an equivalent XPath | |
334 | expression. This allows you to use CSS selectors when working with the XML | |
335 | package as it can only evaluate XPath expressions. Also provided are | |
336 | convenience functions useful for using CSS selectors on XML nodes. This | |
337 | package is a port of the Python package @code{cssselect}.") | |
338 | (license license:bsd-3))) | |
339 | ||
948740b0 CR |
340 | (define-public r-reprex |
341 | (package | |
342 | (name "r-reprex") | |
bd9f1479 | 343 | (version "0.3.0") |
948740b0 CR |
344 | (source |
345 | (origin | |
346 | (method url-fetch) | |
347 | (uri (cran-uri "reprex" version)) | |
348 | (sha256 | |
349 | (base32 | |
bd9f1479 | 350 | "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10")))) |
948740b0 CR |
351 | (build-system r-build-system) |
352 | (propagated-inputs | |
353 | `(("r-callr" ,r-callr) | |
e3c1e93e | 354 | ("r-clipr" ,r-clipr) |
1c9906c2 | 355 | ("r-fs" ,r-fs) |
e3c1e93e | 356 | ("r-rlang" ,r-rlang) |
948740b0 | 357 | ("r-rmarkdown" ,r-rmarkdown) |
e3c1e93e RW |
358 | ("r-whisker" ,r-whisker) |
359 | ("r-withr" ,r-withr))) | |
948740b0 CR |
360 | (home-page "https://github.com/tidyverse/reprex") |
361 | (synopsis "Prepare reproducible R code examples for sharing") | |
362 | (description | |
363 | "This package provides a convenience wrapper that uses the | |
364 | @code{rmarkdown} package to render small snippets of code to target formats | |
365 | that include both code and output. The goal is to encourage the sharing of | |
366 | small, reproducible, and runnable examples on code-oriented websites or email. | |
367 | @code{reprex} also extracts clean, runnable R code from various common formats, | |
368 | such as copy/paste from an R session.") | |
369 | (license license:expat))) | |
370 | ||
10487c30 CR |
371 | (define-public r-callr |
372 | (package | |
373 | (name "r-callr") | |
8fa78874 | 374 | (version "3.3.2") |
10487c30 CR |
375 | (source |
376 | (origin | |
377 | (method url-fetch) | |
378 | (uri (cran-uri "callr" version)) | |
379 | (sha256 | |
380 | (base32 | |
8fa78874 | 381 | "12dbqzjngbyaqdyw0yq1blyfx8pagcvx1vqj2jm451hs25nhdrnh")))) |
10487c30 CR |
382 | (build-system r-build-system) |
383 | (propagated-inputs | |
527c6055 | 384 | `(("r-r6" ,r-r6) |
6034a62a | 385 | ("r-processx" ,r-processx))) |
10487c30 CR |
386 | (home-page "https://github.com/r-lib/callr#readme") |
387 | (synopsis "Call R from R") | |
388 | (description | |
389 | "It is sometimes useful to perform a computation in a separate R process, | |
b3fed5ed | 390 | without affecting the current R process at all. This package does exactly |
10487c30 CR |
391 | that.") |
392 | (license license:expat))) | |
393 | ||
d7637e5e CR |
394 | (define-public r-readxl |
395 | (package | |
396 | (name "r-readxl") | |
50d063b5 | 397 | (version "1.3.1") |
d7637e5e CR |
398 | (source |
399 | (origin | |
400 | (method url-fetch) | |
401 | (uri (cran-uri "readxl" version)) | |
402 | (sha256 | |
403 | (base32 | |
50d063b5 | 404 | "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14")))) |
d7637e5e CR |
405 | (build-system r-build-system) |
406 | (propagated-inputs | |
407 | `(("r-cellranger" ,r-cellranger) | |
b140569e | 408 | ("r-progress" ,r-progress) |
d7637e5e CR |
409 | ("r-rcpp" ,r-rcpp) |
410 | ("r-tibble" ,r-tibble))) | |
411 | (home-page "https://readxl.tidyverse.org") | |
412 | (synopsis "Read Excel files") | |
413 | (description | |
414 | "This package lets you import Excel files into R. It supports | |
415 | @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via | |
416 | the embedded @code{RapidXML} C++ library.") | |
417 | ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and | |
418 | ;; 'rapidxml' which is Boost. | |
419 | (license (list license:gpl3 license:bsd-2 license:boost1.0)))) | |
420 | ||
9a91c925 CR |
421 | (define-public r-modelr |
422 | (package | |
423 | (name "r-modelr") | |
7ef25083 | 424 | (version "0.1.5") |
9a91c925 CR |
425 | (source |
426 | (origin | |
427 | (method url-fetch) | |
428 | (uri (cran-uri "modelr" version)) | |
429 | (sha256 | |
430 | (base32 | |
7ef25083 | 431 | "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5")))) |
9a91c925 CR |
432 | (build-system r-build-system) |
433 | (propagated-inputs | |
434 | `(("r-broom" ,r-broom) | |
435 | ("r-dplyr" ,r-dplyr) | |
9a91c925 CR |
436 | ("r-magrittr" ,r-magrittr) |
437 | ("r-purrr" ,r-purrr) | |
7ef25083 | 438 | ("r-rlang" ,r-rlang) |
9a91c925 CR |
439 | ("r-tibble" ,r-tibble) |
440 | ("r-tidyr" ,r-tidyr))) | |
441 | (home-page "https://github.com/tidyverse/modelr") | |
442 | (synopsis "Helper functions for modelling in pipelines") | |
443 | (description | |
444 | "Functions for modelling that help you seamlessly integrate modelling | |
445 | into a pipeline of data manipulation and visualisation.") | |
446 | (license license:gpl3))) | |
447 | ||
92ce1883 RW |
448 | (define-public r-httpuv |
449 | (package | |
450 | (name "r-httpuv") | |
a1f43994 | 451 | (version "1.5.2") |
92ce1883 RW |
452 | (source (origin |
453 | (method url-fetch) | |
454 | (uri (cran-uri "httpuv" version)) | |
455 | (sha256 | |
456 | (base32 | |
a1f43994 | 457 | "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk")))) |
92ce1883 | 458 | (build-system r-build-system) |
92ce1883 RW |
459 | (propagated-inputs |
460 | `(("r-bh" ,r-bh) | |
461 | ("r-later" ,r-later) | |
2391e97c RW |
462 | ("r-promises" ,r-promises) |
463 | ("r-r6" ,r-r6) | |
464 | ("r-rcpp" ,r-rcpp))) | |
92ce1883 RW |
465 | (home-page "https://github.com/rstudio/httpuv") |
466 | (synopsis "HTTP and WebSocket server library for R") | |
467 | (description | |
468 | "The httpuv package provides low-level socket and protocol support for | |
469 | handling HTTP and WebSocket requests directly from within R. It is primarily | |
470 | intended as a building block for other packages, rather than making it | |
471 | particularly easy to create complete web applications using httpuv alone.") | |
472 | ;; This package includes third-party code that was originally released | |
473 | ;; under various non-copyleft licenses. Full licensing information can be | |
474 | ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE | |
475 | (license license:gpl3+))) | |
476 | ||
477 | (define-public r-jsonlite | |
478 | (package | |
479 | (name "r-jsonlite") | |
a2315c67 | 480 | (version "1.6") |
92ce1883 RW |
481 | (source (origin |
482 | (method url-fetch) | |
483 | (uri (cran-uri "jsonlite" version)) | |
484 | (sha256 | |
485 | (base32 | |
a2315c67 | 486 | "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8")))) |
92ce1883 RW |
487 | (build-system r-build-system) |
488 | (home-page "http://arxiv.org/abs/1403.2805") | |
489 | (synopsis "Robust, high performance JSON parser and generator for R") | |
490 | (description | |
491 | "The jsonlite package provides a fast JSON parser and generator optimized | |
492 | for statistical data and the web. It offers flexible, robust, high | |
493 | performance tools for working with JSON in R and is particularly powerful for | |
494 | building pipelines and interacting with a web API. In addition to converting | |
495 | JSON data from/to R objects, jsonlite contains functions to stream, validate, | |
496 | and prettify JSON data. The unit tests included with the package verify that | |
497 | all edge cases are encoded and decoded consistently for use with dynamic data | |
498 | in systems and applications.") | |
499 | (license license:expat))) | |
500 | ||
501 | (define-public r-servr | |
502 | (package | |
503 | (name "r-servr") | |
f503ed92 | 504 | (version "0.15") |
92ce1883 RW |
505 | (source (origin |
506 | (method url-fetch) | |
507 | (uri (cran-uri "servr" version)) | |
508 | (sha256 | |
509 | (base32 | |
f503ed92 | 510 | "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi")))) |
92ce1883 RW |
511 | (build-system r-build-system) |
512 | (propagated-inputs | |
513 | `(("r-httpuv" ,r-httpuv) | |
514 | ("r-jsonlite" ,r-jsonlite) | |
515 | ("r-mime" ,r-mime) | |
516 | ("r-xfun" ,r-xfun))) | |
517 | (home-page "https://github.com/yihui/servr") | |
518 | (synopsis "Simple HTTP server to serve static files or dynamic documents") | |
519 | (description | |
520 | "Servr provides an HTTP server in R to serve static files, or dynamic | |
521 | documents that can be converted to HTML files (e.g., R Markdown) under a given | |
522 | directory.") | |
523 | (license license:expat))) | |
524 | ||
525 | (define-public r-htmltools | |
526 | (package | |
527 | (name "r-htmltools") | |
528 | (version "0.3.6") | |
529 | (source (origin | |
530 | (method url-fetch) | |
531 | (uri (cran-uri "htmltools" version)) | |
532 | (sha256 | |
533 | (base32 | |
534 | "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4")))) | |
535 | (build-system r-build-system) | |
536 | (arguments | |
537 | `(#:phases | |
538 | (modify-phases %standard-phases | |
539 | ;; See https://github.com/rstudio/htmltools/pull/68 | |
540 | ;; The resource files are in the store and have mode 444. After | |
541 | ;; copying the files R fails to remove them again because it doesn't | |
542 | ;; have write access to them. | |
543 | (add-after 'unpack 'copy-files-without-mode | |
544 | (lambda _ | |
545 | (substitute* "R/html_dependency.R" | |
546 | (("file.copy\\(from, to, " prefix) | |
547 | (string-append prefix | |
548 | "copy.mode = FALSE, "))) | |
549 | #t))))) | |
550 | (propagated-inputs | |
551 | `(("r-digest" ,r-digest) | |
552 | ("r-rcpp" ,r-rcpp))) | |
553 | (home-page "https://cran.r-project.org/web/packages/htmltools") | |
554 | (synopsis "R tools for HTML") | |
555 | (description | |
556 | "This package provides tools for HTML generation and output in R.") | |
557 | (license license:expat))) | |
558 | ||
559 | (define-public r-htmlwidgets | |
560 | (package | |
561 | (name "r-htmlwidgets") | |
562 | (version "1.3") | |
563 | (source (origin | |
564 | (method url-fetch) | |
565 | (uri (cran-uri "htmlwidgets" version)) | |
566 | (sha256 | |
567 | (base32 | |
568 | "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i")))) | |
569 | (build-system r-build-system) | |
570 | (propagated-inputs | |
571 | `(("r-htmltools" ,r-htmltools) | |
572 | ("r-jsonlite" ,r-jsonlite) | |
573 | ("r-yaml" ,r-yaml))) | |
574 | (home-page "https://github.com/ramnathv/htmlwidgets") | |
575 | (synopsis "HTML Widgets for R") | |
576 | (description | |
577 | "HTML widgets is a framework for creating HTML widgets that render in | |
578 | various contexts including the R console, R Markdown documents, and Shiny web | |
579 | applications.") | |
580 | (license license:expat))) | |
581 | ||
582 | (define-public r-htmltable | |
583 | (package | |
584 | (name "r-htmltable") | |
33194de2 | 585 | (version "1.13.2") |
92ce1883 RW |
586 | (source |
587 | (origin | |
588 | (method url-fetch) | |
589 | (uri (cran-uri "htmlTable" version)) | |
590 | (sha256 | |
591 | (base32 | |
33194de2 | 592 | "0h6jslchlx1dzqqdb70c3n9xlapcym9ykycvr0hc4q3450y8qmvh")))) |
92ce1883 RW |
593 | (properties `((upstream-name . "htmlTable"))) |
594 | (build-system r-build-system) | |
595 | (propagated-inputs | |
596 | `(("r-checkmate" ,r-checkmate) | |
597 | ("r-htmltools" ,r-htmltools) | |
598 | ("r-htmlwidgets" ,r-htmlwidgets) | |
599 | ("r-knitr" ,r-knitr) | |
600 | ("r-magrittr" ,r-magrittr) | |
601 | ("r-rstudioapi" ,r-rstudioapi) | |
602 | ("r-stringr" ,r-stringr))) | |
603 | (home-page "http://gforge.se/packages/") | |
604 | (synopsis "Advanced tables for Markdown/HTML") | |
605 | (description | |
606 | "This package provides functions to build tables with advanced layout | |
607 | elements such as row spanners, column spanners, table spanners, zebra | |
608 | striping, and more. While allowing advanced layout, the underlying | |
609 | CSS-structure is simple in order to maximize compatibility with word | |
610 | processors such as LibreOffice. The package also contains a few text | |
611 | formatting functions that help outputting text compatible with HTML or | |
612 | LaTeX.") | |
613 | (license license:gpl3+))) | |
614 | ||
615 | (define-public r-curl | |
616 | (package | |
617 | (name "r-curl") | |
65ddcce3 | 618 | (version "4.2") |
92ce1883 RW |
619 | (source (origin |
620 | (method url-fetch) | |
621 | (uri (cran-uri "curl" version)) | |
622 | (sha256 | |
623 | (base32 | |
65ddcce3 | 624 | "0xh227gvb056wlipjxxbf555z1i1qcs7rr1igvs6k6645y9irrlp")))) |
92ce1883 RW |
625 | (build-system r-build-system) |
626 | (arguments | |
627 | `(#:phases | |
628 | (modify-phases %standard-phases | |
629 | ;; The environment variable CURL_CA_BUNDLE is only respected when | |
630 | ;; running Windows, so we disable the platform checks. | |
631 | ;; This can be removed once the libcurl has been patched. | |
632 | (add-after 'unpack 'allow-CURL_CA_BUNDLE | |
633 | (lambda _ | |
634 | (substitute* "R/onload.R" | |
635 | (("if \\(!grepl\\(\"mingw\".*") | |
636 | "if (FALSE)\n")) | |
637 | (substitute* "src/handle.c" | |
638 | (("#ifdef _WIN32") "#if 1")) | |
639 | #t))))) | |
640 | (inputs | |
646e1ef0 RW |
641 | `(("libcurl" ,curl) |
642 | ("zlib" ,zlib))) | |
643 | (native-inputs | |
644 | `(("pkg-config" ,pkg-config))) | |
92ce1883 RW |
645 | (home-page "https://github.com/jeroenooms/curl") |
646 | (synopsis "HTTP client for R") | |
647 | (description | |
648 | "The @code{curl()} and @code{curl_download()} functions provide highly | |
649 | configurable drop-in replacements for base @code{url()} and | |
650 | @code{download.file()} with better performance, support for encryption, gzip | |
651 | compression, authentication, and other @code{libcurl} goodies. The core of | |
652 | the package implements a framework for performing fully customized requests | |
653 | where data can be processed either in memory, on disk, or streaming via the | |
654 | callback or connection interfaces.") | |
655 | (license license:expat))) | |
656 | ||
657 | (define-public r-hwriter | |
658 | (package | |
659 | (name "r-hwriter") | |
660 | (version "1.3.2") | |
661 | (source | |
662 | (origin | |
663 | (method url-fetch) | |
664 | (uri (cran-uri "hwriter" version)) | |
665 | (sha256 | |
666 | (base32 | |
667 | "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb")))) | |
668 | (build-system r-build-system) | |
669 | (home-page "https://cran.r-project.org/web/packages/hwriter") | |
670 | (synopsis "Output R objects in HTML format") | |
671 | (description | |
672 | "This package provides easy-to-use and versatile functions to output R | |
673 | objects in HTML format.") | |
674 | (license license:lgpl2.1+))) | |
675 | ||
676 | (define-public r-rjson | |
677 | (package | |
678 | (name "r-rjson") | |
679 | (version "0.2.20") | |
680 | (source | |
681 | (origin | |
682 | (method url-fetch) | |
683 | (uri (cran-uri "rjson" version)) | |
684 | (sha256 | |
685 | (base32 | |
686 | "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) | |
687 | (build-system r-build-system) | |
688 | (home-page "https://cran.r-project.org/web/packages/rjson") | |
689 | (synopsis "JSON library for R") | |
690 | (description | |
691 | "This package provides functions to convert R objects into JSON objects | |
692 | and vice-versa.") | |
693 | (license license:gpl2+))) | |
694 | ||
695 | (define-public r-shiny | |
696 | (package | |
697 | (name "r-shiny") | |
d235cf72 | 698 | (version "1.2.0") |
92ce1883 RW |
699 | (source |
700 | (origin | |
701 | (method git-fetch) | |
702 | (uri (git-reference | |
703 | (url "https://github.com/rstudio/shiny.git") | |
704 | (commit (string-append "v" version)))) | |
705 | (file-name (git-file-name name version)) | |
706 | (sha256 | |
707 | (base32 | |
d235cf72 | 708 | "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4")))) |
92ce1883 RW |
709 | (build-system r-build-system) |
710 | (arguments | |
711 | `(#:modules ((guix build r-build-system) | |
712 | (guix build minify-build-system) | |
713 | (guix build utils) | |
714 | (ice-9 match)) | |
715 | #:imported-modules (,@%r-build-system-modules | |
716 | (guix build minify-build-system)) | |
717 | #:phases | |
718 | (modify-phases (@ (guix build r-build-system) %standard-phases) | |
719 | (add-after 'unpack 'replace-bundled-minified-JavaScript | |
720 | (lambda* (#:key inputs #:allow-other-keys) | |
721 | (let ((replace-file (lambda (old new) | |
722 | (format #t "replacing ~a with ~a\n" old new) | |
723 | (delete-file old) | |
724 | (symlink new old)))) | |
725 | ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ | |
726 | ;; contain just data. They are not minified code, so we don't | |
727 | ;; replace them. | |
728 | (with-directory-excursion "inst/www/shared" | |
729 | (replace-file "bootstrap/shim/respond.min.js" | |
730 | (string-append (assoc-ref inputs "js-respond") | |
731 | "/share/javascript/respond.min.js")) | |
732 | (replace-file "bootstrap/shim/html5shiv.min.js" | |
733 | (string-append (assoc-ref inputs "js-html5shiv") | |
734 | "/share/javascript/html5shiv.min.js")) | |
735 | (replace-file "json2-min.js" | |
736 | (string-append (assoc-ref inputs "js-json2") | |
737 | "/share/javascript/json2.min.js")) | |
738 | (replace-file "strftime/strftime-min.js" | |
739 | (string-append (assoc-ref inputs "js-strftime") | |
740 | "/share/javascript/strftime.min.js")) | |
741 | (replace-file "highlight/highlight.pack.js" | |
742 | (string-append (assoc-ref inputs "js-highlight") | |
743 | "/share/javascript/highlight.min.js")) | |
744 | (replace-file "datatables/js/jquery.dataTables.min.js" | |
745 | (string-append (assoc-ref inputs "js-datatables") | |
746 | "/share/javascript/jquery.dataTables.min.js")) | |
747 | (replace-file "selectize/js/selectize.min.js" | |
748 | (string-append (assoc-ref inputs "js-selectize") | |
749 | "/share/javascript/selectize.min.js")) | |
750 | (replace-file "selectize/js/es5-shim.min.js" | |
751 | (string-append (assoc-ref inputs "js-es5-shim") | |
752 | "/share/javascript/es5-shim.min.js")) | |
753 | (for-each (match-lambda | |
754 | ((source . target) | |
755 | (delete-file target) | |
756 | (minify source #:target target))) | |
757 | '(("jqueryui/jquery-ui.js" . | |
758 | "jqueryui/jquery-ui.min.js") | |
92ce1883 RW |
759 | ("datepicker/js/bootstrap-datepicker.js" . |
760 | "datepicker/js/bootstrap-datepicker.min.js") | |
761 | ("ionrangeslider/js/ion.rangeSlider.js" . | |
762 | "ionrangeslider/js/ion.rangeSlider.min.js") | |
763 | ("bootstrap/js/bootstrap.js" . | |
764 | "bootstrap/js/bootstrap.min.js") | |
765 | ("shiny.js" . | |
766 | "shiny.min.js") | |
767 | ("jquery.js" . | |
768 | "jquery.min.js"))))) | |
769 | #t))))) | |
770 | (propagated-inputs | |
771 | `(("r-crayon" ,r-crayon) | |
772 | ("r-httpuv" ,r-httpuv) | |
773 | ("r-mime" ,r-mime) | |
774 | ("r-jsonlite" ,r-jsonlite) | |
775 | ("r-xtable" ,r-xtable) | |
776 | ("r-digest" ,r-digest) | |
777 | ("r-htmltools" ,r-htmltools) | |
778 | ("r-r6" ,r-r6) | |
779 | ("r-sourcetools" ,r-sourcetools))) | |
780 | (inputs | |
781 | `(("js-datatables" ,js-datatables) | |
782 | ("js-html5shiv" ,js-html5shiv) | |
783 | ("js-json2" ,js-json2) | |
784 | ("js-respond" ,js-respond) | |
785 | ("js-selectize" ,js-selectize) | |
786 | ("js-strftime" ,js-strftime) | |
787 | ("js-highlight" ,js-highlight) | |
788 | ("js-es5-shim" ,js-es5-shim))) | |
8916034a RW |
789 | (native-inputs |
790 | `(("uglify-js" ,uglify-js))) | |
92ce1883 RW |
791 | (home-page "http://shiny.rstudio.com") |
792 | (synopsis "Easy interactive web applications with R") | |
793 | (description | |
794 | "Makes it incredibly easy to build interactive web applications | |
795 | with R. Automatic \"reactive\" binding between inputs and outputs and | |
796 | extensive prebuilt widgets make it possible to build beautiful, | |
797 | responsive, and powerful applications with minimal effort.") | |
798 | (license license:artistic2.0))) | |
799 | ||
41b8b05c RW |
800 | ;; This package includes minified JavaScript files. When upgrading please |
801 | ;; check that there are no new minified JavaScript files. | |
802 | (define-public r-shinytree | |
803 | (package | |
804 | (name "r-shinytree") | |
805 | (version "0.2.7") | |
806 | (source | |
807 | (origin | |
808 | (method url-fetch) | |
809 | (uri (cran-uri "shinyTree" version)) | |
810 | (sha256 | |
811 | (base32 | |
812 | "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3")) | |
813 | (modules '((guix build utils))) | |
814 | (snippet | |
815 | '(begin | |
816 | ;; Delete minified JavaScript | |
817 | (for-each delete-file | |
818 | '("inst/www/jsTree-3.3.7/libs/require.js" | |
819 | "inst/www/jsTree-3.3.7/libs/jquery.js" | |
820 | "inst/www/jsTree-3.3.7/jstree.min.js")) | |
821 | #t)))) | |
822 | (properties `((upstream-name . "shinyTree"))) | |
823 | (build-system r-build-system) | |
824 | (arguments | |
825 | `(#:modules ((guix build utils) | |
826 | (guix build r-build-system) | |
827 | (srfi srfi-1) | |
828 | (ice-9 popen)) | |
829 | #:phases | |
830 | (modify-phases %standard-phases | |
831 | (add-after 'unpack 'replace-minified-javascript | |
832 | (lambda* (#:key inputs #:allow-other-keys) | |
833 | (with-directory-excursion "inst/www/jsTree-3.3.7/" | |
834 | (symlink (string-append (assoc-ref inputs "js-requirejs") | |
835 | "/share/javascript/require.min.js") | |
836 | "libs/require.js") | |
837 | (call-with-values | |
838 | (lambda () | |
839 | (unzip2 | |
840 | `((,(assoc-ref inputs "js-jquery") | |
841 | "libs/jquery.js") | |
842 | ("jstree.js" | |
843 | "jstree.min.js")))) | |
844 | (lambda (sources targets) | |
845 | (for-each (lambda (source target) | |
846 | (format #t "Processing ~a --> ~a~%" | |
847 | source target) | |
848 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
849 | (call-with-output-file target | |
850 | (lambda (port) | |
851 | (dump-port minified port))))) | |
852 | sources targets)))) | |
853 | #t))))) | |
854 | (propagated-inputs | |
855 | `(("r-htmlwidgets" ,r-htmlwidgets) | |
856 | ("r-jsonlite" ,r-jsonlite) | |
857 | ("r-promises" ,r-promises) | |
858 | ("r-shiny" ,r-shiny) | |
859 | ("r-stringr" ,r-stringr))) | |
860 | (inputs | |
861 | `(("js-requirejs" ,js-requirejs))) | |
862 | (native-inputs | |
863 | `(("uglify-js" ,uglify-js) | |
864 | ("js-jquery" | |
865 | ,(origin | |
866 | (method url-fetch) | |
867 | (uri "https://code.jquery.com/jquery-3.3.1.js") | |
868 | (sha256 | |
869 | (base32 | |
870 | "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))))) | |
871 | (home-page "https://cran.r-project.org/web/packages/shinyTree/") | |
872 | (synopsis "jsTree bindings for Shiny") | |
873 | (description | |
874 | "This package exposes R bindings to jsTree, a JavaScript library that | |
875 | supports interactive trees, to enable rich, editable trees in Shiny.") | |
876 | (license license:expat))) | |
877 | ||
92ce1883 RW |
878 | (define-public r-shinydashboard |
879 | (package | |
880 | (name "r-shinydashboard") | |
881 | (version "0.7.1") | |
882 | (source (origin | |
883 | (method url-fetch) | |
884 | (uri (cran-uri "shinydashboard" version)) | |
885 | (sha256 | |
886 | (base32 | |
887 | "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) | |
888 | (build-system r-build-system) | |
889 | ;; The directory inst/AdminLTE/ contains a minified JavaScript file. | |
890 | ;; Regenerate it from the included sources. | |
891 | (arguments | |
892 | `(#:modules ((guix build utils) | |
893 | (guix build r-build-system) | |
894 | (ice-9 popen)) | |
895 | #:phases | |
896 | (modify-phases %standard-phases | |
897 | (add-after 'unpack 'generate-minified-javascript | |
898 | (lambda _ | |
899 | (with-directory-excursion "inst/AdminLTE" | |
900 | (delete-file "app.min.js") | |
901 | (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js"))) | |
902 | (call-with-output-file "app.min.js" | |
903 | (lambda (port) | |
904 | (dump-port minified port)))))))))) | |
905 | (propagated-inputs | |
906 | `(("r-htmltools" ,r-htmltools) | |
907 | ("r-promises" ,r-promises) | |
908 | ("r-shiny" ,r-shiny))) | |
909 | (native-inputs | |
910 | `(("uglify-js" ,uglify-js))) | |
911 | (home-page "http://rstudio.github.io/shinydashboard/") | |
912 | (synopsis "Create dashboards with shiny") | |
913 | (description "This package provides an extension to the Shiny web | |
914 | application framework for R, making it easy to create attractive dashboards.") | |
915 | ;; This package includes software that was released under the Expat | |
916 | ;; license, but the whole package is released under GPL version 2 or | |
917 | ;; later. | |
918 | (license license:gpl2+))) | |
919 | ||
920 | (define-public r-shinyfiles | |
921 | (package | |
922 | (name "r-shinyfiles") | |
8bc8cea9 | 923 | (version "0.7.3") |
92ce1883 RW |
924 | (source |
925 | (origin | |
926 | (method url-fetch) | |
927 | (uri (cran-uri "shinyFiles" version)) | |
928 | (sha256 | |
929 | (base32 | |
8bc8cea9 | 930 | "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i")))) |
92ce1883 RW |
931 | (properties `((upstream-name . "shinyFiles"))) |
932 | (build-system r-build-system) | |
933 | (propagated-inputs | |
934 | `(("r-fs" ,r-fs) | |
935 | ("r-htmltools" ,r-htmltools) | |
936 | ("r-jsonlite" ,r-jsonlite) | |
937 | ("r-shiny" ,r-shiny) | |
938 | ("r-tibble" ,r-tibble))) | |
939 | (home-page "https://github.com/thomasp85/shinyFiles") | |
940 | (synopsis "Server-side file system viewer for Shiny") | |
941 | (description | |
942 | "This package provides functionality for client-side navigation of the | |
943 | server side file system in shiny apps. In case the app is running locally | |
944 | this gives the user direct access to the file system without the need to | |
945 | \"download\" files to a temporary location. Both file and folder selection as | |
946 | well as file saving is available.") | |
947 | (license license:gpl2+))) | |
948 | ||
fc3719cc RW |
949 | (define-public r-shinythemes |
950 | (package | |
951 | (name "r-shinythemes") | |
952 | (version "1.1.2") | |
953 | (source | |
954 | (origin | |
955 | (method url-fetch) | |
956 | (uri (cran-uri "shinythemes" version)) | |
957 | (sha256 | |
958 | (base32 | |
959 | "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf")))) | |
960 | (properties `((upstream-name . "shinythemes"))) | |
961 | (build-system r-build-system) | |
962 | (propagated-inputs `(("r-shiny" ,r-shiny))) | |
963 | (home-page "http://rstudio.github.io/shinythemes/") | |
964 | (synopsis "Themes for Shiny") | |
965 | (description | |
966 | "This package provides themes for use with Shiny. It includes several | |
967 | Bootstrap themes, which are packaged for use with Shiny applications.") | |
968 | ;; The package is released under version 3 of the GPL, but it includes | |
969 | ;; source files that are covered by the Expat license. It also includes | |
970 | ;; fonts under SIL or the ASL. | |
971 | (license (list license:gpl3 license:expat | |
972 | license:silofl1.1 license:asl2.0)))) | |
973 | ||
983906bb RW |
974 | ;; The package sources include minified variants of d3.js and non-minified |
975 | ;; source code of d3-jetpack. | |
976 | (define-public r-d3r | |
977 | (package | |
978 | (name "r-d3r") | |
52aacfbd | 979 | (version "0.8.7") |
983906bb RW |
980 | (source |
981 | (origin | |
982 | (method url-fetch) | |
983 | (uri (cran-uri "d3r" version)) | |
984 | (sha256 | |
985 | (base32 | |
52aacfbd | 986 | "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a")))) |
983906bb RW |
987 | (build-system r-build-system) |
988 | (arguments | |
989 | `(#:modules ((guix build utils) | |
990 | (guix build r-build-system) | |
991 | (srfi srfi-1) | |
992 | (ice-9 popen)) | |
993 | #:phases | |
994 | (modify-phases %standard-phases | |
995 | (add-after 'unpack 'process-javascript | |
996 | (lambda* (#:key inputs #:allow-other-keys) | |
997 | (with-directory-excursion "inst/www/d3/" | |
998 | (call-with-values | |
999 | (lambda () | |
1000 | (unzip2 | |
1001 | `((,(assoc-ref inputs "d3.v3.js") | |
1002 | "v3/dist/d3.min.js") | |
1003 | (,(assoc-ref inputs "d3.v4.js") | |
1004 | "v4/dist/d3.min.js") | |
1005 | (,(assoc-ref inputs "d3.v5.js") | |
1006 | "v5/dist/d3.min.js")))) | |
1007 | (lambda (sources targets) | |
1008 | (for-each (lambda (source target) | |
1009 | (format #t "Processing ~a --> ~a~%" | |
1010 | source target) | |
1011 | (delete-file target) | |
1012 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
1013 | (call-with-output-file target | |
1014 | (lambda (port) | |
1015 | (dump-port minified port))))) | |
1016 | sources targets)))) | |
1017 | #t))))) | |
1018 | (propagated-inputs | |
1019 | `(("r-dplyr" ,r-dplyr) | |
1020 | ("r-htmltools" ,r-htmltools) | |
1021 | ("r-tidyr" ,r-tidyr))) | |
1022 | (native-inputs | |
1023 | `(("uglify-js" ,uglify-js) | |
1024 | ("d3.v3.js" | |
1025 | ,(origin | |
1026 | (method url-fetch) | |
1027 | (uri "https://d3js.org/d3.v3.js") | |
1028 | (sha256 | |
1029 | (base32 | |
1030 | "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) | |
1031 | ("d3.v4.js" | |
1032 | ,(origin | |
1033 | (method url-fetch) | |
1034 | (uri "https://d3js.org/d3.v4.js") | |
1035 | (sha256 | |
1036 | (base32 | |
1037 | "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))) | |
1038 | ("d3.v5.js" | |
1039 | ,(origin | |
1040 | (method url-fetch) | |
1041 | (uri "https://d3js.org/d3.v5.js") | |
1042 | (sha256 | |
1043 | (base32 | |
1044 | "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))))) | |
1045 | (home-page "https://github.com/timelyportfolio/d3r") | |
1046 | (synopsis "d3.js utilities for R") | |
1047 | (description | |
1048 | "This package provides a suite of functions to help ease the use of the | |
1049 | d3.js visualization library in R. These helpers include | |
1050 | @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion | |
1051 | tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame} | |
1052 | R objects into the JSON format that the d3.js library expects.") | |
1053 | (license license:bsd-3))) | |
1054 | ||
b03dd5cf RW |
1055 | ;; We use the latest commit here because the last release was in 2016 while |
1056 | ;; the latest commit was in 2018. | |
1057 | (define-public r-sankeyd3 | |
1058 | (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc") | |
1059 | (revision "1")) | |
1060 | (package | |
1061 | (name "r-sankeyd3") | |
1062 | (version (git-version "0.3.2" revision commit)) | |
1063 | (source | |
1064 | (origin | |
1065 | (method git-fetch) | |
1066 | (uri (git-reference | |
1067 | (url "https://github.com/fbreitwieser/sankeyD3.git") | |
1068 | (commit commit))) | |
1069 | (file-name (git-file-name name version)) | |
1070 | (sha256 | |
1071 | (base32 | |
1072 | "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) | |
1073 | (build-system r-build-system) | |
1074 | (propagated-inputs | |
1075 | `(("r-d3r" ,r-d3r) | |
1076 | ("r-htmlwidgets" ,r-htmlwidgets) | |
1077 | ("r-shiny" ,r-shiny) | |
1078 | ("r-magrittr" ,r-magrittr))) | |
1079 | (home-page "https://github.com/fbreitwieser/sankeyD3") | |
1080 | (synopsis "Sankey network graphs from R") | |
1081 | (description | |
1082 | "This package provides an R library to generate Sankey network graphs | |
1083 | in R and Shiny via the D3 visualization library.") | |
1084 | ;; The R code is licensed under GPLv3+. It includes the non-minified | |
1085 | ;; JavaScript source code of d3-sankey, which is released under the | |
1086 | ;; 3-clause BSD license. | |
1087 | (license (list license:gpl3+ license:bsd-3))))) | |
1088 | ||
92ce1883 RW |
1089 | (define-public r-crosstalk |
1090 | (package | |
1091 | (name "r-crosstalk") | |
1092 | (version "1.0.0") | |
1093 | (source | |
1094 | (origin | |
1095 | (method url-fetch) | |
1096 | (uri (cran-uri "crosstalk" version)) | |
1097 | (sha256 | |
1098 | (base32 | |
1099 | "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk")))) | |
1100 | (build-system r-build-system) | |
1101 | (propagated-inputs | |
1102 | `(("r-ggplot2" ,r-ggplot2) | |
1103 | ("r-htmltools" ,r-htmltools) | |
1104 | ("r-jsonlite" ,r-jsonlite) | |
1105 | ("r-lazyeval" ,r-lazyeval) | |
1106 | ("r-r6" ,r-r6) | |
1107 | ("r-shiny" ,r-shiny))) | |
1108 | (home-page "https://rstudio.github.io/crosstalk/") | |
1109 | (synopsis "Inter-widget interactivity for HTML widgets") | |
1110 | (description | |
1111 | "This package provides building blocks for allowing HTML widgets to | |
1112 | communicate with each other, with Shiny or without (i.e. static @code{.html} | |
1113 | files). It currently supports linked brushing and filtering.") | |
1114 | (license license:expat))) | |
1115 | ||
1116 | (define-public r-rook | |
1117 | (package | |
1118 | (name "r-rook") | |
1119 | (version "1.1-1") | |
1120 | (source | |
1121 | (origin | |
1122 | (method url-fetch) | |
1123 | (uri (cran-uri "Rook" version)) | |
1124 | (sha256 | |
1125 | (base32 | |
1126 | "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) | |
1127 | (properties `((upstream-name . "Rook"))) | |
1128 | (build-system r-build-system) | |
1129 | (propagated-inputs `(("r-brew" ,r-brew))) | |
1130 | (home-page "https://cran.r-project.org/web/packages/Rook") | |
1131 | (synopsis "Web server interface for R") | |
1132 | (description | |
1133 | "This package contains the Rook specification and convenience software | |
1134 | for building and running Rook applications. A Rook application is an R | |
1135 | reference class object that implements a @code{call} method or an R closure | |
1136 | that takes exactly one argument, an environment, and returns a list with three | |
1137 | named elements: the @code{status}, the @code{headers}, and the @code{body}.") | |
1138 | (license license:gpl2))) | |
1139 | ||
1140 | (define-public r-miniui | |
1141 | (package | |
1142 | (name "r-miniui") | |
1143 | (version "0.1.1.1") | |
1144 | (source | |
1145 | (origin | |
1146 | (method url-fetch) | |
1147 | (uri (cran-uri "miniUI" version)) | |
1148 | (sha256 | |
1149 | (base32 | |
1150 | "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) | |
1151 | (properties `((upstream-name . "miniUI"))) | |
1152 | (build-system r-build-system) | |
1153 | (propagated-inputs | |
1154 | `(("r-htmltools" ,r-htmltools) | |
1155 | ("r-shiny" ,r-shiny))) | |
1156 | (home-page "https://cran.r-project.org/web/packages/miniUI/") | |
1157 | (synopsis "Shiny UI widgets for small screens") | |
1158 | (description | |
1159 | "This package provides UI widget and layout functions for writing Shiny apps that | |
1160 | work well on small screens.") | |
1161 | (license license:gpl3))) | |
1162 | ||
60a166c6 RW |
1163 | (define-public r-feather |
1164 | (package | |
1165 | (name "r-feather") | |
e48e476f | 1166 | (version "0.3.5") |
60a166c6 RW |
1167 | (source |
1168 | (origin | |
1169 | (method url-fetch) | |
1170 | (uri (cran-uri "feather" version)) | |
1171 | (sha256 | |
1172 | (base32 | |
e48e476f | 1173 | "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh")))) |
60a166c6 RW |
1174 | (build-system r-build-system) |
1175 | (propagated-inputs | |
1176 | `(("r-hms" ,r-hms) | |
1177 | ("r-rcpp" ,r-rcpp) | |
1178 | ("r-tibble" ,r-tibble))) | |
1179 | (home-page "https://github.com/wesm/feather") | |
1180 | (synopsis "R Bindings to the Feather API") | |
1181 | (description "Read and write feather files, a lightweight binary columnar | |
1182 | data store designed for maximum speed.") | |
1183 | (license license:asl2.0))) | |
1184 | ||
2a2760a0 RW |
1185 | (define-public r-maps |
1186 | (package | |
1187 | (name "r-maps") | |
1188 | (version "3.3.0") | |
1189 | (source | |
1190 | (origin | |
1191 | (method url-fetch) | |
1192 | (uri (cran-uri "maps" version)) | |
1193 | (sha256 | |
1194 | (base32 | |
1195 | "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr")))) | |
1196 | (build-system r-build-system) | |
1197 | (home-page "https://cran.r-project.org/web/packages/maps") | |
1198 | (synopsis "Draw geographical maps") | |
1199 | (description "This package provides an R module for display of maps. | |
36a4366d EF |
1200 | Projection code and larger maps are in separate packages (@code{mapproj} and |
1201 | @code{mapdata}).") | |
2a2760a0 RW |
1202 | (license license:gpl2))) |
1203 | ||
1204 | (define-public r-mapproj | |
1205 | (package | |
1206 | (name "r-mapproj") | |
1207 | (version "1.2.6") | |
1208 | (source | |
1209 | (origin | |
1210 | (method url-fetch) | |
1211 | (uri (cran-uri "mapproj" version)) | |
1212 | (sha256 | |
1213 | (base32 | |
1214 | "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2")))) | |
1215 | (build-system r-build-system) | |
1216 | (propagated-inputs `(("r-maps" ,r-maps))) | |
1217 | (home-page "https://cran.r-project.org/web/packages/mapproj") | |
1218 | (synopsis "Map projection in R") | |
1219 | (description "This package converts latitude/longitude into projected | |
1220 | coordinates.") | |
1221 | (license (list license:gpl2 ; The R interface | |
1222 | (license:non-copyleft ; The C code | |
1223 | "https://www.gnu.org/licenses/license-list.en.html#lucent102" | |
1224 | "Lucent Public License Version 1.02"))))) | |
1225 | ||
1226 | (define-public r-rgooglemaps | |
1227 | (package | |
1228 | (name "r-rgooglemaps") | |
6d879bb6 | 1229 | (version "1.4.4") |
2a2760a0 RW |
1230 | (source |
1231 | (origin | |
1232 | (method url-fetch) | |
1233 | (uri (cran-uri "RgoogleMaps" version)) | |
1234 | (sha256 | |
1235 | (base32 | |
6d879bb6 | 1236 | "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x")))) |
2a2760a0 RW |
1237 | (properties `((upstream-name . "RgoogleMaps"))) |
1238 | (build-system r-build-system) | |
1239 | (propagated-inputs `(("r-png" ,r-png))) | |
1240 | (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") | |
1241 | (synopsis "Use Google Maps in R") | |
1242 | (description "This package serves two purposes: | |
1243 | @enumerate | |
1244 | @item Provide a comfortable R interface to query the Google server for static | |
1245 | maps, and | |
1246 | @item Use the map as a background image to overlay plots within R. This | |
1247 | requires proper coordinate scaling. | |
1248 | @end enumerate\n") | |
1249 | (license license:gpl2+))) | |
1250 | ||
1251 | (define-public r-geosphere | |
1252 | (package | |
1253 | (name "r-geosphere") | |
f43ec9e9 | 1254 | (version "1.5-10") |
2a2760a0 RW |
1255 | (source |
1256 | (origin | |
1257 | (method url-fetch) | |
1258 | (uri (cran-uri "geosphere" version)) | |
1259 | (sha256 | |
1260 | (base32 | |
f43ec9e9 | 1261 | "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan")))) |
2a2760a0 RW |
1262 | (build-system r-build-system) |
1263 | (propagated-inputs `(("r-sp" ,r-sp))) | |
1264 | (home-page "https://cran.r-project.org/web/packages/geosphere") | |
1265 | (synopsis "Spherical trigonometry") | |
1266 | (description "This package computes spherical trigonometry for geographic | |
1267 | applications. That is, compute distances and related measures for angular | |
1268 | (longitude/latitude) locations.") | |
1269 | (license license:gpl3+))) | |
1270 | ||
1271 | (define-public r-ggmap | |
1272 | (package | |
1273 | (name "r-ggmap") | |
20662a30 | 1274 | (version "3.0.0") |
2a2760a0 RW |
1275 | (source |
1276 | (origin | |
1277 | (method url-fetch) | |
1278 | (uri (cran-uri "ggmap" version)) | |
1279 | (sha256 | |
1280 | (base32 | |
20662a30 | 1281 | "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) |
2a2760a0 RW |
1282 | (build-system r-build-system) |
1283 | (propagated-inputs | |
20662a30 RW |
1284 | `(("r-bitops" ,r-bitops) |
1285 | ("r-digest" ,r-digest) | |
1286 | ("r-dplyr" ,r-dplyr) | |
2a2760a0 | 1287 | ("r-ggplot2" ,r-ggplot2) |
20662a30 RW |
1288 | ("r-glue" ,r-glue) |
1289 | ("r-httr" ,r-httr) | |
2a2760a0 | 1290 | ("r-jpeg" ,r-jpeg) |
20662a30 | 1291 | ("r-magrittr" ,r-magrittr) |
2a2760a0 RW |
1292 | ("r-plyr" ,r-plyr) |
1293 | ("r-png" ,r-png) | |
20662a30 | 1294 | ("r-purrr" ,r-purrr) |
2a2760a0 RW |
1295 | ("r-rgooglemaps" ,r-rgooglemaps) |
1296 | ("r-rjson" ,r-rjson) | |
20662a30 RW |
1297 | ("r-scales" ,r-scales) |
1298 | ("r-stringr" ,r-stringr) | |
1299 | ("r-tibble" ,r-tibble) | |
1300 | ("r-tidyr" ,r-tidyr))) | |
2a2760a0 RW |
1301 | (home-page "https://github.com/dkahle/ggmap") |
1302 | (synopsis "Spatial visualization with ggplot2") | |
1303 | (description "This package provides a collection of functions to visualize | |
1304 | spatial data and models on top of static maps from various online sources (e.g | |
1305 | Google Maps and Stamen Maps). It includes tools common to those tasks, | |
1306 | including functions for geolocation and routing.") | |
1307 | (license license:gpl2))) | |
1308 | ||
d2a507ef CR |
1309 | (define-public r-haven |
1310 | (package | |
1311 | (name "r-haven") | |
b89805fe | 1312 | (version "2.1.1") |
d2a507ef CR |
1313 | (source |
1314 | (origin | |
1315 | (method url-fetch) | |
1316 | (uri (cran-uri "haven" version)) | |
1317 | (sha256 | |
1318 | (base32 | |
b89805fe | 1319 | "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h")))) |
d2a507ef | 1320 | (build-system r-build-system) |
35b32367 TGR |
1321 | (inputs |
1322 | `(("zlib" ,zlib))) | |
d2a507ef CR |
1323 | (propagated-inputs |
1324 | `(("r-forcats" ,r-forcats) | |
1325 | ("r-hms" ,r-hms) | |
1326 | ("r-rcpp" ,r-rcpp) | |
1327 | ("r-readr" ,r-readr) | |
1328 | ("r-tibble" ,r-tibble))) | |
1329 | (home-page "https://haven.tidyverse.org") | |
1330 | (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files") | |
1331 | (description | |
1332 | "This package lets you mport foreign statistical formats into R via the | |
1333 | embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") | |
1334 | (license license:expat))) | |
1335 | ||
996bed06 RJ |
1336 | (define-public r-amap |
1337 | (package | |
1338 | (name "r-amap") | |
c86da03a | 1339 | (version "0.8-17") |
996bed06 RJ |
1340 | (source (origin |
1341 | (method url-fetch) | |
1342 | (uri (cran-uri "amap" version)) | |
1343 | (sha256 | |
1344 | (base32 | |
c86da03a | 1345 | "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b")))) |
996bed06 | 1346 | (build-system r-build-system) |
c86da03a | 1347 | (native-inputs |
996bed06 RJ |
1348 | `(("gfortran" ,gfortran))) |
1349 | (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") | |
1350 | (synopsis "Another multidimensional analysis package") | |
1351 | (description "This package provides tools for clustering and principal | |
1352 | component analysis (with robust methods, and parallelized functions).") | |
1353 | (license license:gpl2+))) | |
1354 | ||
53cc59a1 RW |
1355 | (define-public r-ape |
1356 | (package | |
1357 | (name "r-ape") | |
8e91ad0b | 1358 | (version "5.3") |
53cc59a1 RW |
1359 | (source |
1360 | (origin | |
1361 | (method url-fetch) | |
1362 | (uri (cran-uri "ape" version)) | |
1363 | (sha256 | |
1364 | (base32 | |
8e91ad0b | 1365 | "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08")))) |
53cc59a1 RW |
1366 | (build-system r-build-system) |
1367 | (propagated-inputs | |
1368 | `(("r-lattice" ,r-lattice) | |
1369 | ("r-nlme" ,r-nlme) | |
1370 | ("r-rcpp" ,r-rcpp))) | |
1371 | (home-page "http://ape-package.ird.fr/") | |
1372 | (synopsis "Analyses of phylogenetics and evolution") | |
1373 | (description | |
1374 | "This package provides functions for reading, writing, plotting, and | |
1375 | manipulating phylogenetic trees, analyses of comparative data in a | |
1376 | phylogenetic framework, ancestral character analyses, analyses of | |
1377 | diversification and macroevolution, computing distances from DNA sequences, | |
1378 | and several other tools.") | |
1379 | (license license:gpl2+))) | |
1380 | ||
109b2f7c VV |
1381 | (define-public r-abbyyr |
1382 | (package | |
1383 | (name "r-abbyyr") | |
4ae5f18a | 1384 | (version "0.5.5") |
109b2f7c VV |
1385 | (source |
1386 | (origin | |
1387 | (method url-fetch) | |
1388 | (uri (cran-uri "abbyyR" version)) | |
1389 | (sha256 | |
1390 | (base32 | |
4ae5f18a | 1391 | "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r")))) |
109b2f7c VV |
1392 | (properties `((upstream-name . "abbyyR"))) |
1393 | (build-system r-build-system) | |
1394 | (propagated-inputs | |
1395 | `(("r-curl" ,r-curl) | |
1396 | ("r-httr" ,r-httr) | |
1397 | ("r-plyr" ,r-plyr) | |
1398 | ("r-progress" ,r-progress) | |
1399 | ("r-readr" ,r-readr) | |
1400 | ("r-xml" ,r-xml))) | |
1401 | (home-page "https://github.com/soodoku/abbyyR") | |
1402 | (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") | |
1403 | (description | |
1404 | "This package provides tools to get text from images of text using Abbyy | |
1405 | Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily | |
1406 | OCR images, barcodes, forms, documents with machine readable zones, e.g. | |
1407 | passports and get the results in a variety of formats including plain text and | |
1408 | XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") | |
1409 | (license license:expat))) | |
1410 | ||
056468dc RW |
1411 | (define-public r-colorspace |
1412 | (package | |
1413 | (name "r-colorspace") | |
f9bc918b | 1414 | (version "1.4-1") |
056468dc RW |
1415 | (source |
1416 | (origin | |
1417 | (method url-fetch) | |
1418 | (uri (cran-uri "colorspace" version)) | |
1419 | (sha256 | |
f9bc918b | 1420 | (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9")))) |
056468dc | 1421 | (build-system r-build-system) |
e9960d8c | 1422 | (home-page "https://cran.r-project.org/web/packages/colorspace") |
056468dc RW |
1423 | (synopsis "Color space manipulation") |
1424 | (description | |
1425 | "This package carries out a mapping between assorted color spaces | |
1426 | including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar | |
1427 | CIELAB. Qualitative, sequential, and diverging color palettes based on HCL | |
1428 | colors are provided.") | |
1429 | (license license:bsd-3))) | |
5bee6bf4 RW |
1430 | |
1431 | (define-public r-glue | |
1432 | (package | |
1433 | (name "r-glue") | |
b21eb347 | 1434 | (version "1.3.1") |
5bee6bf4 RW |
1435 | (source |
1436 | (origin | |
1437 | (method url-fetch) | |
1438 | (uri (cran-uri "glue" version)) | |
1439 | (sha256 | |
1440 | (base32 | |
b21eb347 | 1441 | "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag")))) |
5bee6bf4 RW |
1442 | (build-system r-build-system) |
1443 | (home-page "https://github.com/tidyverse/glue") | |
1444 | (synopsis "Interpreted string literals") | |
1445 | (description | |
1446 | "This package provides an implementation of interpreted string literals, | |
1447 | inspired by Python's Literal String Interpolation (PEP-0498) and | |
1448 | Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") | |
1449 | (license license:expat))) | |
847b4572 | 1450 | |
ddbf2a98 RJ |
1451 | (define-public r-pastecs |
1452 | (package | |
1453 | (name "r-pastecs") | |
1454 | (version "1.3.21") | |
1455 | (source (origin | |
1456 | (method url-fetch) | |
1457 | (uri (cran-uri "pastecs" version)) | |
1458 | (sha256 | |
1459 | (base32 | |
1460 | "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) | |
1461 | (build-system r-build-system) | |
1462 | (propagated-inputs | |
1463 | `(("r-boot" ,r-boot))) | |
1464 | (home-page "http://www.sciviews.org/pastecs") | |
1465 | (synopsis "Analysis of space-time ecological series") | |
1466 | (description | |
1467 | "This package provides functions for regulation, decomposition and analysis | |
1468 | of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER | |
1469 | initiative to bring PASSTEC 2000 functionalities to R.") | |
1470 | (license license:gpl2+))) | |
1471 | ||
847b4572 RW |
1472 | (define-public r-plogr |
1473 | (package | |
1474 | (name "r-plogr") | |
0e947804 | 1475 | (version "0.2.0") |
847b4572 RW |
1476 | (source |
1477 | (origin | |
1478 | (method url-fetch) | |
1479 | (uri (cran-uri "plogr" version)) | |
1480 | (sha256 | |
1481 | (base32 | |
0e947804 | 1482 | "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf")))) |
847b4572 RW |
1483 | (build-system r-build-system) |
1484 | (home-page "https://github.com/krlmlr/plogr") | |
1485 | (synopsis "R bindings for the plog C++ logging library") | |
1486 | (description | |
1487 | "This package provides the header files for a stripped-down version of | |
1488 | the plog header-only C++ logging library, and a method to log to R's standard | |
1489 | error stream.") | |
1490 | (license license:expat))) | |
a8cba9dd | 1491 | |
a86049d9 TGR |
1492 | (define-public r-pls |
1493 | (package | |
1494 | (name "r-pls") | |
4c9a3173 | 1495 | (version "2.7-2") |
a86049d9 TGR |
1496 | (source |
1497 | (origin | |
1498 | (method url-fetch) | |
1499 | (uri (cran-uri "pls" version)) | |
1500 | (sha256 | |
4c9a3173 | 1501 | (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7")))) |
a86049d9 TGR |
1502 | (build-system r-build-system) |
1503 | (home-page "http://mevik.net/work/software/pls.html") | |
1504 | (synopsis "Partial Least Squares and Principal Component Regression") | |
1505 | (description | |
1506 | "The pls package implements multivariate regression methods: Partial Least | |
1507 | Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and | |
1508 | Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports: | |
1509 | ||
1510 | @itemize | |
1511 | @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS | |
1512 | algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd} | |
1513 | @item multi-response models (or @dfn{PLS2}) | |
1514 | @item flexible cross-validation | |
1515 | @item Jackknife variance estimates of regression coefficients | |
1516 | @item extensive and flexible plots: scores, loadings, predictions, coefficients, | |
1517 | (R)MSEP, R², and correlation loadings | |
1518 | @item formula interface, modelled after @code{lm()}, with methods for predict, | |
1519 | print, summary, plot, update, etc. | |
1520 | @item extraction functions for coefficients, scores, and loadings | |
1521 | @item MSEP, RMSEP, and R² estimates | |
1522 | @item multiplicative scatter correction (@dfn{MSC}) | |
1523 | @end itemize\n") | |
1524 | (license license:gpl2))) | |
1525 | ||
b55e64d4 TGR |
1526 | (define-public r-ps |
1527 | (package | |
1528 | (name "r-ps") | |
422dea17 | 1529 | (version "1.3.0") |
b55e64d4 TGR |
1530 | (source |
1531 | (origin | |
1532 | (method url-fetch) | |
1533 | (uri (cran-uri "ps" version)) | |
1534 | (sha256 | |
422dea17 | 1535 | (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498")))) |
b55e64d4 TGR |
1536 | (build-system r-build-system) |
1537 | (home-page "http://ps.r-lib.org") | |
1538 | (synopsis "List, query, and manipulate system processes") | |
1539 | (description | |
1540 | "The ps package implements an API to list, query, and manipulate system | |
1541 | processes. Most of its code is based on the @code{psutil} Python package.") | |
1542 | (license license:bsd-3))) | |
1543 | ||
4f8247b5 RW |
1544 | (define-public r-pkgbuild |
1545 | (package | |
1546 | (name "r-pkgbuild") | |
ef93de84 | 1547 | (version "1.0.5") |
4f8247b5 RW |
1548 | (source |
1549 | (origin | |
1550 | (method url-fetch) | |
1551 | (uri (cran-uri "pkgbuild" version)) | |
1552 | (sha256 | |
1553 | (base32 | |
ef93de84 | 1554 | "0y4i85axwajrk67h3w6fiqfm6wxmhn3dr240w5l2nvqg3ahpxc8q")))) |
4f8247b5 RW |
1555 | (build-system r-build-system) |
1556 | (propagated-inputs | |
1557 | `(("r-callr" ,r-callr) | |
2657e666 | 1558 | ("r-cli" ,r-cli) |
4f8247b5 RW |
1559 | ("r-crayon" ,r-crayon) |
1560 | ("r-desc" ,r-desc) | |
2657e666 | 1561 | ("r-prettyunits" ,r-prettyunits) |
4f8247b5 RW |
1562 | ("r-r6" ,r-r6) |
1563 | ("r-rprojroot" ,r-rprojroot) | |
1564 | ("r-withr" ,r-withr))) | |
1565 | (home-page "https://github.com/r-pkgs/pkgbuild") | |
1566 | (synopsis "Find tools needed to build R packages") | |
1567 | (description | |
1568 | "This package provides functions used to build R packages. It locates | |
1569 | compilers needed to build R packages on various platforms and ensures the PATH | |
1570 | is configured appropriately so R can use them.") | |
1571 | (license license:gpl3))) | |
1572 | ||
e362be8e RW |
1573 | (define-public r-pkgload |
1574 | (package | |
1575 | (name "r-pkgload") | |
65dd0e67 | 1576 | (version "1.0.2") |
e362be8e RW |
1577 | (source |
1578 | (origin | |
1579 | (method url-fetch) | |
1580 | (uri (cran-uri "pkgload" version)) | |
1581 | (sha256 | |
1582 | (base32 | |
65dd0e67 | 1583 | "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii")))) |
e362be8e RW |
1584 | (build-system r-build-system) |
1585 | (propagated-inputs | |
1586 | `(("r-desc" ,r-desc) | |
1587 | ("r-pkgbuild" ,r-pkgbuild) | |
1588 | ("r-rlang" ,r-rlang) | |
1589 | ("r-rprojroot" ,r-rprojroot) | |
1590 | ("r-rstudioapi" ,r-rstudioapi) | |
1591 | ("r-withr" ,r-withr))) | |
1592 | (home-page "https://github.com/r-lib/pkgload") | |
1593 | (synopsis "Simulate package installation and attach") | |
1594 | (description | |
1595 | "This package simulates the process of installing a package and then | |
1596 | attaching it. This is a key part of the @code{devtools} package as it allows | |
1597 | you to rapidly iterate while developing a package.") | |
1598 | (license license:gpl3))) | |
1599 | ||
a8cba9dd RW |
1600 | (define-public r-rcpp |
1601 | (package | |
1602 | (name "r-rcpp") | |
4522ec86 | 1603 | (version "1.0.2") |
a8cba9dd RW |
1604 | (source |
1605 | (origin | |
1606 | (method url-fetch) | |
1607 | (uri (cran-uri "Rcpp" version)) | |
1608 | (sha256 | |
4522ec86 | 1609 | (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd")))) |
a8cba9dd | 1610 | (build-system r-build-system) |
f87a18e6 RW |
1611 | (native-inputs |
1612 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
a8cba9dd RW |
1613 | (home-page "http://www.rcpp.org") |
1614 | (synopsis "Seamless R and C++ integration") | |
1615 | (description | |
1616 | "The Rcpp package provides R functions as well as C++ classes which offer | |
1617 | a seamless integration of R and C++. Many R data types and objects can be | |
1618 | mapped back and forth to C++ equivalents which facilitates both writing of new | |
1619 | code as well as easier integration of third-party libraries. Documentation | |
1620 | about Rcpp is provided by several vignettes included in this package, via the | |
36a4366d | 1621 | @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel |
a8cba9dd | 1622 | and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see |
36a4366d | 1623 | @code{citation(\"Rcpp\")} for details on these last two.") |
a8cba9dd | 1624 | (license license:gpl2+))) |
eed58a08 RW |
1625 | |
1626 | (define-public r-bindr | |
1627 | (package | |
1628 | (name "r-bindr") | |
eb575e95 | 1629 | (version "0.1.1") |
eed58a08 RW |
1630 | (source |
1631 | (origin | |
1632 | (method url-fetch) | |
1633 | (uri (cran-uri "bindr" version)) | |
1634 | (sha256 | |
1635 | (base32 | |
eb575e95 | 1636 | "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) |
eed58a08 RW |
1637 | (build-system r-build-system) |
1638 | (home-page "https://github.com/krlmlr/bindr") | |
1639 | (synopsis "Parametrized active bindings") | |
1640 | (description | |
1641 | "This package provides a simple interface for creating active bindings | |
1642 | where the bound function accepts additional arguments.") | |
1643 | (license license:expat))) | |
4bb0b4cc RW |
1644 | |
1645 | (define-public r-bindrcpp | |
1646 | (package | |
1647 | (name "r-bindrcpp") | |
9f17c056 | 1648 | (version "0.2.2") |
4bb0b4cc RW |
1649 | (source |
1650 | (origin | |
1651 | (method url-fetch) | |
1652 | (uri (cran-uri "bindrcpp" version)) | |
1653 | (sha256 | |
1654 | (base32 | |
9f17c056 | 1655 | "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) |
4bb0b4cc RW |
1656 | (build-system r-build-system) |
1657 | (propagated-inputs | |
1658 | `(("r-bindr" ,r-bindr) | |
1659 | ("r-plogr" ,r-plogr) | |
1660 | ("r-rcpp" ,r-rcpp))) | |
1661 | (home-page "https://github.com/krlmlr/bindrcpp") | |
1662 | (synopsis "Rcpp interface to active bindings") | |
1663 | (description | |
1664 | "This package provides an easy way to fill an environment with active | |
1665 | bindings that call a C++ function.") | |
1666 | (license license:expat))) | |
33ce12e2 RW |
1667 | |
1668 | (define-public r-auc | |
1669 | (package | |
1670 | (name "r-auc") | |
1671 | (version "0.3.0") | |
1672 | (source | |
1673 | (origin | |
1674 | (method url-fetch) | |
1675 | (uri (cran-uri "AUC" version)) | |
1676 | (sha256 | |
1677 | (base32 | |
1678 | "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7")))) | |
1679 | (properties `((upstream-name . "AUC"))) | |
1680 | (build-system r-build-system) | |
e9960d8c | 1681 | (home-page "https://cran.r-project.org/web/packages/AUC") |
33ce12e2 RW |
1682 | (synopsis "Compute the area under the curve of selected measures") |
1683 | (description | |
1684 | "This package includes functions to compute the area under the curve of | |
1685 | selected measures: the area under the sensitivity curve (AUSEC), the area | |
1686 | under the specificity curve (AUSPC), the area under the accuracy | |
1687 | curve (AUACC), and the area under the receiver operating characteristic | |
1688 | curve (AUROC). The curves can also be visualized. Support for partial areas | |
1689 | is provided.") | |
1690 | (license license:gpl2+))) | |
c69d27db RW |
1691 | |
1692 | (define-public r-calibrate | |
1693 | (package | |
1694 | (name "r-calibrate") | |
934f7e31 | 1695 | (version "1.7.5") |
c69d27db RW |
1696 | (source |
1697 | (origin | |
1698 | (method url-fetch) | |
1699 | (uri (cran-uri "calibrate" version)) | |
1700 | (sha256 | |
934f7e31 | 1701 | (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k")))) |
c69d27db RW |
1702 | (build-system r-build-system) |
1703 | (propagated-inputs | |
1704 | `(("r-mass" ,r-mass))) | |
e9960d8c | 1705 | (home-page "https://cran.r-project.org/web/packages/calibrate") |
c69d27db RW |
1706 | (synopsis "Calibration of scatterplot and biplot axes") |
1707 | (description | |
1708 | "This is a package for drawing calibrated scales with tick marks | |
1709 | on (non-orthogonal) variable vectors in scatterplots and biplots.") | |
1710 | (license license:gpl2))) | |
2bdb5c3f RW |
1711 | |
1712 | (define-public r-shape | |
1713 | (package | |
1714 | (name "r-shape") | |
fe5b8893 | 1715 | (version "1.4.4") |
2bdb5c3f RW |
1716 | (source |
1717 | (origin | |
1718 | (method url-fetch) | |
1719 | (uri (cran-uri "shape" version)) | |
1720 | (sha256 | |
1721 | (base32 | |
fe5b8893 | 1722 | "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl")))) |
2bdb5c3f | 1723 | (build-system r-build-system) |
e9960d8c | 1724 | (home-page "https://cran.r-project.org/web/packages/shape") |
2bdb5c3f RW |
1725 | (synopsis "Functions for plotting graphical shapes") |
1726 | (description | |
1727 | "This package provides functions for plotting graphical shapes such as | |
1728 | ellipses, circles, cylinders, arrows, ...") | |
1729 | (license license:gpl3+))) | |
4847a62e RW |
1730 | |
1731 | (define-public r-globaloptions | |
1732 | (package | |
1733 | (name "r-globaloptions") | |
bc11837c | 1734 | (version "0.1.1") |
4847a62e RW |
1735 | (source |
1736 | (origin | |
1737 | (method url-fetch) | |
1738 | (uri (cran-uri "GlobalOptions" version)) | |
1739 | (sha256 | |
bc11837c | 1740 | (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2")))) |
4847a62e RW |
1741 | (properties `((upstream-name . "GlobalOptions"))) |
1742 | (build-system r-build-system) | |
1743 | (home-page "https://github.com/jokergoo/GlobalOptions") | |
1744 | (synopsis "Generate functions to get or set global options") | |
1745 | (description | |
1746 | "This package provides more controls on the option values such as | |
1747 | validation and filtering on the values, making options invisible or private.") | |
1748 | (license license:gpl2+))) | |
2856369f RW |
1749 | |
1750 | (define-public r-circlize | |
1751 | (package | |
1752 | (name "r-circlize") | |
4557f447 | 1753 | (version "0.4.8") |
2856369f RW |
1754 | (source |
1755 | (origin | |
1756 | (method url-fetch) | |
1757 | (uri (cran-uri "circlize" version)) | |
1758 | (sha256 | |
1759 | (base32 | |
4557f447 | 1760 | "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2")))) |
2856369f RW |
1761 | (build-system r-build-system) |
1762 | (propagated-inputs | |
1763 | `(("r-colorspace" ,r-colorspace) | |
1764 | ("r-globaloptions" ,r-globaloptions) | |
1765 | ("r-shape" ,r-shape))) | |
1766 | (home-page "https://github.com/jokergoo/circlize") | |
1767 | (synopsis "Circular visualization") | |
1768 | (description | |
031462ba TGR |
1769 | "Circular layout is an efficient way to visualise huge amounts of |
1770 | information. This package provides an implementation of circular layout | |
1771 | generation in R as well as an enhancement of available software. Its | |
1772 | flexibility is based on the usage of low-level graphics functions such that | |
1773 | self-defined high-level graphics can be easily implemented by users for | |
1774 | specific purposes. Together with the seamless connection between the powerful | |
1775 | computational and visual environment in R, it gives users more convenience and | |
1776 | freedom to design figures for better understanding complex patterns behind | |
1777 | multi-dimensional data.") | |
2856369f | 1778 | (license license:gpl2+))) |
5cc79c9c RW |
1779 | |
1780 | (define-public r-powerlaw | |
1781 | (package | |
1782 | (name "r-powerlaw") | |
397dba01 | 1783 | (version "0.70.2") |
5cc79c9c RW |
1784 | (source |
1785 | (origin | |
1786 | (method url-fetch) | |
1787 | (uri (cran-uri "poweRlaw" version)) | |
1788 | (sha256 | |
1789 | (base32 | |
397dba01 | 1790 | "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4")))) |
5cc79c9c RW |
1791 | (properties `((upstream-name . "poweRlaw"))) |
1792 | (build-system r-build-system) | |
1793 | (propagated-inputs | |
1794 | `(("r-vgam" ,r-vgam))) | |
1795 | (home-page "https://github.com/csgillespie/poweRlaw") | |
1796 | (synopsis "Tools for the analysis of heavy tailed distributions") | |
1797 | (description | |
1798 | "This package provides an implementation of maximum likelihood estimators | |
1799 | for a variety of heavy tailed distributions, including both the discrete and | |
1800 | continuous power law distributions. Additionally, a goodness-of-fit based | |
1801 | approach is used to estimate the lower cut-off for the scaling region.") | |
1802 | ;; Any of these GPL versions. | |
1803 | (license (list license:gpl2 license:gpl3)))) | |
05486604 RW |
1804 | |
1805 | (define-public r-compare | |
1806 | (package | |
1807 | (name "r-compare") | |
1808 | (version "0.2-6") | |
1809 | (source | |
1810 | (origin | |
1811 | (method url-fetch) | |
1812 | (uri (cran-uri "compare" version)) | |
1813 | (sha256 | |
1814 | (base32 | |
1815 | "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw")))) | |
1816 | (build-system r-build-system) | |
e9960d8c | 1817 | (home-page "https://cran.r-project.org/web/packages/compare") |
05486604 RW |
1818 | (synopsis "Comparing objects for differences") |
1819 | (description | |
1820 | "This package provides functions to compare a model object to a | |
1821 | comparison object. If the objects are not identical, the functions can be | |
1822 | instructed to explore various modifications of the objects (e.g., sorting | |
1823 | rows, dropping names) to see if the modified versions are identical.") | |
1824 | (license license:gpl2+))) | |
d3c67e1b RW |
1825 | |
1826 | (define-public r-dendextend | |
1827 | (package | |
1828 | (name "r-dendextend") | |
089ac9af | 1829 | (version "1.12.0") |
d3c67e1b RW |
1830 | (source |
1831 | (origin | |
1832 | (method url-fetch) | |
1833 | (uri (cran-uri "dendextend" version)) | |
1834 | (sha256 | |
1835 | (base32 | |
089ac9af | 1836 | "0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl")))) |
d3c67e1b RW |
1837 | (build-system r-build-system) |
1838 | (propagated-inputs | |
089ac9af | 1839 | `(("r-ggplot2" ,r-ggplot2) |
d3c67e1b | 1840 | ("r-magrittr" ,r-magrittr) |
089ac9af | 1841 | ("r-viridis" ,r-viridis))) |
d3c67e1b RW |
1842 | (home-page "https://cran.r-project.org/web/packages/dendextend") |
1843 | (synopsis "Extending 'dendrogram' functionality in R") | |
1844 | (description | |
1845 | "This package offers a set of functions for extending @code{dendrogram} | |
1846 | objects in R, letting you visualize and compare trees of hierarchical | |
1847 | clusterings. You can adjust a tree's graphical parameters (the color, size, | |
1848 | type, etc of its branches, nodes and labels) and visually and statistically | |
1849 | compare different dendrograms to one another.") | |
1850 | ;; Any of these versions | |
1851 | (license (list license:gpl2 license:gpl3)))) | |
e0268ff2 RW |
1852 | |
1853 | (define-public r-getoptlong | |
1854 | (package | |
1855 | (name "r-getoptlong") | |
5fa9be11 | 1856 | (version "0.1.7") |
e0268ff2 RW |
1857 | (source |
1858 | (origin | |
1859 | (method url-fetch) | |
1860 | (uri (cran-uri "GetoptLong" version)) | |
1861 | (sha256 | |
1862 | (base32 | |
5fa9be11 | 1863 | "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr")))) |
e0268ff2 RW |
1864 | (properties `((upstream-name . "GetoptLong"))) |
1865 | (build-system r-build-system) | |
1866 | (inputs | |
1867 | `(("perl" ,perl))) | |
1868 | (propagated-inputs | |
1869 | `(("r-globaloptions" ,r-globaloptions) | |
1870 | ("r-rjson" ,r-rjson))) | |
1871 | (home-page "https://github.com/jokergoo/GetoptLong") | |
1872 | (synopsis "Parsing command-line arguments and variable interpolation") | |
1873 | (description | |
1874 | "This is yet another command-line argument parser which wraps the | |
1875 | powerful Perl module @code{Getopt::Long} and with some adaptation for easier | |
1876 | use in R. It also provides a simple way for variable interpolation in R.") | |
1877 | (license license:gpl2+))) | |
f2e974e1 RW |
1878 | |
1879 | (define-public r-fastmatch | |
1880 | (package | |
1881 | (name "r-fastmatch") | |
1882 | (version "1.1-0") | |
1883 | (source | |
1884 | (origin | |
1885 | (method url-fetch) | |
1886 | (uri (cran-uri "fastmatch" version)) | |
1887 | (sha256 | |
1888 | (base32 | |
1889 | "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) | |
1890 | (build-system r-build-system) | |
1891 | (home-page "http://www.rforge.net/fastmatch") | |
1892 | (synopsis "Fast match function") | |
1893 | (description | |
1894 | "This package provides a fast @code{match} replacement for cases that | |
1895 | require repeated look-ups. It is slightly faster that R's built-in | |
1896 | @code{match} function on first match against a table, but extremely fast on | |
1897 | any subsequent lookup as it keeps the hash table in memory.") | |
1898 | (license license:gpl2))) | |
a7f0faa2 RW |
1899 | |
1900 | (define-public r-ff | |
1901 | (package | |
1902 | (name "r-ff") | |
207c497e | 1903 | (version "2.2-14") |
a7f0faa2 RW |
1904 | (source |
1905 | (origin | |
1906 | (method url-fetch) | |
1907 | (uri (cran-uri "ff" version)) | |
1908 | (sha256 | |
1909 | (base32 | |
207c497e | 1910 | "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw")))) |
a7f0faa2 RW |
1911 | (build-system r-build-system) |
1912 | (propagated-inputs `(("r-bit" ,r-bit))) | |
1913 | (home-page "http://ff.r-forge.r-project.org/") | |
1914 | (synopsis "Memory-efficient storage of large data on disk and access functions") | |
1915 | (description | |
1916 | "This package provides data structures that are stored on disk but | |
1917 | behave (almost) as if they were in RAM by transparently mapping only a section | |
1918 | in main memory.") | |
a6e67d86 EF |
1919 | ;; error Architecture not supported. |
1920 | (supported-systems (delete "aarch64-linux" %supported-systems)) | |
a7f0faa2 | 1921 | (license license:gpl2))) |
49c9c297 RW |
1922 | |
1923 | (define-public r-ffbase | |
1924 | (package | |
1925 | (name "r-ffbase") | |
ec0ee085 | 1926 | (version "0.12.7") |
49c9c297 RW |
1927 | (source |
1928 | (origin | |
1929 | (method url-fetch) | |
1930 | (uri (cran-uri "ffbase" version)) | |
1931 | (sha256 | |
1932 | (base32 | |
ec0ee085 | 1933 | "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw")))) |
49c9c297 RW |
1934 | (build-system r-build-system) |
1935 | (propagated-inputs | |
1936 | `(("r-bit" ,r-bit) | |
1937 | ("r-fastmatch" ,r-fastmatch) | |
1938 | ("r-ff" ,r-ff))) | |
1939 | (home-page "http://github.com/edwindj/ffbase") | |
1940 | (synopsis "Basic statistical functions for package 'ff'") | |
1941 | (description | |
1942 | "This package extends the out of memory vectors of @code{ff} with | |
1943 | statistical functions and other utilities to ease their usage.") | |
1944 | (license license:gpl3))) | |
18a16ceb RW |
1945 | |
1946 | (define-public r-prettyunits | |
1947 | (package | |
1948 | (name "r-prettyunits") | |
1949 | (version "1.0.2") | |
1950 | (source | |
1951 | (origin | |
1952 | (method url-fetch) | |
1953 | (uri (cran-uri "prettyunits" version)) | |
1954 | (sha256 | |
1955 | (base32 | |
1956 | "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m")))) | |
1957 | (build-system r-build-system) | |
1958 | (propagated-inputs | |
1959 | `(("r-assertthat" ,r-assertthat) | |
1960 | ("r-magrittr" ,r-magrittr))) | |
1961 | (home-page "https://github.com/gaborcsardi/prettyunits") | |
1962 | (synopsis "Pretty, human readable formatting of quantities") | |
1963 | (description | |
1964 | "This package provides tools for pretty, human readable formatting of | |
1965 | quantities.") | |
1966 | (license license:expat))) | |
71be51d5 RW |
1967 | |
1968 | (define-public r-reshape | |
1969 | (package | |
1970 | (name "r-reshape") | |
2b8126a4 | 1971 | (version "0.8.8") |
71be51d5 RW |
1972 | (source |
1973 | (origin | |
1974 | (method url-fetch) | |
1975 | (uri (cran-uri "reshape" version)) | |
1976 | (sha256 | |
1977 | (base32 | |
2b8126a4 | 1978 | "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) |
71be51d5 RW |
1979 | (build-system r-build-system) |
1980 | (propagated-inputs | |
1981 | `(("r-plyr" ,r-plyr) | |
1982 | ("r-rcpp" ,r-rcpp))) | |
1983 | (home-page "http://had.co.nz/reshape") | |
1984 | (synopsis "Flexibly reshape data") | |
1985 | (description | |
1986 | "Flexibly restructure and aggregate data using just two functions: | |
1987 | @code{melt} and @code{cast}. This package provides them.") | |
1988 | (license license:expat))) | |
c9c6f4b5 RW |
1989 | |
1990 | (define-public r-progress | |
1991 | (package | |
1992 | (name "r-progress") | |
7e8ac56a | 1993 | (version "1.2.2") |
c9c6f4b5 RW |
1994 | (source |
1995 | (origin | |
1996 | (method url-fetch) | |
1997 | (uri (cran-uri "progress" version)) | |
1998 | (sha256 | |
1999 | (base32 | |
7e8ac56a | 2000 | "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l")))) |
c9c6f4b5 RW |
2001 | (build-system r-build-system) |
2002 | (propagated-inputs | |
9de9dcd9 RW |
2003 | `(("r-crayon" ,r-crayon) |
2004 | ("r-hms" ,r-hms) | |
2005 | ("r-prettyunits" ,r-prettyunits) | |
c9c6f4b5 RW |
2006 | ("r-r6" ,r-r6))) |
2007 | (home-page "https://github.com/gaborcsardi/progress") | |
2008 | (synopsis "Terminal progress bars") | |
2009 | (description | |
2010 | "This package provides configurable progress bars. They may include | |
2011 | percentage, elapsed time, and/or the estimated completion time. They work in | |
2012 | terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The | |
2013 | package also provides a C++ API, that works with or without Rcpp.") | |
2014 | (license license:expat))) | |
ac840207 RW |
2015 | |
2016 | (define-public r-ggally | |
2017 | (package | |
2018 | (name "r-ggally") | |
9944399a | 2019 | (version "1.4.0") |
ac840207 RW |
2020 | (source |
2021 | (origin | |
2022 | (method url-fetch) | |
2023 | (uri (cran-uri "GGally" version)) | |
2024 | (sha256 | |
2025 | (base32 | |
9944399a | 2026 | "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws")))) |
ac840207 RW |
2027 | (properties `((upstream-name . "GGally"))) |
2028 | (build-system r-build-system) | |
9944399a RW |
2029 | (inputs |
2030 | `(("libressl" ,libressl))) | |
ac840207 RW |
2031 | (propagated-inputs |
2032 | `(("r-ggplot2" ,r-ggplot2) | |
2033 | ("r-gtable" ,r-gtable) | |
2034 | ("r-plyr" ,r-plyr) | |
2035 | ("r-progress" ,r-progress) | |
2036 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9944399a RW |
2037 | ("r-reshape" ,r-reshape) |
2038 | ("r-rlang" ,r-rlang))) | |
ac840207 RW |
2039 | (home-page "https://ggobi.github.io/ggally") |
2040 | (synopsis "Extension to ggplot2") | |
2041 | (description | |
2042 | "The R package ggplot2 is a plotting system based on the grammar of | |
2043 | graphics. GGally extends ggplot2 by adding several functions to reduce the | |
2044 | complexity of combining geometric objects with transformed data. Some of | |
2045 | these functions include a pairwise plot matrix, a two group pairwise plot | |
2046 | matrix, a parallel coordinates plot, a survival plot, and several functions to | |
2047 | plot networks.") | |
2048 | (license license:gpl2+))) | |
3349faec RW |
2049 | |
2050 | (define-public r-proxy | |
2051 | (package | |
2052 | (name "r-proxy") | |
e190d9af | 2053 | (version "0.4-23") |
3349faec RW |
2054 | (source |
2055 | (origin | |
2056 | (method url-fetch) | |
2057 | (uri (cran-uri "proxy" version)) | |
2058 | (sha256 | |
2059 | (base32 | |
e190d9af | 2060 | "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x")))) |
3349faec | 2061 | (build-system r-build-system) |
e9960d8c | 2062 | (home-page "https://cran.r-project.org/web/packages/proxy") |
3349faec RW |
2063 | (synopsis "Distance and similarity measures") |
2064 | (description | |
2065 | "This package provides an extensible framework for the efficient | |
2066 | calculation of auto- and cross-proximities, along with implementations of the | |
2067 | most popular ones.") | |
2068 | (license license:gpl2))) | |
bc0081e7 RW |
2069 | |
2070 | (define-public r-sp | |
2071 | (package | |
2072 | (name "r-sp") | |
d87130cb | 2073 | (version "1.3-1") |
bc0081e7 RW |
2074 | (source |
2075 | (origin | |
2076 | (method url-fetch) | |
2077 | (uri (cran-uri "sp" version)) | |
2078 | (sha256 | |
2079 | (base32 | |
d87130cb | 2080 | "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p")))) |
bc0081e7 RW |
2081 | (build-system r-build-system) |
2082 | (propagated-inputs | |
2083 | `(("r-lattice" ,r-lattice))) | |
e9960d8c | 2084 | (home-page "https://cran.r-project.org/web/packages/sp") |
bc0081e7 RW |
2085 | (synopsis "Classes and methods for spatial data") |
2086 | (description | |
2087 | "This package provides classes and methods for spatial data; the classes | |
2088 | document where the spatial location information resides, for 2D or 3D data. | |
2089 | Utility functions are provided, e.g. for plotting data as maps, spatial | |
2090 | selection, as well as methods for retrieving coordinates, for subsetting, | |
2091 | print, summary, etc.") | |
2092 | (license license:gpl2+))) | |
e389d10f RW |
2093 | |
2094 | (define-public r-rmtstat | |
2095 | (package | |
2096 | (name "r-rmtstat") | |
2097 | (version "0.3") | |
2098 | (source | |
2099 | (origin | |
2100 | (method url-fetch) | |
2101 | (uri (cran-uri "RMTstat" version)) | |
2102 | (sha256 | |
2103 | (base32 | |
2104 | "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1")))) | |
2105 | (properties `((upstream-name . "RMTstat"))) | |
2106 | (build-system r-build-system) | |
e9960d8c | 2107 | (home-page "https://cran.r-project.org/web/packages/RMTstat") |
e389d10f RW |
2108 | (synopsis "Distributions, statistics and tests derived from random matrix theory") |
2109 | (description | |
2110 | "This package provides functions for working with the Tracy-Widom laws | |
2111 | and other distributions related to the eigenvalues of large Wishart | |
2112 | matrices.") | |
2113 | (license license:bsd-3))) | |
6427e620 | 2114 | |
94989d4b RJ |
2115 | (define-public r-rmpi |
2116 | (package | |
2117 | (name "r-rmpi") | |
5e8282a4 | 2118 | (version "0.6-9") |
94989d4b RJ |
2119 | (source (origin |
2120 | (method url-fetch) | |
2121 | (uri (cran-uri "Rmpi" version)) | |
2122 | (sha256 | |
2123 | (base32 | |
5e8282a4 | 2124 | "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) |
94989d4b RJ |
2125 | (properties `((upstream-name . "Rmpi"))) |
2126 | (build-system r-build-system) | |
2127 | (arguments | |
56d447ba EB |
2128 | `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"") |
2129 | #:phases (modify-phases %standard-phases | |
2130 | (add-before 'install 'mpi-setup | |
2131 | ,%openmpi-setup)))) | |
94989d4b RJ |
2132 | (inputs |
2133 | `(("openmpi" ,openmpi))) | |
9ebfdcd3 RW |
2134 | (native-inputs |
2135 | `(("pkg-config" ,pkg-config))) | |
94989d4b RJ |
2136 | (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") |
2137 | (synopsis "R interface to message-passing interface (MPI)") | |
2138 | (description | |
2139 | "This package provides an interface (wrapper) to MPI APIs. It also | |
2140 | provides an interactive R manager and worker environment.") | |
2141 | (license license:gpl2+))) | |
2142 | ||
6427e620 RW |
2143 | (define-public r-lmoments |
2144 | (package | |
2145 | (name "r-lmoments") | |
739135b2 | 2146 | (version "1.3-1") |
6427e620 RW |
2147 | (source |
2148 | (origin | |
2149 | (method url-fetch) | |
2150 | (uri (cran-uri "Lmoments" version)) | |
2151 | (sha256 | |
2152 | (base32 | |
739135b2 | 2153 | "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw")))) |
6427e620 RW |
2154 | (properties `((upstream-name . "Lmoments"))) |
2155 | (build-system r-build-system) | |
739135b2 RW |
2156 | (propagated-inputs |
2157 | `(("r-rcpp" ,r-rcpp) | |
2158 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
6427e620 RW |
2159 | (home-page "http://www.tilastotiede.fi/juha_karvanen.html") |
2160 | (synopsis "L-moments and quantile mixtures") | |
2161 | (description | |
2162 | "This package contains functions to estimate L-moments and trimmed | |
2163 | L-moments from the data. It also contains functions to estimate the | |
2164 | parameters of the normal polynomial quantile mixture and the Cauchy polynomial | |
2165 | quantile mixture from L-moments and trimmed L-moments.") | |
2166 | (license license:gpl2))) | |
28476b4b RW |
2167 | |
2168 | (define-public r-distillery | |
2169 | (package | |
2170 | (name "r-distillery") | |
5686da76 | 2171 | (version "1.0-6") |
28476b4b RW |
2172 | (source |
2173 | (origin | |
2174 | (method url-fetch) | |
2175 | (uri (cran-uri "distillery" version)) | |
2176 | (sha256 | |
2177 | (base32 | |
5686da76 | 2178 | "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429")))) |
28476b4b RW |
2179 | (build-system r-build-system) |
2180 | (home-page "http://www.ral.ucar.edu/staff/ericg") | |
2181 | (synopsis "Functions for confidence intervals and object information") | |
2182 | (description | |
2183 | "This package provides some very simple method functions for confidence | |
2184 | interval calculation and to distill pertinent information from a potentially | |
2185 | complex object; primarily used in common with the packages extRemes and | |
2186 | SpatialVx.") | |
2187 | (license license:gpl2+))) | |
58db98c9 RW |
2188 | |
2189 | (define-public r-extremes | |
2190 | (package | |
2191 | (name "r-extremes") | |
987b0804 | 2192 | (version "2.0-10") |
58db98c9 RW |
2193 | (source |
2194 | (origin | |
2195 | (method url-fetch) | |
2196 | (uri (cran-uri "extRemes" version)) | |
2197 | (sha256 | |
2198 | (base32 | |
987b0804 | 2199 | "08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic")))) |
58db98c9 RW |
2200 | (properties `((upstream-name . "extRemes"))) |
2201 | (build-system r-build-system) | |
2202 | (propagated-inputs | |
987b0804 | 2203 | `(("r-distillery" ,r-distillery) |
58db98c9 RW |
2204 | ("r-lmoments" ,r-lmoments))) |
2205 | (home-page "http://www.assessment.ucar.edu/toolkit/") | |
2206 | (synopsis "Extreme value analysis") | |
2207 | (description | |
2208 | "ExtRemes is a suite of functions for carrying out analyses on the | |
2209 | extreme values of a process of interest; be they block maxima over long blocks | |
2210 | or excesses over a high threshold.") | |
2211 | (license license:gpl2+))) | |
062b6dbd RW |
2212 | |
2213 | (define-public r-lmtest | |
2214 | (package | |
2215 | (name "r-lmtest") | |
0b5b9d69 | 2216 | (version "0.9-37") |
062b6dbd RW |
2217 | (source |
2218 | (origin | |
2219 | (method url-fetch) | |
2220 | (uri (cran-uri "lmtest" version)) | |
2221 | (sha256 | |
2222 | (base32 | |
0b5b9d69 | 2223 | "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx")))) |
062b6dbd RW |
2224 | (build-system r-build-system) |
2225 | (propagated-inputs | |
2226 | `(("r-zoo" ,r-zoo))) | |
2227 | (native-inputs | |
2228 | `(("gfortran" ,gfortran))) | |
e9960d8c | 2229 | (home-page "https://cran.r-project.org/web/packages/lmtest") |
062b6dbd RW |
2230 | (synopsis "Testing linear regression models") |
2231 | (description | |
2232 | "This package provides a collection of tests, data sets, and examples for | |
2233 | diagnostic checking in linear regression models. Furthermore, some generic | |
2234 | tools for inference in parametric models are provided.") | |
2235 | ;; Either version is okay | |
2236 | (license (list license:gpl2 license:gpl3)))) | |
d6b156dc | 2237 | |
c974008d RJ |
2238 | (define-public r-idr |
2239 | (package | |
2240 | (name "r-idr") | |
2241 | (version "1.2") | |
2242 | (source (origin | |
2243 | (method url-fetch) | |
2244 | (uri (cran-uri "idr" version)) | |
2245 | (sha256 | |
2246 | (base32 | |
2247 | "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb")))) | |
2248 | (build-system r-build-system) | |
2249 | (home-page "https://cran.r-project.org/web/packages/idr/") | |
2250 | (synopsis "Irreproducible discovery rate") | |
2251 | (description | |
2252 | "This is a package for estimating the copula mixture model and plotting | |
2253 | correspondence curves in \"Measuring reproducibility of high-throughput | |
2254 | experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, | |
2255 | by Li, Brown, Huang, and Bickel") | |
2256 | (license license:gpl2+))) | |
2257 | ||
d6b156dc RW |
2258 | (define-public r-inline |
2259 | (package | |
2260 | (name "r-inline") | |
0acbf8bb | 2261 | (version "0.3.15") |
d6b156dc RW |
2262 | (source (origin |
2263 | (method url-fetch) | |
2264 | (uri (cran-uri "inline" version)) | |
2265 | (sha256 | |
2266 | (base32 | |
0acbf8bb | 2267 | "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z")))) |
d6b156dc | 2268 | (build-system r-build-system) |
e9960d8c | 2269 | (home-page "https://cran.r-project.org/web/packages/inline") |
d6b156dc RW |
2270 | (synopsis "Functions to inline C, C++, Fortran function calls from R") |
2271 | (description | |
2272 | "This package provides functionality to dynamically define R functions | |
2273 | and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and | |
2274 | @code{.Call} calling conventions.") | |
2275 | ;; Any version of the LGPL. | |
2276 | (license license:lgpl3+))) | |
8c72b830 RW |
2277 | |
2278 | (define-public r-bbmle | |
2279 | (package | |
2280 | (name "r-bbmle") | |
84078220 | 2281 | (version "1.0.20") |
8c72b830 RW |
2282 | (source |
2283 | (origin | |
2284 | (method url-fetch) | |
2285 | (uri (cran-uri "bbmle" version)) | |
2286 | (sha256 | |
2287 | (base32 | |
84078220 | 2288 | "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc")))) |
8c72b830 RW |
2289 | (build-system r-build-system) |
2290 | (propagated-inputs | |
2291 | `(("r-lattice" ,r-lattice) | |
2292 | ("r-mass" ,r-mass) | |
2293 | ("r-numderiv" ,r-numderiv))) | |
e9960d8c | 2294 | (home-page "https://cran.r-project.org/web/packages/bbmle") |
8c72b830 RW |
2295 | (synopsis "Tools for General Maximum Likelihood Estimation") |
2296 | (description | |
c151b0b6 RW |
2297 | "This package provides methods and functions for fitting maximum |
2298 | likelihood models in R. This package modifies and extends the @code{mle} | |
2299 | classes in the @code{stats4} package.") | |
8c72b830 | 2300 | ;; Any version of the GPL |
c151b0b6 | 2301 | (license license:gpl2+))) |
b31e4a96 RW |
2302 | |
2303 | (define-public r-emdbook | |
2304 | (package | |
2305 | (name "r-emdbook") | |
59c51342 | 2306 | (version "1.3.11") |
b31e4a96 RW |
2307 | (source |
2308 | (origin | |
2309 | (method url-fetch) | |
2310 | (uri (cran-uri "emdbook" version)) | |
2311 | (sha256 | |
2312 | (base32 | |
59c51342 | 2313 | "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q")))) |
b31e4a96 RW |
2314 | (build-system r-build-system) |
2315 | (propagated-inputs | |
2316 | `(("r-bbmle" ,r-bbmle) | |
2317 | ("r-coda" ,r-coda) | |
2318 | ("r-lattice" ,r-lattice) | |
2319 | ("r-mass" ,r-mass) | |
2320 | ("r-plyr" ,r-plyr) | |
2321 | ("r-rcpp" ,r-rcpp))) | |
2322 | (home-page "http://www.math.mcmaster.ca/bolker/emdbook") | |
2323 | (synopsis "Support functions and data for \"Ecological Models and Data\"") | |
2324 | (description | |
2325 | "This package provides auxiliary functions and data sets for \"Ecological | |
2326 | Models and Data\", a book presenting maximum likelihood estimation and related | |
2327 | topics for ecologists (ISBN 978-0-691-12522-0).") | |
2328 | ;; Any GPL version | |
2329 | (license (list license:gpl2 license:gpl3)))) | |
a3e36d37 RW |
2330 | |
2331 | (define-public r-lpsolve | |
2332 | (package | |
2333 | (name "r-lpsolve") | |
bf9a8236 | 2334 | (version "5.6.13.3") |
a3e36d37 RW |
2335 | (source |
2336 | (origin | |
2337 | (method url-fetch) | |
2338 | (uri (cran-uri "lpSolve" version)) | |
2339 | (sha256 | |
2340 | (base32 | |
bf9a8236 | 2341 | "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6")))) |
a3e36d37 RW |
2342 | (properties `((upstream-name . "lpSolve"))) |
2343 | (build-system r-build-system) | |
e9960d8c | 2344 | (home-page "https://cran.r-project.org/web/packages/lpSolve") |
a3e36d37 RW |
2345 | (synopsis "R interface to Lp_solve to solve linear/integer programs") |
2346 | (description | |
2347 | "Lp_solve is software for solving linear, integer and mixed integer | |
2348 | programs. This implementation supplies a \"wrapper\" function in C and some R | |
2349 | functions that solve general linear/integer problems, assignment problems, and | |
2350 | transportation problems.") | |
2351 | (license license:lgpl2.0))) | |
521e0703 RW |
2352 | |
2353 | (define-public r-limsolve | |
2354 | (package | |
2355 | (name "r-limsolve") | |
2356 | (version "1.5.5.3") | |
2357 | (source | |
2358 | (origin | |
2359 | (method url-fetch) | |
2360 | (uri (cran-uri "limSolve" version)) | |
2361 | (sha256 | |
2362 | (base32 | |
2363 | "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg")))) | |
2364 | (properties `((upstream-name . "limSolve"))) | |
2365 | (build-system r-build-system) | |
2366 | (propagated-inputs | |
2367 | `(("r-lpsolve" ,r-lpsolve) | |
2368 | ("r-mass" ,r-mass) | |
2369 | ("r-quadprog" ,r-quadprog))) | |
2370 | (native-inputs `(("gfortran" ,gfortran))) | |
e9960d8c | 2371 | (home-page "https://cran.r-project.org/web/packages/limSolve") |
521e0703 RW |
2372 | (synopsis "Solving linear inverse models") |
2373 | (description | |
2374 | "This package provides functions that: | |
2375 | ||
2376 | @enumerate | |
2377 | @item find the minimum/maximum of a linear or quadratic function, | |
2378 | @item sample an underdetermined or overdetermined system, | |
2379 | @item solve a linear system Ax=B for the unknown x. | |
2380 | @end enumerate | |
2381 | ||
2382 | It includes banded and tridiagonal linear systems. The package calls Fortran | |
2383 | functions from LINPACK.") | |
2384 | ;; Any GPL version. | |
2385 | (license (list license:gpl2+ license:gpl3+)))) | |
6b4a9aec RW |
2386 | |
2387 | (define-public r-fitdistrplus | |
2388 | (package | |
2389 | (name "r-fitdistrplus") | |
9e0162df | 2390 | (version "1.0-14") |
6b4a9aec RW |
2391 | (source |
2392 | (origin | |
2393 | (method url-fetch) | |
2394 | (uri (cran-uri "fitdistrplus" version)) | |
2395 | (sha256 | |
2396 | (base32 | |
9e0162df | 2397 | "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245")))) |
6b4a9aec RW |
2398 | (build-system r-build-system) |
2399 | (propagated-inputs | |
2400 | `(("r-mass" ,r-mass) | |
8c456dff | 2401 | ("r-npsurv" ,r-npsurv) |
6b4a9aec RW |
2402 | ("r-survival" ,r-survival))) |
2403 | (home-page "http://riskassessment.r-forge.r-project.org") | |
2404 | (synopsis "Fitting a parametric distribution from data") | |
2405 | (description | |
2406 | "This package extends the @code{fitdistr} function of the MASS package | |
2407 | with several functions to help the fit of a parametric distribution to | |
2408 | non-censored or censored data. Censored data may contain left-censored, | |
2409 | right-censored and interval-censored values, with several lower and upper | |
2410 | bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package | |
2411 | provides moment matching (MME), quantile matching (QME) and maximum | |
2412 | goodness-of-fit estimation (MGE) methods (available only for non-censored | |
2413 | data). Weighted versions of MLE, MME and QME are available.") | |
2414 | (license license:gpl2+))) | |
8d220073 RW |
2415 | |
2416 | (define-public r-energy | |
2417 | (package | |
2418 | (name "r-energy") | |
3337fd1d | 2419 | (version "1.7-6") |
8d220073 RW |
2420 | (source |
2421 | (origin | |
2422 | (method url-fetch) | |
2423 | (uri (cran-uri "energy" version)) | |
2424 | (sha256 | |
2425 | (base32 | |
3337fd1d | 2426 | "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh")))) |
8d220073 RW |
2427 | (build-system r-build-system) |
2428 | (propagated-inputs | |
2429 | `(("r-boot" ,r-boot) | |
2430 | ("r-rcpp" ,r-rcpp))) | |
e9960d8c | 2431 | (home-page "https://cran.r-project.org/web/packages/energy") |
8d220073 RW |
2432 | (synopsis "Multivariate inference via the energy of data") |
2433 | (description | |
2434 | "This package provides e-statistics (energy) tests and statistics for | |
2435 | multivariate and univariate inference, including distance correlation, | |
2436 | one-sample, two-sample, and multi-sample tests for comparing multivariate | |
2437 | distributions, are implemented. Measuring and testing multivariate | |
2438 | independence based on distance correlation, partial distance correlation, | |
2439 | multivariate goodness-of-fit tests, clustering based on energy distance, | |
2440 | testing for multivariate normality, distance components (disco) for | |
2441 | non-parametric analysis of structured data, and other energy | |
2442 | statistics/methods are implemented.") | |
2443 | (license license:gpl2+))) | |
abcb8494 RW |
2444 | |
2445 | (define-public r-suppdists | |
2446 | (package | |
2447 | (name "r-suppdists") | |
2448 | (version "1.1-9.4") | |
2449 | (source | |
2450 | (origin | |
2451 | (method url-fetch) | |
2452 | (uri (cran-uri "SuppDists" version)) | |
2453 | (sha256 | |
2454 | (base32 | |
2455 | "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw")))) | |
2456 | (properties `((upstream-name . "SuppDists"))) | |
2457 | (build-system r-build-system) | |
e9960d8c | 2458 | (home-page "https://cran.r-project.org/web/packages/SuppDists") |
abcb8494 RW |
2459 | (synopsis "Supplementary distributions") |
2460 | (description | |
2461 | "This package provides ten distributions supplementing those built into | |
2462 | R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, | |
2463 | Spearman's rho, maximum F ratio, the Pearson product moment correlation | |
2464 | coefficient, Johnson distributions, normal scores and generalized | |
2465 | hypergeometric distributions. In addition two random number generators of | |
2466 | George Marsaglia are included.") | |
2467 | (license license:gpl2+))) | |
05e8a3ef RW |
2468 | |
2469 | (define-public r-ksamples | |
2470 | (package | |
2471 | (name "r-ksamples") | |
beb82eb9 | 2472 | (version "1.2-9") |
05e8a3ef RW |
2473 | (source |
2474 | (origin | |
2475 | (method url-fetch) | |
2476 | (uri (cran-uri "kSamples" version)) | |
2477 | (sha256 | |
2478 | (base32 | |
beb82eb9 | 2479 | "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms")))) |
05e8a3ef RW |
2480 | (properties `((upstream-name . "kSamples"))) |
2481 | (build-system r-build-system) | |
2482 | (propagated-inputs | |
2483 | `(("r-suppdists" ,r-suppdists))) | |
e9960d8c | 2484 | (home-page "https://cran.r-project.org/web/packages/kSamples") |
05e8a3ef RW |
2485 | (synopsis "K-Sample rank tests and their combinations") |
2486 | (description | |
2487 | "This package provides tools to compares k samples using the | |
2488 | Anderson-Darling test, Kruskal-Wallis type tests with different rank score | |
2489 | criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) | |
2490 | test. It computes asymptotic, simulated or (limited) exact P-values, all | |
2491 | valid under randomization, with or without ties, or conditionally under random | |
2492 | sampling from populations, given the observed tie pattern. Except for Steel's | |
2493 | test and the JT test it also combines these tests across several blocks of | |
2494 | samples.") | |
2495 | (license license:gpl2+))) | |
f97ce815 RW |
2496 | |
2497 | (define-public r-cvst | |
2498 | (package | |
2499 | (name "r-cvst") | |
b13b5674 | 2500 | (version "0.2-2") |
f97ce815 RW |
2501 | (source |
2502 | (origin | |
2503 | (method url-fetch) | |
2504 | (uri (cran-uri "CVST" version)) | |
2505 | (sha256 | |
2506 | (base32 | |
b13b5674 | 2507 | "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5")))) |
f97ce815 RW |
2508 | (properties `((upstream-name . "CVST"))) |
2509 | (build-system r-build-system) | |
2510 | (propagated-inputs | |
2511 | `(("r-kernlab" ,r-kernlab) | |
2512 | ("r-matrix" ,r-matrix))) | |
e9960d8c | 2513 | (home-page "https://cran.r-project.org/web/packages/CVST") |
f97ce815 RW |
2514 | (synopsis "Fast cross-validation via sequential testing") |
2515 | (description | |
2516 | "This package implements the fast cross-validation via sequential | |
2517 | testing (CVST) procedure. CVST is an improved cross-validation procedure | |
2518 | which uses non-parametric testing coupled with sequential analysis to | |
2519 | determine the best parameter set on linearly increasing subsets of the data. | |
2520 | Additionally to the CVST the package contains an implementation of the | |
2521 | ordinary k-fold cross-validation with a flexible and powerful set of helper | |
2522 | objects and methods to handle the overall model selection process. The | |
2523 | implementations of the Cochran's Q test with permutations and the sequential | |
2524 | testing framework of Wald are generic and can therefore also be used in other | |
2525 | contexts.") | |
2526 | (license license:gpl2+))) | |
797e1dfb | 2527 | |
c5f033e0 RW |
2528 | (define-public r-squarem |
2529 | (package | |
2530 | (name "r-squarem") | |
2531 | (version "2017.10-1") | |
2532 | (source | |
2533 | (origin | |
2534 | (method url-fetch) | |
2535 | (uri (cran-uri "SQUAREM" version)) | |
2536 | (sha256 | |
2537 | (base32 | |
2538 | "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv")))) | |
2539 | (properties `((upstream-name . "SQUAREM"))) | |
2540 | (build-system r-build-system) | |
2541 | (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html") | |
2542 | (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms") | |
2543 | (description | |
2544 | "This package provides algorithms for accelerating the convergence of | |
2545 | slow, monotone sequences from smooth, contraction mapping such as the EM | |
2546 | algorithm. It can be used to accelerate any smooth, linearly convergent | |
2547 | acceleration scheme. A tutorial style introduction to this package is | |
2548 | available in a vignette.") | |
2549 | (license license:gpl2+))) | |
2550 | ||
797e1dfb RW |
2551 | (define-public r-lava |
2552 | (package | |
2553 | (name "r-lava") | |
099b7c55 | 2554 | (version "1.6.6") |
797e1dfb RW |
2555 | (source |
2556 | (origin | |
2557 | (method url-fetch) | |
2558 | (uri (cran-uri "lava" version)) | |
2559 | (sha256 | |
2560 | (base32 | |
099b7c55 | 2561 | "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s")))) |
797e1dfb RW |
2562 | (build-system r-build-system) |
2563 | (propagated-inputs | |
2564 | `(("r-numderiv" ,r-numderiv) | |
92e4534c | 2565 | ("r-squarem" ,r-squarem) |
797e1dfb RW |
2566 | ("r-survival" ,r-survival))) |
2567 | (home-page "https://github.com/kkholst/lava") | |
2568 | (synopsis "Latent variable models") | |
2569 | (description | |
2570 | "This package provides tools for the estimation and simulation of latent | |
2571 | variable models.") | |
2572 | (license license:gpl3))) | |
d26b7c1b RW |
2573 | |
2574 | (define-public r-drr | |
2575 | (package | |
2576 | (name "r-drr") | |
0f001b3c | 2577 | (version "0.0.3") |
d26b7c1b RW |
2578 | (source |
2579 | (origin | |
2580 | (method url-fetch) | |
2581 | (uri (cran-uri "DRR" version)) | |
2582 | (sha256 | |
2583 | (base32 | |
0f001b3c | 2584 | "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl")))) |
d26b7c1b RW |
2585 | (properties `((upstream-name . "DRR"))) |
2586 | (build-system r-build-system) | |
2587 | (propagated-inputs | |
2588 | `(("r-cvst" ,r-cvst) | |
2589 | ("r-kernlab" ,r-kernlab) | |
2590 | ("r-matrix" ,r-matrix))) | |
e9960d8c | 2591 | (home-page "https://cran.r-project.org/web/packages/DRR") |
d26b7c1b RW |
2592 | (synopsis "Dimensionality reduction via regression") |
2593 | (description | |
2594 | "This package provides an implementation of dimensionality reduction via | |
2595 | regression using Kernel Ridge Regression.") | |
2596 | (license license:gpl3))) | |
9dd707f0 RW |
2597 | |
2598 | (define-public r-prodlim | |
2599 | (package | |
2600 | (name "r-prodlim") | |
9ee81a36 | 2601 | (version "2018.04.18") |
9dd707f0 RW |
2602 | (source |
2603 | (origin | |
2604 | (method url-fetch) | |
2605 | (uri (cran-uri "prodlim" version)) | |
2606 | (sha256 | |
2607 | (base32 | |
9ee81a36 | 2608 | "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb")))) |
9dd707f0 RW |
2609 | (build-system r-build-system) |
2610 | (propagated-inputs | |
2611 | `(("r-kernsmooth" ,r-kernsmooth) | |
2612 | ("r-lava" ,r-lava) | |
2613 | ("r-rcpp" ,r-rcpp) | |
2614 | ("r-survival" ,r-survival))) | |
e9960d8c | 2615 | (home-page "https://cran.r-project.org/web/packages/prodlim") |
9dd707f0 RW |
2616 | (synopsis "Product-limit estimation for censored event history analysis") |
2617 | (description | |
2618 | "This package provides a fast and user-friendly implementation of | |
2619 | nonparametric estimators for censored event history (survival) analysis with | |
2620 | the Kaplan-Meier and Aalen-Johansen methods.") | |
2621 | (license license:gpl2+))) | |
b561f563 RW |
2622 | |
2623 | (define-public r-dimred | |
2624 | (package | |
2625 | (name "r-dimred") | |
7a67bca1 | 2626 | (version "0.2.3") |
b561f563 RW |
2627 | (source |
2628 | (origin | |
2629 | (method url-fetch) | |
2630 | (uri (cran-uri "dimRed" version)) | |
2631 | (sha256 | |
2632 | (base32 | |
7a67bca1 | 2633 | "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6")))) |
b561f563 RW |
2634 | (properties `((upstream-name . "dimRed"))) |
2635 | (build-system r-build-system) | |
77f97229 RW |
2636 | (propagated-inputs |
2637 | `(("r-drr" ,r-drr) | |
2638 | ("r-magrittr" ,r-magrittr))) | |
b561f563 RW |
2639 | (home-page "https://github.com/gdkrmr/dimRed") |
2640 | (synopsis "Framework for dimensionality reduction") | |
2641 | (description | |
2642 | "This package provides a collection of dimensionality reduction | |
2643 | techniques from R packages and provides a common interface for calling the | |
2644 | methods.") | |
2645 | (license license:gpl3))) | |
1b663184 RW |
2646 | |
2647 | (define-public r-timedate | |
2648 | (package | |
2649 | (name "r-timedate") | |
51b7b0e3 | 2650 | (version "3043.102") |
1b663184 RW |
2651 | (source |
2652 | (origin | |
2653 | (method url-fetch) | |
2654 | (uri (cran-uri "timeDate" version)) | |
2655 | (sha256 | |
2656 | (base32 | |
51b7b0e3 | 2657 | "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p")))) |
1b663184 RW |
2658 | (properties `((upstream-name . "timeDate"))) |
2659 | (build-system r-build-system) | |
2660 | (home-page "https://www.rmetrics.org") | |
2661 | (synopsis "Chronological and calendar objects") | |
2662 | (description | |
2663 | "This package provides an environment for teaching \"Financial | |
2664 | Engineering and Computational Finance\" and for managing chronological and | |
2665 | calendar objects.") | |
2666 | (license license:gpl2+))) | |
f57b883e | 2667 | |
ce4e81cb RW |
2668 | (define-public r-magic |
2669 | (package | |
2670 | (name "r-magic") | |
bba80fad | 2671 | (version "1.5-9") |
ce4e81cb RW |
2672 | (source |
2673 | (origin | |
2674 | (method url-fetch) | |
2675 | (uri (cran-uri "magic" version)) | |
2676 | (sha256 | |
2677 | (base32 | |
bba80fad | 2678 | "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) |
ce4e81cb RW |
2679 | (build-system r-build-system) |
2680 | (propagated-inputs | |
2681 | `(("r-abind" ,r-abind))) | |
2682 | (home-page "https://github.com/RobinHankin/magic.git") | |
2683 | (synopsis "Create and investigate magic squares") | |
2684 | (description | |
2685 | "This package provides a collection of efficient, vectorized algorithms | |
2686 | for the creation and investigation of magic squares and hypercubes, including | |
2687 | a variety of functions for the manipulation and analysis of arbitrarily | |
2688 | dimensioned arrays.") | |
2689 | (license license:gpl2))) | |
2690 | ||
d9bec9a8 RW |
2691 | (define-public r-rmysql |
2692 | (package | |
2693 | (name "r-rmysql") | |
937e1557 | 2694 | (version "0.10.17") |
d9bec9a8 RW |
2695 | (source |
2696 | (origin | |
2697 | (method url-fetch) | |
2698 | (uri (cran-uri "RMySQL" version)) | |
2699 | (sha256 | |
2700 | (base32 | |
937e1557 | 2701 | "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm")))) |
d9bec9a8 RW |
2702 | (properties `((upstream-name . "RMySQL"))) |
2703 | (build-system r-build-system) | |
d9bec9a8 RW |
2704 | (inputs |
2705 | `(("mariadb" ,mariadb) | |
2706 | ("zlib" ,zlib))) | |
2707 | (propagated-inputs | |
2708 | `(("r-dbi" ,r-dbi))) | |
2709 | (home-page "https://github.com/r-dbi/RMySQL") | |
2710 | (synopsis "Database interface and MySQL driver for R") | |
2711 | (description | |
2712 | "This package provides a DBI interface to MySQL / MariaDB. The RMySQL | |
2713 | package contains an old implementation based on legacy code from S-PLUS which | |
2714 | is being phased out. A modern MySQL client based on Rcpp is available from | |
2715 | the RMariaDB package.") | |
2716 | (license license:gpl2))) | |
2717 | ||
5574cb81 RW |
2718 | (define-public r-rpostgresql |
2719 | (package | |
2720 | (name "r-rpostgresql") | |
2721 | (version "0.6-2") | |
2722 | (source | |
2723 | (origin | |
2724 | (method url-fetch) | |
2725 | (uri (cran-uri "RPostgreSQL" version)) | |
2726 | (sha256 | |
2727 | (base32 | |
2728 | "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) | |
2729 | (properties `((upstream-name . "RPostgreSQL"))) | |
2730 | (build-system r-build-system) | |
2731 | (inputs | |
2732 | `(("postgresql" ,postgresql))) | |
2733 | (propagated-inputs | |
2734 | `(("r-dbi" ,r-dbi))) | |
2735 | (home-page "https://github.com/tomoakin/RPostgreSQL") | |
2736 | (synopsis "R interface to the PostgreSQL database system") | |
2737 | (description | |
2738 | "This package provides a Database Interface (DBI) compliant driver for R | |
2739 | to access PostgreSQL database systems.") | |
2740 | ;; The whole package is released under GPL version 2. It includes code | |
2741 | ;; under the PostgreSQL license. | |
2742 | (license license:gpl2))) | |
2743 | ||
f3640cee RW |
2744 | (define-public r-linprog |
2745 | (package | |
2746 | (name "r-linprog") | |
2747 | (version "0.9-2") | |
2748 | (source | |
2749 | (origin | |
2750 | (method url-fetch) | |
2751 | (uri (cran-uri "linprog" version)) | |
2752 | (sha256 | |
2753 | (base32 | |
2754 | "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9")))) | |
2755 | (build-system r-build-system) | |
2756 | (propagated-inputs `(("r-lpsolve" ,r-lpsolve))) | |
2757 | (home-page "http://linprog.r-forge.r-project.org/") | |
2758 | (synopsis "Linear programming and optimization") | |
2759 | (description | |
2760 | "This package can be used to solve Linear Programming / Linear | |
2761 | Optimization problems by using the simplex algorithm.") | |
2762 | (license license:gpl2+))) | |
2763 | ||
9604429d RW |
2764 | (define-public r-geometry |
2765 | (package | |
2766 | (name "r-geometry") | |
9960ad55 | 2767 | (version "0.4.4") |
9604429d RW |
2768 | (source |
2769 | (origin | |
2770 | (method url-fetch) | |
2771 | (uri (cran-uri "geometry" version)) | |
2772 | (sha256 | |
2773 | (base32 | |
9960ad55 | 2774 | "1mx5n5mw63nij4n6crs9165mlls4fnh1ipw5ch467rjsidgl0mg8")))) |
9604429d | 2775 | (build-system r-build-system) |
a023d43d BG |
2776 | (propagated-inputs |
2777 | `(("r-magic" ,r-magic) | |
a80620b9 | 2778 | ("r-linprog" ,r-linprog) |
a023d43d BG |
2779 | ("r-lpsolve" ,r-lpsolve) |
2780 | ("r-rcpp" ,r-rcpp) | |
3d17dc5d | 2781 | ("r-rcppprogress" ,r-rcppprogress))) |
9604429d RW |
2782 | (home-page "http://geometry.r-forge.r-project.org/") |
2783 | (synopsis "Mesh generation and surface tesselation") | |
2784 | (description | |
2785 | "This package makes the qhull library available in R, in a similar manner | |
2786 | as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace | |
2787 | intersections about a point, Voronoi diagrams, furthest-site Delaunay | |
2788 | triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, | |
2789 | and higher dimensions. It implements the Quickhull algorithm for computing | |
2790 | the convex hull. Qhull does not support constrained Delaunay triangulations, | |
2791 | or mesh generation of non-convex objects, but the package does include some R | |
2792 | functions that allow for this. Currently the package only gives access to | |
2793 | Delaunay triangulation and convex hull computation.") | |
2794 | ;; The Qhull sources are included and are distributed under a custom | |
2795 | ;; non-copyleft license. The R sources are released under GPL version 2. | |
2796 | (license (list license:gpl2 | |
2797 | (license:non-copyleft "http://www.qhull.org/COPYING.txt"))))) | |
2798 | ||
f57b883e RW |
2799 | (define-public r-ddalpha |
2800 | (package | |
2801 | (name "r-ddalpha") | |
a315d496 | 2802 | (version "1.3.9") |
f57b883e RW |
2803 | (source |
2804 | (origin | |
2805 | (method url-fetch) | |
2806 | (uri (cran-uri "ddalpha" version)) | |
2807 | (sha256 | |
2808 | (base32 | |
a315d496 | 2809 | "1vzs0cvl6xw3h9i00rg3hs02xwgxcnh8326y10kxmhs3qq4m7nb2")))) |
f57b883e RW |
2810 | (build-system r-build-system) |
2811 | (propagated-inputs | |
2812 | `(("r-bh" ,r-bh) | |
2813 | ("r-class" ,r-class) | |
4f184233 | 2814 | ("r-geometry" ,r-geometry) |
f57b883e RW |
2815 | ("r-mass" ,r-mass) |
2816 | ("r-rcpp" ,r-rcpp) | |
e90456b9 RW |
2817 | ("r-robustbase" ,r-robustbase) |
2818 | ("r-sfsmisc" ,r-sfsmisc))) | |
2819 | (native-inputs | |
2820 | `(("gfortran" ,gfortran))) | |
e9960d8c | 2821 | (home-page "https://cran.r-project.org/web/packages/ddalpha") |
f57b883e RW |
2822 | (synopsis "Depth-Based classification and calculation of data depth") |
2823 | (description | |
2824 | "This package contains procedures for depth-based supervised learning, | |
2825 | which are entirely non-parametric, in particular the DDalpha-procedure (Lange, | |
2826 | Mosler and Mozharovskyi, 2014). The training data sample is transformed by a | |
2827 | statistical depth function to a compact low-dimensional space, where the final | |
2828 | classification is done. It also offers an extension to functional data and | |
2829 | routines for calculating certain notions of statistical depth functions. 50 | |
2830 | multivariate and 5 functional classification problems are included.") | |
2831 | (license license:gpl2))) | |
5a87093f RW |
2832 | |
2833 | (define-public r-gower | |
2834 | (package | |
2835 | (name "r-gower") | |
1541f0a0 | 2836 | (version "0.2.1") |
5a87093f RW |
2837 | (source |
2838 | (origin | |
2839 | (method url-fetch) | |
2840 | (uri (cran-uri "gower" version)) | |
2841 | (sha256 | |
2842 | (base32 | |
1541f0a0 | 2843 | "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg")))) |
5a87093f | 2844 | (build-system r-build-system) |
5a87093f RW |
2845 | (home-page "https://github.com/markvanderloo/gower") |
2846 | (synopsis "Gower's distance") | |
2847 | (description | |
2848 | "This package provides tools to compute Gower's distance (or similarity) | |
2849 | coefficient between records, and to compute the top-n matches between records. | |
2850 | Core algorithms are executed in parallel on systems supporting OpenMP.") | |
2851 | (license license:gpl3))) | |
649cf27c RW |
2852 | |
2853 | (define-public r-rcpproll | |
2854 | (package | |
2855 | (name "r-rcpproll") | |
d0396c8e | 2856 | (version "0.3.0") |
649cf27c RW |
2857 | (source |
2858 | (origin | |
2859 | (method url-fetch) | |
2860 | (uri (cran-uri "RcppRoll" version)) | |
2861 | (sha256 | |
2862 | (base32 | |
d0396c8e | 2863 | "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) |
649cf27c RW |
2864 | (properties `((upstream-name . "RcppRoll"))) |
2865 | (build-system r-build-system) | |
2866 | (propagated-inputs | |
2867 | `(("r-rcpp" ,r-rcpp))) | |
e9960d8c | 2868 | (home-page "https://cran.r-project.org/web/packages/RcppRoll") |
649cf27c RW |
2869 | (synopsis "Efficient rolling and windowed operations") |
2870 | (description | |
2871 | "This package provides fast and efficient routines for common rolling / | |
2872 | windowed operations. Routines for the efficient computation of windowed mean, | |
2873 | median, sum, product, minimum, maximum, standard deviation and variance are | |
2874 | provided.") | |
2875 | (license license:gpl2+))) | |
6c3d42d6 RW |
2876 | |
2877 | (define-public r-ipred | |
2878 | (package | |
2879 | (name "r-ipred") | |
5fce9013 | 2880 | (version "0.9-9") |
6c3d42d6 RW |
2881 | (source |
2882 | (origin | |
2883 | (method url-fetch) | |
2884 | (uri (cran-uri "ipred" version)) | |
2885 | (sha256 | |
2886 | (base32 | |
5fce9013 | 2887 | "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d")))) |
6c3d42d6 RW |
2888 | (build-system r-build-system) |
2889 | (propagated-inputs | |
2890 | `(("r-class" ,r-class) | |
2891 | ("r-mass" ,r-mass) | |
2892 | ("r-nnet" ,r-nnet) | |
2893 | ("r-prodlim" ,r-prodlim) | |
2894 | ("r-rpart" ,r-rpart) | |
2895 | ("r-survival" ,r-survival))) | |
e9960d8c | 2896 | (home-page "https://cran.r-project.org/web/packages/ipred") |
6c3d42d6 RW |
2897 | (synopsis "Improved predictors") |
2898 | (description | |
2899 | "This package provides improved predictive models by indirect | |
2900 | classification and bagging for classification, regression and survival | |
2901 | problems as well as resampling based estimators of prediction error.") | |
2902 | (license license:gpl2+))) | |
ba4527ab | 2903 | |
cdc129dc RW |
2904 | (define-public r-psych |
2905 | (package | |
2906 | (name "r-psych") | |
523762e3 | 2907 | (version "1.8.12") |
cdc129dc RW |
2908 | (source |
2909 | (origin | |
2910 | (method url-fetch) | |
2911 | (uri (cran-uri "psych" version)) | |
2912 | (sha256 | |
2913 | (base32 | |
523762e3 | 2914 | "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf")))) |
cdc129dc RW |
2915 | (build-system r-build-system) |
2916 | (propagated-inputs | |
2917 | `(("r-foreign" ,r-foreign) | |
2918 | ("r-lattice" ,r-lattice) | |
2919 | ("r-mnormt" ,r-mnormt) | |
2920 | ("r-nlme" ,r-nlme))) | |
e9960d8c | 2921 | (home-page "https://cran.r-project.org/web/packages/psych/") |
cdc129dc RW |
2922 | (synopsis "Procedures for psychological, psychometric, and personality research") |
2923 | (description | |
2924 | "This package provides a general purpose toolbox for personality, | |
2925 | psychometric theory and experimental psychology. Functions are primarily for | |
2926 | multivariate analysis and scale construction using factor analysis, principal | |
2927 | component analysis, cluster analysis and reliability analysis, although others | |
2928 | provide basic descriptive statistics. Item Response Theory is done using | |
2929 | factor analysis of tetrachoric and polychoric correlations. Functions for | |
2930 | analyzing data at multiple levels include within and between group statistics, | |
2931 | including correlations and factor analysis. Functions for simulating and | |
2932 | testing particular item and test structures are included. Several functions | |
2933 | serve as a useful front end for structural equation modeling. Graphical | |
2934 | displays of path diagrams, factor analysis and structural equation models are | |
2935 | created using basic graphics.") | |
2936 | (license license:gpl2+))) | |
2937 | ||
25c67ecf RW |
2938 | (define-public r-generics |
2939 | (package | |
2940 | (name "r-generics") | |
2941 | (version "0.0.2") | |
2942 | (source | |
2943 | (origin | |
2944 | (method url-fetch) | |
2945 | (uri (cran-uri "generics" version)) | |
2946 | (sha256 | |
2947 | (base32 | |
2948 | "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) | |
2949 | (build-system r-build-system) | |
2950 | (home-page "https://github.com/r-lib/generics") | |
2951 | (synopsis "Common S3 generics not provided by base R methods") | |
2952 | (description | |
2953 | "In order to reduce potential package dependencies and conflicts, | |
2954 | generics provides a number of commonly used S3 generics that are not provided | |
2955 | by base R methods related to model fitting.") | |
2956 | (license license:gpl2))) | |
2957 | ||
6c8c8c6b RW |
2958 | (define-public r-broom |
2959 | (package | |
2960 | (name "r-broom") | |
1235f0d3 | 2961 | (version "0.5.2") |
6c8c8c6b RW |
2962 | (source |
2963 | (origin | |
2964 | (method url-fetch) | |
2965 | (uri (cran-uri "broom" version)) | |
2966 | (sha256 | |
2967 | (base32 | |
1235f0d3 | 2968 | "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn")))) |
6c8c8c6b RW |
2969 | (build-system r-build-system) |
2970 | (propagated-inputs | |
45c156bf RW |
2971 | `(("r-backports" ,r-backports) |
2972 | ("r-dplyr" ,r-dplyr) | |
813d9c51 | 2973 | ("r-generics" ,r-generics) |
6c8c8c6b | 2974 | ("r-nlme" ,r-nlme) |
45c156bf | 2975 | ("r-purrr" ,r-purrr) |
6c8c8c6b RW |
2976 | ("r-reshape2" ,r-reshape2) |
2977 | ("r-stringr" ,r-stringr) | |
45c156bf | 2978 | ("r-tibble" ,r-tibble) |
6c8c8c6b | 2979 | ("r-tidyr" ,r-tidyr))) |
6e19d50e | 2980 | (home-page "https://github.com/tidyverse/broom") |
6c8c8c6b RW |
2981 | (synopsis "Convert statistical analysis objects into tidy data frames") |
2982 | (description | |
2983 | "This package provides tools to convert statistical analysis objects from | |
2984 | R into tidy data frames, so that they can more easily be combined, reshaped | |
2985 | and otherwise processed with tools like @code{dplyr}, @code{tidyr} and | |
2986 | @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which | |
2987 | summarizes a model's statistical findings such as coefficients of a | |
2988 | regression; @code{augment}, which adds columns to the original data such as | |
2989 | predictions, residuals and cluster assignments; and @code{glance}, which | |
2990 | provides a one-row summary of model-level statistics.") | |
2991 | (license license:expat))) | |
2992 | ||
ba4527ab RW |
2993 | (define-public r-recipes |
2994 | (package | |
2995 | (name "r-recipes") | |
e85f0503 | 2996 | (version "0.1.7") |
ba4527ab RW |
2997 | (source |
2998 | (origin | |
2999 | (method url-fetch) | |
3000 | (uri (cran-uri "recipes" version)) | |
3001 | (sha256 | |
3002 | (base32 | |
e85f0503 | 3003 | "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98")))) |
ba4527ab RW |
3004 | (build-system r-build-system) |
3005 | (propagated-inputs | |
decea6ee RW |
3006 | `(("r-dplyr" ,r-dplyr) |
3007 | ("r-generics" ,r-generics) | |
3008 | ("r-glue" ,r-glue) | |
ba4527ab RW |
3009 | ("r-gower" ,r-gower) |
3010 | ("r-ipred" ,r-ipred) | |
3011 | ("r-lubridate" ,r-lubridate) | |
3012 | ("r-magrittr" ,r-magrittr) | |
18a11c6d | 3013 | ("r-matrix" ,r-matrix) |
ba4527ab | 3014 | ("r-purrr" ,r-purrr) |
ba4527ab RW |
3015 | ("r-rlang" ,r-rlang) |
3016 | ("r-tibble" ,r-tibble) | |
decea6ee | 3017 | ("r-tidyr" ,r-tidyr) |
ba4527ab | 3018 | ("r-tidyselect" ,r-tidyselect) |
57039918 RW |
3019 | ("r-timedate" ,r-timedate) |
3020 | ("r-withr" ,r-withr))) | |
ba4527ab RW |
3021 | (home-page "https://github.com/topepo/recipes") |
3022 | (synopsis "Preprocessing tools to create design matrices") | |
3023 | (description | |
3024 | "Recipes is an extensible framework to create and preprocess design | |
3025 | matrices. Recipes consist of one or more data manipulation and analysis | |
3026 | \"steps\". Statistical parameters for the steps can be estimated from an | |
3027 | initial data set and then applied to other data sets. The resulting design | |
3028 | matrices can then be used as inputs into statistical or machine learning | |
3029 | models.") | |
3030 | (license license:gpl2))) | |
1ab867be RW |
3031 | |
3032 | (define-public r-pdist | |
3033 | (package | |
3034 | (name "r-pdist") | |
3035 | (version "1.2") | |
3036 | (source | |
3037 | (origin | |
3038 | (method url-fetch) | |
3039 | (uri (cran-uri "pdist" version)) | |
3040 | (sha256 | |
3041 | (base32 | |
3042 | "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd")))) | |
3043 | (build-system r-build-system) | |
3044 | (home-page "https://github.com/jeffwong/pdist") | |
3045 | (synopsis "Partitioned distance function") | |
3046 | (description | |
3047 | "Pdist computes the euclidean distance between rows of a matrix X and | |
3048 | rows of another matrix Y. Previously, this could be done by binding the two | |
3049 | matrices together and calling @code{dist}, but this creates unnecessary | |
3050 | computation by computing the distances between a row of X and another row of | |
3051 | X, and likewise for Y. Pdist strictly computes distances across the two | |
3052 | matrices, not within the same matrix, making computations significantly faster | |
3053 | for certain use cases.") | |
3054 | (license license:gpl3+))) | |
81e0b625 RW |
3055 | |
3056 | (define-public r-ggrepel | |
3057 | (package | |
3058 | (name "r-ggrepel") | |
00399a78 | 3059 | (version "0.8.1") |
81e0b625 RW |
3060 | (source |
3061 | (origin | |
3062 | (method url-fetch) | |
3063 | (uri (cran-uri "ggrepel" version)) | |
3064 | (sha256 | |
3065 | (base32 | |
00399a78 | 3066 | "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m")))) |
81e0b625 RW |
3067 | (build-system r-build-system) |
3068 | (propagated-inputs | |
3069 | `(("r-ggplot2" ,r-ggplot2) | |
3070 | ("r-rcpp" ,r-rcpp) | |
3071 | ("r-scales" ,r-scales))) | |
3072 | (home-page "http://github.com/slowkow/ggrepel") | |
3073 | (synopsis "Repulsive text and label geometries for ggplot2") | |
3074 | (description | |
3075 | "This package provides text and label geometries for ggplot2 that help to | |
3076 | avoid overlapping text labels. Labels repel away from each other and away | |
3077 | from the data points.") | |
3078 | (license license:gpl3))) | |
6b968c4c RW |
3079 | |
3080 | (define-public r-corrplot | |
3081 | (package | |
3082 | (name "r-corrplot") | |
3083 | (version "0.84") | |
3084 | (source | |
3085 | (origin | |
3086 | (method url-fetch) | |
3087 | (uri (cran-uri "corrplot" version)) | |
3088 | (sha256 | |
3089 | (base32 | |
3090 | "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd")))) | |
3091 | (build-system r-build-system) | |
3092 | (home-page "https://github.com/taiyun/corrplot") | |
3093 | (synopsis "Visualization of a correlation matrix") | |
3094 | (description | |
3095 | "This package provides a graphical display of a correlation matrix or | |
3096 | general matrix. It also contains some algorithms to do matrix reordering. In | |
3097 | addition, corrplot is good at details, including choosing color, text labels, | |
3098 | color labels, layout, etc.") | |
3099 | ;; Any version of the GPL | |
3100 | (license license:gpl2+))) | |
a40a04fd RW |
3101 | |
3102 | (define-public r-stringdist | |
3103 | (package | |
3104 | (name "r-stringdist") | |
8e0267f6 | 3105 | (version "0.9.5.2") |
a40a04fd RW |
3106 | (source |
3107 | (origin | |
3108 | (method url-fetch) | |
3109 | (uri (cran-uri "stringdist" version)) | |
3110 | (sha256 | |
3111 | (base32 | |
8e0267f6 | 3112 | "0nw8c317qkfq63pr0prl0hx522ddfq4cbgixb5r4pq3fxk9z303l")))) |
a40a04fd RW |
3113 | (build-system r-build-system) |
3114 | (home-page "https://github.com/markvanderloo/stringdist") | |
3115 | (synopsis "Approximate string matching and string distance functions") | |
3116 | (description | |
3117 | "This package implements an approximate string matching version of R's | |
3118 | native @code{match} function. It can calculate various string distances based | |
3119 | on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), | |
3120 | qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, | |
3121 | Jaro-Winkler). An implementation of soundex is provided as well. Distances | |
3122 | can be computed between character vectors while taking proper care of encoding | |
3123 | or between integer vectors representing generic sequences.") | |
3124 | (license license:gpl3+))) | |
10e16fa9 | 3125 | |
dc668352 RW |
3126 | (define-public r-ucminf |
3127 | (package | |
3128 | (name "r-ucminf") | |
3129 | (version "1.1-4") | |
3130 | (source | |
3131 | (origin | |
3132 | (method url-fetch) | |
3133 | (uri (cran-uri "ucminf" version)) | |
3134 | (sha256 | |
3135 | (base32 | |
3136 | "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) | |
3137 | (build-system r-build-system) | |
3138 | (native-inputs `(("gfortran" ,gfortran))) | |
3139 | (home-page "https://cran.r-project.org/web/packages/ucminf/") | |
3140 | (synopsis "General-purpose unconstrained non-linear optimization") | |
3141 | (description | |
3142 | "This package provides an implementation of an algorithm for | |
3143 | general-purpose unconstrained non-linear optimization. The algorithm is of | |
3144 | quasi-Newton type with BFGS updating of the inverse Hessian and soft line | |
3145 | search with a trust region type monitoring of the input to the line search | |
3146 | algorithm. The interface of @code{ucminf} is designed for easy interchange | |
3147 | with the package @code{optim}.") | |
3148 | (license license:gpl2+))) | |
3149 | ||
b8f6e2f8 RW |
3150 | (define-public r-ordinal |
3151 | (package | |
3152 | (name "r-ordinal") | |
779174e4 | 3153 | (version "2019.4-25") |
b8f6e2f8 RW |
3154 | (source |
3155 | (origin | |
3156 | (method url-fetch) | |
3157 | (uri (cran-uri "ordinal" version)) | |
3158 | (sha256 | |
3159 | (base32 | |
779174e4 | 3160 | "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8")))) |
b8f6e2f8 RW |
3161 | (build-system r-build-system) |
3162 | (propagated-inputs | |
3163 | `(("r-mass" ,r-mass) | |
3164 | ("r-matrix" ,r-matrix) | |
3165 | ("r-numderiv" ,r-numderiv) | |
3166 | ("r-ucminf" ,r-ucminf))) | |
3167 | (home-page "https://github.com/runehaubo/ordinal") | |
3168 | (synopsis "Regression models for ordinal data") | |
3169 | (description | |
3170 | "This package provides an implementation of cumulative link (mixed) | |
3171 | models also known as ordered regression models, proportional odds models, | |
3172 | proportional hazards models for grouped survival times and ordered models. | |
3173 | Estimation is via maximum likelihood and mixed models are fitted with the | |
3174 | Laplace approximation and adaptive Gauss-Hermite quadrature.") | |
3175 | (license license:gpl2+))) | |
3176 | ||
fe1495e3 RW |
3177 | (define-public r-jomo |
3178 | (package | |
3179 | (name "r-jomo") | |
bed34246 | 3180 | (version "2.6-9") |
fe1495e3 RW |
3181 | (source |
3182 | (origin | |
3183 | (method url-fetch) | |
3184 | (uri (cran-uri "jomo" version)) | |
3185 | (sha256 | |
3186 | (base32 | |
bed34246 | 3187 | "16ychdhhv8cii8zrdfdf5gzgnvmfaq573bmi00xqdf323q3lf3xr")))) |
fe1495e3 RW |
3188 | (build-system r-build-system) |
3189 | (propagated-inputs | |
3190 | `(("r-lme4" ,r-lme4) | |
fccb2450 | 3191 | ("r-mass" ,r-mass) |
e7630cc9 | 3192 | ("r-ordinal" ,r-ordinal) |
fe1495e3 RW |
3193 | ("r-survival" ,r-survival))) |
3194 | (home-page "https://cran.r-project.org/web/packages/jomo/") | |
3195 | (synopsis "Multilevel Joint Modelling Multiple Imputation") | |
3196 | (description | |
3197 | "Similarly to Schafer's package pan, jomo is a package for multilevel | |
3198 | joint modelling multiple imputation @url{Carpenter and Kenward (2013), | |
3199 | http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the | |
3200 | possibility of handling binary and categorical data through latent normal | |
3201 | variables, the option to use cluster-specific covariance matrices and to | |
3202 | impute compatibly with the substantive model.") | |
3203 | (license license:gpl2))) | |
3204 | ||
03e718fb RW |
3205 | (define-public r-pan |
3206 | (package | |
3207 | (name "r-pan") | |
a7265593 | 3208 | (version "1.6") |
03e718fb RW |
3209 | (source |
3210 | (origin | |
3211 | (method url-fetch) | |
3212 | (uri (cran-uri "pan" version)) | |
3213 | (sha256 | |
3214 | (base32 | |
a7265593 | 3215 | "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) |
03e718fb RW |
3216 | (build-system r-build-system) |
3217 | (native-inputs `(("gfortran" ,gfortran))) | |
3218 | (home-page "https://cran.r-project.org/web/packages/pan/") | |
3219 | (synopsis "Multiple imputation for multivariate panel or clustered data") | |
3220 | (description | |
3221 | "This package implements multiple imputation for multivariate panel or | |
3222 | clustered data.") | |
3223 | (license license:gpl3))) | |
3224 | ||
84e7147a RW |
3225 | (define-public r-mitml |
3226 | (package | |
3227 | (name "r-mitml") | |
1c6d199e | 3228 | (version "0.3-7") |
84e7147a RW |
3229 | (source |
3230 | (origin | |
3231 | (method url-fetch) | |
3232 | (uri (cran-uri "mitml" version)) | |
3233 | (sha256 | |
3234 | (base32 | |
1c6d199e | 3235 | "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) |
84e7147a RW |
3236 | (build-system r-build-system) |
3237 | (propagated-inputs | |
3238 | `(("r-haven" ,r-haven) | |
3239 | ("r-jomo" ,r-jomo) | |
3240 | ("r-pan" ,r-pan))) | |
3241 | (home-page "https://cran.r-project.org/web/packages/mitml/") | |
3242 | (synopsis "Tools for multiple imputation in multilevel modeling") | |
3243 | (description | |
3244 | "This package provides tools for multiple imputation of missing data in | |
3245 | multilevel modeling. It includes a user-friendly interface to the packages | |
3246 | pan and jomo, and several functions for visualization, data management and the | |
3247 | analysis of multiply imputed data sets.") | |
3248 | (license license:gpl2+))) | |
3249 | ||
10e16fa9 RW |
3250 | (define-public r-mice |
3251 | (package | |
3252 | (name "r-mice") | |
04d42a9d | 3253 | (version "3.6.0") |
10e16fa9 RW |
3254 | (source |
3255 | (origin | |
3256 | (method url-fetch) | |
3257 | (uri (cran-uri "mice" version)) | |
3258 | (sha256 | |
3259 | (base32 | |
04d42a9d | 3260 | "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv")))) |
10e16fa9 RW |
3261 | (build-system r-build-system) |
3262 | (propagated-inputs | |
aea3be25 RW |
3263 | `(("r-broom" ,r-broom) |
3264 | ("r-dplyr" ,r-dplyr) | |
3265 | ("r-lattice" ,r-lattice) | |
10e16fa9 | 3266 | ("r-mass" ,r-mass) |
aea3be25 | 3267 | ("r-mitml" ,r-mitml) |
10e16fa9 RW |
3268 | ("r-nnet" ,r-nnet) |
3269 | ("r-rcpp" ,r-rcpp) | |
aea3be25 | 3270 | ("r-rlang" ,r-rlang) |
10e16fa9 RW |
3271 | ("r-rpart" ,r-rpart) |
3272 | ("r-survival" ,r-survival))) | |
3273 | (home-page "https://cran.r-project.org/web/packages/mice/") | |
3274 | (synopsis "Multivariate imputation by chained equations") | |
3275 | (description | |
3276 | "Multiple imputation using @dfn{Fully Conditional Specification} (FCS) | |
3277 | implemented by the MICE algorithm as described in @url{Van Buuren and | |
3278 | Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each | |
3279 | variable has its own imputation model. Built-in imputation models are | |
3280 | provided for continuous data (predictive mean matching, normal), binary | |
3281 | data (logistic regression), unordered categorical data (polytomous logistic | |
3282 | regression) and ordered categorical data (proportional odds). MICE can also | |
3283 | impute continuous two-level data (normal model, pan, second-level variables). | |
3284 | Passive imputation can be used to maintain consistency between variables. | |
3285 | Various diagnostic plots are available to inspect the quality of the | |
3286 | imputations.") | |
3287 | ;; Any of these two versions. | |
3288 | (license (list license:gpl2 license:gpl3)))) | |
7fd5f60b | 3289 | |
02cdb45f RW |
3290 | (define-public r-truncnorm |
3291 | (package | |
3292 | (name "r-truncnorm") | |
9d6f3925 | 3293 | (version "1.0-8") |
02cdb45f RW |
3294 | (source |
3295 | (origin | |
3296 | (method url-fetch) | |
3297 | (uri (cran-uri "truncnorm" version)) | |
3298 | (sha256 | |
3299 | (base32 | |
9d6f3925 | 3300 | "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9")))) |
02cdb45f | 3301 | (build-system r-build-system) |
e9960d8c | 3302 | (home-page "https://cran.r-project.org/web/packages/truncnorm/") |
02cdb45f RW |
3303 | (synopsis "Truncated normal distribution") |
3304 | (description "This package provides functions for the truncated normal | |
3305 | distribution with mean equal to @code{mean} and standard deviation equal to | |
3306 | @code{sd}. It includes density, distribution, quantile, and expected value | |
3307 | functions, as well as a random generation function.") | |
3308 | (license license:gpl2))) | |
3309 | ||
cb8b4c11 RW |
3310 | (define-public r-rsolnp |
3311 | (package | |
3312 | (name "r-rsolnp") | |
3313 | (version "1.16") | |
3314 | (source | |
3315 | (origin | |
3316 | (method url-fetch) | |
3317 | (uri (cran-uri "Rsolnp" version)) | |
3318 | (sha256 | |
3319 | (base32 | |
3320 | "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii")))) | |
3321 | (properties `((upstream-name . "Rsolnp"))) | |
3322 | (build-system r-build-system) | |
3323 | (propagated-inputs | |
3324 | `(("r-truncnorm" ,r-truncnorm))) | |
e9960d8c | 3325 | (home-page "https://cran.r-project.org/web/packages/Rsolnp/") |
cb8b4c11 RW |
3326 | (synopsis "General non-linear optimization") |
3327 | (description "The Rsolnp package implements a general non-linear augmented | |
3328 | Lagrange multiplier method solver, a @dfn{sequential quadratic | |
3329 | programming} (SQP) based solver).") | |
3330 | ;; Any version of the GPL. | |
3331 | (license license:gpl2+))) | |
3332 | ||
7fd5f60b RW |
3333 | (define-public r-hardyweinberg |
3334 | (package | |
3335 | (name "r-hardyweinberg") | |
83e3e72a | 3336 | (version "1.6.3") |
7fd5f60b RW |
3337 | (source |
3338 | (origin | |
3339 | (method url-fetch) | |
3340 | (uri (cran-uri "HardyWeinberg" version)) | |
3341 | (sha256 | |
3342 | (base32 | |
83e3e72a | 3343 | "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f")))) |
7fd5f60b RW |
3344 | (properties `((upstream-name . "HardyWeinberg"))) |
3345 | (build-system r-build-system) | |
3346 | (propagated-inputs | |
3347 | `(("r-mice" ,r-mice) | |
d0394944 RW |
3348 | ("r-rcpp" ,r-rcpp) |
3349 | ("r-rsolnp" ,r-rsolnp))) | |
7fd5f60b RW |
3350 | (home-page "https://cran.r-project.org/package=HardyWeinberg") |
3351 | (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") | |
3352 | (description | |
3353 | "This package contains tools for exploring Hardy-Weinberg equilibrium for | |
3354 | diallelic genetic marker data. All classical tests (chi-square, exact, | |
3355 | likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are | |
3356 | included in the package, as well as functions for power computation and for | |
3357 | the simulation of marker data under equilibrium and disequilibrium. Routines | |
3358 | for dealing with markers on the X-chromosome are included. Functions for | |
3359 | testing equilibrium in the presence of missing data by using multiple | |
3360 | imputation are also provided. Implements several graphics for exploring the | |
3361 | equilibrium status of a large set of diallelic markers: ternary plots with | |
3362 | acceptance regions, log-ratio plots and Q-Q plots.") | |
3363 | (license license:gpl2+))) | |
3a22732c RW |
3364 | |
3365 | (define-public r-sm | |
3366 | (package | |
3367 | (name "r-sm") | |
5621b840 | 3368 | (version "2.2-5.6") |
3a22732c RW |
3369 | (source |
3370 | (origin | |
3371 | (method url-fetch) | |
3372 | (uri (cran-uri "sm" version)) | |
3373 | (sha256 | |
3374 | (base32 | |
5621b840 | 3375 | "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q")))) |
3a22732c RW |
3376 | (build-system r-build-system) |
3377 | (native-inputs `(("gfortran" ,gfortran))) | |
3378 | (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") | |
3379 | (synopsis "Smoothing methods for nonparametric regression and density estimation") | |
3380 | (description | |
3381 | "This is software accompanying the book 'Applied Smoothing Techniques for | |
3382 | Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford | |
3383 | University Press. It provides smoothing methods for nonparametric regression | |
3384 | and density estimation") | |
3385 | (license license:gpl2+))) | |
9232cac4 | 3386 | |
6174db2b RJ |
3387 | (define-public r-venndiagram |
3388 | (package | |
3389 | (name "r-venndiagram") | |
3390 | (version "1.6.20") | |
3391 | (source (origin | |
3392 | (method url-fetch) | |
3393 | (uri (cran-uri "VennDiagram" version)) | |
3394 | (sha256 | |
3395 | (base32 | |
3396 | "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775")))) | |
3397 | (properties `((upstream-name . "VennDiagram"))) | |
3398 | (build-system r-build-system) | |
3399 | (propagated-inputs | |
3400 | `(("r-futile-logger" ,r-futile-logger))) | |
3401 | (home-page "https://cran.r-project.org/web/packages/VennDiagram/") | |
3402 | (synopsis "Generate High-Resolution Venn and Euler Plots") | |
3403 | (description | |
3404 | "This package provides a set of functions to generate high-resolution | |
3405 | Venn and Euler plots. It includes handling for several special cases, | |
3406 | including two-case scaling, and extensive customization of plot shape and | |
3407 | structure.") | |
3408 | (license license:gpl2+))) | |
3409 | ||
9232cac4 RW |
3410 | (define-public r-vioplot |
3411 | (package | |
3412 | (name "r-vioplot") | |
70980197 | 3413 | (version "0.3.2") |
9232cac4 RW |
3414 | (source |
3415 | (origin | |
3416 | (method url-fetch) | |
3417 | (uri (cran-uri "vioplot" version)) | |
3418 | (sha256 | |
3419 | (base32 | |
70980197 | 3420 | "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv")))) |
9232cac4 | 3421 | (build-system r-build-system) |
7d4b9818 RW |
3422 | (propagated-inputs |
3423 | `(("r-sm" ,r-sm) | |
3424 | ("r-zoo" ,r-zoo))) | |
9232cac4 RW |
3425 | (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") |
3426 | (synopsis "Violin plot") | |
3427 | (description | |
3428 | "This package provides a violin plot, which is a combination of a box | |
3429 | plot and a kernel density plot.") | |
3430 | (license license:bsd-3))) | |
7b0569c0 RW |
3431 | |
3432 | (define-public r-rsofia | |
3433 | (package | |
3434 | (name "r-rsofia") | |
3435 | (version "1.1") | |
3436 | (source (origin | |
3437 | (method url-fetch) | |
3438 | ;; This package has been removed from CRAN, so we can | |
3439 | ;; only fetch it from the archives. | |
3440 | (uri (string-append "https://cran.r-project.org/src/" | |
3441 | "contrib/Archive/RSofia/RSofia_" | |
3442 | version ".tar.gz")) | |
3443 | (sha256 | |
3444 | (base32 | |
3445 | "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn")))) | |
3446 | (properties `((upstream-name . "RSofia"))) | |
3447 | (build-system r-build-system) | |
3448 | (propagated-inputs | |
3449 | `(("r-rcpp" ,r-rcpp))) | |
3450 | (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") | |
3451 | (synopsis "Port of sofia-ml to R") | |
3452 | (description "This package is a port of sofia-ml to R. Sofia-ml is a | |
3453 | suite of fast incremental algorithms for machine learning that can be used for | |
3454 | training models for classification or ranking.") | |
3455 | (license license:asl2.0))) | |
738dda83 | 3456 | |
3699383e RW |
3457 | (define-public r-xts |
3458 | (package | |
3459 | (name "r-xts") | |
cea8a607 | 3460 | (version "0.11-2") |
3699383e RW |
3461 | (source |
3462 | (origin | |
3463 | (method url-fetch) | |
3464 | (uri (cran-uri "xts" version)) | |
3465 | (sha256 | |
3466 | (base32 | |
cea8a607 | 3467 | "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj")))) |
3699383e RW |
3468 | (build-system r-build-system) |
3469 | (propagated-inputs `(("r-zoo" ,r-zoo))) | |
3699383e RW |
3470 | (home-page "https://github.com/joshuaulrich/xts") |
3471 | (synopsis "Extensible time series") | |
3472 | (description | |
3473 | "This package provides for uniform handling of R's different time-based | |
3474 | data classes by extending @code{zoo}, maximizing native format information | |
3475 | preservation and allowing for user-level customization and extension, while | |
3476 | simplifying cross-class interoperability.") | |
3477 | (license license:gpl2+))) | |
b72b42cf RW |
3478 | |
3479 | (define-public r-performanceanalytics | |
3480 | (package | |
3481 | (name "r-performanceanalytics") | |
1f7e8d49 | 3482 | (version "1.5.3") |
b72b42cf RW |
3483 | (source |
3484 | (origin | |
3485 | (method url-fetch) | |
3486 | (uri (cran-uri "PerformanceAnalytics" version)) | |
3487 | (sha256 | |
3488 | (base32 | |
1f7e8d49 | 3489 | "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd")))) |
b72b42cf RW |
3490 | (properties |
3491 | `((upstream-name . "PerformanceAnalytics"))) | |
3492 | (build-system r-build-system) | |
3493 | (propagated-inputs | |
081d143d RW |
3494 | `(("r-quadprog" ,r-quadprog) |
3495 | ("r-xts" ,r-xts) | |
b72b42cf | 3496 | ("r-zoo" ,r-zoo))) |
d062957a | 3497 | (home-page "https://r-forge.r-project.org/projects/returnanalytics/") |
b72b42cf RW |
3498 | (synopsis "Econometric tools for performance and risk analysis") |
3499 | (description "This is a collection of econometric functions for | |
3500 | performance and risk analysis. This package aims to aid practitioners and | |
3501 | researchers in utilizing the latest research in analysis of non-normal return | |
3502 | streams. In general, it is most tested on return (rather than price) data on | |
3503 | a regular scale, but most functions will work with irregular return data as | |
3504 | well, and increasing numbers of functions will work with P&L or price data | |
3505 | where possible.") | |
3506 | ;; Either version may be picked. | |
3507 | (license (list license:gpl2 license:gpl3)))) | |
018cf270 RW |
3508 | |
3509 | (define-public r-laeken | |
3510 | (package | |
3511 | (name "r-laeken") | |
ed46a05c | 3512 | (version "0.5.0") |
018cf270 RW |
3513 | (source |
3514 | (origin | |
3515 | (method url-fetch) | |
3516 | (uri (cran-uri "laeken" version)) | |
3517 | (sha256 | |
3518 | (base32 | |
ed46a05c | 3519 | "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa")))) |
018cf270 RW |
3520 | (build-system r-build-system) |
3521 | (propagated-inputs | |
3522 | `(("r-boot" ,r-boot) | |
3523 | ("r-mass" ,r-mass))) | |
e9960d8c | 3524 | (home-page "https://cran.r-project.org/web/packages/laeken/") |
018cf270 RW |
3525 | (synopsis "Estimation of indicators on social exclusion and poverty") |
3526 | (description "This package provides tools for the estimation of indicators | |
3527 | on social exclusion and poverty, as well as an implementation of Pareto tail | |
3528 | modeling for empirical income distributions.") | |
3529 | (license license:gpl2+))) | |
e5c17b8d RW |
3530 | |
3531 | (define-public r-vcd | |
3532 | (package | |
3533 | (name "r-vcd") | |
2960f965 | 3534 | (version "1.4-4") |
e5c17b8d RW |
3535 | (source |
3536 | (origin | |
3537 | (method url-fetch) | |
3538 | (uri (cran-uri "vcd" version)) | |
3539 | (sha256 | |
3540 | (base32 | |
2960f965 | 3541 | "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5")))) |
e5c17b8d RW |
3542 | (build-system r-build-system) |
3543 | (propagated-inputs | |
3544 | `(("r-colorspace" ,r-colorspace) | |
3545 | ("r-lmtest" ,r-lmtest) | |
3546 | ("r-mass" ,r-mass))) | |
e9960d8c | 3547 | (home-page "https://cran.r-project.org/web/packages/vcd/") |
e5c17b8d RW |
3548 | (synopsis "Visualizing categorical data") |
3549 | (description "This package provides visualization techniques, data sets, | |
3550 | summary and inference procedures aimed particularly at categorical data. | |
3551 | Special emphasis is given to highly extensible grid graphics. The package was | |
3552 | originally inspired by the book \"Visualizing Categorical Data\" by Michael | |
3553 | Friendly and is now the main support package for a new book, \"Discrete Data | |
3554 | Analysis with R\" by Michael Friendly and David Meyer (2015).") | |
3555 | (license license:gpl2))) | |
ae164260 RW |
3556 | |
3557 | (define-public r-ica | |
3558 | (package | |
3559 | (name "r-ica") | |
fabf0993 | 3560 | (version "1.0-2") |
ae164260 RW |
3561 | (source |
3562 | (origin | |
3563 | (method url-fetch) | |
3564 | (uri (cran-uri "ica" version)) | |
3565 | (sha256 | |
3566 | (base32 | |
fabf0993 | 3567 | "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7")))) |
ae164260 | 3568 | (build-system r-build-system) |
e9960d8c | 3569 | (home-page "https://cran.r-project.org/web/packages/ica/") |
ae164260 RW |
3570 | (synopsis "Independent component analysis") |
3571 | (description "This package provides tools for @dfn{Independent Component | |
3572 | Analysis} (ICA) using various algorithms: FastICA, | |
3573 | Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization | |
3574 | of Eigenmatrices} (JADE).") | |
3575 | (license license:gpl2+))) | |
bf025ff6 RW |
3576 | |
3577 | (define-public r-dtw | |
3578 | (package | |
3579 | (name "r-dtw") | |
fa859675 | 3580 | (version "1.21-3") |
bf025ff6 RW |
3581 | (source |
3582 | (origin | |
3583 | (method url-fetch) | |
3584 | (uri (cran-uri "dtw" version)) | |
3585 | (sha256 | |
3586 | (base32 | |
fa859675 | 3587 | "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s")))) |
bf025ff6 RW |
3588 | (build-system r-build-system) |
3589 | (propagated-inputs `(("r-proxy" ,r-proxy))) | |
3590 | (home-page "http://dtw.r-forge.r-project.org/") | |
3591 | (synopsis "Dynamic Time Warping Algorithms") | |
3592 | (description "This package provides a comprehensive implementation of | |
3593 | @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the | |
3594 | optimal (least cumulative distance) alignment between points of two time | |
3595 | series. Common DTW variants covered include local (slope) and global (window) | |
3596 | constraints, subsequence matches, arbitrary distance definitions, | |
3597 | normalizations, minimum variance matching, and so on.") | |
3598 | (license license:gpl2+))) | |
15ef07f0 RW |
3599 | |
3600 | (define-public r-sdmtools | |
3601 | (package | |
3602 | (name "r-sdmtools") | |
5ac82ee3 | 3603 | (version "1.1-221.1") |
15ef07f0 RW |
3604 | (source |
3605 | (origin | |
3606 | (method url-fetch) | |
3607 | (uri (cran-uri "SDMTools" version)) | |
3608 | (sha256 | |
3609 | (base32 | |
5ac82ee3 | 3610 | "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q")))) |
15ef07f0 RW |
3611 | (properties `((upstream-name . "SDMTools"))) |
3612 | (build-system r-build-system) | |
3613 | (propagated-inputs `(("r-r-utils" ,r-r-utils))) | |
3614 | (home-page "http://www.rforge.net/SDMTools/") | |
3615 | (synopsis "Species distribution modelling tools") | |
9c98e0e7 | 3616 | (description "This package provides a set of tools for post processing |
15ef07f0 RW |
3617 | the outcomes of species distribution modeling exercises. It includes novel |
3618 | methods for comparing models and tracking changes in distributions through | |
3619 | time. It further includes methods for visualizing outcomes, selecting | |
3620 | thresholds, calculating measures of accuracy and landscape fragmentation | |
3621 | statistics, etc.") | |
3622 | (license license:gpl3+))) | |
ae3f2079 RW |
3623 | |
3624 | (define-public r-scatterplot3d | |
3625 | (package | |
3626 | (name "r-scatterplot3d") | |
5ade82bb | 3627 | (version "0.3-41") |
ae3f2079 RW |
3628 | (source |
3629 | (origin | |
3630 | (method url-fetch) | |
3631 | (uri (cran-uri "scatterplot3d" version)) | |
3632 | (sha256 | |
3633 | (base32 | |
5ade82bb | 3634 | "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc")))) |
ae3f2079 | 3635 | (build-system r-build-system) |
e9960d8c | 3636 | (home-page "https://cran.r-project.org/web/packages/scatterplot3d/") |
ae3f2079 RW |
3637 | (synopsis "3D scatter plot") |
3638 | (description "This package provides an implementation of scatter plots for | |
3639 | plotting. a three dimensional point cloud.") | |
3640 | (license license:gpl2))) | |
f90018e5 RW |
3641 | |
3642 | (define-public r-ggridges | |
3643 | (package | |
3644 | (name "r-ggridges") | |
16a39c2d | 3645 | (version "0.5.1") |
f90018e5 RW |
3646 | (source |
3647 | (origin | |
3648 | (method url-fetch) | |
3649 | (uri (cran-uri "ggridges" version)) | |
3650 | (sha256 | |
3651 | (base32 | |
16a39c2d | 3652 | "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01")))) |
f90018e5 RW |
3653 | (build-system r-build-system) |
3654 | (propagated-inputs | |
3655 | `(("r-ggplot2" ,r-ggplot2) | |
3656 | ("r-plyr" ,r-plyr) | |
0edd2fd1 RW |
3657 | ("r-scales" ,r-scales) |
3658 | ("r-withr" ,r-withr))) | |
f90018e5 RW |
3659 | (home-page "https://github.com/clauswilke/ggridges") |
3660 | (synopsis "Ridgeline plots in ggplot2") | |
3661 | (description | |
3662 | "Ridgeline plots provide a convenient way of visualizing changes in | |
3663 | distributions over time or space. This package enables the creation of such | |
3664 | plots in @code{ggplot2}.") | |
3665 | (license license:gpl2))) | |
007f6d98 RW |
3666 | |
3667 | (define-public r-ggjoy | |
3668 | (package | |
3669 | (name "r-ggjoy") | |
c36745cf | 3670 | (version "0.4.1") |
007f6d98 RW |
3671 | (source |
3672 | (origin | |
3673 | (method url-fetch) | |
3674 | (uri (cran-uri "ggjoy" version)) | |
3675 | (sha256 | |
3676 | (base32 | |
c36745cf | 3677 | "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) |
007f6d98 RW |
3678 | (build-system r-build-system) |
3679 | (propagated-inputs | |
3680 | `(("r-ggplot2" ,r-ggplot2) | |
3681 | ("r-ggridges" ,r-ggridges))) | |
3682 | (home-page "https://github.com/clauswilke/ggjoy") | |
3683 | (synopsis "Joyplots in ggplot2") | |
3684 | (description "Joyplots provide a convenient way of visualizing changes in | |
3685 | distributions over time or space. This package enables the creation of such | |
3686 | plots in @code{ggplot2}.") | |
3687 | (license license:gpl2))) | |
2976f304 RW |
3688 | |
3689 | (define-public r-cli | |
3690 | (package | |
3691 | (name "r-cli") | |
78e29738 | 3692 | (version "1.1.0") |
2976f304 RW |
3693 | (source |
3694 | (origin | |
3695 | (method url-fetch) | |
3696 | (uri (cran-uri "cli" version)) | |
3697 | (sha256 | |
3698 | (base32 | |
78e29738 | 3699 | "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g")))) |
2976f304 RW |
3700 | (build-system r-build-system) |
3701 | (propagated-inputs | |
3702 | `(("r-assertthat" ,r-assertthat) | |
3703 | ("r-crayon" ,r-crayon))) | |
3704 | (home-page "https://github.com/r-lib/cli#readme") | |
3705 | (synopsis "Helpers for developing command line interfaces") | |
3706 | (description "This package provides a suite of tools designed to build | |
3707 | attractive command line interfaces (CLIs). It includes tools for drawing | |
3708 | rules, boxes, trees, and Unicode symbols with ASCII alternatives.") | |
3709 | (license license:expat))) | |
55577393 RW |
3710 | |
3711 | (define-public r-argparser | |
3712 | (package | |
3713 | (name "r-argparser") | |
3714 | (version "0.4") | |
3715 | (source | |
3716 | (origin | |
3717 | (method url-fetch) | |
3718 | (uri (cran-uri "argparser" version)) | |
3719 | (sha256 | |
3720 | (base32 | |
3721 | "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9")))) | |
3722 | (build-system r-build-system) | |
3723 | (home-page "https://bitbucket.org/djhshih/argparser") | |
3724 | (synopsis "Command-line argument parser") | |
3725 | (description | |
3726 | "This package provides a cross-platform command-line argument parser | |
3727 | written purely in R with no external dependencies. It is useful with the | |
3728 | Rscript front-end and facilitates turning an R script into an executable | |
3729 | script.") | |
3730 | (license license:gpl3+))) | |
a3257d42 RW |
3731 | |
3732 | (define-public r-debugme | |
3733 | (package | |
3734 | (name "r-debugme") | |
3735 | (version "1.1.0") | |
3736 | (source | |
3737 | (origin | |
3738 | (method url-fetch) | |
3739 | (uri (cran-uri "debugme" version)) | |
3740 | (sha256 | |
3741 | (base32 | |
3742 | "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) | |
3743 | (build-system r-build-system) | |
3744 | (propagated-inputs `(("r-crayon" ,r-crayon))) | |
3745 | (home-page "https://github.com/r-lib/debugme#readme") | |
3746 | (synopsis "Debug R packages") | |
3747 | (description | |
3748 | "This package allows the user to specify debug messages as special string | |
3749 | constants, and control debugging of packages via environment variables.") | |
3750 | (license license:expat))) | |
2058e37d RW |
3751 | |
3752 | (define-public r-processx | |
3753 | (package | |
3754 | (name "r-processx") | |
503d5b5a | 3755 | (version "3.4.1") |
2058e37d RW |
3756 | (source |
3757 | (origin | |
3758 | (method url-fetch) | |
3759 | (uri (cran-uri "processx" version)) | |
3760 | (sha256 | |
3761 | (base32 | |
503d5b5a | 3762 | "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi")))) |
2058e37d RW |
3763 | (build-system r-build-system) |
3764 | (propagated-inputs | |
0e87bf01 RW |
3765 | `(("r-ps" ,r-ps) |
3766 | ("r-r6" ,r-r6))) | |
2058e37d RW |
3767 | (home-page "https://github.com/r-lib/processx3") |
3768 | (synopsis "Execute and control system processes") | |
3769 | (description | |
3770 | "This package provides portable tools to run system processes in the | |
3771 | background. It can check if a background process is running; wait on a | |
3772 | background process to finish; get the exit status of finished processes; kill | |
3773 | background processes and their children; restart processes. It can read the | |
3774 | standard output and error of the processes, using non-blocking connections. | |
3775 | @code{processx} can poll a process for standard output or error, with a | |
3776 | timeout. It can also poll several processes at once.") | |
3777 | (license license:expat))) | |
f285346a RW |
3778 | |
3779 | (define-public r-tsp | |
3780 | (package | |
3781 | (name "r-tsp") | |
130314d8 | 3782 | (version "1.1-7") |
f285346a RW |
3783 | (source |
3784 | (origin | |
3785 | (method url-fetch) | |
3786 | (uri (cran-uri "TSP" version)) | |
3787 | (sha256 | |
3788 | (base32 | |
130314d8 | 3789 | "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb")))) |
f285346a RW |
3790 | (properties `((upstream-name . "TSP"))) |
3791 | (build-system r-build-system) | |
3792 | (propagated-inputs `(("r-foreach" ,r-foreach))) | |
3793 | (home-page "https://cran.r-project.org/web/packages/TSP/") | |
3794 | (synopsis "Traveling salesperson problem (TSP)") | |
3795 | (description "This package provides basic infrastructure and some | |
3796 | algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the | |
3797 | traveling salesman problem).") | |
3798 | (license license:gpl3))) | |
ffb59bce RW |
3799 | |
3800 | (define-public r-qap | |
3801 | (package | |
3802 | (name "r-qap") | |
3803 | (version "0.1-1") | |
3804 | (source | |
3805 | (origin | |
3806 | (method url-fetch) | |
3807 | (uri (cran-uri "qap" version)) | |
3808 | (sha256 | |
3809 | (base32 | |
3810 | "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) | |
3811 | (build-system r-build-system) | |
3812 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 3813 | (home-page "https://cran.r-project.org/web/packages/qap/") |
ffb59bce RW |
3814 | (synopsis "Heuristics for the quadratic assignment problem (QAP)") |
3815 | (description "This package implements heuristics for the @dfn{quadratic | |
3816 | assignment problem} (QAP). Currently only a simulated annealing heuristic is | |
3817 | available.") | |
3818 | (license license:gpl3))) | |
7fe49f2a RW |
3819 | |
3820 | (define-public r-gclus | |
3821 | (package | |
3822 | (name "r-gclus") | |
111516f9 | 3823 | (version "1.3.2") |
7fe49f2a RW |
3824 | (source |
3825 | (origin | |
3826 | (method url-fetch) | |
3827 | (uri (cran-uri "gclus" version)) | |
3828 | (sha256 | |
3829 | (base32 | |
111516f9 | 3830 | "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) |
7fe49f2a RW |
3831 | (build-system r-build-system) |
3832 | (propagated-inputs `(("r-cluster" ,r-cluster))) | |
d062957a | 3833 | (home-page "https://cran.r-project.org/web/packages/gclus/") |
7fe49f2a RW |
3834 | (synopsis "Clustering graphics") |
3835 | (description "This package orders panels in scatterplot matrices and | |
3836 | parallel coordinate displays by some merit index. It contains various indices | |
3837 | of merit, ordering functions, and enhanced versions of @code{pairs} and | |
3838 | @code{parcoord} which color panels according to their merit level.") | |
3839 | (license license:gpl2+))) | |
8e5e26d2 RW |
3840 | |
3841 | (define-public r-webshot | |
3842 | (package | |
3843 | (name "r-webshot") | |
8871a513 | 3844 | (version "0.5.1") |
8e5e26d2 RW |
3845 | (source |
3846 | (origin | |
3847 | (method url-fetch) | |
3848 | (uri (cran-uri "webshot" version)) | |
3849 | (sha256 | |
3850 | (base32 | |
8871a513 | 3851 | "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr")))) |
8e5e26d2 RW |
3852 | (build-system r-build-system) |
3853 | (propagated-inputs | |
8871a513 RW |
3854 | `(("r-callr" ,r-callr) |
3855 | ("r-jsonlite" ,r-jsonlite) | |
3856 | ("r-magrittr" ,r-magrittr))) | |
8e5e26d2 RW |
3857 | (home-page "https://github.com/wch/webshot/") |
3858 | (synopsis "Take screenshots of web pages") | |
3859 | (description | |
3860 | "Webshot makes it easy to take screenshots of web pages from within R. | |
3861 | It can also run Shiny applications locally and take screenshots of the | |
3862 | application; and it can render and screenshot static as well as interactive R | |
3863 | Markdown documents.") | |
3864 | (license license:gpl2))) | |
2e9d187b RW |
3865 | |
3866 | (define-public r-seriation | |
3867 | (package | |
3868 | (name "r-seriation") | |
bd8710b4 | 3869 | (version "1.2-8") |
2e9d187b RW |
3870 | (source |
3871 | (origin | |
3872 | (method url-fetch) | |
3873 | (uri (cran-uri "seriation" version)) | |
3874 | (sha256 | |
3875 | (base32 | |
bd8710b4 | 3876 | "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk")))) |
2e9d187b RW |
3877 | (build-system r-build-system) |
3878 | (propagated-inputs | |
3879 | `(("r-cluster" ,r-cluster) | |
3880 | ("r-colorspace" ,r-colorspace) | |
3881 | ("r-dendextend" ,r-dendextend) | |
3882 | ("r-gclus" ,r-gclus) | |
3883 | ("r-gplots" ,r-gplots) | |
3884 | ("r-mass" ,r-mass) | |
3885 | ("r-qap" ,r-qap) | |
3886 | ("r-registry" ,r-registry) | |
3887 | ("r-tsp" ,r-tsp))) | |
3888 | (native-inputs `(("gfortran" ,gfortran))) | |
3889 | (home-page "http://s2.smu.edu/IDA/seriation/") | |
3890 | (synopsis "Infrastructure for ordering objects using seriation") | |
3891 | (description | |
3892 | "This package provides infrastructure for seriation with an | |
3893 | implementation of several seriation/sequencing techniques to reorder matrices, | |
3894 | dissimilarity matrices, and dendrograms. It also provides (optimally) | |
3895 | reordered heatmaps, color images and clustering visualizations like | |
3896 | dissimilarity plots, and visual assessment of cluster tendency plots (VAT and | |
3897 | iVAT).") | |
3898 | (license license:gpl3))) | |
e9e78d2c | 3899 | |
f6d2b45c RW |
3900 | (define-public r-xfun |
3901 | (package | |
3902 | (name "r-xfun") | |
7e099141 | 3903 | (version "0.10") |
f6d2b45c RW |
3904 | (source |
3905 | (origin | |
3906 | (method url-fetch) | |
3907 | (uri (cran-uri "xfun" version)) | |
3908 | (sha256 | |
7e099141 | 3909 | (base32 "065ygh046ah43p5aqyrkv2vkxcnvnb4j7blfdygysg6hmqzp4pbv")))) |
f6d2b45c RW |
3910 | (build-system r-build-system) |
3911 | (home-page "https://github.com/yihui/xfun") | |
3912 | (synopsis "Miscellaneous functions") | |
3913 | (description | |
3914 | "This package provides miscellaneous functions commonly used in other | |
3915 | packages maintained by Yihui Xie.") | |
3916 | (license license:expat))) | |
f2442968 RW |
3917 | |
3918 | (define-public r-utf8 | |
3919 | (package | |
3920 | (name "r-utf8") | |
65ea783f | 3921 | (version "1.1.4") |
f2442968 RW |
3922 | (source |
3923 | (origin | |
3924 | (method url-fetch) | |
3925 | (uri (cran-uri "utf8" version)) | |
3926 | (sha256 | |
3927 | (base32 | |
65ea783f | 3928 | "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) |
f2442968 RW |
3929 | (build-system r-build-system) |
3930 | (home-page "https://github.com/patperry/r-utf8") | |
3931 | (synopsis "Unicode text processing") | |
3932 | (description | |
3933 | "This package provides tools to process and print UTF-8 encoded | |
3934 | international text (Unicode). Input, validate, normalize, encode, format, and | |
3935 | display.") | |
3936 | (license license:asl2.0))) | |
c555ccab | 3937 | |
c87a3358 RW |
3938 | (define-public r-zeallot |
3939 | (package | |
3940 | (name "r-zeallot") | |
3941 | (version "0.1.0") | |
3942 | (source | |
3943 | (origin | |
3944 | (method url-fetch) | |
3945 | (uri (cran-uri "zeallot" version)) | |
3946 | (sha256 | |
3947 | (base32 | |
3948 | "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3")))) | |
3949 | (build-system r-build-system) | |
3950 | (home-page "https://github.com/nteetor/zeallot") | |
3951 | (synopsis "Multiple, unpacking, and destructuring assignment") | |
3952 | (description | |
3953 | "This package provides a @code{%<-%} operator to perform multiple, | |
3954 | unpacking, and destructuring assignment in R. The operator unpacks the | |
3955 | right-hand side of an assignment into multiple values and assigns these values | |
3956 | to variables on the left-hand side of the assignment.") | |
3957 | (license license:expat))) | |
3958 | ||
6004bc1a RW |
3959 | (define-public r-vctrs |
3960 | (package | |
3961 | (name "r-vctrs") | |
56444d18 | 3962 | (version "0.2.0") |
6004bc1a RW |
3963 | (source |
3964 | (origin | |
3965 | (method url-fetch) | |
3966 | (uri (cran-uri "vctrs" version)) | |
3967 | (sha256 | |
3968 | (base32 | |
56444d18 | 3969 | "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv")))) |
6004bc1a RW |
3970 | (build-system r-build-system) |
3971 | (propagated-inputs | |
3972 | `(("r-backports" ,r-backports) | |
3973 | ("r-digest" ,r-digest) | |
56444d18 | 3974 | ("r-ellipsis" ,r-ellipsis) |
6004bc1a RW |
3975 | ("r-glue" ,r-glue) |
3976 | ("r-rlang" ,r-rlang) | |
3977 | ("r-zeallot" ,r-zeallot))) | |
3978 | (home-page "https://github.com/r-lib/vctrs") | |
3979 | (synopsis "Vector helpers") | |
3980 | (description | |
3981 | "There are three main goals to the @code{vctrs} package: | |
3982 | ||
3983 | @enumerate | |
3984 | @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to | |
3985 | @code{length()} and @code{class()}. These definitions are paired with a | |
3986 | framework for type-coercion and size-recycling. | |
3987 | @item To define type- and size-stability as desirable function properties, use | |
3988 | them to analyse existing base function, and to propose better alternatives. | |
3989 | This work has been particularly motivated by thinking about the ideal | |
3990 | properties of @code{c()}, @code{ifelse()}, and @code{rbind()}. | |
3991 | @item To provide a new @code{vctr} base class that makes it easy to create new | |
3992 | S3 vectors. @code{vctrs} provides methods for many base generics in terms of | |
3993 | a few new @code{vctrs} generics, making implementation considerably simpler | |
3994 | and more robust. | |
3995 | @end enumerate\n") | |
3996 | (license license:gpl3))) | |
3997 | ||
c555ccab RW |
3998 | (define-public r-pillar |
3999 | (package | |
4000 | (name "r-pillar") | |
9f8f2d9b | 4001 | (version "1.4.2") |
c555ccab RW |
4002 | (source |
4003 | (origin | |
4004 | (method url-fetch) | |
4005 | (uri (cran-uri "pillar" version)) | |
4006 | (sha256 | |
4007 | (base32 | |
9f8f2d9b | 4008 | "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms")))) |
c555ccab RW |
4009 | (build-system r-build-system) |
4010 | (propagated-inputs | |
4011 | `(("r-cli" ,r-cli) | |
4012 | ("r-crayon" ,r-crayon) | |
6f5b157e | 4013 | ("r-fansi" ,r-fansi) |
c555ccab | 4014 | ("r-rlang" ,r-rlang) |
33ba8135 RW |
4015 | ("r-utf8" ,r-utf8) |
4016 | ("r-vctrs" ,r-vctrs))) | |
c555ccab RW |
4017 | (home-page "https://github.com/r-lib/pillar") |
4018 | (synopsis "Coloured formatting for columns") | |
4019 | (description | |
4020 | "This package provides a @code{pillar} generic designed for formatting | |
4021 | columns of data using the full range of colours provided by modern | |
4022 | terminals.") | |
4023 | (license license:gpl3))) | |
1c791925 RW |
4024 | |
4025 | (define-public r-uuid | |
4026 | (package | |
4027 | (name "r-uuid") | |
4028 | (version "0.1-2") | |
4029 | (source | |
4030 | (origin | |
4031 | (method url-fetch) | |
4032 | (uri (cran-uri "uuid" version)) | |
4033 | (sha256 | |
4034 | (base32 | |
4035 | "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx")))) | |
4036 | (build-system r-build-system) | |
4037 | (home-page "http://www.rforge.net/uuid") | |
4038 | (synopsis "Tools for generating and handling of UUIDs") | |
4039 | (description | |
4040 | "This package provides tools for generating and handling of | |
4041 | @dfn{Universally Unique Identifiers} (UUIDs).") | |
4042 | (license license:expat))) | |
846f4c23 RW |
4043 | |
4044 | (define-public r-tinytex | |
4045 | (package | |
4046 | (name "r-tinytex") | |
290c75fc | 4047 | (version "0.16") |
846f4c23 RW |
4048 | (source |
4049 | (origin | |
4050 | (method url-fetch) | |
4051 | (uri (cran-uri "tinytex" version)) | |
4052 | (sha256 | |
4053 | (base32 | |
290c75fc | 4054 | "1dadq9l0527v038b1k1dyfs0dklsgxnmplls3qhqprfgskif8mga")))) |
846f4c23 | 4055 | (build-system r-build-system) |
8b0701d9 TGR |
4056 | (propagated-inputs |
4057 | `(("r-xfun" ,r-xfun))) | |
846f4c23 RW |
4058 | (home-page "https://github.com/yihui/tinytex") |
4059 | (synopsis "Helper functions for TeX Live and compiling LaTeX documents") | |
4060 | (description | |
4061 | "This package provides helper functions to install and maintain the LaTeX | |
4062 | distribution named TinyTeX, a lightweight, cross-platform, portable, and | |
4063 | easy-to-maintain version of TeX Live. This package also contains helper | |
4064 | functions to compile LaTeX documents, and install missing LaTeX packages | |
4065 | automatically.") | |
4066 | (license license:expat))) | |
4376166b RW |
4067 | |
4068 | (define-public r-metap | |
4069 | (package | |
4070 | (name "r-metap") | |
87bb1b8c | 4071 | (version "1.1") |
4376166b RW |
4072 | (source |
4073 | (origin | |
4074 | (method url-fetch) | |
4075 | (uri (cran-uri "metap" version)) | |
4076 | (sha256 | |
4077 | (base32 | |
87bb1b8c | 4078 | "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0")))) |
4376166b RW |
4079 | (build-system r-build-system) |
4080 | (propagated-inputs | |
e32368c1 RW |
4081 | `(("r-lattice" ,r-lattice) |
4082 | ("r-rdpack" ,r-rdpack))) | |
4376166b RW |
4083 | (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") |
4084 | (synopsis "Meta-analysis of significance values") | |
4085 | (description | |
4086 | "The canonical way to perform meta-analysis involves using effect sizes. | |
4087 | When they are not available this package provides a number of methods for | |
4088 | meta-analysis of significance values including the methods of Edgington, | |
4089 | Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate | |
4090 | published results; and a routine for graphical display.") | |
4091 | (license license:gpl2))) | |
5f4565b1 RW |
4092 | |
4093 | (define-public r-network | |
4094 | (package | |
4095 | (name "r-network") | |
20a48579 | 4096 | (version "1.15") |
5f4565b1 RW |
4097 | (source |
4098 | (origin | |
4099 | (method url-fetch) | |
4100 | (uri (cran-uri "network" version)) | |
4101 | (sha256 | |
4102 | (base32 | |
20a48579 | 4103 | "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw")))) |
5f4565b1 | 4104 | (build-system r-build-system) |
75cbc800 RW |
4105 | (propagated-inputs |
4106 | `(("r-magrittr" ,r-magrittr) | |
4107 | ("r-tibble" ,r-tibble))) | |
40862677 | 4108 | (home-page "https://statnet.org/") |
5f4565b1 RW |
4109 | (synopsis "Classes for relational data") |
4110 | (description | |
4111 | "This package provides tools to create and modify network objects. The | |
4112 | @code{network} class can represent a range of relational data types, and | |
4113 | supports arbitrary vertex/edge/graph attributes.") | |
4114 | (license license:gpl2+))) | |
07a2f34d RW |
4115 | |
4116 | (define-public r-statnet-common | |
4117 | (package | |
4118 | (name "r-statnet-common") | |
f7f65cba | 4119 | (version "4.3.0") |
07a2f34d RW |
4120 | (source |
4121 | (origin | |
4122 | (method url-fetch) | |
4123 | (uri (cran-uri "statnet.common" version)) | |
4124 | (sha256 | |
4125 | (base32 | |
f7f65cba | 4126 | "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3")))) |
07a2f34d RW |
4127 | (properties |
4128 | `((upstream-name . "statnet.common"))) | |
4129 | (build-system r-build-system) | |
1268a995 RW |
4130 | (propagated-inputs |
4131 | `(("r-coda" ,r-coda))) | |
40862677 | 4132 | (home-page "https://statnet.org") |
07a2f34d RW |
4133 | (synopsis "R scripts and utilities used by the Statnet software") |
4134 | (description "This package provides non-statistical utilities used by the | |
4135 | software developed by the Statnet Project.") | |
4136 | (license license:gpl3))) | |
1088744d RW |
4137 | |
4138 | (define-public r-sna | |
4139 | (package | |
4140 | (name "r-sna") | |
4141 | (version "2.4") | |
4142 | (source | |
4143 | (origin | |
4144 | (method url-fetch) | |
4145 | (uri (cran-uri "sna" version)) | |
4146 | (sha256 | |
4147 | (base32 | |
4148 | "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2")))) | |
4149 | (build-system r-build-system) | |
4150 | (propagated-inputs | |
4151 | `(("r-network" ,r-network) | |
4152 | ("r-statnet-common" ,r-statnet-common))) | |
40862677 | 4153 | (home-page "https://statnet.org") |
1088744d RW |
4154 | (synopsis "Tools for social network analysis") |
4155 | (description | |
4156 | "This package provides a range of tools for social network analysis, | |
4157 | including node and graph-level indices, structural distance and covariance | |
4158 | methods, structural equivalence detection, network regression, random graph | |
4159 | generation, and 2D/3D network visualization.") | |
4160 | (license license:gpl2+))) | |
93c21ddc RW |
4161 | |
4162 | (define-public r-ttr | |
4163 | (package | |
4164 | (name "r-ttr") | |
9655b1d4 | 4165 | (version "0.23-5") |
93c21ddc RW |
4166 | (source |
4167 | (origin | |
4168 | (method url-fetch) | |
4169 | (uri (cran-uri "TTR" version)) | |
4170 | (sha256 | |
4171 | (base32 | |
9655b1d4 | 4172 | "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6")))) |
93c21ddc RW |
4173 | (properties `((upstream-name . "TTR"))) |
4174 | (build-system r-build-system) | |
4175 | (propagated-inputs | |
4176 | `(("r-curl" ,r-curl) | |
4177 | ("r-xts" ,r-xts) | |
4178 | ("r-zoo" ,r-zoo))) | |
93c21ddc RW |
4179 | (home-page "https://github.com/joshuaulrich/TTR") |
4180 | (synopsis "Technical trading rules") | |
4181 | (description | |
4182 | "This package provides functions and data to construct technical trading | |
4183 | rules with R.") | |
4184 | (license license:gpl2))) | |
0b64332c RW |
4185 | |
4186 | (define-public r-leaps | |
4187 | (package | |
4188 | (name "r-leaps") | |
4189 | (version "3.0") | |
4190 | (source | |
4191 | (origin | |
4192 | (method url-fetch) | |
4193 | (uri (cran-uri "leaps" version)) | |
4194 | (sha256 | |
4195 | (base32 | |
4196 | "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m")))) | |
4197 | (build-system r-build-system) | |
4198 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4199 | (home-page "https://cran.r-project.org/web/packages/leaps/") |
0b64332c RW |
4200 | (synopsis "Regression subset selection") |
4201 | (description | |
4202 | "This package provides tools for regression subset selection, including | |
4203 | exhaustive search.") | |
4204 | (license license:gpl2+))) | |
d3cb62e5 RW |
4205 | |
4206 | (define-public r-splus2r | |
4207 | (package | |
4208 | (name "r-splus2r") | |
4209 | (version "1.2-2") | |
4210 | (source | |
4211 | (origin | |
4212 | (method url-fetch) | |
4213 | (uri (cran-uri "splus2R" version)) | |
4214 | (sha256 | |
4215 | (base32 | |
4216 | "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz")))) | |
4217 | (properties `((upstream-name . "splus2R"))) | |
4218 | (build-system r-build-system) | |
4219 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4220 | (home-page "https://cran.r-project.org/web/packages/splus2R/") |
d3cb62e5 RW |
4221 | (synopsis "Supplemental S-PLUS functionality in R") |
4222 | (description | |
4223 | "Currently there are many functions in S-PLUS that are missing in R. To | |
4224 | facilitate the conversion of S-PLUS packages to R packages, this package | |
4225 | provides some missing S-PLUS functionality in R.") | |
4226 | (license license:gpl2))) | |
034ac9d6 RW |
4227 | |
4228 | (define-public r-ifultools | |
4229 | (package | |
4230 | (name "r-ifultools") | |
d8787b33 | 4231 | (version "2.0-5") |
034ac9d6 RW |
4232 | (source |
4233 | (origin | |
4234 | (method url-fetch) | |
4235 | (uri (cran-uri "ifultools" version)) | |
4236 | (sha256 | |
4237 | (base32 | |
d8787b33 | 4238 | "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j")))) |
034ac9d6 RW |
4239 | (build-system r-build-system) |
4240 | (propagated-inputs | |
4241 | `(("r-mass" ,r-mass) | |
4242 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 4243 | (home-page "https://cran.r-project.org/web/packages/ifultools/") |
034ac9d6 RW |
4244 | (synopsis "Insightful research tools") |
4245 | (description "This package provides C code used by the wmtsa, fractal, and | |
4246 | sapa R packages.") | |
4247 | (license license:gpl2))) | |
0be7effe RW |
4248 | |
4249 | (define-public r-sapa | |
4250 | (package | |
4251 | (name "r-sapa") | |
4252 | (version "2.0-2") | |
4253 | (source | |
4254 | (origin | |
4255 | (method url-fetch) | |
4256 | (uri (cran-uri "sapa" version)) | |
4257 | (sha256 | |
4258 | (base32 | |
4259 | "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds")))) | |
4260 | (build-system r-build-system) | |
4261 | (propagated-inputs | |
4262 | `(("r-ifultools" ,r-ifultools) | |
4263 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 4264 | (home-page "https://cran.r-project.org/web/packages/sapa/") |
0be7effe RW |
4265 | (synopsis "Spectral analysis for physical applications") |
4266 | (description "This package provides software for the book Spectral | |
4267 | Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, | |
4268 | Cambridge University Press, 1993.") | |
4269 | (license license:gpl2))) | |
dceb1592 | 4270 | |
3a4c6288 RW |
4271 | (define-public r-aggregation |
4272 | (package | |
4273 | (name "r-aggregation") | |
4274 | (version "1.0.1") | |
4275 | (source | |
4276 | (origin | |
4277 | (method url-fetch) | |
4278 | (uri (cran-uri "aggregation" version)) | |
4279 | (sha256 | |
4280 | (base32 | |
4281 | "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46")))) | |
4282 | (build-system r-build-system) | |
4283 | (home-page "https://cran.r-project.org/web/packages/aggregation/") | |
4284 | (synopsis "Methods for p-value aggregation") | |
4285 | (description | |
4286 | "This package contains functionality for performing the following methods | |
4287 | of p-value aggregation: Fisher's method, the Lancaster method (weighted | |
4288 | Fisher's method), and Sidak correction.") | |
4289 | (license license:gpl3))) | |
4290 | ||
dceb1592 RW |
4291 | (define-public r-quantmod |
4292 | (package | |
4293 | (name "r-quantmod") | |
22b2d8b9 | 4294 | (version "0.4-15") |
dceb1592 RW |
4295 | (source |
4296 | (origin | |
4297 | (method url-fetch) | |
4298 | (uri (cran-uri "quantmod" version)) | |
4299 | (sha256 | |
4300 | (base32 | |
22b2d8b9 | 4301 | "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky")))) |
dceb1592 RW |
4302 | (build-system r-build-system) |
4303 | (propagated-inputs | |
4304 | `(("r-curl" ,r-curl) | |
4305 | ("r-ttr" ,r-ttr) | |
4306 | ("r-xts" ,r-xts) | |
4307 | ("r-zoo" ,r-zoo))) | |
d062957a | 4308 | (home-page "https://cran.r-project.org/web/packages/quantmod/") |
dceb1592 RW |
4309 | (synopsis "Quantitative financial modelling framework") |
4310 | (description "This package provides a quantitative financial modelling | |
4311 | framework to allow users to specify, build, trade, and analyse quantitative | |
4312 | financial trading strategies.") | |
4313 | (license license:gpl3))) | |
b6dc3255 RW |
4314 | |
4315 | (define-public r-tseries | |
4316 | (package | |
4317 | (name "r-tseries") | |
9ce3d17e | 4318 | (version "0.10-47") |
b6dc3255 RW |
4319 | (source |
4320 | (origin | |
4321 | (method url-fetch) | |
4322 | (uri (cran-uri "tseries" version)) | |
4323 | (sha256 | |
4324 | (base32 | |
9ce3d17e | 4325 | "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0")))) |
b6dc3255 RW |
4326 | (build-system r-build-system) |
4327 | (propagated-inputs | |
4328 | `(("r-quadprog" ,r-quadprog) | |
4329 | ("r-quantmod" ,r-quantmod) | |
4330 | ("r-zoo" ,r-zoo))) | |
4331 | (native-inputs | |
4332 | `(("gfortran" ,gfortran))) | |
d062957a | 4333 | (home-page "https://cran.r-project.org/web/packages/tseries/") |
b6dc3255 RW |
4334 | (synopsis "Time series analysis and computational finance") |
4335 | (description | |
4336 | "This package provides functions relating to time series analysis and | |
4337 | computational finance.") | |
4338 | (license license:gpl2))) | |
a2c079a7 RW |
4339 | |
4340 | (define-public r-wmtsa | |
4341 | (package | |
4342 | (name "r-wmtsa") | |
4343 | (version "2.0-3") | |
4344 | (source | |
4345 | (origin | |
4346 | (method url-fetch) | |
4347 | (uri (cran-uri "wmtsa" version)) | |
4348 | (sha256 | |
4349 | (base32 | |
4350 | "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) | |
4351 | (build-system r-build-system) | |
4352 | (propagated-inputs | |
4353 | `(("r-ifultools" ,r-ifultools) | |
4354 | ("r-mass" ,r-mass) | |
4355 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 4356 | (home-page "https://cran.r-project.org/web/packages/wmtsa/") |
a2c079a7 RW |
4357 | (synopsis "Wavelet methods for time series analysis") |
4358 | (description | |
4359 | "This package provides software to accompany the book \"Wavelet Methods | |
4360 | for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge | |
4361 | University Press, 2000.") | |
4362 | (license license:gpl2))) | |
4993a02a RW |
4363 | |
4364 | (define-public r-tsa | |
4365 | (package | |
4366 | (name "r-tsa") | |
1fe9919a | 4367 | (version "1.2") |
4993a02a RW |
4368 | (source |
4369 | (origin | |
4370 | (method url-fetch) | |
4371 | (uri (cran-uri "TSA" version)) | |
4372 | (sha256 | |
4373 | (base32 | |
1fe9919a | 4374 | "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q")))) |
4993a02a RW |
4375 | (properties `((upstream-name . "TSA"))) |
4376 | (build-system r-build-system) | |
4377 | (propagated-inputs | |
4378 | `(("r-leaps" ,r-leaps) | |
4379 | ("r-locfit" ,r-locfit) | |
1fe9919a | 4380 | ("r-mgcv" ,r-mgcv))) |
4993a02a RW |
4381 | (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm") |
4382 | (synopsis "Time series analysis") | |
4383 | (description | |
4384 | "This package contains R functions and datasets detailed in the book | |
4385 | \"Time Series Analysis with Applications in R (second edition)\" by Jonathan | |
4386 | Cryer and Kung-Sik Chan.") | |
4387 | (license license:gpl2+))) | |
19da7fe3 RW |
4388 | |
4389 | (define-public r-extradistr | |
4390 | (package | |
4391 | (name "r-extradistr") | |
e0cd8f73 | 4392 | (version "1.8.11") |
19da7fe3 RW |
4393 | (source |
4394 | (origin | |
4395 | (method url-fetch) | |
4396 | (uri (cran-uri "extraDistr" version)) | |
4397 | (sha256 | |
4398 | (base32 | |
e0cd8f73 | 4399 | "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3")))) |
19da7fe3 RW |
4400 | (properties `((upstream-name . "extraDistr"))) |
4401 | (build-system r-build-system) | |
4402 | (propagated-inputs | |
4403 | `(("r-rcpp" ,r-rcpp))) | |
4404 | (home-page "https://github.com/twolodzko/extraDistr") | |
4405 | (synopsis "Additional univariate and multivariate distributions") | |
4406 | (description | |
4407 | "This package implements density, distribution functions, quantile | |
4408 | functions and random generation functions for a large number of univariate and | |
4409 | multivariate distributions.") | |
4410 | (license license:gpl2))) | |
5b25bc55 RW |
4411 | |
4412 | (define-public r-fractal | |
4413 | (package | |
4414 | (name "r-fractal") | |
4415 | (version "2.0-4") | |
4416 | (source | |
4417 | (origin | |
4418 | (method url-fetch) | |
4419 | (uri (cran-uri "fractal" version)) | |
4420 | (sha256 | |
4421 | (base32 | |
4422 | "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) | |
4423 | (build-system r-build-system) | |
4424 | (propagated-inputs | |
4425 | `(("r-ifultools" ,r-ifultools) | |
4426 | ("r-mass" ,r-mass) | |
4427 | ("r-sapa" ,r-sapa) | |
4428 | ("r-scatterplot3d" ,r-scatterplot3d) | |
4429 | ("r-splus2r" ,r-splus2r) | |
4430 | ("r-wmtsa" ,r-wmtsa))) | |
d062957a | 4431 | (home-page "https://cran.r-project.org/web/packages/fractal/") |
5b25bc55 RW |
4432 | (synopsis "Fractal time series modeling and analysis") |
4433 | (description | |
4434 | "This package provides tools for stochastic fractal and deterministic | |
4435 | chaotic time series analysis.") | |
4436 | (license license:gpl2))) | |
6615a364 RW |
4437 | |
4438 | (define-public r-urca | |
4439 | (package | |
4440 | (name "r-urca") | |
4441 | (version "1.3-0") | |
4442 | (source | |
4443 | (origin | |
4444 | (method url-fetch) | |
4445 | (uri (cran-uri "urca" version)) | |
4446 | (sha256 | |
4447 | (base32 | |
4448 | "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732")))) | |
4449 | (build-system r-build-system) | |
4450 | (propagated-inputs `(("r-nlme" ,r-nlme))) | |
4451 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4452 | (home-page "https://cran.r-project.org/web/packages/urca/") |
6615a364 RW |
4453 | (synopsis "Unit root and cointegration tests for time series data") |
4454 | (description | |
4455 | "This package provides unit root and cointegration tests encountered in | |
4456 | applied econometric analysis.") | |
4457 | (license license:gpl2+))) | |
d32e5724 RW |
4458 | |
4459 | (define-public r-cubature | |
4460 | (package | |
4461 | (name "r-cubature") | |
5f1f1104 | 4462 | (version "2.0.3") |
d32e5724 RW |
4463 | (source |
4464 | (origin | |
4465 | (method url-fetch) | |
4466 | (uri (cran-uri "cubature" version)) | |
4467 | (sha256 | |
4468 | (base32 | |
5f1f1104 | 4469 | "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr")))) |
d32e5724 RW |
4470 | (build-system r-build-system) |
4471 | (propagated-inputs | |
4472 | `(("r-rcpp" ,r-rcpp))) | |
4473 | (home-page "https://github.com/bnaras/cubature") | |
4474 | (synopsis "Adaptive multivariate integration over hypercubes") | |
4475 | (description | |
4476 | "This package is an R wrapper around the cubature C library for adaptive | |
4477 | multivariate integration over hypercubes. This version provides both | |
4478 | @code{hcubature} and @code{pcubature} routines in addition to a vector | |
4479 | interface.") | |
4480 | ;; The included cubature C library is released under GPLv2+, but the | |
4481 | ;; wrapper declares the license to be GPLv3+. | |
4482 | (license (list license:gpl2+ license:gpl3+)))) | |
7531ee84 RW |
4483 | |
4484 | (define-public r-trend | |
4485 | (package | |
4486 | (name "r-trend") | |
cd4abb6d | 4487 | (version "1.1.1") |
7531ee84 RW |
4488 | (source |
4489 | (origin | |
4490 | (method url-fetch) | |
4491 | (uri (cran-uri "trend" version)) | |
4492 | (sha256 | |
4493 | (base32 | |
cd4abb6d | 4494 | "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q")))) |
7531ee84 RW |
4495 | (build-system r-build-system) |
4496 | (propagated-inputs | |
4497 | `(("r-extradistr" ,r-extradistr))) | |
4498 | (native-inputs | |
4499 | `(("gfortran" ,gfortran))) | |
d062957a | 4500 | (home-page "https://cran.r-project.org/web/packages/trend/") |
7531ee84 RW |
4501 | (synopsis "Non-parametric trend tests and change-point detection") |
4502 | (description | |
4503 | "The analysis of environmental data often requires the detection of | |
4504 | trends and change-points. This package includes tests for trend | |
4505 | detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) | |
4506 | Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) | |
4507 | Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman | |
4508 | correlation trend test), change-point detection (Lanzante's test procedures, | |
4509 | Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal | |
4510 | Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency | |
4511 | Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two | |
4512 | sample Robust Rank-Order Distributional Test.") | |
4513 | (license license:gpl3))) | |
f96eda90 RW |
4514 | |
4515 | (define-public r-expm | |
4516 | (package | |
4517 | (name "r-expm") | |
a11d29b4 | 4518 | (version "0.999-4") |
f96eda90 RW |
4519 | (source |
4520 | (origin | |
4521 | (method url-fetch) | |
4522 | (uri (cran-uri "expm" version)) | |
4523 | (sha256 | |
4524 | (base32 | |
a11d29b4 | 4525 | "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q")))) |
f96eda90 RW |
4526 | (build-system r-build-system) |
4527 | (propagated-inputs `(("r-matrix" ,r-matrix))) | |
4528 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4529 | (home-page "https://r-forge.r-project.org/projects/expm/") |
f96eda90 RW |
4530 | (synopsis "Tools for matrix exponentials and related quantities") |
4531 | (description | |
4532 | "This package provides tools for the computation of the matrix | |
4533 | exponential, logarithm, square root, and related quantities.") | |
4534 | (license license:gpl2+))) | |
68b6a67e RW |
4535 | |
4536 | (define-public r-complexplus | |
4537 | (package | |
4538 | (name "r-complexplus") | |
4539 | (version "2.1") | |
4540 | (source | |
4541 | (origin | |
4542 | (method url-fetch) | |
4543 | (uri (cran-uri "complexplus" version)) | |
4544 | (sha256 | |
4545 | (base32 | |
4546 | "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) | |
4547 | (build-system r-build-system) | |
4548 | (propagated-inputs | |
4549 | `(("r-expm" ,r-expm) | |
4550 | ("r-matrix" ,r-matrix))) | |
d062957a | 4551 | (home-page "https://cran.r-project.org/web/packages/complexplus/") |
68b6a67e RW |
4552 | (synopsis "Functions of complex or real variables") |
4553 | (description | |
4554 | "This package extends several functions to the complex domain, including | |
4555 | the matrix exponential and logarithm, and the determinant.") | |
4556 | (license license:gpl2))) | |
7b81a7ea RW |
4557 | |
4558 | (define-public r-phontools | |
4559 | (package | |
4560 | (name "r-phontools") | |
4561 | (version "0.2-2.1") | |
4562 | (source | |
4563 | (origin | |
4564 | (method url-fetch) | |
4565 | (uri (cran-uri "phonTools" version)) | |
4566 | (sha256 | |
4567 | (base32 | |
4568 | "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7")))) | |
4569 | (properties `((upstream-name . "phonTools"))) | |
4570 | (build-system r-build-system) | |
4571 | (home-page "http://www.santiagobarreda.com/rscripts.html") | |
4572 | (synopsis "Tools for phonetic and acoustic analyses") | |
4573 | (description | |
4574 | "This package contains tools for the organization, display, and analysis | |
4575 | of the sorts of data frequently encountered in phonetics research and | |
4576 | experimentation, including the easy creation of IPA vowel plots, and the | |
4577 | creation and manipulation of WAVE audio files.") | |
4578 | (license license:bsd-2))) | |
d976454c RW |
4579 | |
4580 | (define-public r-np | |
4581 | (package | |
4582 | (name "r-np") | |
02c57c01 | 4583 | (version "0.60-9") |
d976454c RW |
4584 | (source |
4585 | (origin | |
4586 | (method url-fetch) | |
4587 | (uri (cran-uri "np" version)) | |
4588 | (sha256 | |
4589 | (base32 | |
02c57c01 | 4590 | "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy")))) |
d976454c RW |
4591 | (build-system r-build-system) |
4592 | (propagated-inputs | |
4593 | `(("r-boot" ,r-boot) | |
4594 | ("r-cubature" ,r-cubature) | |
65d66b3e | 4595 | ("r-quadprog" ,r-quadprog) |
d976454c RW |
4596 | ("r-quantreg" ,r-quantreg))) |
4597 | (home-page "https://github.com/JeffreyRacine/R-Package-np") | |
4598 | (synopsis "Non-parametric kernel smoothing methods for mixed data types") | |
4599 | (description "This package provides non-parametric (and semi-parametric) | |
4600 | kernel methods that seamlessly handle a mix of continuous, unordered, and | |
4601 | ordered factor data types.") | |
4602 | ;; Any version of the GPL. | |
4603 | (license license:gpl3+))) | |
2a112be0 RW |
4604 | |
4605 | (define-public r-powerplus | |
4606 | (package | |
4607 | (name "r-powerplus") | |
4608 | (version "3.1") | |
4609 | (source | |
4610 | (origin | |
4611 | (method url-fetch) | |
4612 | (uri (cran-uri "powerplus" version)) | |
4613 | (sha256 | |
4614 | (base32 | |
4615 | "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) | |
4616 | (build-system r-build-system) | |
4617 | (propagated-inputs | |
4618 | `(("r-complexplus" ,r-complexplus) | |
4619 | ("r-expm" ,r-expm) | |
4620 | ("r-mass" ,r-mass) | |
4621 | ("r-matrix" ,r-matrix) | |
4622 | ("r-phontools" ,r-phontools))) | |
d062957a | 4623 | (home-page "https://cran.r-project.org/web/packages/powerplus/") |
2a112be0 RW |
4624 | (synopsis "Exponentiation operations") |
4625 | (description | |
4626 | "This package provides tools for the computation of matrix and scalar | |
4627 | exponentiation.") | |
4628 | (license license:gpl2))) | |
021caafa RW |
4629 | |
4630 | (define-public r-heatmaply | |
4631 | (package | |
4632 | (name "r-heatmaply") | |
5da9918d | 4633 | (version "0.16.0") |
021caafa RW |
4634 | (source |
4635 | (origin | |
4636 | (method url-fetch) | |
4637 | (uri (cran-uri "heatmaply" version)) | |
4638 | (sha256 | |
4639 | (base32 | |
5da9918d | 4640 | "1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1")))) |
021caafa RW |
4641 | (build-system r-build-system) |
4642 | (propagated-inputs | |
4643 | `(("r-assertthat" ,r-assertthat) | |
4644 | ("r-colorspace" ,r-colorspace) | |
4645 | ("r-dendextend" ,r-dendextend) | |
4646 | ("r-ggplot2" ,r-ggplot2) | |
021caafa RW |
4647 | ("r-htmlwidgets" ,r-htmlwidgets) |
4648 | ("r-magrittr" ,r-magrittr) | |
4649 | ("r-plotly" ,r-plotly) | |
4650 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4651 | ("r-reshape2" ,r-reshape2) | |
4652 | ("r-scales" ,r-scales) | |
4653 | ("r-seriation" ,r-seriation) | |
4654 | ("r-viridis" ,r-viridis) | |
4655 | ("r-webshot" ,r-webshot))) | |
4656 | (home-page "https://cran.r-project.org/package=heatmaply") | |
4657 | (synopsis "Interactive cluster heat maps using plotly") | |
4658 | (description | |
4659 | "This package enables you to create interactive cluster heatmaps that can | |
4660 | be saved as a stand-alone HTML file, embedded in R Markdown documents or in a | |
4661 | Shiny app, and made available in the RStudio viewer pane. Hover the mouse | |
4662 | pointer over a cell to show details or drag a rectangle to zoom. A heatmap is | |
4663 | a popular graphical method for visualizing high-dimensional data, in which a | |
4664 | table of numbers is encoded as a grid of colored cells. The rows and columns | |
4665 | of the matrix are ordered to highlight patterns and are often accompanied by | |
4666 | dendrograms.") | |
4667 | ;; Either version of the license. | |
4668 | (license (list license:gpl2 license:gpl3)))) | |
b2dc4cb4 | 4669 | |
ff939ef4 RW |
4670 | (define-public r-h5 |
4671 | (package | |
4672 | (name "r-h5") | |
4673 | (version "0.9.9") | |
4674 | (source | |
4675 | (origin | |
4676 | (method url-fetch) | |
4677 | (uri (cran-uri "h5" version)) | |
4678 | (sha256 | |
4679 | (base32 | |
4680 | "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) | |
4681 | (build-system r-build-system) | |
4682 | (inputs | |
4683 | `(("zlib" ,zlib) | |
4684 | ("hdf5" ,hdf5))) | |
4685 | (native-inputs | |
4686 | `(("which" ,which))) | |
4687 | (propagated-inputs | |
4688 | `(("r-rcpp" ,r-rcpp))) | |
4689 | (home-page "https://github.com/mannau/h5") | |
4690 | (synopsis "Interface to the HDF5 Library") | |
4691 | (description | |
4692 | "This package provides an S4 interface to the HDF5 library supporting | |
4693 | fast storage and retrieval of R-objects like vectors, matrices and arrays to | |
4694 | binary files in a language independent format. The HDF5 format can therefore | |
4695 | be used as an alternative to R's save/load mechanism. Since h5 is able to | |
4696 | access only subsets of stored data it can also handle data sets which do not | |
4697 | fit into memory.") | |
4698 | (license license:bsd-2))) | |
4699 | ||
b2dc4cb4 RW |
4700 | (define-public r-cgdsr |
4701 | (package | |
4702 | (name "r-cgdsr") | |
dacf52e0 | 4703 | (version "1.3.0") |
b2dc4cb4 RW |
4704 | (source |
4705 | (origin | |
4706 | (method url-fetch) | |
4707 | (uri (cran-uri "cgdsr" version)) | |
4708 | (sha256 | |
4709 | (base32 | |
dacf52e0 | 4710 | "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) |
b2dc4cb4 RW |
4711 | (build-system r-build-system) |
4712 | (propagated-inputs | |
dacf52e0 RW |
4713 | `(("r-httr" ,r-httr) |
4714 | ("r-r-methodss3" ,r-r-methodss3) | |
b2dc4cb4 RW |
4715 | ("r-r-oo" ,r-r-oo))) |
4716 | (home-page "https://github.com/cBioPortal/cgdsr") | |
4717 | (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") | |
4718 | (description | |
4719 | "This package provides a basic set of R functions for querying the Cancer | |
4720 | Genomics Data Server (CGDS), hosted by the Computational Biology Center at | |
4721 | Memorial-Sloan-Kettering Cancer Center (MSKCC).") | |
4722 | (license license:lgpl3))) | |
a00968b7 RW |
4723 | |
4724 | (define-public r-import | |
4725 | (package | |
4726 | (name "r-import") | |
4727 | (version "1.1.0") | |
4728 | (source | |
4729 | (origin | |
4730 | (method url-fetch) | |
4731 | (uri (cran-uri "import" version)) | |
4732 | (sha256 | |
4733 | (base32 | |
4734 | "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji")))) | |
4735 | (build-system r-build-system) | |
4736 | (home-page "https://github.com/smbache/import") | |
4737 | (synopsis "Import mechanism for R") | |
4738 | (description | |
4739 | "This is an alternative mechanism for importing objects from packages. | |
4740 | The syntax allows for importing multiple objects from a package with a single | |
4741 | command in an expressive way. The import package bridges some of the gap | |
4742 | between using @code{library} (or @code{require}) and direct (single-object) | |
4743 | imports. Furthermore the imported objects are not placed in the current | |
4744 | environment. It is also possible to import objects from stand-alone @code{.R} | |
4745 | files.") | |
4746 | (license license:expat))) | |
5d9b82ac RW |
4747 | |
4748 | (define-public r-shinyace | |
4749 | (package | |
4750 | (name "r-shinyace") | |
cd5d6e26 | 4751 | (version "0.4.1") |
5d9b82ac RW |
4752 | (source |
4753 | (origin | |
4754 | (method url-fetch) | |
4755 | (uri (cran-uri "shinyAce" version)) | |
4756 | (sha256 | |
4757 | (base32 | |
cd5d6e26 | 4758 | "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn")))) |
5d9b82ac RW |
4759 | (properties `((upstream-name . "shinyAce"))) |
4760 | (build-system r-build-system) | |
4761 | (propagated-inputs | |
e86d3cc5 RW |
4762 | `(("r-shiny" ,r-shiny) |
4763 | ("r-jsonlite" ,r-jsonlite))) | |
5d9b82ac RW |
4764 | (home-page "http://cran.r-project.org/web/packages/shinyAce") |
4765 | (synopsis "Ace editor bindings for Shiny") | |
4766 | (description | |
4767 | "This package provides Ace editor bindings to enable a rich text editing | |
4768 | environment within Shiny.") | |
4769 | (license license:expat))) | |
f64fea1d | 4770 | |
72032c9d RW |
4771 | (define-public r-base64url |
4772 | (package | |
4773 | (name "r-base64url") | |
4774 | (version "1.4") | |
4775 | (source | |
4776 | (origin | |
4777 | (method url-fetch) | |
4778 | (uri (cran-uri "base64url" version)) | |
4779 | (sha256 | |
4780 | (base32 | |
4781 | "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x")))) | |
4782 | (build-system r-build-system) | |
4783 | (propagated-inputs | |
4784 | `(("r-backports" ,r-backports))) | |
4785 | (home-page "https://github.com/mllg/base64url") | |
4786 | (synopsis "Fast and URL-safe base64 encoder and decoder") | |
4787 | (description | |
4788 | "This package provides a URL-safe base64 encoder and decoder. In | |
4789 | contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-}, | |
4790 | the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the | |
4791 | encoder does not fill the string with trailing @code{=}. The resulting | |
4792 | encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]} | |
4793 | and thus are safe to use in URLs or for file names. The package also comes | |
4794 | with a simple base32 encoder/decoder suited for case insensitive file | |
4795 | systems.") | |
4796 | (license license:gpl3))) | |
4797 | ||
f64fea1d RW |
4798 | (define-public r-radiant-data |
4799 | (package | |
4800 | (name "r-radiant-data") | |
a7146013 | 4801 | (version "1.0.6") |
f64fea1d RW |
4802 | (source |
4803 | (origin | |
4804 | (method url-fetch) | |
4805 | (uri (cran-uri "radiant.data" version)) | |
4806 | (sha256 | |
4807 | (base32 | |
a7146013 | 4808 | "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg")) |
f64fea1d RW |
4809 | (modules '((guix build utils))) |
4810 | (snippet | |
4811 | '(begin | |
4812 | ;; Delete files that are under CC-NC-SA. | |
4813 | (delete-file-recursively "inst/app/tools/help") | |
4814 | #t)))) | |
4815 | (properties `((upstream-name . "radiant.data"))) | |
4816 | (build-system r-build-system) | |
4817 | (propagated-inputs | |
4818 | `(("r-base64enc" ,r-base64enc) | |
4819 | ("r-broom" ,r-broom) | |
4820 | ("r-car" ,r-car) | |
4821 | ("r-curl" ,r-curl) | |
4822 | ("r-dplyr" ,r-dplyr) | |
4823 | ("r-dt" ,r-dt) | |
36dc3591 | 4824 | ("r-glue" ,r-glue) |
f64fea1d RW |
4825 | ("r-ggplot2" ,r-ggplot2) |
4826 | ("r-gridextra" ,r-gridextra) | |
4827 | ("r-import" ,r-import) | |
4828 | ("r-jsonlite" ,r-jsonlite) | |
4829 | ("r-knitr" ,r-knitr) | |
4830 | ("r-lubridate" ,r-lubridate) | |
4831 | ("r-magrittr" ,r-magrittr) | |
4832 | ("r-markdown" ,r-markdown) | |
36dc3591 | 4833 | ("r-plotly" ,r-plotly) |
f64fea1d RW |
4834 | ("r-psych" ,r-psych) |
4835 | ("r-readr" ,r-readr) | |
36dc3591 RW |
4836 | ("r-readxl" ,r-readxl) |
4837 | ("r-rlang" ,r-rlang) | |
f64fea1d RW |
4838 | ("r-rmarkdown" ,r-rmarkdown) |
4839 | ("r-rstudioapi" ,r-rstudioapi) | |
4840 | ("r-scales" ,r-scales) | |
4841 | ("r-shiny" ,r-shiny) | |
e5f9e9fa | 4842 | ("r-shinyfiles" ,r-shinyfiles) |
f64fea1d | 4843 | ("r-shinyace" ,r-shinyace) |
cb40b6eb | 4844 | ("r-stringi" ,r-stringi) |
f64fea1d | 4845 | ("r-tibble" ,r-tibble) |
36dc3591 RW |
4846 | ("r-tidyr" ,r-tidyr) |
4847 | ("r-writexl" ,r-writexl))) | |
f64fea1d RW |
4848 | (home-page "https://github.com/radiant-rstats/radiant.data") |
4849 | (synopsis "Data menu for Radiant: business analytics using R and Shiny") | |
4850 | (description | |
4851 | "The Radiant Data menu includes interfaces for loading, saving, viewing, | |
4852 | visualizing, summarizing, transforming, and combining data. It also contains | |
4853 | functionality to generate reproducible reports of the analyses conducted in | |
4854 | the application.") | |
4855 | (license license:agpl3))) | |
e2cafc24 RW |
4856 | |
4857 | (define-public r-algdesign | |
4858 | (package | |
4859 | (name "r-algdesign") | |
4860 | (version "1.1-7.3") | |
4861 | (source | |
4862 | (origin | |
4863 | (method url-fetch) | |
4864 | (uri (cran-uri "AlgDesign" version)) | |
4865 | (sha256 | |
4866 | (base32 | |
4867 | "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz")))) | |
4868 | (properties `((upstream-name . "AlgDesign"))) | |
4869 | (build-system r-build-system) | |
4870 | (home-page "https://github.com/jvbraun/AlgDesign") | |
4871 | (synopsis "Algorithmic experimental design") | |
4872 | (description | |
4873 | "This package provides tools to calculate exact and approximate theory | |
4874 | experimental designs for D, A, and I criteria. Very large designs may be | |
4875 | created. Experimental designs may be blocked or blocked designs created from | |
4876 | a candidate list, using several criteria. The blocking can be done when whole | |
4877 | and within plot factors interact.") | |
4878 | (license license:gpl2+))) | |
35b0c051 RW |
4879 | |
4880 | (define-public r-signal | |
4881 | (package | |
4882 | (name "r-signal") | |
4883 | (version "0.7-6") | |
4884 | (source | |
4885 | (origin | |
4886 | (method url-fetch) | |
4887 | (uri (cran-uri "signal" version)) | |
4888 | (sha256 | |
4889 | (base32 | |
4890 | "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b")))) | |
4891 | (build-system r-build-system) | |
4892 | (propagated-inputs `(("r-mass" ,r-mass))) | |
4893 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4894 | (home-page "https://cran.r-project.org/web/packages/signal/") |
35b0c051 RW |
4895 | (synopsis "Signal processing") |
4896 | (description | |
4897 | "This package provides a set of signal processing functions originally | |
4898 | written for Matlab and GNU Octave. It includes filter generation utilities, | |
4899 | filtering functions, resampling routines, and visualization of filter models. | |
4900 | It also includes interpolation functions.") | |
4901 | (license license:gpl2))) | |
db80dd4a | 4902 | |
3dab50d9 RW |
4903 | (define-public r-gsubfn |
4904 | (package | |
4905 | (name "r-gsubfn") | |
2acc0e5f | 4906 | (version "0.7") |
3dab50d9 RW |
4907 | (source |
4908 | (origin | |
4909 | (method url-fetch) | |
4910 | (uri (cran-uri "gsubfn" version)) | |
4911 | (sha256 | |
4912 | (base32 | |
2acc0e5f | 4913 | "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) |
3dab50d9 RW |
4914 | (build-system r-build-system) |
4915 | (propagated-inputs `(("r-proto" ,r-proto))) | |
4916 | (home-page "http://gsubfn.googlecode.com") | |
4917 | (synopsis "Utilities for strings and function arguments.") | |
4918 | (description | |
4919 | "This package provides @code{gsubfn} which is like @code{gsub} but can | |
4920 | take a replacement function or certain other objects instead of the | |
4921 | replacement string. Matches and back references are input to the replacement | |
4922 | function and replaced by the function output. @code{gsubfn} can be used to | |
4923 | split strings based on content rather than delimiters and for quasi-perl-style | |
4924 | string interpolation. The package also has facilities for translating | |
4925 | formulas to functions and allowing such formulas in function calls instead of | |
4926 | functions.") | |
4927 | (license license:gpl2+))) | |
3a563a41 RW |
4928 | |
4929 | (define-public r-sqldf | |
4930 | (package | |
4931 | (name "r-sqldf") | |
4932 | (version "0.4-11") | |
4933 | (source | |
4934 | (origin | |
4935 | (method url-fetch) | |
4936 | (uri (cran-uri "sqldf" version)) | |
4937 | (sha256 | |
4938 | (base32 | |
4939 | "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff")))) | |
4940 | (build-system r-build-system) | |
4941 | (propagated-inputs | |
4942 | `(("r-chron" ,r-chron) | |
4943 | ("r-dbi" ,r-dbi) | |
4944 | ("r-gsubfn" ,r-gsubfn) | |
4945 | ("r-proto" ,r-proto) | |
4946 | ("r-rsqlite" ,r-rsqlite))) | |
4947 | (home-page "https://github.com/ggrothendieck/sqldf") | |
4948 | (synopsis "Manipulate R data frames using SQL") | |
4949 | (description | |
4950 | "The @code{sqldf} function is typically passed a single argument which is | |
4951 | an SQL select statement where the table names are ordinary R data frame names. | |
4952 | @code{sqldf} transparently sets up a database, imports the data frames into | |
4953 | that database, performs the SQL statement and returns the result using a | |
4954 | heuristic to determine which class to assign to each column of the returned | |
4955 | data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be | |
4956 | used to read filtered files into R even if the original files are larger than | |
4957 | R itself can handle.") | |
4958 | (license license:gpl2))) | |
94e46cab RW |
4959 | |
4960 | (define-public r-abind | |
4961 | (package | |
4962 | (name "r-abind") | |
4963 | (version "1.4-5") | |
4964 | (source | |
4965 | (origin | |
4966 | (method url-fetch) | |
4967 | (uri (cran-uri "abind" version)) | |
4968 | (sha256 | |
4969 | (base32 | |
4970 | "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) | |
4971 | (build-system r-build-system) | |
d062957a | 4972 | (home-page "https://cran.r-project.org/web/packages/abind/") |
94e46cab RW |
4973 | (synopsis "Combine multidimensional arrays") |
4974 | (description | |
4975 | "This package provides tools to combine multidimensional arrays into a | |
4976 | single array. This is a generalization of @code{cbind} and @code{rbind}. It | |
4977 | works with vectors, matrices, and higher-dimensional arrays. It also provides | |
4978 | the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating, | |
4979 | extracting and replacing data in arrays.") | |
4980 | (license license:lgpl2.0+))) | |
fc784b66 RW |
4981 | |
4982 | (define-public r-prroc | |
4983 | (package | |
4984 | (name "r-prroc") | |
0430eb66 | 4985 | (version "1.3.1") |
fc784b66 RW |
4986 | (source |
4987 | (origin | |
4988 | (method url-fetch) | |
4989 | (uri (cran-uri "PRROC" version)) | |
4990 | (sha256 | |
4991 | (base32 | |
0430eb66 | 4992 | "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7")))) |
fc784b66 RW |
4993 | (properties `((upstream-name . "PRROC"))) |
4994 | (build-system r-build-system) | |
d062957a | 4995 | (home-page "https://cran.r-project.org/web/packages/PRROC/") |
fc784b66 RW |
4996 | (synopsis "Precision-Recall and ROC curves for weighted and unweighted data") |
4997 | (description | |
4998 | "This package computes the areas under the @dfn{precision-recall} (PR) | |
4999 | and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In | |
5000 | contrast to other implementations, the interpolation between points of the PR | |
5001 | curve is done by a non-linear piecewise function. In addition to the areas | |
5002 | under the curves, the curves themselves can also be computed and plotted by a | |
5003 | specific S3-method.") | |
5004 | (license license:gpl3))) | |
661bb51e RW |
5005 | |
5006 | (define-public r-vim | |
5007 | (package | |
5008 | (name "r-vim") | |
8b2c80b8 | 5009 | (version "4.8.0") |
661bb51e RW |
5010 | (source |
5011 | (origin | |
5012 | (method url-fetch) | |
5013 | (uri (cran-uri "VIM" version)) | |
5014 | (sha256 | |
5015 | (base32 | |
8b2c80b8 | 5016 | "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw")))) |
661bb51e RW |
5017 | (properties `((upstream-name . "VIM"))) |
5018 | (build-system r-build-system) | |
5019 | (propagated-inputs | |
5020 | `(("r-car" ,r-car) | |
5021 | ("r-colorspace" ,r-colorspace) | |
5022 | ("r-data-table" ,r-data-table) | |
5023 | ("r-e1071" ,r-e1071) | |
5024 | ("r-laeken" ,r-laeken) | |
5025 | ("r-mass" ,r-mass) | |
5026 | ("r-nnet" ,r-nnet) | |
8b2c80b8 | 5027 | ("r-ranger" ,r-ranger) |
661bb51e RW |
5028 | ("r-rcpp" ,r-rcpp) |
5029 | ("r-robustbase" ,r-robustbase) | |
5030 | ("r-sp" ,r-sp) | |
5031 | ("r-vcd" ,r-vcd))) | |
5032 | (home-page "https://github.com/alexkowa/VIM") | |
5033 | (synopsis "Visualization and imputation of missing values") | |
5034 | (description | |
5035 | "This package provides tools for the visualization of missing and/or | |
5036 | imputed values are introduced, which can be used for exploring the data and | |
5037 | the structure of the missing and/or imputed values. Depending on this | |
5038 | structure of the missing values, the corresponding methods may help to | |
5039 | identify the mechanism generating the missing values and allows to explore the | |
5040 | data including missing values. In addition, the quality of imputation can be | |
5041 | visually explored using various univariate, bivariate, multiple and | |
5042 | multivariate plot methods.") | |
5043 | (license license:gpl2+))) | |
d10b0952 RW |
5044 | |
5045 | (define-public r-fnn | |
5046 | (package | |
5047 | (name "r-fnn") | |
b9b10413 | 5048 | (version "1.1.3") |
d10b0952 RW |
5049 | (source |
5050 | (origin | |
5051 | (method url-fetch) | |
5052 | (uri (cran-uri "FNN" version)) | |
5053 | (sha256 | |
5054 | (base32 | |
b9b10413 | 5055 | "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny")))) |
d10b0952 RW |
5056 | (properties `((upstream-name . "FNN"))) |
5057 | (build-system r-build-system) | |
1b5905fe | 5058 | (home-page "https://cran.r-project.org/web/packages/FNN") |
d10b0952 RW |
5059 | (synopsis "Fast nearest neighbor search algorithms and applications") |
5060 | (description | |
5061 | "This package provides cover-tree and kd-tree fast k-nearest neighbor | |
5062 | search algorithms. Related applications including KNN classification, | |
5063 | regression and information measures are implemented.") | |
5064 | ;; The DESCRIPTION file erroneously states that GPL version 2.1 or | |
5065 | ;; later can be used. | |
5066 | (license license:gpl2+))) | |
be815dbd RW |
5067 | |
5068 | (define-public r-smoother | |
5069 | (package | |
5070 | (name "r-smoother") | |
5071 | (version "1.1") | |
5072 | (source | |
5073 | (origin | |
5074 | (method url-fetch) | |
5075 | (uri (cran-uri "smoother" version)) | |
5076 | (sha256 | |
5077 | (base32 | |
5078 | "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci")))) | |
5079 | (build-system r-build-system) | |
5080 | (propagated-inputs | |
5081 | `(("r-ttr" ,r-ttr))) | |
5082 | (home-page "http://cran.r-project.org/web/packages/smoother") | |
5083 | (synopsis "Functions relating to the smoothing of numerical data") | |
5084 | (description | |
5085 | "This package provides a collection of methods for smoothing numerical | |
5086 | data, commencing with a port of the Matlab gaussian window smoothing function. | |
5087 | In addition, several functions typically used in smoothing of financial data | |
5088 | are included.") | |
5089 | (license license:gpl2))) | |
0efd09ac RW |
5090 | |
5091 | (define-public r-riverplot | |
5092 | (package | |
5093 | (name "r-riverplot") | |
5094 | (version "0.6") | |
5095 | (source | |
5096 | (origin | |
5097 | (method url-fetch) | |
5098 | (uri (cran-uri "riverplot" version)) | |
5099 | (sha256 | |
5100 | (base32 | |
5101 | "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z")))) | |
5102 | (build-system r-build-system) | |
5103 | (home-page "https://logfc.wordpress.com") | |
5104 | (synopsis "Sankey or ribbon plots") | |
5105 | (description | |
5106 | "Sankey plots are a type of diagram that is convenient to illustrate how | |
5107 | flow of information, resources etc. separates and joins, much like observing | |
5108 | how rivers split and merge. For example, they can be used to compare | |
5109 | different clusterings. This package provides an implementation of Sankey | |
5110 | plots for R.") | |
5111 | (license license:gpl2+))) | |
c56739df SY |
5112 | |
5113 | (define-public r-dyn | |
5114 | (package | |
5115 | (name "r-dyn") | |
5116 | (version "0.2-9.6") | |
5117 | (source | |
5118 | (origin | |
5119 | (method url-fetch) | |
5120 | (uri (cran-uri "dyn" version)) | |
5121 | (sha256 | |
5122 | (base32 | |
5123 | "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb")))) | |
5124 | (build-system r-build-system) | |
5125 | (propagated-inputs | |
5126 | `(("r-zoo" ,r-zoo))) | |
5127 | (home-page "https://cran.r-project.org/web/packages/dyn") | |
5128 | (synopsis "Time series regression") | |
5129 | (description | |
5130 | "This package provides the dyn class interfaces @code{ts}, @code{irts}, | |
5131 | @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm}, | |
5132 | @code{loess}, @code{quantreg::rq}, @code{MASS::rlm}, | |
5133 | @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()}, | |
5134 | @code{randomForest::randomForest()} and other regression functions, allowing | |
5135 | those functions to be used with time series including specifications that may | |
5136 | contain lags, diffs and missing values.") | |
5137 | ;; Any GPL version. | |
5138 | (license license:gpl2+))) | |
24fa6bca SY |
5139 | |
5140 | (define-public r-catdap | |
5141 | (package | |
5142 | (name "r-catdap") | |
5143 | (version "1.3.4") | |
5144 | (source | |
5145 | (origin | |
5146 | (method url-fetch) | |
5147 | (uri (cran-uri "catdap" version)) | |
5148 | (sha256 | |
5149 | (base32 | |
5150 | "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2")))) | |
5151 | (build-system r-build-system) | |
5152 | (native-inputs | |
5153 | `(("gfortran" ,gfortran))) | |
5154 | (home-page "https://cran.r-project.org/web/packages/catdap/") | |
5155 | (synopsis "Tools for categorical data analysis") | |
5156 | (description | |
5157 | "This package provides functions for analyzing multivariate data. | |
5158 | Dependencies of the distribution of the specified variable (response | |
5159 | variable) to other variables (explanatory variables) are derived and | |
5160 | evaluated by the @dfn{Akaike Information Criterion} (AIC).") | |
5161 | (license license:gpl2+))) | |
96e22362 SS |
5162 | |
5163 | (define-public r-arules | |
5164 | (package | |
5165 | (name "r-arules") | |
2586cfd3 | 5166 | (version "1.6-4") |
96e22362 SS |
5167 | (source |
5168 | (origin | |
5169 | (method url-fetch) | |
5170 | (uri (cran-uri "arules" version)) | |
5171 | (sha256 | |
5172 | (base32 | |
2586cfd3 | 5173 | "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n")))) |
96e22362 SS |
5174 | (build-system r-build-system) |
5175 | (propagated-inputs | |
5176 | `(("r-matrix" ,r-matrix))) | |
5177 | (home-page "https://github.com/mhahsler/arules") | |
5178 | (synopsis "Mining association rules and frequent itemsets") | |
5179 | (description | |
5180 | "This package provides an infrastructure for representing, manipulating | |
5181 | and analyzing transaction data and patterns (frequent itemsets and association rules). | |
5182 | It also provides C implementations of the association mining algorithms Apriori | |
5183 | and Eclat.") | |
5184 | (license license:gpl3))) | |
1cde7467 KH |
5185 | |
5186 | (define-public r-parsedate | |
5187 | (package | |
5188 | (name "r-parsedate") | |
86ad5dbc | 5189 | (version "1.2.0") |
1cde7467 KH |
5190 | (source |
5191 | (origin | |
5192 | (method url-fetch) | |
5193 | (uri (cran-uri "parsedate" version)) | |
5194 | (sha256 | |
5195 | (base32 | |
86ad5dbc | 5196 | "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr")))) |
1cde7467 | 5197 | (build-system r-build-system) |
86ad5dbc RW |
5198 | (propagated-inputs |
5199 | `(("r-rematch2" ,r-rematch2))) | |
1cde7467 KH |
5200 | (home-page "https://github.com/gaborcsardi/parsedate") |
5201 | (synopsis | |
5202 | "Recognize and parse dates in various formats") | |
5203 | (description | |
5204 | "This package provides three functions for dealing with dates: | |
5205 | @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and | |
5206 | time formats, @code{parse_date} parses dates in unspecified formats, | |
5207 | and @code{format_iso_8601} formats a date in ISO 8601 format.") | |
5208 | (license license:gpl2))) | |
2a27c0bb SY |
5209 | |
5210 | (define-public r-abc-data | |
5211 | (package | |
5212 | (name "r-abc-data") | |
5213 | (version "1.0") | |
5214 | (source | |
5215 | (origin | |
5216 | (method url-fetch) | |
5217 | (uri (cran-uri "abc.data" version)) | |
5218 | (sha256 | |
5219 | (base32 | |
5220 | "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj")))) | |
5221 | (properties `((upstream-name . "abc.data"))) | |
5222 | (build-system r-build-system) | |
5223 | (home-page "https://cran.r-project.org/web/packages/abc.data/") | |
5224 | (synopsis "Data for Approximate Bayesian Computation (ABC) package") | |
5225 | (description | |
5226 | "This package contains data which are used by functions of the abc | |
5227 | package which implements several @dfn{Approximate Bayesian Computation} (ABC) | |
5228 | algorithms for performing parameter estimation, model selection, and | |
5229 | goodness-of-fit.") | |
5230 | (license license:gpl3+))) | |
82c8e0ae SY |
5231 | |
5232 | (define-public r-abc | |
5233 | (package | |
5234 | (name "r-abc") | |
5235 | (version "2.1") | |
5236 | (source | |
5237 | (origin | |
5238 | (method url-fetch) | |
5239 | (uri (cran-uri "abc" version)) | |
5240 | (sha256 | |
5241 | (base32 | |
5242 | "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) | |
5243 | (build-system r-build-system) | |
5244 | (propagated-inputs | |
5245 | `(("r-abc-data" ,r-abc-data) | |
5246 | ("r-locfit" ,r-locfit) | |
5247 | ("r-mass" ,r-mass) | |
5248 | ("r-nnet" ,r-nnet) | |
5249 | ("r-quantreg" ,r-quantreg))) | |
5250 | (home-page "https://cran.r-project.org/web/packages/abc/") | |
5251 | (synopsis "Tools for Approximate Bayesian Computation (ABC)") | |
5252 | (description | |
5253 | "This package implements several @dfn{Approximate Bayesian | |
5254 | Computation} (ABC) algorithms for performing parameter estimation, model | |
5255 | selection, and goodness-of-fit. Cross-validation tools are also available for | |
5256 | measuring the accuracy of ABC estimates, and to calculate the | |
5257 | misclassification probabilities of different models.") | |
5258 | (license license:gpl3+))) | |
4b1f7a3e | 5259 | |
d182828f RW |
5260 | (define-public r-zip |
5261 | (package | |
5262 | (name "r-zip") | |
59fd6915 | 5263 | (version "2.0.4") |
d182828f RW |
5264 | (source |
5265 | (origin | |
5266 | (method url-fetch) | |
5267 | (uri (cran-uri "zip" version)) | |
5268 | (sha256 | |
5269 | (base32 | |
59fd6915 | 5270 | "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb")))) |
d182828f RW |
5271 | (build-system r-build-system) |
5272 | (home-page "https://github.com/gaborcsardi/zip") | |
5273 | (synopsis "Cross-platform Zip compression") | |
5274 | (description | |
5275 | "This package provides a cross-platform Zip compression library for R. | |
5276 | It is a replacement for the @code{zip} function, that does not require any | |
5277 | additional external tools on any platform.") | |
5278 | (license license:cc0))) | |
5279 | ||
4b1f7a3e RW |
5280 | (define-public r-openxlsx |
5281 | (package | |
5282 | (name "r-openxlsx") | |
9dd35123 | 5283 | (version "4.1.0.1") |
4b1f7a3e RW |
5284 | (source |
5285 | (origin | |
5286 | (method url-fetch) | |
5287 | (uri (cran-uri "openxlsx" version)) | |
5288 | (sha256 | |
5289 | (base32 | |
9dd35123 | 5290 | "1lflygpi1z4rlb1c6g6wsmi334maiiy7jhpg6ph4sw8lpvg12w4b")))) |
4b1f7a3e | 5291 | (build-system r-build-system) |
a8b4677b RW |
5292 | (propagated-inputs |
5293 | `(("r-rcpp" ,r-rcpp) | |
5294 | ("r-zip" ,r-zip))) | |
4b1f7a3e RW |
5295 | (home-page "https://github.com/awalker89/openxlsx") |
5296 | (synopsis "Read, write and edit XLSX files") | |
5297 | (description | |
5298 | "This package simplifies the creation of Excel @code{.xlsx} files by | |
5299 | providing a high level interface to writing, styling and editing worksheets. | |
5300 | Through the use of Rcpp, read/write times are comparable to the @code{xlsx} | |
5301 | and @code{XLConnect} packages with the added benefit of removing the | |
5302 | dependency on Java.") | |
5303 | (license license:gpl3))) | |
c9920f25 RW |
5304 | |
5305 | (define-public r-rio | |
5306 | (package | |
5307 | (name "r-rio") | |
1417d5f1 | 5308 | (version "0.5.16") |
c9920f25 RW |
5309 | (source |
5310 | (origin | |
5311 | (method url-fetch) | |
5312 | (uri (cran-uri "rio" version)) | |
5313 | (sha256 | |
5314 | (base32 | |
1417d5f1 | 5315 | "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) |
c9920f25 RW |
5316 | (build-system r-build-system) |
5317 | (propagated-inputs | |
5318 | `(("r-curl" ,r-curl) | |
5319 | ("r-data-table" ,r-data-table) | |
5320 | ("r-foreign" ,r-foreign) | |
5321 | ("r-haven" ,r-haven) | |
5322 | ("r-openxlsx" ,r-openxlsx) | |
5323 | ("r-readxl" ,r-readxl) | |
5324 | ("r-tibble" ,r-tibble))) | |
5325 | (home-page "https://github.com/leeper/rio") | |
5326 | (synopsis "Swiss-army knife for data I/O") | |
5327 | (description | |
5328 | "This package provides streamlined data import and export infrastructure | |
5329 | by making assumptions that the user is probably willing to make: @code{import} | |
5330 | and @code{export} determine the data structure from the file extension, | |
5331 | reasonable defaults are used for data import and export (e.g., | |
5332 | @code{stringsAsFactors=FALSE}), web-based import is natively | |
5333 | supported (including from SSL/HTTPS), compressed files can be read directly | |
5334 | without explicit decompression, and fast import packages are used where | |
5335 | appropriate. An additional convenience function, @code{convert}, provides a | |
5336 | simple method for converting between file types.") | |
5337 | (license license:gpl2))) | |
08dac3d9 RW |
5338 | |
5339 | (define-public r-maptools | |
5340 | (package | |
5341 | (name "r-maptools") | |
bbe94211 | 5342 | (version "0.9-5") |
08dac3d9 RW |
5343 | (source |
5344 | (origin | |
5345 | (method url-fetch) | |
5346 | (uri (cran-uri "maptools" version)) | |
5347 | (sha256 | |
5348 | (base32 | |
bbe94211 | 5349 | "1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax")))) |
08dac3d9 RW |
5350 | (build-system r-build-system) |
5351 | (propagated-inputs | |
5352 | `(("r-foreign" ,r-foreign) | |
5353 | ("r-lattice" ,r-lattice) | |
5354 | ("r-sp" ,r-sp))) | |
5355 | (home-page "http://r-forge.r-project.org/projects/maptools/") | |
5356 | (synopsis "Tools for reading and handling spatial objects") | |
5357 | (description | |
5358 | "This package provides a set of tools for manipulating and reading | |
5359 | geographic data, in particular ESRI Shapefiles. It includes binary access to | |
5360 | GSHHG shoreline files. The package also provides interface wrappers for | |
5361 | exchanging spatial objects with other R packages.") | |
5362 | ;; The C source files from shapelib are released under the Expat license. | |
5363 | ;; The R code is released under GPL version 2 or later. | |
5364 | (license (list license:gpl2+ | |
5365 | license:expat)))) | |
284179bb RW |
5366 | |
5367 | (define-public r-later | |
5368 | (package | |
5369 | (name "r-later") | |
00fb3203 | 5370 | (version "0.8.0") |
284179bb RW |
5371 | (source |
5372 | (origin | |
5373 | (method url-fetch) | |
5374 | (uri (cran-uri "later" version)) | |
5375 | (sha256 | |
5376 | (base32 | |
00fb3203 | 5377 | "08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb")))) |
284179bb RW |
5378 | (build-system r-build-system) |
5379 | (propagated-inputs | |
5380 | `(("r-bh" ,r-bh) | |
5381 | ("r-rcpp" ,r-rcpp) | |
5382 | ("r-rlang" ,r-rlang))) | |
5383 | (home-page "https://github.com/r-lib/later") | |
5384 | (synopsis "Utilities for delaying function execution") | |
5385 | (description | |
5386 | "This package provides tools to execute arbitrary R or C functions some | |
5387 | time after the current time, after the R execution stack has emptied.") | |
5388 | (license license:gpl2+))) | |
d9d66ba9 RW |
5389 | |
5390 | (define-public r-promises | |
5391 | (package | |
5392 | (name "r-promises") | |
5393 | (version "1.0.1") | |
5394 | (source | |
5395 | (origin | |
5396 | (method url-fetch) | |
5397 | (uri (cran-uri "promises" version)) | |
5398 | (sha256 | |
5399 | (base32 | |
5400 | "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2")))) | |
5401 | (build-system r-build-system) | |
5402 | (propagated-inputs | |
5403 | `(("r-later" ,r-later) | |
5404 | ("r-magrittr" ,r-magrittr) | |
5405 | ("r-r6" ,r-r6) | |
5406 | ("r-rcpp" ,r-rcpp) | |
5407 | ("r-rlang" ,r-rlang))) | |
5408 | (home-page "https://rstudio.github.io/promises") | |
5409 | (synopsis "Abstractions for promise-based asynchronous programming") | |
5410 | (description | |
5411 | "This package provides fundamental abstractions for doing asynchronous | |
5412 | programming in R using promises. Asynchronous programming is useful for | |
5413 | allowing a single R process to orchestrate multiple tasks in the background | |
5414 | while also attending to something else. Semantics are similar to JavaScript | |
5415 | promises, but with a syntax that is idiomatic R.") | |
5416 | (license license:expat))) | |
3cf9ae2f RW |
5417 | |
5418 | (define-public r-dosnow | |
5419 | (package | |
5420 | (name "r-dosnow") | |
e3abc134 | 5421 | (version "1.0.18") |
3cf9ae2f RW |
5422 | (source |
5423 | (origin | |
5424 | (method url-fetch) | |
5425 | (uri (cran-uri "doSNOW" version)) | |
5426 | (sha256 | |
5427 | (base32 | |
e3abc134 | 5428 | "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh")))) |
3cf9ae2f RW |
5429 | (properties `((upstream-name . "doSNOW"))) |
5430 | (build-system r-build-system) | |
5431 | (propagated-inputs | |
5432 | `(("r-foreach" ,r-foreach) | |
5433 | ("r-iterators" ,r-iterators) | |
5434 | ("r-snow" ,r-snow))) | |
5435 | (home-page "https://cran.r-project.org/web/packages/doSNOW") | |
5436 | (synopsis "Foreach parallel adaptor for the snow package") | |
5437 | (description | |
5438 | "This package provides a parallel backend for the @code{%dopar%} function | |
5439 | using the @code{snow} package.") | |
5440 | (license license:gpl2))) | |
fdc3a05d RJ |
5441 | |
5442 | (define-public r-snowfall | |
5443 | (package | |
5444 | (name "r-snowfall") | |
5445 | (version "1.84-6.1") | |
5446 | (source (origin | |
5447 | (method url-fetch) | |
5448 | (uri (cran-uri "snowfall" version)) | |
5449 | (sha256 | |
5450 | (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) | |
5451 | (build-system r-build-system) | |
5452 | (propagated-inputs | |
5453 | `(("r-snow" ,r-snow))) | |
5454 | (home-page "http://cran.r-project.org/web/packages/snowfall/") | |
5455 | (synopsis "Easier cluster computing") | |
5456 | (description "This package is a usability wrapper around snow for easier | |
5457 | development of parallel R programs. This package offers e.g. extended error | |
5458 | checks, and additional functions. All functions work in sequential mode, too, | |
5459 | if no cluster is present or wished. The package is also designed as connector | |
5460 | to the cluster management tool @code{sfCluster}, but can also used without | |
5461 | it.") | |
5462 | (license license:gpl2+))) | |
e09d74ec | 5463 | |
94a8990f RW |
5464 | (define-public r-rappdirs |
5465 | (package | |
5466 | (name "r-rappdirs") | |
5467 | (version "0.3.1") | |
5468 | (source | |
5469 | (origin | |
5470 | (method url-fetch) | |
5471 | (uri (cran-uri "rappdirs" version)) | |
5472 | (sha256 | |
5473 | (base32 | |
5474 | "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g")))) | |
5475 | (build-system r-build-system) | |
5476 | (home-page "https://cran.r-project.org/web/packages/rappdirs/") | |
5477 | (synopsis "Determine where to save data, caches, and logs") | |
5478 | (description | |
5479 | "This package provides an easy way to determine which directories on the | |
5480 | user's computer should be used to save data, caches and logs. It is a port of | |
5481 | Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") | |
5482 | (license license:expat))) | |
2b47ebe1 RW |
5483 | |
5484 | (define-public r-learnr | |
5485 | (package | |
5486 | (name "r-learnr") | |
7d0370ed | 5487 | (version "0.9.2.1") |
2b47ebe1 RW |
5488 | (source |
5489 | (origin | |
5490 | (method url-fetch) | |
5491 | (uri (cran-uri "learnr" version)) | |
5492 | (sha256 | |
5493 | (base32 | |
7d0370ed | 5494 | "0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5")))) |
2b47ebe1 RW |
5495 | (build-system r-build-system) |
5496 | (propagated-inputs | |
5497 | `(("r-evaluate" ,r-evaluate) | |
5498 | ("r-htmltools" ,r-htmltools) | |
5499 | ("r-htmlwidgets" ,r-htmlwidgets) | |
5500 | ("r-jsonlite" ,r-jsonlite) | |
5501 | ("r-knitr" ,r-knitr) | |
5502 | ("r-markdown" ,r-markdown) | |
5503 | ("r-rappdirs" ,r-rappdirs) | |
5504 | ("r-rmarkdown" ,r-rmarkdown) | |
5505 | ("r-rprojroot" ,r-rprojroot) | |
5506 | ("r-shiny" ,r-shiny) | |
5507 | ("r-withr" ,r-withr))) | |
5508 | (home-page "https://rstudio.github.io/learnr/") | |
5509 | (synopsis "Interactive tutorials for R") | |
5510 | (description | |
5511 | "This package provides tools to create interactive tutorials using R | |
5512 | Markdown. Use a combination of narrative, figures, videos, exercises, and | |
5513 | quizzes to create self-paced tutorials for learning about R and R packages.") | |
5514 | (license license:asl2.0))) | |
12591673 RW |
5515 | |
5516 | (define-public r-analytics | |
5517 | (package | |
5518 | (name "r-analytics") | |
7a06cdfa | 5519 | (version "3.0") |
12591673 RW |
5520 | (source |
5521 | (origin | |
5522 | (method url-fetch) | |
5523 | (uri (cran-uri "analytics" version)) | |
5524 | (sha256 | |
5525 | (base32 | |
7a06cdfa | 5526 | "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) |
12591673 RW |
5527 | (build-system r-build-system) |
5528 | (propagated-inputs | |
5529 | `(("r-car" ,r-car) | |
5530 | ("r-cluster" ,r-cluster) | |
5531 | ("r-fractal" ,r-fractal) | |
5532 | ("r-lmtest" ,r-lmtest) | |
5533 | ("r-mass" ,r-mass) | |
5534 | ("r-np" ,r-np) | |
5535 | ("r-powerplus" ,r-powerplus) | |
5536 | ("r-robust" ,r-robust) | |
5537 | ("r-trend" ,r-trend) | |
5538 | ("r-tsa" ,r-tsa) | |
7a06cdfa RW |
5539 | ("r-urca" ,r-urca) |
5540 | ("r-vim" ,r-vim))) | |
12591673 RW |
5541 | (home-page "https://cran.r-project.org/web/packages/analytics/") |
5542 | (synopsis "Collection of data analysis tools") | |
5543 | (description | |
5544 | "This package is a collection of data analysis tools. It includes tools | |
5545 | for regression outlier detection in a fitted linear model, stationary | |
5546 | bootstrap using a truncated geometric distribution, a comprehensive test for | |
5547 | weak stationarity, column means by group, weighted biplots, and a heuristic to | |
5548 | obtain a better initial configuration in non-metric MDS.") | |
5549 | (license license:gpl2))) | |
9f56ceec RW |
5550 | |
5551 | (define-public r-reticulate | |
5552 | (package | |
5553 | (name "r-reticulate") | |
2d363778 | 5554 | (version "1.13") |
9f56ceec RW |
5555 | (source |
5556 | (origin | |
5557 | (method url-fetch) | |
5558 | (uri (cran-uri "reticulate" version)) | |
5559 | (sha256 | |
5560 | (base32 | |
2d363778 | 5561 | "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd")))) |
9f56ceec RW |
5562 | (build-system r-build-system) |
5563 | (inputs `(("python" ,python))) | |
5564 | (propagated-inputs | |
5565 | `(("r-jsonlite" ,r-jsonlite) | |
5566 | ("r-matrix" ,r-matrix) | |
5567 | ("r-rcpp" ,r-rcpp))) | |
5568 | (home-page "https://github.com/rstudio/reticulate") | |
5569 | (synopsis "R interface to Python") | |
5570 | (description | |
5571 | "This package provides an interface from R to Python modules, classes, | |
5572 | and functions. When calling into Python, R data types are automatically | |
5573 | converted to their equivalent Python types. When values are returned from | |
5574 | Python to R they are converted back to R types.") | |
5575 | (license license:asl2.0))) | |
11de8673 RW |
5576 | |
5577 | (define-public r-bibtex | |
5578 | (package | |
5579 | (name "r-bibtex") | |
5580 | (version "0.4.2") | |
5581 | (source | |
5582 | (origin | |
5583 | (method url-fetch) | |
5584 | (uri (cran-uri "bibtex" version)) | |
5585 | (sha256 | |
5586 | (base32 | |
5587 | "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz")))) | |
5588 | (build-system r-build-system) | |
5589 | (propagated-inputs `(("r-stringr" ,r-stringr))) | |
5590 | (home-page "https://github.com/romainfrancois/bibtex") | |
5591 | (synopsis "Bibtex parser") | |
5592 | (description "This package provides a utility for R to parse a bibtex | |
5593 | file.") | |
5594 | (license license:gpl2+))) | |
e67acae7 RW |
5595 | |
5596 | (define-public r-ggseqlogo | |
5597 | (package | |
5598 | (name "r-ggseqlogo") | |
5599 | (version "0.1") | |
5600 | (source | |
5601 | (origin | |
5602 | (method url-fetch) | |
5603 | (uri (cran-uri "ggseqlogo" version)) | |
5604 | (sha256 | |
5605 | (base32 | |
5606 | "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1")))) | |
5607 | (build-system r-build-system) | |
5608 | (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) | |
5609 | (home-page "https://github.com/omarwagih/ggseqlogo") | |
5610 | (synopsis "ggplot2 extension for drawing genetic sequence logos") | |
5611 | (description | |
5612 | "The range of functions provided by this package makes it possible to | |
5613 | draw highly versatile genomic sequence logos. Features include, but are not | |
5614 | limited to, modifying colour schemes and fonts used to draw the logo, | |
5615 | generating multiple logo plots, and aiding the visualisation with annotations. | |
5616 | Sequence logos can easily be combined with other ggplot2 plots.") | |
5617 | ;; Unspecified version of the LGPL. | |
5618 | (license license:lgpl3+))) | |
85df1a86 RW |
5619 | |
5620 | (define-public r-ggsci | |
5621 | (package | |
5622 | (name "r-ggsci") | |
5623 | (version "2.9") | |
5624 | (source | |
5625 | (origin | |
5626 | (method url-fetch) | |
5627 | (uri (cran-uri "ggsci" version)) | |
5628 | (sha256 | |
5629 | (base32 | |
5630 | "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) | |
5631 | (build-system r-build-system) | |
5632 | (propagated-inputs | |
5633 | `(("r-ggplot2" ,r-ggplot2) | |
5634 | ("r-scales" ,r-scales))) | |
5635 | (home-page "https://nanx.me/ggsci/") | |
5636 | (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") | |
5637 | (description | |
5638 | "This package provides a collection of ggplot2 color palettes inspired by | |
5639 | plots in scientific journals, data visualization libraries, science fiction | |
5640 | movies, and TV shows.") | |
5641 | (license license:gpl3))) | |
5219c5c5 RW |
5642 | |
5643 | (define-public r-ggsignif | |
5644 | (package | |
5645 | (name "r-ggsignif") | |
d099499e | 5646 | (version "0.6.0") |
5219c5c5 RW |
5647 | (source |
5648 | (origin | |
5649 | (method url-fetch) | |
5650 | (uri (cran-uri "ggsignif" version)) | |
5651 | (sha256 | |
5652 | (base32 | |
d099499e | 5653 | "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg")))) |
5219c5c5 RW |
5654 | (build-system r-build-system) |
5655 | (propagated-inputs | |
5656 | `(("r-ggplot2" ,r-ggplot2))) | |
5657 | (home-page "https://github.com/const-ae/ggsignif") | |
5658 | (synopsis "Significance brackets for ggplot2") | |
5659 | (description | |
5660 | "Enrich your ggplots with group-wise comparisons. This package provides | |
5661 | an easy way to indicate if two groups are significantly different. Commonly | |
5662 | this is shown by a bracket on top connecting the groups of interest which | |
5663 | itself is annotated with the level of significance. The package provides a | |
5664 | single layer that takes the groups for comparison and the test as arguments | |
5665 | and adds the annotation to the plot.") | |
5666 | (license license:gpl3))) | |
5cbaaee8 RW |
5667 | |
5668 | (define-public r-ggpubr | |
5669 | (package | |
5670 | (name "r-ggpubr") | |
f11920c7 | 5671 | (version "0.2.3") |
5cbaaee8 RW |
5672 | (source |
5673 | (origin | |
5674 | (method url-fetch) | |
5675 | (uri (cran-uri "ggpubr" version)) | |
5676 | (sha256 | |
5677 | (base32 | |
f11920c7 | 5678 | "0i81mmz4qn9yzcgfa6dhkcrx4ddlflkm2c3b40isc8all43rm8rn")))) |
5cbaaee8 RW |
5679 | (build-system r-build-system) |
5680 | (propagated-inputs | |
5681 | `(("r-cowplot" ,r-cowplot) | |
5682 | ("r-dplyr" ,r-dplyr) | |
5683 | ("r-ggplot2" ,r-ggplot2) | |
5684 | ("r-ggrepel" ,r-ggrepel) | |
5685 | ("r-ggsci" ,r-ggsci) | |
5686 | ("r-ggsignif" ,r-ggsignif) | |
caaec886 | 5687 | ("r-glue" ,r-glue) |
5cbaaee8 RW |
5688 | ("r-gridextra" ,r-gridextra) |
5689 | ("r-magrittr" ,r-magrittr) | |
caaec886 | 5690 | ("r-polynom" ,r-polynom) |
5cbaaee8 | 5691 | ("r-purrr" ,r-purrr) |
2132e922 | 5692 | ("r-rlang" ,r-rlang) |
5cbaaee8 RW |
5693 | ("r-scales" ,r-scales) |
5694 | ("r-tidyr" ,r-tidyr))) | |
5695 | (home-page "http://www.sthda.com/english/rpkgs/ggpubr") | |
5696 | (synopsis "ggplot2-based publication-ready plots") | |
5697 | (description | |
5698 | "The ggplot2 package is an excellent and flexible package for elegant | |
5699 | data visualization in R. However the default generated plots require some | |
5700 | formatting before we can send them for publication. The ggpubr package | |
5701 | provides some easy-to-use functions for creating and customizing ggplot2-based | |
5702 | publication-ready plots.") | |
5703 | (license license:gpl2))) | |
141e43bd RW |
5704 | |
5705 | (define-public r-ellipse | |
5706 | (package | |
5707 | (name "r-ellipse") | |
5708 | (version "0.4.1") | |
5709 | (source | |
5710 | (origin | |
5711 | (method url-fetch) | |
5712 | (uri (cran-uri "ellipse" version)) | |
5713 | (sha256 | |
5714 | (base32 | |
5715 | "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs")))) | |
5716 | (build-system r-build-system) | |
5717 | (home-page "https://cran.r-project.org/web/packages/ellipse/") | |
5718 | (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") | |
5719 | (description | |
5720 | "This package contains various routines for drawing ellipses and | |
5721 | ellipse-like confidence regions, implementing the plots described in Murdoch | |
5722 | and Chow (1996), A graphical display of large correlation matrices, The | |
5723 | American Statistician 50, 178-180. There are also routines implementing the | |
5724 | profile plots described in Bates and Watts (1988), Nonlinear Regression | |
5725 | Analysis and its Applications.") | |
5726 | (license license:gpl2+))) | |
cbf6017d RW |
5727 | |
5728 | (define-public r-flashclust | |
5729 | (package | |
5730 | (name "r-flashclust") | |
5731 | (version "1.01-2") | |
5732 | (source | |
5733 | (origin | |
5734 | (method url-fetch) | |
5735 | (uri (cran-uri "flashClust" version)) | |
5736 | (sha256 | |
5737 | (base32 | |
5738 | "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) | |
5739 | (properties `((upstream-name . "flashClust"))) | |
5740 | (build-system r-build-system) | |
5741 | (native-inputs `(("gfortran" ,gfortran))) | |
5742 | (home-page "https://cran.r-project.org/web/packages/flashClust/") | |
5743 | (synopsis "Implementation of optimal hierarchical clustering") | |
5744 | (description | |
5745 | "This package provides a fast implementation of hierarchical | |
5746 | clustering.") | |
5747 | (license license:gpl2+))) | |
e83841a2 RW |
5748 | |
5749 | (define-public r-factominer | |
5750 | (package | |
5751 | (name "r-factominer") | |
c187e8f6 | 5752 | (version "1.42") |
e83841a2 RW |
5753 | (source |
5754 | (origin | |
5755 | (method url-fetch) | |
5756 | (uri (cran-uri "FactoMineR" version)) | |
5757 | (sha256 | |
5758 | (base32 | |
c187e8f6 | 5759 | "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac")))) |
e83841a2 RW |
5760 | (properties `((upstream-name . "FactoMineR"))) |
5761 | (build-system r-build-system) | |
5762 | (propagated-inputs | |
5763 | `(("r-car" ,r-car) | |
5764 | ("r-cluster" ,r-cluster) | |
5765 | ("r-ellipse" ,r-ellipse) | |
5766 | ("r-flashclust" ,r-flashclust) | |
5767 | ("r-lattice" ,r-lattice) | |
5768 | ("r-leaps" ,r-leaps) | |
5769 | ("r-mass" ,r-mass) | |
5770 | ("r-scatterplot3d" ,r-scatterplot3d))) | |
5771 | (home-page "http://factominer.free.fr") | |
5772 | (synopsis "Multivariate exploratory data analysis and data mining") | |
5773 | (description | |
5774 | "This package provides exploratory data analysis methods to summarize, | |
5775 | visualize and describe datasets. The main principal component methods are | |
5776 | available, those with the largest potential in terms of applications: | |
5777 | principal component analysis (PCA) when variables are quantitative, | |
5778 | correspondence analysis (CA) and multiple correspondence analysis (MCA) when | |
5779 | variables are categorical, Multiple Factor Analysis when variables are | |
5780 | structured in groups, etc. and hierarchical cluster analysis.") | |
5781 | (license license:gpl2+))) | |
f22bfee9 RW |
5782 | |
5783 | (define-public r-factoextra | |
5784 | (package | |
5785 | (name "r-factoextra") | |
5786 | (version "1.0.5") | |
5787 | (source | |
5788 | (origin | |
5789 | (method url-fetch) | |
5790 | (uri (cran-uri "factoextra" version)) | |
5791 | (sha256 | |
5792 | (base32 | |
5793 | "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1")))) | |
5794 | (build-system r-build-system) | |
5795 | (propagated-inputs | |
5796 | `(("r-abind" ,r-abind) | |
5797 | ("r-cluster" ,r-cluster) | |
5798 | ("r-dendextend" ,r-dendextend) | |
5799 | ("r-factominer" ,r-factominer) | |
5800 | ("r-ggplot2" ,r-ggplot2) | |
5801 | ("r-ggpubr" ,r-ggpubr) | |
5802 | ("r-ggrepel" ,r-ggrepel) | |
5803 | ("r-reshape2" ,r-reshape2) | |
5804 | ("r-tidyr" ,r-tidyr))) | |
5805 | (home-page "http://www.sthda.com/english/rpkgs/factoextra") | |
5806 | (synopsis "Extract and visualize the results of multivariate data analyses") | |
5807 | (description | |
5808 | "This package provides some easy-to-use functions to extract and | |
5809 | visualize the output of multivariate data analyses, including | |
6ccd88e8 RW |
5810 | @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence |
5811 | Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor | |
5812 | Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and | |
f22bfee9 RW |
5813 | @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R |
5814 | packages. It contains also functions for simplifying some clustering analysis | |
5815 | steps and provides ggplot2-based elegant data visualization.") | |
5816 | (license license:gpl2))) | |
0c9868aa | 5817 | |
356230da RW |
5818 | (define-public r-fansi |
5819 | (package | |
5820 | (name "r-fansi") | |
08645fcf | 5821 | (version "0.4.0") |
356230da RW |
5822 | (source |
5823 | (origin | |
5824 | (method url-fetch) | |
5825 | (uri (cran-uri "fansi" version)) | |
5826 | (sha256 | |
5827 | (base32 | |
08645fcf | 5828 | "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171")))) |
356230da RW |
5829 | (build-system r-build-system) |
5830 | (native-inputs | |
5831 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
5832 | (home-page "https://github.com/brodieG/fansi") | |
5833 | (synopsis "ANSI control sequence aware string functions") | |
5834 | (description | |
5835 | "This package provides counterparts to R string manipulation functions | |
5836 | that account for the effects of ANSI text formatting control sequences.") | |
5837 | (license license:gpl2+))) | |
5838 | ||
0c9868aa RW |
5839 | (define-public r-nbclust |
5840 | (package | |
5841 | (name "r-nbclust") | |
5842 | (version "3.0") | |
5843 | (source | |
5844 | (origin | |
5845 | (method url-fetch) | |
5846 | (uri (cran-uri "NbClust" version)) | |
5847 | (sha256 | |
5848 | (base32 | |
5849 | "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c")))) | |
5850 | (properties `((upstream-name . "NbClust"))) | |
5851 | (build-system r-build-system) | |
5852 | (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package") | |
5853 | (synopsis "Determine the best number of clusters in a data set") | |
5854 | (description | |
5855 | "NbClust provides 30 indexes for determining the optimal number of | |
5856 | clusters in a data set and offers the best clustering scheme from different | |
5857 | results to the user.") | |
5858 | (license license:gpl2))) | |
546fc4aa RW |
5859 | |
5860 | (define-public r-hdf5r | |
5861 | (package | |
5862 | (name "r-hdf5r") | |
17ae31b7 | 5863 | (version "1.2.0") |
546fc4aa RW |
5864 | (source |
5865 | (origin | |
5866 | (method url-fetch) | |
5867 | (uri (cran-uri "hdf5r" version)) | |
5868 | (sha256 | |
5869 | (base32 | |
17ae31b7 | 5870 | "10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq")))) |
546fc4aa RW |
5871 | (build-system r-build-system) |
5872 | (inputs | |
5873 | `(("hdf5" ,hdf5) | |
5874 | ("zlib" ,zlib))) | |
5875 | (propagated-inputs | |
5876 | `(("r-bit64" ,r-bit64) | |
5877 | ("r-r6" ,r-r6))) | |
5878 | (home-page "https://hhoeflin.github.io/hdf5r") | |
5879 | (synopsis "Interface to the HDF5 binary data format") | |
5880 | (description | |
5881 | "HDF5 is a data model, library and file format for storing and managing | |
5882 | large amounts of data. This package provides a nearly feature complete, | |
5883 | object oriented wrapper for the HDF5 API using R6 classes. Additionally, | |
5884 | functionality is added so that HDF5 objects behave very similar to their | |
5885 | corresponding R counterparts.") | |
5886 | (license license:asl2.0))) | |
846325a8 | 5887 | |
3568b823 RW |
5888 | (define-public r-itertools |
5889 | (package | |
5890 | (name "r-itertools") | |
5891 | (version "0.1-3") | |
5892 | (source | |
5893 | (origin | |
5894 | (method url-fetch) | |
5895 | (uri (cran-uri "itertools" version)) | |
5896 | (sha256 | |
5897 | (base32 | |
5898 | "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn")))) | |
5899 | (build-system r-build-system) | |
5900 | (propagated-inputs | |
5901 | `(("r-iterators" ,r-iterators))) | |
5902 | (home-page "https://cran.r-project.org/web/packages/itertools/") | |
5903 | (synopsis "Iterator tools") | |
5904 | (description | |
5905 | "This package provides various tools for creating iterators, many | |
5906 | patterned after functions in the Python @code{itertools} module, and others | |
5907 | patterned after functions in the snow package.") | |
5908 | (license license:gpl2))) | |
5909 | ||
53718658 RW |
5910 | (define-public r-polynom |
5911 | (package | |
5912 | (name "r-polynom") | |
3be585cf | 5913 | (version "1.4-0") |
53718658 RW |
5914 | (source |
5915 | (origin | |
5916 | (method url-fetch) | |
5917 | (uri (cran-uri "polynom" version)) | |
5918 | (sha256 | |
5919 | (base32 | |
3be585cf | 5920 | "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5")))) |
53718658 RW |
5921 | (build-system r-build-system) |
5922 | (home-page "https://cran.r-project.org/web/packages/polynom/") | |
5923 | (synopsis "Functions for univariate polynomial manipulations") | |
5924 | (description | |
5925 | "This package provides a collection of functions to implement a class for | |
5926 | univariate polynomial manipulations.") | |
5927 | (license license:gpl2))) | |
5928 | ||
dd954dd7 RW |
5929 | (define-public r-gbrd |
5930 | (package | |
5931 | (name "r-gbrd") | |
5932 | (version "0.4-11") | |
5933 | (source | |
5934 | (origin | |
5935 | (method url-fetch) | |
5936 | (uri (cran-uri "gbRd" version)) | |
5937 | (sha256 | |
5938 | (base32 | |
5939 | "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82")))) | |
5940 | (properties `((upstream-name . "gbRd"))) | |
5941 | (build-system r-build-system) | |
5942 | (home-page "https://cran.r-project.org/web/packages/gbRd/") | |
5943 | (synopsis "Utilities for processing Rd objects and files") | |
5944 | (description | |
5945 | "This package provides utilities for processing Rd objects and files. | |
5946 | Extract argument descriptions and other parts of the help pages of | |
5947 | functions.") | |
5948 | (license license:gpl2+))) | |
5949 | ||
0c92f373 RW |
5950 | (define-public r-rjags |
5951 | (package | |
5952 | (name "r-rjags") | |
86e243a2 | 5953 | (version "4-9") |
0c92f373 RW |
5954 | (source |
5955 | (origin | |
5956 | (method url-fetch) | |
5957 | (uri (cran-uri "rjags" version)) | |
5958 | (sha256 | |
5959 | (base32 | |
86e243a2 | 5960 | "1vrmxxfnia2mkmfkp5yaq5qrlh4xg3ggab6fnj14mrp1231wb91a")))) |
0c92f373 RW |
5961 | (build-system r-build-system) |
5962 | (propagated-inputs | |
5963 | `(("r-coda" ,r-coda))) | |
5964 | (inputs | |
5965 | `(("jags" ,jags))) | |
5966 | (native-inputs | |
5967 | `(("pkg-config" ,pkg-config))) | |
5968 | (home-page "http://mcmc-jags.sourceforge.net") | |
5969 | (synopsis "Bayesian graphical models using MCMC") | |
5970 | (description | |
5971 | "This package provides an R interface to the JAGS MCMC library. JAGS is | |
5972 | Just Another Gibbs Sampler. It is a program for analysis of Bayesian | |
5973 | hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") | |
5974 | (license license:gpl2))) | |
5975 | ||
6a846975 RW |
5976 | (define-public r-rdpack |
5977 | (package | |
5978 | (name "r-rdpack") | |
f0826fec | 5979 | (version "0.11-0") |
6a846975 RW |
5980 | (source |
5981 | (origin | |
5982 | (method url-fetch) | |
5983 | (uri (cran-uri "Rdpack" version)) | |
5984 | (sha256 | |
5985 | (base32 | |
f0826fec | 5986 | "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g")))) |
6a846975 RW |
5987 | (properties `((upstream-name . "Rdpack"))) |
5988 | (build-system r-build-system) | |
5989 | (propagated-inputs | |
5990 | `(("r-bibtex" ,r-bibtex) | |
5991 | ("r-gbrd" ,r-gbrd))) | |
5992 | (home-page "https://github.com/GeoBosh/Rdpack") | |
5993 | (synopsis "Update and manipulate Rd documentation objects") | |
5994 | (description | |
5995 | "This package provides functions for manipulation of R documentation | |
5996 | objects, including functions @code{reprompt()} and @code{ereprompt()} for | |
5997 | updating Rd documentation for functions, methods and classes; it also includes | |
5998 | Rd macros for citations and import of references from bibtex files for use in | |
5999 | Rd files and roxygen2 comments, as well as many functions for manipulation of | |
6000 | references and Rd files.") | |
6001 | (license license:gpl2+))) | |
6002 | ||
c183fa26 RW |
6003 | (define-public r-officer |
6004 | (package | |
6005 | (name "r-officer") | |
0d2e2662 | 6006 | (version "0.3.5") |
c183fa26 RW |
6007 | (source |
6008 | (origin | |
6009 | (method url-fetch) | |
6010 | (uri (cran-uri "officer" version)) | |
6011 | (sha256 | |
6012 | (base32 | |
0d2e2662 | 6013 | "005kaxjhr40shpav2pg7s7gj8f49579r7rbgwlncbwv16nn0rbbg")))) |
c183fa26 RW |
6014 | (build-system r-build-system) |
6015 | (propagated-inputs | |
6016 | `(("r-base64enc" ,r-base64enc) | |
6017 | ("r-digest" ,r-digest) | |
6018 | ("r-htmltools" ,r-htmltools) | |
6019 | ("r-magrittr" ,r-magrittr) | |
6020 | ("r-r6" ,r-r6) | |
6021 | ("r-rcpp" ,r-rcpp) | |
fd1a17a5 | 6022 | ("r-rlang" ,r-rlang) |
c183fa26 RW |
6023 | ("r-uuid" ,r-uuid) |
6024 | ("r-xml2" ,r-xml2) | |
6025 | ("r-zip" ,r-zip))) | |
6026 | (home-page "https://davidgohel.github.io/officer") | |
6027 | (synopsis "Manipulation of Word and PowerPoint documents") | |
6028 | (description | |
6029 | "This package provides tools to access and manipulate Word and PowerPoint | |
6030 | documents from R. The package focuses on tabular and graphical reporting from | |
6031 | R; it also provides two functions that let users get document content into | |
6032 | data objects. A set of functions lets add and remove images, tables and | |
6033 | paragraphs of text in new or existing documents. When working with PowerPoint | |
6034 | presentations, slides can be added or removed; shapes inside slides can also | |
6035 | be added or removed. When working with Word documents, a cursor can be used | |
6036 | to help insert or delete content at a specific location in the document.") | |
6037 | (license license:gpl3))) | |
6038 | ||
488dc4e1 RW |
6039 | (define-public r-abn |
6040 | (package | |
6041 | (name "r-abn") | |
72c967e2 | 6042 | (version "2.1") |
488dc4e1 RW |
6043 | (source |
6044 | (origin | |
6045 | (method url-fetch) | |
6046 | (uri (cran-uri "abn" version)) | |
6047 | (sha256 | |
6048 | (base32 | |
72c967e2 | 6049 | "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b")))) |
488dc4e1 RW |
6050 | (build-system r-build-system) |
6051 | (inputs | |
6052 | `(("gsl" ,gsl))) | |
6053 | (propagated-inputs | |
72c967e2 | 6054 | `(("r-lme4" ,r-lme4) |
488dc4e1 RW |
6055 | ("r-mass" ,r-mass) |
6056 | ("r-nnet" ,r-nnet) | |
6057 | ("r-rcpp" ,r-rcpp) | |
6058 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6059 | ("r-rjags" ,r-rjags))) | |
6060 | (home-page "http://www.r-bayesian-networks.org") | |
6061 | (synopsis "Modelling multivariate data with additive bayesian networks") | |
6062 | (description | |
6063 | "Bayesian network analysis is a form of probabilistic graphical models | |
6064 | which derives from empirical data a directed acyclic graph, DAG, describing | |
6065 | the dependency structure between random variables. An additive Bayesian | |
6066 | network model consists of a form of a DAG where each node comprises a | |
6067 | @dfn{generalized linear model} (GLM). Additive Bayesian network models are | |
6068 | equivalent to Bayesian multivariate regression using graphical modelling, they | |
6069 | generalises the usual multivariable regression, GLM, to multiple dependent | |
6070 | variables. This package provides routines to help determine optimal Bayesian | |
6071 | network models for a given data set, where these models are used to identify | |
6072 | statistical dependencies in messy, complex data.") | |
6073 | (license license:gpl2+))) | |
6074 | ||
ffdeda3c RW |
6075 | (define-public r-acd |
6076 | (package | |
6077 | (name "r-acd") | |
6078 | (version "1.5.3") | |
6079 | (source | |
6080 | (origin | |
6081 | (method url-fetch) | |
6082 | (uri (cran-uri "ACD" version)) | |
6083 | (sha256 | |
6084 | (base32 | |
6085 | "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6")))) | |
6086 | (properties `((upstream-name . "ACD"))) | |
6087 | (build-system r-build-system) | |
6088 | (home-page "https://cran.r-project.org/web/packages/ACD/") | |
6089 | (synopsis "Categorical data analysis with complete or missing responses") | |
6090 | (description | |
6091 | "This package provides tools for categorical data analysis with complete | |
6092 | or missing responses.") | |
6093 | (license license:gpl2+))) | |
6094 | ||
acbf23da RW |
6095 | (define-public r-acdm |
6096 | (package | |
6097 | (name "r-acdm") | |
6098 | (version "1.0.4") | |
6099 | (source | |
6100 | (origin | |
6101 | (method url-fetch) | |
6102 | (uri (cran-uri "ACDm" version)) | |
6103 | (sha256 | |
6104 | (base32 | |
6105 | "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil")))) | |
6106 | (properties `((upstream-name . "ACDm"))) | |
6107 | (build-system r-build-system) | |
6108 | (propagated-inputs | |
6109 | `(("r-dplyr" ,r-dplyr) | |
6110 | ("r-ggplot2" ,r-ggplot2) | |
6111 | ("r-plyr" ,r-plyr) | |
6112 | ("r-rsolnp" ,r-rsolnp) | |
6113 | ("r-zoo" ,r-zoo))) | |
6114 | (home-page "https://cran.r-project.org/web/packages/ACDm/") | |
6115 | (synopsis "Tools for Autoregressive Conditional Duration Models") | |
6116 | (description | |
6117 | "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle | |
6118 | and Russell, 1998) models. It creates trade, price or volume durations from | |
6119 | transactions (tic) data, performs diurnal adjustments, fits various ACD models | |
6120 | and tests them.") | |
6121 | (license license:gpl2+))) | |
6122 | ||
08bf097a RW |
6123 | (define-public r-overlap |
6124 | (package | |
6125 | (name "r-overlap") | |
6126 | (version "0.3.2") | |
6127 | (source | |
6128 | (origin | |
6129 | (method url-fetch) | |
6130 | (uri (cran-uri "overlap" version)) | |
6131 | (sha256 | |
6132 | (base32 | |
6133 | "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy")))) | |
6134 | (build-system r-build-system) | |
6135 | (home-page "https://cran.r-project.org/web/packages/overlap/") | |
6136 | (synopsis "Estimates of coefficient of overlapping for animal activity patterns") | |
6137 | (description | |
6138 | "This package provides functions to fit kernel density functions to data | |
6139 | on temporal activity patterns of animals; estimate coefficients of overlapping | |
6140 | of densities for two species; and calculate bootstrap estimates of confidence | |
6141 | intervals.") | |
6142 | (license license:gpl3+))) | |
6143 | ||
bfee9ce8 RW |
6144 | (define-public r-snakecase |
6145 | (package | |
6146 | (name "r-snakecase") | |
794c9e7d | 6147 | (version "0.11.0") |
bfee9ce8 RW |
6148 | (source |
6149 | (origin | |
6150 | (method url-fetch) | |
6151 | (uri (cran-uri "snakecase" version)) | |
6152 | (sha256 | |
6153 | (base32 | |
794c9e7d | 6154 | "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r")))) |
bfee9ce8 RW |
6155 | (build-system r-build-system) |
6156 | (propagated-inputs | |
6157 | `(("r-stringi" ,r-stringi) | |
6158 | ("r-stringr" ,r-stringr))) | |
6159 | (home-page "https://github.com/Tazinho/snakecase") | |
6160 | (synopsis "Convert strings into any case") | |
6161 | (description | |
6162 | "This package provides a consistent, flexible and easy to use tool to | |
6163 | parse and convert strings into cases like snake or camel among others.") | |
6164 | (license license:gpl3))) | |
6165 | ||
de059e4b RW |
6166 | (define-public r-prediction |
6167 | (package | |
6168 | (name "r-prediction") | |
c3447a92 | 6169 | (version "0.3.14") |
de059e4b RW |
6170 | (source |
6171 | (origin | |
6172 | (method url-fetch) | |
6173 | (uri (cran-uri "prediction" version)) | |
6174 | (sha256 | |
6175 | (base32 | |
c3447a92 | 6176 | "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx")))) |
de059e4b RW |
6177 | (build-system r-build-system) |
6178 | (propagated-inputs | |
6179 | `(("r-data-table" ,r-data-table))) | |
6180 | (home-page "https://github.com/leeper/prediction") | |
6181 | (synopsis "Tidy, type-safe prediction methods") | |
6182 | (description | |
6183 | "This package provides the @code{prediction()} function, a type-safe | |
6184 | alternative to @code{predict()} that always returns a data frame. The package | |
6185 | currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"}) | |
6186 | from the @code{stats} package, as well as numerous other model classes from | |
6187 | other add-on packages.") | |
6188 | (license license:expat))) | |
6189 | ||
d14c770d RW |
6190 | (define-public r-insight |
6191 | (package | |
6192 | (name "r-insight") | |
c90eebf7 | 6193 | (version "0.5.0") |
d14c770d RW |
6194 | (source |
6195 | (origin | |
6196 | (method url-fetch) | |
6197 | (uri (cran-uri "insight" version)) | |
6198 | (sha256 | |
6199 | (base32 | |
c90eebf7 | 6200 | "0lrh2l9n2zd9n3zzknsxz6nlasnrayx3bplxlz7m616g56gr5nfp")))) |
d14c770d RW |
6201 | (build-system r-build-system) |
6202 | (home-page "https://easystats.github.io/insight/") | |
6203 | (synopsis "Easy access to model information for various model objects") | |
6204 | (description | |
6205 | "This package provides a tool to provide an easy, intuitive and | |
6206 | consistent access to information contained in various R models, like model | |
6207 | formulas, model terms, information about random effects, data that was used to | |
6208 | fit the model or data from response variables. The package mainly revolves | |
6209 | around two types of functions: Functions that find (the names of) information, | |
6210 | starting with @code{find_}, and functions that get the underlying data, | |
6211 | starting with @code{get_}. The package has a consistent syntax and works with | |
6212 | many different model objects, where otherwise functions to access these | |
6213 | information are missing.") | |
6214 | (license license:gpl3))) | |
6215 | ||
cfc06314 RW |
6216 | (define-public r-sjlabelled |
6217 | (package | |
6218 | (name "r-sjlabelled") | |
3ab3f7f3 | 6219 | (version "1.1.1") |
cfc06314 RW |
6220 | (source |
6221 | (origin | |
6222 | (method url-fetch) | |
6223 | (uri (cran-uri "sjlabelled" version)) | |
6224 | (sha256 | |
6225 | (base32 | |
3ab3f7f3 | 6226 | "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz")))) |
cfc06314 RW |
6227 | (build-system r-build-system) |
6228 | (propagated-inputs | |
bc418c97 | 6229 | `(("r-haven" ,r-haven) |
5e16dff9 | 6230 | ("r-insight" ,r-insight) |
cfc06314 | 6231 | ("r-magrittr" ,r-magrittr) |
cfc06314 | 6232 | ("r-purrr" ,r-purrr) |
bc418c97 RW |
6233 | ("r-rlang" ,r-rlang) |
6234 | ("r-tidyselect" ,r-tidyselect))) | |
cfc06314 RW |
6235 | (home-page "https://github.com/strengejacke/sjlabelled") |
6236 | (synopsis "Labelled data utility functions") | |
6237 | (description | |
6238 | "This package provides a collection of functions dealing with labelled | |
6239 | data, like reading and writing data between R and other statistical software | |
6240 | packages. This includes easy ways to get, set or change value and variable | |
6241 | label attributes, to convert labelled vectors into factors or numeric (and | |
6242 | vice versa), or to deal with multiple declared missing values.") | |
6243 | (license license:gpl3))) | |
6244 | ||
1f560b9c RW |
6245 | (define-public r-sjmisc |
6246 | (package | |
6247 | (name "r-sjmisc") | |
14c3e7bb | 6248 | (version "2.8.2") |
1f560b9c RW |
6249 | (source |
6250 | (origin | |
6251 | (method url-fetch) | |
6252 | (uri (cran-uri "sjmisc" version)) | |
6253 | (sha256 | |
6254 | (base32 | |
14c3e7bb | 6255 | "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2")))) |
1f560b9c RW |
6256 | (build-system r-build-system) |
6257 | (propagated-inputs | |
31af2e7f | 6258 | `(("r-dplyr" ,r-dplyr) |
45dcc89d | 6259 | ("r-insight" ,r-insight) |
1f560b9c | 6260 | ("r-magrittr" ,r-magrittr) |
1f560b9c RW |
6261 | ("r-purrr" ,r-purrr) |
6262 | ("r-rlang" ,r-rlang) | |
14c3e7bb RW |
6263 | ("r-sjlabelled" ,r-sjlabelled) |
6264 | ("r-tidyselect" ,r-tidyselect))) | |
1f560b9c RW |
6265 | (home-page "https://github.com/strengejacke/sjmisc") |
6266 | (synopsis "Data and variable transformation functions") | |
6267 | (description | |
6268 | "This package is a collection of miscellaneous utility functions, | |
6269 | supporting data transformation tasks like recoding, dichotomizing or grouping | |
6270 | variables, setting and replacing missing values. The data transformation | |
6271 | functions also support labelled data, and all integrate seamlessly into a | |
6272 | tidyverse workflow.") | |
6273 | (license license:gpl3))) | |
6274 | ||
aaed237d RW |
6275 | (define-public r-nortest |
6276 | (package | |
6277 | (name "r-nortest") | |
6278 | (version "1.0-4") | |
6279 | (source | |
6280 | (origin | |
6281 | (method url-fetch) | |
6282 | (uri (cran-uri "nortest" version)) | |
6283 | (sha256 | |
6284 | (base32 | |
6285 | "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3")))) | |
6286 | (build-system r-build-system) | |
6287 | (home-page "https://cran.r-project.org/web/packages/nortest/") | |
6288 | (synopsis "Tests for normality") | |
6289 | (description | |
6290 | "This package provides five omnibus tests for testing the composite | |
6291 | hypothesis of normality.") | |
6292 | (license license:gpl2+))) | |
6293 | ||
0fd7d59d RW |
6294 | (define-public r-moonbook |
6295 | (package | |
6296 | (name "r-moonbook") | |
6297 | (version "0.2.3") | |
6298 | (source | |
6299 | (origin | |
6300 | (method url-fetch) | |
6301 | (uri (cran-uri "moonBook" version)) | |
6302 | (sha256 | |
6303 | (base32 | |
6304 | "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6")))) | |
6305 | (properties `((upstream-name . "moonBook"))) | |
6306 | (build-system r-build-system) | |
6307 | (propagated-inputs | |
6308 | `(("r-magrittr" ,r-magrittr) | |
6309 | ("r-nortest" ,r-nortest) | |
6310 | ("r-purrr" ,r-purrr) | |
6311 | ("r-sjmisc" ,r-sjmisc) | |
6312 | ("r-stringr" ,r-stringr) | |
6313 | ("r-survival" ,r-survival))) | |
6314 | (home-page "https://github.com/cardiomoon/moonBook") | |
6315 | (synopsis "Functions and datasets for the book by Keon-Woong Moon") | |
6316 | (description | |
6317 | "This package provides several analysis-related functions for the book | |
6318 | entitled \"R statistics and graph for medical articles\" (written in Korean), | |
6319 | version 1, by Keon-Woong Moon with Korean demographic data with several plot | |
6320 | functions.") | |
6321 | (license license:gpl2))) | |
6322 | ||
589bd1c4 RW |
6323 | (define-public r-flextable |
6324 | (package | |
6325 | (name "r-flextable") | |
c46a1640 | 6326 | (version "0.5.5") |
589bd1c4 RW |
6327 | (source |
6328 | (origin | |
6329 | (method url-fetch) | |
6330 | (uri (cran-uri "flextable" version)) | |
6331 | (sha256 | |
6332 | (base32 | |
c46a1640 | 6333 | "1q6x9mfk5gikqjbbra1dn8hs1rq5ws99jdjav3m113gx9f2j5yxh")))) |
589bd1c4 RW |
6334 | (build-system r-build-system) |
6335 | (propagated-inputs | |
30918ce8 RW |
6336 | `(("r-base64enc" ,r-base64enc) |
6337 | ("r-data-table" ,r-data-table) | |
e89d5427 | 6338 | ("r-gdtools" ,r-gdtools) |
589bd1c4 RW |
6339 | ("r-htmltools" ,r-htmltools) |
6340 | ("r-knitr" ,r-knitr) | |
6341 | ("r-officer" ,r-officer) | |
e89d5427 | 6342 | ("r-rlang" ,r-rlang) |
589bd1c4 | 6343 | ("r-rmarkdown" ,r-rmarkdown) |
589bd1c4 RW |
6344 | ("r-xml2" ,r-xml2))) |
6345 | (home-page "https://davidgohel.github.io/flextable") | |
6346 | (synopsis "Functions for tabular reporting") | |
6347 | (description | |
6348 | "This package provides tools to create pretty tables for HTML documents | |
6349 | and other formats. Functions are provided to let users create tables, modify | |
6350 | and format their content. It extends the @code{officer} package and can be | |
6351 | used within R markdown documents when rendering to HTML and to Word | |
6352 | documents.") | |
6353 | (license license:gpl3))) | |
6354 | ||
846325a8 RW |
6355 | (define-public r-writexl |
6356 | (package | |
6357 | (name "r-writexl") | |
04a18a81 | 6358 | (version "1.1") |
846325a8 RW |
6359 | (source |
6360 | (origin | |
6361 | (method url-fetch) | |
6362 | (uri (cran-uri "writexl" version)) | |
6363 | (sha256 | |
6364 | (base32 | |
04a18a81 | 6365 | "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46")))) |
846325a8 RW |
6366 | (build-system r-build-system) |
6367 | (inputs `(("zlib" ,zlib))) | |
6368 | (home-page "https://github.com/ropensci/writexl") | |
6369 | (synopsis "Export data frames to xlsx format") | |
6370 | (description | |
6371 | "This package provides a data frame to xlsx exporter based on | |
6372 | libxlsxwriter.") | |
6373 | (license license:bsd-2))) | |
64abd245 RW |
6374 | |
6375 | (define-public r-biasedurn | |
6376 | (package | |
6377 | (name "r-biasedurn") | |
6378 | (version "1.07") | |
6379 | (source | |
6380 | (origin | |
6381 | (method url-fetch) | |
6382 | (uri (cran-uri "BiasedUrn" version)) | |
6383 | (sha256 | |
6384 | (base32 | |
6385 | "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) | |
6386 | (properties `((upstream-name . "BiasedUrn"))) | |
6387 | (build-system r-build-system) | |
6388 | (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") | |
6389 | (synopsis "Biased Urn model distributions") | |
6390 | (description | |
6391 | "This package provides statistical models of biased sampling in the form | |
6392 | of univariate and multivariate noncentral hypergeometric distributions, | |
6393 | including Wallenius' noncentral hypergeometric distribution and Fisher's | |
6394 | noncentral hypergeometric distribution (also called extended hypergeometric | |
6395 | distribution).") | |
6396 | (license license:gpl3))) | |
87ba9508 RW |
6397 | |
6398 | (define-public r-goplot | |
6399 | (package | |
6400 | (name "r-goplot") | |
6401 | (version "1.0.2") | |
6402 | (source | |
6403 | (origin | |
6404 | (method url-fetch) | |
6405 | (uri (cran-uri "GOplot" version)) | |
6406 | (sha256 | |
6407 | (base32 | |
6408 | "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix")))) | |
6409 | (properties `((upstream-name . "GOplot"))) | |
6410 | (build-system r-build-system) | |
6411 | (propagated-inputs | |
6412 | `(("r-ggdendro" ,r-ggdendro) | |
6413 | ("r-ggplot2" ,r-ggplot2) | |
6414 | ("r-gridextra" ,r-gridextra) | |
6415 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
6416 | (home-page "https://github.com/wencke/wencke.github.io") | |
6417 | (synopsis "Visualization of functional analysis data") | |
6418 | (description | |
6419 | "This package provides an implementation of multilayered visualizations | |
6420 | for enhanced graphical representation of functional analysis data. It | |
6421 | combines and integrates omics data derived from expression and functional | |
6422 | annotation enrichment analyses. Its plotting functions have been developed | |
6423 | with an hierarchical structure in mind: starting from a general overview to | |
6424 | identify the most enriched categories (modified bar plot, bubble plot) to a | |
6425 | more detailed one displaying different types of relevant information for the | |
6426 | molecules in a given set of categories (circle plot, chord plot, cluster plot, | |
6427 | Venn diagram, heatmap).") | |
6428 | (license license:gpl2))) | |
aec7d6be RW |
6429 | |
6430 | (define-public r-getopt | |
6431 | (package | |
6432 | (name "r-getopt") | |
104ec4c9 | 6433 | (version "1.20.3") |
aec7d6be RW |
6434 | (source |
6435 | (origin | |
6436 | (method url-fetch) | |
6437 | (uri (cran-uri "getopt" version)) | |
6438 | (sha256 | |
6439 | (base32 | |
104ec4c9 | 6440 | "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk")))) |
aec7d6be RW |
6441 | (build-system r-build-system) |
6442 | (home-page "https://github.com/trevorld/getopt") | |
6443 | (synopsis "Command-line option processor for R") | |
6444 | (description | |
6445 | "This package is designed to be used with Rscript to write shebang | |
6446 | scripts that accept short and long options. Many users will prefer to | |
6447 | use the packages @code{optparse} or @code{argparse} which add extra | |
6448 | features like automatically generated help options and usage texts, | |
6449 | support for default values, positional argument support, etc.") | |
6450 | (license license:gpl2+))) | |
3629622b RW |
6451 | |
6452 | (define-public r-findpython | |
6453 | (package | |
6454 | (name "r-findpython") | |
fcb84565 | 6455 | (version "1.0.5") |
3629622b RW |
6456 | (source |
6457 | (origin | |
6458 | (method url-fetch) | |
6459 | (uri (cran-uri "findpython" version)) | |
6460 | (sha256 | |
6461 | (base32 | |
fcb84565 | 6462 | "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy")))) |
3629622b RW |
6463 | (build-system r-build-system) |
6464 | (home-page "https://github.com/trevorld/findpython") | |
6465 | (synopsis "Functions to find an acceptable Python binary") | |
6466 | (description | |
6467 | "This package was designed to find an acceptable Python binary that | |
6468 | matches version and feature constraints.") | |
6469 | (license license:expat))) | |
fa697599 RW |
6470 | |
6471 | ;; This in not the same as "r-argparser" | |
6472 | (define-public r-argparse | |
6473 | (package | |
6474 | (name "r-argparse") | |
37317189 | 6475 | (version "2.0.1") |
fa697599 RW |
6476 | (source |
6477 | (origin | |
6478 | (method url-fetch) | |
6479 | (uri (cran-uri "argparse" version)) | |
6480 | (sha256 | |
6481 | (base32 | |
37317189 | 6482 | "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l")))) |
fa697599 RW |
6483 | (build-system r-build-system) |
6484 | (inputs `(("python" ,python))) | |
6485 | (propagated-inputs | |
6486 | `(("r-findpython" ,r-findpython) | |
fa697599 | 6487 | ("r-jsonlite" ,r-jsonlite) |
11a36548 | 6488 | ("r-r6" ,r-r6))) |
fa697599 RW |
6489 | (home-page "https://github.com/trevorld/argparse") |
6490 | (synopsis "Command line optional and positional argument parser") | |
6491 | (description | |
6492 | "This package provides a command line parser to be used with Rscript to | |
6493 | write shebang scripts that gracefully accept positional and optional arguments | |
6494 | and automatically generate usage notices.") | |
6495 | (license license:gpl2+))) | |
4646d18e RW |
6496 | |
6497 | (define-public r-hash | |
6498 | (package | |
6499 | (name "r-hash") | |
a431c381 | 6500 | (version "2.2.6.1") |
4646d18e RW |
6501 | (source |
6502 | (origin | |
6503 | (method url-fetch) | |
6504 | (uri (cran-uri "hash" version)) | |
6505 | (sha256 | |
6506 | (base32 | |
a431c381 | 6507 | "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056")))) |
4646d18e RW |
6508 | (build-system r-build-system) |
6509 | (home-page "https://cran.r-project.org/web/packages/hash/") | |
6510 | (synopsis "Implementation of hash/associated arrays/dictionaries") | |
6511 | (description | |
6512 | "This package implements a data structure similar to hashes in Perl and | |
6513 | dictionaries in Python but with a purposefully R flavor. For objects of | |
6514 | appreciable size, access using hashes outperforms native named lists and | |
6515 | vectors.") | |
6516 | (license license:gpl2+))) | |
06a45ad6 RW |
6517 | |
6518 | (define-public r-orddom | |
6519 | (package | |
6520 | (name "r-orddom") | |
6521 | (version "3.1") | |
6522 | (source | |
6523 | (origin | |
6524 | (method url-fetch) | |
6525 | (uri (cran-uri "orddom" version)) | |
6526 | (sha256 | |
6527 | (base32 | |
6528 | "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) | |
6529 | (build-system r-build-system) | |
6530 | (propagated-inputs `(("r-psych" ,r-psych))) | |
6531 | (home-page "https://cran.r-project.org/web/packages/orddom/") | |
6532 | (synopsis "Ordinal dominance statistics") | |
6533 | (description | |
6534 | "This package provides tools to compute ordinal, statistics and effect | |
6535 | sizes as an alternative to mean comparison: Cliff's delta or success rate | |
6536 | difference (SRD), Vargha and Delaney's A or the Area Under a Receiver | |
6537 | Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's | |
6538 | Common Language Effect Size (CLES) or Grissom & Kim's Probability of | |
6539 | Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover, | |
6540 | comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of | |
6541 | Group (Non-)Overlap considerations.") | |
6542 | (license license:gpl2))) | |
0fccd15f RW |
6543 | |
6544 | (define-public r-doby | |
6545 | (package | |
6546 | (name "r-doby") | |
cb96d81b | 6547 | (version "4.6-2") |
0fccd15f RW |
6548 | (source |
6549 | (origin | |
6550 | (method url-fetch) | |
6551 | (uri (cran-uri "doBy" version)) | |
6552 | (sha256 | |
6553 | (base32 | |
cb96d81b | 6554 | "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb")))) |
0fccd15f RW |
6555 | (properties `((upstream-name . "doBy"))) |
6556 | (build-system r-build-system) | |
6557 | (propagated-inputs | |
6558 | `(("r-dplyr" ,r-dplyr) | |
6559 | ("r-magrittr" ,r-magrittr) | |
6560 | ("r-mass" ,r-mass) | |
6561 | ("r-matrix" ,r-matrix) | |
6562 | ("r-plyr" ,r-plyr))) | |
6563 | (home-page "http://people.math.aau.dk/~sorenh/software/doBy/") | |
6564 | (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") | |
6565 | (description | |
6566 | "This package contains: | |
6567 | ||
6568 | @itemize | |
6569 | @item facilities for working with grouped data: @code{do} | |
6570 | something to data stratified @code{by} some variables. | |
6571 | @item implementations of least-squares means, general linear contrasts, and | |
6572 | @item miscellaneous other utilities. | |
6573 | @end itemize\n") | |
6574 | (license license:gpl2+))) | |
5850c5b3 RW |
6575 | |
6576 | (define-public r-refgenome | |
6577 | (package | |
6578 | (name "r-refgenome") | |
27abdb11 | 6579 | (version "1.7.7") |
5850c5b3 RW |
6580 | (source |
6581 | (origin | |
6582 | (method url-fetch) | |
6583 | (uri (cran-uri "refGenome" version)) | |
6584 | (sha256 | |
6585 | (base32 | |
27abdb11 | 6586 | "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5")))) |
5850c5b3 RW |
6587 | (properties `((upstream-name . "refGenome"))) |
6588 | (build-system r-build-system) | |
6589 | (propagated-inputs | |
6590 | `(("r-dbi" ,r-dbi) | |
6591 | ("r-doby" ,r-doby) | |
6592 | ("r-rsqlite" ,r-rsqlite))) | |
6593 | (home-page "https://cran.r-project.org/web/packages/refGenome/") | |
6594 | (synopsis | |
6595 | "Gene and splice site annotation using annotation data from Ensembl and UCSC") | |
6596 | (description | |
6597 | "This package contains functionality for importing and managing of | |
6598 | downloaded genome annotation data from the Ensembl genome browser (European | |
6599 | Bioinformatics Institute) and from the UCSC genome browser (University of | |
6600 | California, Santa Cruz) and annotation routines for genomic positions and | |
6601 | splice site positions.") | |
6602 | (license license:gpl2))) | |
ff7d53a7 RW |
6603 | |
6604 | (define-public r-basix | |
6605 | (package | |
6606 | (name "r-basix") | |
6607 | (version "1.1") | |
6608 | (source | |
6609 | (origin | |
6610 | (method url-fetch) | |
6611 | (uri (cran-uri "BASIX" version)) | |
6612 | (sha256 | |
6613 | (base32 | |
6614 | "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id")))) | |
6615 | (properties `((upstream-name . "BASIX"))) | |
6616 | (build-system r-build-system) | |
6617 | (home-page "https://cran.r-project.org/web/packages/BASIX/") | |
6618 | (synopsis "Efficient C/C++ toolset for R") | |
6619 | (description | |
6620 | "BASIX provides some efficient C/C++ implementations of native R | |
6621 | procedures to speed up calculations in R.") | |
6622 | (license license:gpl2))) | |
65e74814 RW |
6623 | |
6624 | (define-public r-blockfest | |
6625 | (package | |
6626 | (name "r-blockfest") | |
6627 | (version "1.6") | |
6628 | (source | |
6629 | (origin | |
6630 | (method url-fetch) | |
6631 | (uri (cran-uri "BlockFeST" version)) | |
6632 | (sha256 | |
6633 | (base32 | |
6634 | "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) | |
6635 | (properties `((upstream-name . "BlockFeST"))) | |
6636 | (build-system r-build-system) | |
6637 | (propagated-inputs `(("r-basix" ,r-basix))) | |
6638 | (home-page "https://cran.r-project.org/web/packages/BlockFeST/") | |
6639 | (synopsis "Bayesian calculation of region-specific fixation index") | |
6640 | (description | |
6641 | "This package provides an R implementation of an extension of the | |
6642 | BayeScan software for codominant markers, adding the option to group | |
6643 | individual SNPs into pre-defined blocks. A typical application of this new | |
6644 | approach is the identification of genomic regions, genes, or gene sets | |
6645 | containing one or more SNPs that evolved under directional selection.") | |
6646 | (license license:gpl2))) | |
b9ff2599 | 6647 | |
fbdf05b1 RW |
6648 | (define-public r-proc |
6649 | (package | |
6650 | (name "r-proc") | |
a510dc60 | 6651 | (version "1.15.3") |
fbdf05b1 RW |
6652 | (source |
6653 | (origin | |
6654 | (method url-fetch) | |
6655 | (uri (cran-uri "pROC" version)) | |
6656 | (sha256 | |
6657 | (base32 | |
a510dc60 | 6658 | "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h")))) |
fbdf05b1 RW |
6659 | (properties `((upstream-name . "pROC"))) |
6660 | (build-system r-build-system) | |
6661 | (propagated-inputs | |
a3daf011 | 6662 | `(("r-plyr" ,r-plyr) |
fbdf05b1 RW |
6663 | ("r-rcpp" ,r-rcpp))) |
6664 | (home-page "http://expasy.org/tools/pROC/") | |
6665 | (synopsis "Display and analyze ROC curves") | |
6666 | (description | |
6667 | "This package provides tools for visualizing, smoothing and comparing | |
6668 | receiver operating characteristic (ROC curves). The area under the | |
6669 | curve (AUC) can be compared with statistical tests based on U-statistics or | |
6670 | bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") | |
6671 | (license license:gpl3+))) | |
cea4d360 RW |
6672 | |
6673 | (define-public r-rootsolve | |
6674 | (package | |
6675 | (name "r-rootsolve") | |
6676 | (version "1.7") | |
6677 | (source | |
6678 | (origin | |
6679 | (method url-fetch) | |
6680 | (uri (cran-uri "rootSolve" version)) | |
6681 | (sha256 | |
6682 | (base32 | |
6683 | "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8")))) | |
6684 | (properties `((upstream-name . "rootSolve"))) | |
6685 | (build-system r-build-system) | |
6686 | (native-inputs `(("gfortran" ,gfortran))) | |
6687 | (home-page "https://cran.r-project.org/web/packages/rootSolve/") | |
6688 | (synopsis "Tools for the analysis of ordinary differential equations") | |
6689 | (description | |
6690 | "This package provides routines to find the root of nonlinear functions, | |
6691 | and to perform steady-state and equilibrium analysis of @dfn{ordinary | |
6692 | differential equations} (ODE). It includes routines that: | |
6693 | ||
6694 | @enumerate | |
6695 | @item generate gradient and jacobian matrices (full and banded), | |
6696 | @item find roots of non-linear equations by the Newton-Raphson method, | |
6697 | @item estimate steady-state conditions of a system of (differential) equations | |
6698 | in full, banded or sparse form, using the Newton-Raphson method, or by | |
6699 | dynamically running, | |
6700 | @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, | |
6701 | and 3-D partial differential equations, that have been converted to ordinary | |
6702 | differential equations by numerical differencing (using the method-of-lines | |
6703 | approach). | |
6704 | @end enumerate\n") | |
6705 | (license license:gpl2+))) | |
c994418b | 6706 | |
6707 | (define-public r-abcanalysis | |
6708 | (package | |
6709 | (name "r-abcanalysis") | |
6710 | (version "1.2.1") | |
6711 | (source | |
6712 | (origin | |
6713 | (method url-fetch) | |
6714 | (uri (cran-uri "ABCanalysis" version)) | |
6715 | (sha256 | |
6716 | (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) | |
6717 | (properties `((upstream-name . "ABCanalysis"))) | |
6718 | (build-system r-build-system) | |
6719 | (propagated-inputs `(("r-plotrix" ,r-plotrix))) | |
6720 | (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") | |
6721 | (synopsis "Computed ABC Analysis") | |
6722 | (description | |
6723 | "Multivariate data sets often differ in several factors or derived statistical | |
6724 | parameters, which have to be selected for a valid interpretation. Basing this | |
6725 | selection on traditional statistical limits leads occasionally to the perception | |
6726 | of losing information from a data set. This package provides tools to calculate | |
6727 | these limits on the basis of the mathematical properties of the distribution of | |
6728 | the analyzed items.") | |
6729 | (license license:gpl3))) | |
87b576aa | 6730 | |
6731 | (define-public r-slam | |
6732 | (package | |
6733 | (name "r-slam") | |
1007b1b6 | 6734 | (version "0.1-45") |
87b576aa | 6735 | (source |
6736 | (origin | |
6737 | (method url-fetch) | |
6738 | (uri (cran-uri "slam" version)) | |
6739 | (sha256 | |
1007b1b6 | 6740 | (base32 "0xvj8va6xd7zkn3l4a5ad7v62s7xmkz8frq7gpcl3b6vqwckkaw4")))) |
87b576aa | 6741 | (build-system r-build-system) |
6742 | (home-page "https://cran.r-project.org/web/packages/slam/") | |
6743 | (synopsis "Sparse lightweight arrays and matrices") | |
6744 | (description | |
6745 | "This package contains data structures and algorithms for sparse arrays and matrices, | |
6746 | based on index arrays and simple triplet representations, respectively.") | |
6747 | (license license:gpl2))) | |
881cc61c | 6748 | |
6749 | (define-public r-manipulatewidget | |
6750 | (package | |
6751 | (name "r-manipulatewidget") | |
6752 | (version "0.10.0") | |
6753 | (source | |
6754 | (origin | |
6755 | (method url-fetch) | |
6756 | (uri (cran-uri "manipulateWidget" version)) | |
6757 | (sha256 | |
6758 | (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x")))) | |
6759 | (properties | |
6760 | `((upstream-name . "manipulateWidget"))) | |
6761 | (build-system r-build-system) | |
6762 | (propagated-inputs | |
6763 | `(("r-base64enc" ,r-base64enc) | |
6764 | ("r-codetools" ,r-codetools) | |
6765 | ("r-htmltools" ,r-htmltools) | |
6766 | ("r-htmlwidgets" ,r-htmlwidgets) | |
6767 | ("r-knitr" ,r-knitr) | |
6768 | ("r-miniui" ,r-miniui) | |
6769 | ("r-shiny" ,r-shiny) | |
6770 | ("r-webshot" ,r-webshot))) | |
6771 | (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") | |
6772 | (synopsis "Add even more interactivity to interactive charts") | |
6773 | (description | |
6774 | "This package lets you create in just a few lines of R code a nice user interface to | |
6775 | modify the data or the graphical parameters of one or multiple interactive | |
6776 | charts. It is useful to quickly explore visually some data or for package | |
6777 | developers to generate user interfaces easy to maintain.") | |
6778 | (license license:gpl2+))) | |
16b0e8da | 6779 | |
6780 | (define-public r-a3 | |
6781 | (package | |
6782 | (name "r-a3") | |
6783 | (version "1.0.0") | |
6784 | (source | |
6785 | (origin | |
6786 | (method url-fetch) | |
6787 | (uri (cran-uri "A3" version)) | |
6788 | (sha256 | |
6789 | (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) | |
6790 | (properties `((upstream-name . "A3"))) | |
6791 | (build-system r-build-system) | |
6792 | (propagated-inputs | |
6793 | `(("r-pbapply" ,r-pbapply) | |
6794 | ("r-xtable" ,r-xtable))) | |
6795 | (home-page "https://cran.r-project.org/web/packages/A3/") | |
6796 | (synopsis "Error metrics for predictive models") | |
6797 | (description | |
6798 | "This package supplies tools for tabulating and analyzing the results of predictive | |
6799 | models. The methods employed are applicable to virtually any predictive model | |
6800 | and make comparisons between different methodologies straightforward.") | |
6801 | (license license:gpl2+))) | |
59b55def RW |
6802 | |
6803 | (define-public r-infotheo | |
6804 | (package | |
6805 | (name "r-infotheo") | |
6806 | (version "1.2.0") | |
6807 | (source | |
6808 | (origin | |
6809 | (method url-fetch) | |
6810 | (uri (cran-uri "infotheo" version)) | |
6811 | (sha256 | |
6812 | (base32 | |
6813 | "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv")))) | |
6814 | (build-system r-build-system) | |
6815 | (home-page "http://homepage.meyerp.com/software") | |
6816 | (synopsis "Information-theoretic measures") | |
6817 | (description | |
6818 | "This package implements various measures of information theory based on | |
6819 | several entropy estimators.") | |
6820 | (license license:gpl3+))) | |
9e21f217 | 6821 | |
6822 | (define-public r-abcoptim | |
6823 | (package | |
6824 | (name "r-abcoptim") | |
6825 | (version "0.15.0") | |
6826 | (source | |
6827 | (origin | |
6828 | (method url-fetch) | |
6829 | (uri (cran-uri "ABCoptim" version)) | |
6830 | (sha256 | |
6831 | (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) | |
6832 | (properties `((upstream-name . "ABCoptim"))) | |
6833 | (build-system r-build-system) | |
6834 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
6835 | (home-page "https://github.com/gvegayon/ABCoptim/") | |
6836 | (synopsis "Optimization of Artificial Bee Colony algorithm") | |
6837 | (description | |
6838 | "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis | |
6839 | Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as | |
6840 | simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) | |
6841 | algorithms, and uses only common control parameters such as colony size and | |
6842 | maximum cycle number. The @code{r-abcoptim} implements the Artificial bee | |
6843 | colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. | |
6844 | This version is a work-in-progress and is written in R code.") | |
6845 | (license license:expat))) | |
40c10917 | 6846 | |
6847 | (define-public r-abcp2 | |
6848 | (package | |
6849 | (name "r-abcp2") | |
6850 | (version "1.2") | |
6851 | (source | |
6852 | (origin | |
6853 | (method url-fetch) | |
6854 | (uri (cran-uri "ABCp2" version)) | |
6855 | (sha256 | |
6856 | (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) | |
6857 | (properties `((upstream-name . "ABCp2"))) | |
6858 | (build-system r-build-system) | |
6859 | (propagated-inputs `(("r-mass" ,r-mass))) | |
6860 | (home-page "https://cran.r-project.org/web/packages/ABCp2/") | |
6861 | (synopsis "Approximate Bayesian Computational Model for Estimating P2") | |
6862 | (description | |
6863 | "This package tests the goodness of fit of a distribution of offspring to the Normal, | |
6864 | Poisson, and Gamma distribution and estimates the proportional paternity of the | |
6865 | second male (P2) based on the best fit distribution.") | |
6866 | (license license:gpl2))) | |
cadc10a5 | 6867 | |
6868 | (define-public r-abcrf | |
6869 | (package | |
6870 | (name "r-abcrf") | |
89afd031 | 6871 | (version "1.8") |
cadc10a5 | 6872 | (source |
6873 | (origin | |
6874 | (method url-fetch) | |
6875 | (uri (cran-uri "abcrf" version)) | |
6876 | (sha256 | |
89afd031 | 6877 | (base32 "0r31ki89z8zzcffm0yvd2zw3q96rk6g6fnwwkql902mgajbrha1f")))) |
cadc10a5 | 6878 | (build-system r-build-system) |
6879 | (propagated-inputs | |
89afd031 RW |
6880 | `(("r-doparallel" ,r-doparallel) |
6881 | ("r-foreach" ,r-foreach) | |
6882 | ("r-mass" ,r-mass) | |
cadc10a5 | 6883 | ("r-matrixstats" ,r-matrixstats) |
6884 | ("r-ranger" ,r-ranger) | |
6885 | ("r-rcpp" ,r-rcpp) | |
6886 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6887 | ("r-readr" ,r-readr) | |
6888 | ("r-stringr" ,r-stringr))) | |
6889 | (home-page "https://cran.r-project.org/web/packages/abcrf/") | |
6890 | (synopsis "Approximate bayesian computation via random forests") | |
6891 | (description | |
6892 | "This package performs approximate bayesian computation (ABC) model choice and | |
6893 | parameter inference via random forests. This machine learning tool named random | |
6894 | forests (RF) can conduct selection among the highly complex models covered by | |
6895 | ABC algorithms.") | |
6896 | (license license:gpl2+))) | |
12da2a5e | 6897 | |
6898 | (define-public r-abctools | |
6899 | (package | |
6900 | (name "r-abctools") | |
6901 | (version "1.1.3") | |
6902 | (source | |
6903 | (origin | |
6904 | (method url-fetch) | |
6905 | (uri (cran-uri "abctools" version)) | |
6906 | (sha256 | |
6907 | (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) | |
6908 | (build-system r-build-system) | |
6909 | (propagated-inputs | |
6910 | `(("r-abc" ,r-abc) | |
6911 | ("r-abind" ,r-abind) | |
6912 | ("r-hmisc" ,r-hmisc) | |
6913 | ("r-plyr" ,r-plyr))) | |
6914 | (home-page "https://github.com/dennisprangle/abctools/") | |
6915 | (synopsis "Tools for ABC analyses") | |
6916 | (description | |
6917 | "This @code{r-abctools} package provides tools for approximate Bayesian computation | |
6918 | including summary statistic selection and assessing coverage. This includes | |
6919 | recent dimension reduction algorithms to tune the choice of summary statistics, | |
6920 | and coverage methods to tune the choice of threshold.") | |
6921 | (license license:gpl2+))) | |
77b33e0e | 6922 | |
6923 | (define-public r-ggstance | |
6924 | (package | |
6925 | (name "r-ggstance") | |
b3aa0d2f | 6926 | (version "0.3.3") |
77b33e0e | 6927 | (source |
6928 | (origin | |
6929 | (method url-fetch) | |
6930 | (uri (cran-uri "ggstance" version)) | |
6931 | (sha256 | |
b3aa0d2f | 6932 | (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh")))) |
77b33e0e | 6933 | (build-system r-build-system) |
6934 | (propagated-inputs | |
6935 | `(("r-ggplot2" ,r-ggplot2) | |
6936 | ("r-plyr" ,r-plyr) | |
6937 | ("r-rlang" ,r-rlang) | |
6938 | ("r-withr" ,r-withr))) | |
6939 | (home-page "https://cran.r-project.org/web/packages/ggstance/") | |
6940 | (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") | |
6941 | (description | |
6942 | "This package is a @code{r-ggplot2} extension that provides flipped components: | |
6943 | @enumerate | |
6944 | @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms; | |
6945 | @item vertical versions of @code{r-ggplot2} positions. | |
6946 | @end enumerate") | |
6947 | (license license:gpl3))) | |
c61f7bc5 | 6948 | |
6949 | (define-public r-mosaiccore | |
6950 | (package | |
6951 | (name "r-mosaiccore") | |
6952 | (version "0.6.0") | |
6953 | (source | |
6954 | (origin | |
6955 | (method url-fetch) | |
6956 | (uri (cran-uri "mosaicCore" version)) | |
6957 | (sha256 | |
6958 | (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z")))) | |
6959 | (properties `((upstream-name . "mosaicCore"))) | |
6960 | (build-system r-build-system) | |
6961 | (propagated-inputs | |
6962 | `(("r-dplyr" ,r-dplyr) | |
6963 | ("r-lazyeval" ,r-lazyeval) | |
6964 | ("r-mass" ,r-mass) | |
6965 | ("r-rlang" ,r-rlang) | |
6966 | ("r-tidyr" ,r-tidyr))) | |
6967 | (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") | |
6968 | (synopsis "Common utilities for mosaic family packages") | |
6969 | (description | |
6970 | "Common utilities used in other Mosaic family packages are collected here.") | |
6971 | (license license:gpl2+))) | |
214452ff | 6972 | |
6973 | (define-public r-ggformula | |
6974 | (package | |
6975 | (name "r-ggformula") | |
9a470682 | 6976 | (version "0.9.2") |
214452ff | 6977 | (source |
6978 | (origin | |
6979 | (method url-fetch) | |
6980 | (uri (cran-uri "ggformula" version)) | |
6981 | (sha256 | |
9a470682 | 6982 | (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr")))) |
214452ff | 6983 | (build-system r-build-system) |
6984 | (propagated-inputs | |
6985 | `(("r-ggplot2" ,r-ggplot2) | |
6986 | ("r-ggstance" ,r-ggstance) | |
6987 | ("r-magrittr" ,r-magrittr) | |
6988 | ("r-mosaiccore" ,r-mosaiccore) | |
6989 | ("r-rlang" ,r-rlang) | |
6990 | ("r-stringr" ,r-stringr) | |
6991 | ("r-tibble" ,r-tibble) | |
6992 | ("r-tidyr" ,r-tidyr))) | |
6993 | (home-page "https://github.com/ProjectMOSAIC/ggformula/") | |
6994 | (synopsis "Formula interface for the @code{r-ggplot2}") | |
6995 | (description | |
6996 | "The @code{r-ggformula} introduces a family of graphics functions, gf_point(), | |
6997 | gf_density(), and so on, bring the formula interface to ggplot(). This captures | |
6998 | and extends the excellent simplicity of the lattice-graphics formula interface, | |
6999 | while providing the intuitive capabilities of @code{r-ggplot2}.") | |
7000 | (license license:expat))) | |
2f195b6f | 7001 | |
7002 | (define-public r-mosaicdata | |
7003 | (package | |
7004 | (name "r-mosaicdata") | |
7005 | (version "0.17.0") | |
7006 | (source | |
7007 | (origin | |
7008 | (method url-fetch) | |
7009 | (uri (cran-uri "mosaicData" version)) | |
7010 | (sha256 | |
7011 | (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9")))) | |
7012 | (properties `((upstream-name . "mosaicData"))) | |
7013 | (build-system r-build-system) | |
7014 | (home-page "https://cran.r-project.org/web/packages/mosaicData/") | |
7015 | (synopsis "Data sets for project Mosaic") | |
7016 | (description | |
7017 | "This package provides data sets from project Mosaic @url{http://mosaic-web.org} | |
7018 | used to teach mathematics, statistics, computation and modeling.") | |
7019 | (license license:gpl2+))) | |
6c6ce2d0 | 7020 | |
82acd43c RW |
7021 | (define-public r-raster |
7022 | (package | |
7023 | (name "r-raster") | |
e7c8c685 | 7024 | (version "3.0-7") |
82acd43c RW |
7025 | (source |
7026 | (origin | |
7027 | (method url-fetch) | |
7028 | (uri (cran-uri "raster" version)) | |
7029 | (sha256 | |
7030 | (base32 | |
e7c8c685 | 7031 | "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn")))) |
82acd43c RW |
7032 | (build-system r-build-system) |
7033 | (propagated-inputs | |
7034 | `(("r-rcpp" ,r-rcpp) | |
7035 | ("r-sp" ,r-sp))) | |
aff13de3 | 7036 | (home-page "https://www.rspatial.org/") |
82acd43c RW |
7037 | (synopsis "Geographic data analysis and modeling") |
7038 | (description | |
7039 | "The package implements basic and high-level functions for reading, | |
7040 | writing, manipulating, analyzing and modeling of gridded spatial data. | |
7041 | Processing of very large files is supported.") | |
7042 | (license license:gpl3+))) | |
7043 | ||
6c6ce2d0 | 7044 | (define-public r-mosaic |
7045 | (package | |
7046 | (name "r-mosaic") | |
7047 | (version "1.4.0") | |
7048 | (source | |
7049 | (origin | |
7050 | (method url-fetch) | |
7051 | (uri (cran-uri "mosaic" version)) | |
7052 | (sha256 | |
7053 | (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2")))) | |
7054 | (build-system r-build-system) | |
7055 | (propagated-inputs | |
7056 | `(("r-broom" ,r-broom) | |
7057 | ("r-dplyr" ,r-dplyr) | |
7058 | ("r-ggdendro" ,r-ggdendro) | |
7059 | ("r-ggformula" ,r-ggformula) | |
7060 | ("r-ggplot2" ,r-ggplot2) | |
7061 | ("r-ggrepel" ,r-ggrepel) | |
7062 | ("r-glue" ,r-glue) | |
7063 | ("r-gridextra" ,r-gridextra) | |
7064 | ("r-lattice" ,r-lattice) | |
7065 | ("r-latticeextra" ,r-latticeextra) | |
7066 | ("r-lazyeval" ,r-lazyeval) | |
7067 | ("r-mass" ,r-mass) | |
7068 | ("r-matrix" ,r-matrix) | |
7069 | ("r-mosaiccore" ,r-mosaiccore) | |
7070 | ("r-mosaicdata" ,r-mosaicdata) | |
7071 | ("r-readr" ,r-readr) | |
7072 | ("r-tidyr" ,r-tidyr))) | |
7073 | (home-page "https://github.com/ProjectMOSAIC/mosaic/") | |
7074 | (synopsis "Mathematics, statistics, and computation teaching utilities") | |
7075 | (description | |
7076 | "This package contain data sets and utilities from | |
7077 | @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics, | |
7078 | statistics, computation and modeling. Project MOSAIC is a community of | |
7079 | educators working to tie together aspects of quantitative work that students | |
7080 | in science, technology, engineering and mathematics will need in their | |
7081 | professional lives, but which are usually taught in isolation, if at all.") | |
7082 | (license license:gpl2+))) | |
cbb0edd1 | 7083 | |
7084 | (define-public r-abd | |
7085 | (package | |
7086 | (name "r-abd") | |
7087 | (version "0.2-8") | |
7088 | (source | |
7089 | (origin | |
7090 | (method url-fetch) | |
7091 | (uri (cran-uri "abd" version)) | |
7092 | (sha256 | |
7093 | (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7")))) | |
7094 | (build-system r-build-system) | |
7095 | (propagated-inputs | |
7096 | `(("r-lattice" ,r-lattice) | |
7097 | ("r-mosaic" ,r-mosaic) | |
7098 | ("r-nlme" ,r-nlme))) | |
7099 | (home-page "https://cran.r-project.org/web/packages/abd/") | |
7100 | (synopsis "Analysis of biological data") | |
7101 | (description | |
7102 | "The @code{r-abd} package contains data sets and sample code for the Analysis of | |
7103 | biological data by Michael Whitlock and Dolph Schluter.") | |
7104 | (license license:gpl2))) | |
01af264d MIP |
7105 | |
7106 | (define-public r-svgui | |
7107 | (package | |
7108 | (name "r-svgui") | |
7109 | (version "1.0.0") | |
7110 | (source | |
7111 | (origin | |
7112 | (method url-fetch) | |
7113 | (uri (cran-uri "svGUI" version)) | |
7114 | (sha256 | |
7115 | (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc")))) | |
7116 | (properties `((upstream-name . "svGUI"))) | |
7117 | (build-system r-build-system) | |
7118 | (home-page "https://github.com/SciViews/svGUI/") | |
7119 | (synopsis "Functions for managing GUI clients in R") | |
7120 | (description | |
7121 | "The SciViews @code{svGUI} package eases the management of Graphical User | |
7122 | Interfaces (GUI) in R. It is independent from any particular GUI widgets. It | |
7123 | centralizes info about GUI elements currently used, and it dispatches GUI | |
7124 | calls to the particular toolkits in use in function of the context.") | |
7125 | (license license:gpl2))) | |
d1ca3d72 | 7126 | |
7127 | (define-public r-svdialogs | |
7128 | (package | |
7129 | (name "r-svdialogs") | |
7130 | (version "1.0.0") | |
7131 | (source | |
7132 | (origin | |
7133 | (method url-fetch) | |
7134 | (uri (cran-uri "svDialogs" version)) | |
7135 | (sha256 | |
7136 | (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97")))) | |
7137 | (properties `((upstream-name . "svDialogs"))) | |
7138 | (build-system r-build-system) | |
7139 | (inputs | |
7140 | `(("yad" ,yad) | |
7141 | ("zenity" ,zenity))) | |
7142 | (propagated-inputs | |
7143 | `(("r-rstudioapi" ,r-rstudioapi) | |
7144 | ("r-svgui" ,r-svgui))) | |
7145 | (home-page "https://github.com/SciViews/svDialogs/") | |
7146 | (synopsis "Portable dialog boxes") | |
7147 | (description | |
7148 | "This package helps to construct standard dialog boxes for your GUI, including | |
7149 | message boxes, input boxes, list, file or directory selection, and others. In | |
7150 | case R cannot display GUI dialog boxes, a simpler command line version of these | |
7151 | interactive elements is also provided as a fallback solution.") | |
7152 | (license license:gpl2))) | |
3cadd3ce | 7153 | |
7154 | (define-public r-abe | |
7155 | (package | |
7156 | (name "r-abe") | |
7157 | (version "3.0.1") | |
7158 | (source | |
7159 | (origin | |
7160 | (method url-fetch) | |
7161 | (uri (cran-uri "abe" version)) | |
7162 | (sha256 | |
7163 | (base32 | |
7164 | "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6")))) | |
7165 | (build-system r-build-system) | |
7166 | (home-page "https://cran.r-project.org/web/packages/abe/") | |
7167 | (synopsis "Augmented backward elimination") | |
7168 | (description | |
7169 | "This package performs augmented backward elimination and checks the | |
7170 | stability of the obtained model. Augmented backward elimination combines | |
7171 | significance or information based criteria with the change in estimate to | |
7172 | either select the optimal model for prediction purposes or to serve as a tool | |
7173 | to obtain a practically sound, highly interpretable model.") | |
7174 | (license license:gpl2+))) | |
ef26400b | 7175 | |
7176 | (define-public r-abf2 | |
7177 | (package | |
7178 | (name "r-abf2") | |
7179 | (version "0.7-1") | |
7180 | (source | |
7181 | (origin | |
7182 | (method url-fetch) | |
7183 | (uri (cran-uri "abf2" version)) | |
7184 | (sha256 | |
7185 | (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx")))) | |
7186 | (build-system r-build-system) | |
7187 | (home-page "https://cran.r-project.org/web/packages/abf2/") | |
7188 | (synopsis "Load gap-free axon @code{r-abf2} files") | |
7189 | (description | |
7190 | "This package loads electrophysiology data from ABF2 files, as created by | |
7191 | Axon Instruments/Molecular Devices software. Only files recorded in gap-free | |
7192 | mode are currently supported.") | |
7193 | (license license:artistic2.0))) | |
1efcd0f1 | 7194 | |
7195 | (define-public r-abhgenotyper | |
7196 | (package | |
7197 | (name "r-abhgenotyper") | |
7198 | (version "1.0.1") | |
7199 | (source | |
7200 | (origin | |
7201 | (method url-fetch) | |
7202 | (uri (cran-uri "ABHgenotypeR" version)) | |
7203 | (sha256 | |
7204 | (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l")))) | |
7205 | (properties `((upstream-name . "ABHgenotypeR"))) | |
7206 | (build-system r-build-system) | |
7207 | (propagated-inputs | |
7208 | `(("r-ggplot2" ,r-ggplot2) | |
7209 | ("r-reshape2" ,r-reshape2))) | |
7210 | (home-page "https://github.com/StefanReuscher/ABHgenotypeR/") | |
7211 | (synopsis "Visualize and manipulate ABH genotypes") | |
7212 | (description | |
7213 | "The @code{r-abhgenotyper} package provides simple imputation, | |
7214 | error-correction and plotting capacities for genotype data. The package is | |
7215 | supposed to serve as an intermediate but independent analysis tool between the | |
7216 | TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities | |
7217 | not found in either TASSEL or @code{r-qtl} in addition to visualization of | |
7218 | genotypes as \"graphical genotypes\".") | |
7219 | (license license:gpl3))) | |
ebb3cdb1 | 7220 | |
6e8b38d3 RW |
7221 | (define-public r-furrr |
7222 | (package | |
7223 | (name "r-furrr") | |
7224 | (version "0.1.0") | |
7225 | (source | |
7226 | (origin | |
7227 | (method url-fetch) | |
7228 | (uri (cran-uri "furrr" version)) | |
7229 | (sha256 | |
7230 | (base32 | |
7231 | "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx")))) | |
7232 | (build-system r-build-system) | |
7233 | (propagated-inputs | |
7234 | `(("r-future" ,r-future) | |
7235 | ("r-globals" ,r-globals) | |
7236 | ("r-purrr" ,r-purrr) | |
7237 | ("r-rlang" ,r-rlang))) | |
7238 | (home-page "https://github.com/DavisVaughan/furrr") | |
7239 | (synopsis "Apply mapping functions in parallel using futures") | |
7240 | (description | |
7241 | "This package provides implementations of the family of @code{map()} | |
7242 | functions from the @code{purrr} package that can be resolved using any | |
7243 | @code{future}-supported backend, e.g. parallel on the local machine or | |
7244 | distributed on a compute cluster.") | |
7245 | (license license:lgpl2.1+))) | |
7246 | ||
ebb3cdb1 | 7247 | (define-public r-abjutils |
7248 | (package | |
7249 | (name "r-abjutils") | |
3d5bcae0 | 7250 | (version "0.2.3") |
ebb3cdb1 | 7251 | (source |
7252 | (origin | |
7253 | (method url-fetch) | |
7254 | (uri (cran-uri "abjutils" version)) | |
7255 | (sha256 | |
3d5bcae0 | 7256 | (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv")))) |
ebb3cdb1 | 7257 | (build-system r-build-system) |
7258 | (propagated-inputs | |
7259 | `(("r-devtools" ,r-devtools) | |
7260 | ("r-dplyr" ,r-dplyr) | |
3d5bcae0 RW |
7261 | ("r-furrr" ,r-furrr) |
7262 | ("r-future" ,r-future) | |
ebb3cdb1 | 7263 | ("r-glue" ,r-glue) |
7264 | ("r-httr" ,r-httr) | |
7265 | ("r-magrittr" ,r-magrittr) | |
ebb3cdb1 | 7266 | ("r-progress" ,r-progress) |
7267 | ("r-purrr" ,r-purrr) | |
3d5bcae0 RW |
7268 | ("r-readr" ,r-readr) |
7269 | ("r-rlang" ,r-rlang) | |
ebb3cdb1 | 7270 | ("r-rstudioapi" ,r-rstudioapi) |
7271 | ("r-scales" ,r-scales) | |
7272 | ("r-stringi" ,r-stringi) | |
7273 | ("r-stringr" ,r-stringr) | |
7274 | ("r-tibble" ,r-tibble) | |
7275 | ("r-tidyr" ,r-tidyr))) | |
7276 | (home-page "https://github.com/abjur/abjutils/") | |
7277 | (synopsis "Collection of tools for jurimetrical analysis") | |
7278 | (description | |
7279 | "This package implements general purpose tools, such as functions for | |
7280 | sampling and basic manipulation of Brazilian lawsuits identification number. | |
7281 | It also implements functions for text cleaning, such as accentuation | |
7282 | removal.") | |
7283 | (license license:expat))) | |
b6afe7b7 | 7284 | |
7285 | (define-public r-abnormality | |
7286 | (package | |
7287 | (name "r-abnormality") | |
7288 | (version "0.1.0") | |
7289 | (source | |
7290 | (origin | |
7291 | (method url-fetch) | |
7292 | (uri (cran-uri "abnormality" version)) | |
7293 | (sha256 | |
7294 | (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) | |
7295 | (build-system r-build-system) | |
7296 | (propagated-inputs | |
7297 | `(("r-mass" ,r-mass) | |
7298 | ("r-matrix" ,r-matrix))) | |
7299 | (home-page "https://cran.r-project.org/web/packages/abnormality/") | |
7300 | (synopsis "Measure a subject's abnormality with respect to a reference population") | |
7301 | (description | |
7302 | "This package contains functions to implement the methodology and | |
7303 | considerations laid out by Marks et al. in the article \"Measuring abnormality | |
7304 | in high dimensional spaces: applications in biomechanical gait analysis\". | |
7305 | Using high-dimensional datasets to measure a subject's overall level of | |
7306 | abnormality as compared to a reference population is often needed in outcomes | |
7307 | research.") | |
7308 | (license license:expat))) | |
016cabf7 | 7309 | |
7310 | (define-public r-abodoutlier | |
7311 | (package | |
7312 | (name "r-abodoutlier") | |
7313 | (version "0.1") | |
7314 | (source | |
7315 | (origin | |
7316 | (method url-fetch) | |
7317 | (uri (cran-uri "abodOutlier" version)) | |
7318 | (sha256 | |
7319 | (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj")))) | |
7320 | (properties `((upstream-name . "abodOutlier"))) | |
7321 | (build-system r-build-system) | |
7322 | (propagated-inputs | |
7323 | `(("r-cluster" ,r-cluster))) | |
7324 | (home-page "https://cran.r-project.org/web/packages/abodOutlier/") | |
7325 | (synopsis "Angle-based outlier detection") | |
7326 | (description | |
7327 | "This package performs angle-based outlier detection on a given data | |
7328 | frame. It offers three methods to process data: | |
7329 | @enumerate | |
7330 | @item full but slow implementation using all the data that has cubic | |
7331 | complexity; | |
7332 | @item a fully randomized method; | |
7333 | @item a method using k-nearest neighbours. | |
7334 | @end enumerate | |
7335 | These algorithms are well suited for high dimensional data outlier | |
7336 | detection.") | |
7337 | (license license:expat))) | |
03c95f04 | 7338 | |
7339 | (define-public r-abps | |
7340 | (package | |
7341 | (name "r-abps") | |
bec74196 | 7342 | (version "0.3") |
03c95f04 | 7343 | (source |
7344 | (origin | |
7345 | (method url-fetch) | |
7346 | (uri (cran-uri "ABPS" version)) | |
7347 | (sha256 | |
bec74196 | 7348 | (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) |
03c95f04 | 7349 | (properties `((upstream-name . "ABPS"))) |
7350 | (build-system r-build-system) | |
7351 | (propagated-inputs `(("r-kernlab" ,r-kernlab))) | |
7352 | (home-page "https://cran.r-project.org/web/packages/ABPS/") | |
7353 | (synopsis "Abnormal blood profile score to detect blood doping") | |
7354 | (description | |
7355 | "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS). | |
7356 | The ABPS is a part of the Athlete biological passport program of the World | |
7357 | anti-doping agency, which combines several blood parameters into a single | |
7358 | score in order to detect blood doping. The package also contains functions to | |
7359 | calculate other scores used in anti-doping programs, such as the ratio of | |
7360 | hemoglobin to reticulocytes (OFF-score), as well as example data.") | |
7361 | (license license:gpl2+))) | |
26358ac5 RW |
7362 | |
7363 | (define-public r-parmigene | |
7364 | (package | |
7365 | (name "r-parmigene") | |
7366 | (version "1.0.2") | |
7367 | (source | |
7368 | (origin | |
7369 | (method url-fetch) | |
7370 | (uri (cran-uri "parmigene" version)) | |
7371 | (sha256 | |
7372 | (base32 | |
7373 | "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d")))) | |
7374 | (build-system r-build-system) | |
7375 | (home-page "https://cran.r-project.org/web/packages/parmigene/") | |
7376 | (synopsis "Mutual information estimation for gene network reconstruction") | |
7377 | (description | |
7378 | "This package provides a parallel estimation of the mutual information | |
7379 | based on entropy estimates from k-nearest neighbors distances and algorithms | |
7380 | for the reconstruction of gene regulatory networks.") | |
7381 | (license license:agpl3+))) | |
b2bf43b2 | 7382 | |
7383 | (define-public r-pscl | |
7384 | (package | |
7385 | (name "r-pscl") | |
7386 | (version "1.5.2") | |
7387 | (source | |
7388 | (origin | |
7389 | (method url-fetch) | |
7390 | (uri (cran-uri "pscl" version)) | |
7391 | (sha256 | |
7392 | (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc")))) | |
7393 | (build-system r-build-system) | |
7394 | (propagated-inputs | |
7395 | `(("r-mass" ,r-mass))) | |
7396 | (home-page "https://github.com/atahk/pscl/") | |
7397 | (synopsis "Political science computational laboratory") | |
7398 | (description | |
7399 | "The @code{pscl} is an R package providing classes and methods for: | |
7400 | @enumerate | |
7401 | @item Bayesian analysis of roll call data (item-response models); | |
7402 | @item elementary Bayesian statistics; | |
7403 | @item maximum likelihood estimation of zero-inflated and hurdle models for count | |
7404 | data; | |
7405 | @item utility functions. | |
7406 | @end enumerate") | |
7407 | (license license:gpl2))) | |
e710d1a4 | 7408 | |
7409 | (define-public r-accelmissing | |
7410 | (package | |
7411 | (name "r-accelmissing") | |
7412 | (version "1.4") | |
7413 | (source | |
7414 | (origin | |
7415 | (method url-fetch) | |
7416 | (uri (cran-uri "accelmissing" version)) | |
7417 | (sha256 | |
7418 | (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) | |
7419 | (build-system r-build-system) | |
7420 | (propagated-inputs | |
7421 | `(("r-mice" ,r-mice) | |
7422 | ("r-pscl" ,r-pscl))) | |
7423 | (home-page "https://cran.r-project.org/web/packages/accelmissing/") | |
7424 | (synopsis "Missing value imputation for accelerometer data") | |
7425 | (description | |
7426 | "This package provides a statistical method to impute the missing values in | |
7427 | accelerometer data. The methodology includes both parametric and | |
7428 | semi-parametric multiple imputations under the zero-inflated Poisson lognormal | |
7429 | model. It also provides multiple functions to preprocess the accelerometer data | |
7430 | previous to the missing data imputation. These include detecting the wearing | |
7431 | and the non-wearing time, selecting valid days and subjects, and creating plots.") | |
7432 | (license license:gpl2+))) | |
f359b115 | 7433 | |
7434 | (define-public r-mhsmm | |
7435 | (package | |
7436 | (name "r-mhsmm") | |
7437 | (version "0.4.16") | |
7438 | (source | |
7439 | (origin | |
7440 | (method url-fetch) | |
7441 | (uri (cran-uri "mhsmm" version)) | |
7442 | (sha256 | |
7443 | (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) | |
7444 | (build-system r-build-system) | |
7445 | (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) | |
7446 | (home-page "https://github.com/jaredo/mhsmm/") | |
7447 | (synopsis "Inference for hidden Markov and semi-Markov models") | |
7448 | (description | |
7449 | "The @code{r-mhsmm} package implements estimation and prediction methods for | |
7450 | hidden Markov and semi-Markov models for multiple observation sequences. Such | |
7451 | techniques are of interest when observed data is thought to be dependent on some | |
7452 | unobserved (or hidden) state. Also, this package is suitable for equidistant | |
7453 | time series data, with multivariate and/or missing data. Allows user defined | |
7454 | emission distributions.") | |
7455 | (license license:gpl2+))) | |
16c5285a | 7456 | |
7457 | (define-public r-nleqslv | |
7458 | (package | |
7459 | (name "r-nleqslv") | |
7460 | (version "3.3.2") | |
7461 | (source | |
7462 | (origin | |
7463 | (method url-fetch) | |
7464 | (uri (cran-uri "nleqslv" version)) | |
7465 | (sha256 | |
7466 | (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) | |
7467 | (build-system r-build-system) | |
7468 | (native-inputs `(("gfortran" ,gfortran))) | |
7469 | (home-page "https://cran.r-project.org/web/packages/nleqslv/") | |
7470 | (synopsis "Solve systems of nonlinear equations") | |
7471 | (description | |
7472 | "The @code{r-nleqslv} package solves a system of nonlinear equations using a | |
7473 | Broyden or a Newton method with a choice of global strategies such as line | |
7474 | search and trust region. There are options for using a numerical or user | |
7475 | supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a | |
7476 | singular or ill-conditioned Jacobian.") | |
7477 | (license license:gpl2+))) | |
63ec2c50 | 7478 | |
7479 | (define-public r-physicalactivity | |
7480 | (package | |
7481 | (name "r-physicalactivity") | |
7482 | (version "0.2-2") | |
7483 | (source | |
7484 | (origin | |
7485 | (method url-fetch) | |
7486 | (uri (cran-uri "PhysicalActivity" version)) | |
7487 | (sha256 | |
7488 | (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln")))) | |
7489 | (properties | |
7490 | `((upstream-name . "PhysicalActivity"))) | |
7491 | (build-system r-build-system) | |
7492 | (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") | |
7493 | (synopsis "Procesing accelerometer data for physical activity measurement") | |
7494 | (description | |
7495 | "This @code{r-physicalactivity} package provides a function @code{wearingMarking} | |
7496 | for classification of monitor wear and nonwear time intervals in accelerometer | |
7497 | data collected to assess physical activity. The package also contains functions | |
7498 | for making plots of accelerometer data and obtaining the summary of various | |
7499 | information including daily monitor wear time and the mean monitor wear time | |
7500 | during valid days. The revised package version 0.2-1 improved the functions | |
7501 | regarding speed, robustness and add better support for time zones and daylight | |
7502 | saving. In addition, several functions were added: | |
7503 | @enumerate | |
7504 | @item the @code{markDelivery} can classify days for ActiGraph delivery by mail; | |
7505 | @item the @code{markPAI} can categorize physical activity intensity level based | |
7506 | on user-defined cut-points of accelerometer counts. | |
7507 | @end enumerate | |
7508 | It also supports importing ActiGraph (AGD) files with @code{readActigraph} and | |
7509 | @code{queryActigraph} functions.") | |
7510 | (license license:gpl3+))) | |
f95d4542 | 7511 | |
7512 | (define-public r-acc | |
7513 | (package | |
7514 | (name "r-acc") | |
7515 | (version "1.3.3") | |
7516 | (source | |
7517 | (origin | |
7518 | (method url-fetch) | |
7519 | (uri (cran-uri "acc" version)) | |
7520 | (sha256 | |
7521 | (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) | |
7522 | (build-system r-build-system) | |
7523 | (propagated-inputs | |
7524 | `(("r-circlize" ,r-circlize) | |
7525 | ("r-dbi" ,r-dbi) | |
7526 | ("r-ggplot2" ,r-ggplot2) | |
7527 | ("r-iterators" ,r-iterators) | |
7528 | ("r-mhsmm" ,r-mhsmm) | |
7529 | ("r-nleqslv" ,r-nleqslv) | |
7530 | ("r-physicalactivity" ,r-physicalactivity) | |
7531 | ("r-plyr" ,r-plyr) | |
7532 | ("r-r-utils" ,r-r-utils) | |
7533 | ("r-rcpp" ,r-rcpp) | |
7534 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
7535 | ("r-rsqlite" ,r-rsqlite) | |
7536 | ("r-zoo" ,r-zoo))) | |
7537 | (home-page "https://cran.r-project.org/web/packages/acc/") | |
7538 | (synopsis "Exploring accelerometer data") | |
7539 | (description | |
7540 | "This package processes accelerometer data from uni-axial and tri-axial devices | |
7541 | and generates data summaries. Also, includes functions to plot, analyze, and | |
7542 | simulate accelerometer data.") | |
7543 | (license license:gpl2+))) | |
f6890c08 | 7544 | |
7545 | (define-public r-rbenchmark | |
7546 | (package | |
7547 | (name "r-rbenchmark") | |
7548 | (version "1.0.0") | |
7549 | (source | |
7550 | (origin | |
7551 | (method url-fetch) | |
7552 | (uri (cran-uri "rbenchmark" version)) | |
7553 | (sha256 | |
7554 | (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9")))) | |
7555 | (build-system r-build-system) | |
7556 | (home-page "https://cran.r-project.org/web/packages/rbenchmark/") | |
7557 | (synopsis "Benchmarking routine for R") | |
7558 | (description | |
7559 | "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark, | |
7560 | and is intended to facilitate benchmarking of arbitrary R code. The library | |
7561 | consists of just one function, benchmark, which is a simple wrapper around | |
7562 | system.time. Given a specification of the benchmarking process (counts of | |
7563 | replications, evaluation environment) and an arbitrary number of expressions, | |
7564 | benchmark evaluates each of the expressions in the specified environment, | |
7565 | replicating the evaluation as many times as specified, and returning the results | |
7566 | conveniently wrapped into a data frame.") | |
7567 | (license license:gpl2+))) | |
7568 | ||
9c4f118b RW |
7569 | (define-public r-mitools |
7570 | (package | |
7571 | (name "r-mitools") | |
7572 | (version "2.4") | |
7573 | (source | |
7574 | (origin | |
7575 | (method url-fetch) | |
7576 | (uri (cran-uri "mitools" version)) | |
7577 | (sha256 | |
7578 | (base32 | |
7579 | "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j")))) | |
7580 | (build-system r-build-system) | |
7581 | (propagated-inputs `(("r-dbi" ,r-dbi))) | |
7582 | (home-page "https://cran.r-project.org/web/packages/mitools/") | |
7583 | (synopsis "Tools for multiple imputation of missing data") | |
7584 | (description | |
7585 | "This package provides tools to perform analyses and combine results from | |
7586 | multiple-imputation datasets.") | |
7587 | (license license:gpl2))) | |
7588 | ||
dab3e92c RW |
7589 | (define-public r-magick |
7590 | (package | |
7591 | (name "r-magick") | |
9c2d9780 | 7592 | (version "2.2") |
dab3e92c RW |
7593 | (source |
7594 | (origin | |
7595 | (method url-fetch) | |
7596 | (uri (cran-uri "magick" version)) | |
7597 | (sha256 | |
7598 | (base32 | |
9c2d9780 | 7599 | "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85")))) |
dab3e92c RW |
7600 | (build-system r-build-system) |
7601 | (inputs | |
7602 | `(("imagemagick" ,imagemagick) | |
7603 | ("zlib" ,zlib))) | |
7604 | (propagated-inputs | |
7605 | `(("r-curl" ,r-curl) | |
7606 | ("r-magrittr" ,r-magrittr) | |
7607 | ("r-rcpp" ,r-rcpp))) | |
7608 | (native-inputs | |
7609 | `(("pkg-config" ,pkg-config))) | |
7610 | (home-page "https://github.com/ropensci/magick") | |
7611 | (synopsis "Advanced graphics and image-processing in R") | |
7612 | (description | |
7613 | "This package provides bindings to ImageMagick, a comprehensive image | |
7614 | processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, | |
7615 | etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All | |
7616 | operations are vectorized via the Magick++ STL meaning they operate either on | |
7617 | a single frame or a series of frames for working with layers, collages, or | |
7618 | animation. In RStudio, images are automatically previewed when printed to the | |
7619 | console, resulting in an interactive editing environment.") | |
7620 | (license license:expat))) | |
7621 | ||
f0bff698 RW |
7622 | (define-public r-survey |
7623 | (package | |
7624 | (name "r-survey") | |
7b18fac4 | 7625 | (version "3.36") |
f0bff698 RW |
7626 | (source |
7627 | (origin | |
7628 | (method url-fetch) | |
7629 | (uri (cran-uri "survey" version)) | |
7630 | (sha256 | |
7631 | (base32 | |
7b18fac4 | 7632 | "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh")))) |
f0bff698 RW |
7633 | (build-system r-build-system) |
7634 | (propagated-inputs | |
7635 | `(("r-lattice" ,r-lattice) | |
7636 | ("r-matrix" ,r-matrix) | |
7637 | ("r-minqa" ,r-minqa) | |
7b18fac4 | 7638 | ("r-mitools" ,r-mitools) |
f0bff698 RW |
7639 | ("r-numderiv" ,r-numderiv) |
7640 | ("r-survival" ,r-survival))) | |
7641 | (home-page "http://r-survey.r-forge.r-project.org/survey/") | |
7642 | (synopsis "Analysis of complex survey samples") | |
7643 | (description | |
7644 | "This package provides tools for the analysis of complex survey samples. | |
7645 | The provided features include: summary statistics, two-sample tests, rank | |
7646 | tests, generalised linear models, cumulative link models, Cox models, | |
7647 | loglinear models, and general maximum pseudolikelihood estimation for | |
7648 | multistage stratified, cluster-sampled, unequally weighted survey samples; | |
7649 | variances by Taylor series linearisation or replicate weights; | |
7650 | post-stratification, calibration, and raking; two-phase subsampling designs; | |
7651 | graphics; PPS sampling without replacement; principal components, and factor | |
7652 | analysis.") | |
7653 | ;; Either version of the GPL. | |
7654 | (license (list license:gpl2 license:gpl3)))) | |
7655 | ||
7af2dd38 | 7656 | (define-public r-dvmisc |
7657 | (package | |
7658 | (name "r-dvmisc") | |
a6a87db8 | 7659 | (version "1.1.3") |
7af2dd38 | 7660 | (source |
7661 | (origin | |
7662 | (method url-fetch) | |
7663 | (uri (cran-uri "dvmisc" version)) | |
7664 | (sha256 | |
a6a87db8 | 7665 | (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv")))) |
7af2dd38 | 7666 | (build-system r-build-system) |
7667 | (propagated-inputs | |
a6a87db8 RW |
7668 | `(("r-cubature" ,r-cubature) |
7669 | ("r-data-table" ,r-data-table) | |
7670 | ("r-dplyr" ,r-dplyr) | |
7671 | ("r-ggplot2" ,r-ggplot2) | |
7672 | ("r-mass" ,r-mass) | |
7673 | ("r-mvtnorm" ,r-mvtnorm) | |
7674 | ("r-pracma" ,r-pracma) | |
7675 | ("r-purrr" ,r-purrr) | |
7af2dd38 | 7676 | ("r-rbenchmark" ,r-rbenchmark) |
a6a87db8 RW |
7677 | ("r-rcpp" ,r-rcpp) |
7678 | ("r-survey" ,r-survey))) | |
7af2dd38 | 7679 | (home-page "https://cran.r-project.org/web/packages/dvmisc/") |
7680 | (synopsis "Faster computation of common statistics and miscellaneous functions") | |
7681 | (description | |
7682 | "This package implements faster versions of base R functions (e.g. mean, standard | |
7683 | deviation, covariance, weighted mean), mostly written in C++, along with | |
7684 | miscellaneous functions for various purposes (e.g. create the histogram with | |
7685 | fitted probability density function or probability mass function curve, create | |
7686 | the body mass index groups, assess the linearity assumption in logistic | |
7687 | regression).") | |
7688 | (license license:gpl2))) | |
d8d8844e | 7689 | |
7690 | (define-public r-accelerometry | |
7691 | (package | |
7692 | (name "r-accelerometry") | |
7693 | (version "3.1.2") | |
7694 | (source | |
7695 | (origin | |
7696 | (method url-fetch) | |
7697 | (uri (cran-uri "accelerometry" version)) | |
7698 | (sha256 | |
7699 | (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) | |
7700 | (build-system r-build-system) | |
7701 | (propagated-inputs | |
7702 | `(("r-dvmisc" ,r-dvmisc) | |
7703 | ("r-rcpp" ,r-rcpp))) | |
7704 | (home-page "https://cran.r-project.org/web/packages/accelerometry/") | |
7705 | (synopsis "Functions for processing accelerometer data") | |
7706 | (description | |
7707 | "This package provides a collection of functions that perform operations on | |
7708 | time-series accelerometer data, such as identify the non-wear time, flag minutes | |
7709 | that are part of an activity bout, and find the maximum 10-minute average count | |
7710 | value. The functions are generally very flexible, allowing for a variety of | |
7711 | algorithms to be implemented.") | |
7712 | (license license:gpl3))) | |
1ddb2b5c | 7713 | |
7714 | (define-public r-absim | |
7715 | (package | |
7716 | (name "r-absim") | |
7717 | (version "0.2.6") | |
7718 | (source | |
7719 | (origin | |
7720 | (method url-fetch) | |
7721 | (uri (cran-uri "AbSim" version)) | |
7722 | (sha256 | |
7723 | (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) | |
7724 | (properties `((upstream-name . "AbSim"))) | |
7725 | (build-system r-build-system) | |
7726 | (propagated-inputs | |
7727 | `(("r-ape" ,r-ape) | |
7728 | ("r-powerlaw" ,r-powerlaw))) | |
7729 | (home-page "https://cran.r-project.org/web/packages/AbSim/") | |
7730 | (synopsis "Time resolved simulations of antibody repertoires") | |
7731 | (description | |
7732 | "This package provides simulation methods for the evolution of antibody repertoires. | |
7733 | The heavy and light chain variable region of both human and C57BL/6 mice can | |
7734 | be simulated in a time-dependent fashion. Both single lineages using one set of | |
7735 | V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins | |
7736 | with an initial V-D-J recombination event, starting the first phylogenetic tree. | |
7737 | Upon completion, the main loop of the algorithm begins, with each iteration | |
7738 | representing one simulated time step. Various mutation events are possible at | |
7739 | each time step, contributing to a diverse final repertoire.") | |
7740 | (license license:gpl2))) | |
c2ffc4fb | 7741 | |
b5a31005 MIP |
7742 | (define-public r-quic |
7743 | (package | |
7744 | (name "r-quic") | |
7745 | (version "1.1") | |
7746 | (source | |
7747 | (origin | |
7748 | (method url-fetch) | |
7749 | (uri (cran-uri "QUIC" version)) | |
7750 | (sha256 | |
7751 | (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) | |
7752 | (properties `((upstream-name . "QUIC"))) | |
7753 | (build-system r-build-system) | |
7754 | (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") | |
7755 | (synopsis "Regularized sparse inverse covariance matrix estimation") | |
7756 | (description | |
7757 | "This package implements the regularized Gaussian maximum likelihood | |
7758 | estimation of the inverse of a covariance matrix. It uses Newton's method and | |
7759 | coordinate descent to solve the regularized inverse covariance matrix | |
7760 | estimation problem.") | |
7761 | ;; The project home page states that the release is under GPLv3 or later. | |
7762 | ;; The CRAN page only says GPL-3. | |
7763 | (license license:gpl3+))) | |
7764 | ||
b509df82 MIP |
7765 | (define-public r-abundant |
7766 | (package | |
7767 | (name "r-abundant") | |
7768 | (version "1.1") | |
7769 | (source | |
7770 | (origin | |
7771 | (method url-fetch) | |
7772 | (uri (cran-uri "abundant" version)) | |
7773 | (sha256 | |
7774 | (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) | |
7775 | (build-system r-build-system) | |
7776 | (propagated-inputs | |
7777 | `(("r-quic" ,r-quic))) | |
7778 | (home-page "https://cran.r-project.org/web/packages/abundant/") | |
7779 | (synopsis "Abundant regression and high-dimensional principal fitted components") | |
7780 | (description | |
7781 | "This package provides tools to fit and predict with the high-dimensional | |
7782 | principal fitted components model. This model is described by Cook, Forzani, | |
7783 | and Rothman (2012) @url{doi:10.1214/11-AOS962}.") | |
7784 | ;; The DESCRIPTION file states GPL-2, but since it directly depends on a | |
7785 | ;; GPLv3+ package (QUIC) this likely means GPLv2+. | |
7786 | (license license:gpl2+))) | |
7787 | ||
c2ffc4fb | 7788 | (define-public r-ac3net |
7789 | (package | |
7790 | (name "r-ac3net") | |
7791 | (version "1.2.2") | |
7792 | (source | |
7793 | (origin | |
7794 | (method url-fetch) | |
7795 | (uri (cran-uri "Ac3net" version)) | |
7796 | (sha256 | |
7797 | (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) | |
7798 | (properties `((upstream-name . "Ac3net"))) | |
7799 | (build-system r-build-system) | |
7800 | (propagated-inputs | |
7801 | `(("r-data-table" ,r-data-table))) | |
7802 | (home-page "https://cran.r-project.org/web/packages/Ac3net/") | |
7803 | (synopsis "Inferring directional conservative causal core gene networks") | |
7804 | (description "This package infers directional Conservative causal core | |
7805 | (gene) networks (C3NET). This is a version of the algorithm C3NET with | |
7806 | directional network.") | |
7807 | (license license:gpl3+))) | |
da333859 | 7808 | |
7809 | (define-public r-aca | |
7810 | (package | |
7811 | (name "r-aca") | |
7812 | (version "1.1") | |
7813 | (source | |
7814 | (origin | |
7815 | (method url-fetch) | |
7816 | (uri (cran-uri "ACA" version)) | |
7817 | (sha256 | |
7818 | (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) | |
7819 | (properties `((upstream-name . "ACA"))) | |
7820 | (build-system r-build-system) | |
7821 | (home-page "https://cran.r-project.org/web/packages/ACA/") | |
7822 | (synopsis "Abrupt change-point or aberration detection in point series") | |
7823 | (description | |
7824 | "This package offers an interactive function for the detection of breakpoints in | |
7825 | series.") | |
7826 | ;; Any version of the GPL | |
7827 | (license (list license:gpl2+ license:gpl3+)))) | |
9c1c2108 | 7828 | |
7829 | (define-public r-acceptancesampling | |
7830 | (package | |
7831 | (name "r-acceptancesampling") | |
ddd168ff | 7832 | (version "1.0-6") |
9c1c2108 | 7833 | (source |
7834 | (origin | |
7835 | (method url-fetch) | |
7836 | (uri (cran-uri "AcceptanceSampling" version)) | |
7837 | (sha256 | |
ddd168ff | 7838 | (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9")))) |
9c1c2108 | 7839 | (properties |
7840 | `((upstream-name . "AcceptanceSampling"))) | |
7841 | (build-system r-build-system) | |
7842 | (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") | |
7843 | (synopsis "Creation and evaluation of acceptance sampling plans") | |
7844 | (description | |
7845 | "This @code{r-acceptancesampling} provides functionality for creating and evaluating | |
7846 | acceptance sampling plans. Acceptance sampling is a methodology commonly used | |
7847 | in quality control and improvement. International standards of acceptance | |
7848 | sampling provide sampling plans for specific circumstances. The aim of this | |
7849 | package is to provide an easy-to-use interface to visualize single, double or | |
7850 | multiple sampling plans. In addition, methods have been provided to enable the | |
7851 | user to assess sampling plans against pre-specified levels of performance, as | |
7852 | measured by the probability of acceptance for a given level of quality in the | |
7853 | lot.") | |
7854 | (license license:gpl3+))) | |
7855 | ||
63781c57 LF |
7856 | (define-public r-acclma |
7857 | (package | |
7858 | (name "r-acclma") | |
7859 | (version "1.0") | |
7860 | (source | |
7861 | (origin | |
7862 | (method url-fetch) | |
7863 | (uri (cran-uri "ACCLMA" version)) | |
7864 | (sha256 | |
7865 | (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) | |
7866 | (properties `((upstream-name . "ACCLMA"))) | |
7867 | (build-system r-build-system) | |
7868 | (home-page "https://cran.r-project.org/web/packages/ACCLMA/") | |
7869 | (synopsis "ACC & LMA graph plotting") | |
7870 | (description | |
666fb288 LC |
7871 | "This package contains a function that imports data from a @acronym{CSV, |
7872 | Comma-Separated Values} file, or uses manually entered data from the format (x, | |
7873 | y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration | |
7874 | Curve} vs @acronym{LOI, Line of Independence} graph and | |
7875 | @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main | |
7876 | function is @code{plotLMA} (source file, header) that takes a data set and plots the | |
63781c57 LF |
7877 | appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a |
7878 | string) was passed, a manual data entry window is opened. The header parameter | |
7879 | indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has | |
7880 | a header row or not. The dataset should contain only one independent variable | |
7881 | (x) and one dependent variable (y) and can contain a weight for each | |
7882 | observation.") | |
7883 | (license license:gpl2))) | |
b55697fb LL |
7884 | |
7885 | (define-public r-aspi | |
7886 | (package | |
7887 | (name "r-aspi") | |
7888 | (version "0.2.0") | |
7889 | (source | |
7890 | (origin | |
7891 | (method url-fetch) | |
7892 | (uri (cran-uri "aspi" version)) | |
7893 | (sha256 | |
7894 | (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) | |
7895 | (build-system r-build-system) | |
7896 | (home-page | |
7897 | "https://cran.r-project.org/web/packages/aspi/") | |
7898 | (synopsis | |
7899 | "Analysis of symmetry of parasitic infections") | |
7900 | (description | |
7901 | "This package provides tools for the analysis and visualization of bilateral | |
7902 | asymmetry in parasitic infections.") | |
7903 | (license license:gpl3+))) | |
302db585 RW |
7904 | |
7905 | (define-public r-sandwich | |
7906 | (package | |
7907 | (name "r-sandwich") | |
0eb306d3 | 7908 | (version "2.5-1") |
302db585 RW |
7909 | (source |
7910 | (origin | |
7911 | (method url-fetch) | |
7912 | (uri (cran-uri "sandwich" version)) | |
7913 | (sha256 | |
7914 | (base32 | |
0eb306d3 | 7915 | "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv")))) |
302db585 RW |
7916 | (build-system r-build-system) |
7917 | (propagated-inputs | |
7918 | `(("r-zoo" ,r-zoo))) | |
7919 | (home-page "https://cran.r-project.org/web/packages/sandwich/") | |
7920 | (synopsis "Robust Covariance Matrix Estimators") | |
7921 | (description | |
7922 | "This package provides model-robust standard error estimators for | |
7923 | cross-sectional, time series, clustered, panel, and longitudinal data.") | |
7924 | ;; Either version of the license. | |
7925 | (license (list license:gpl2 license:gpl3)))) | |
6ce07cf9 RW |
7926 | |
7927 | (define-public r-th-data | |
7928 | (package | |
7929 | (name "r-th-data") | |
62595ee3 | 7930 | (version "1.0-10") |
6ce07cf9 RW |
7931 | (source |
7932 | (origin | |
7933 | (method url-fetch) | |
7934 | (uri (cran-uri "TH.data" version)) | |
7935 | (sha256 | |
7936 | (base32 | |
62595ee3 | 7937 | "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1")))) |
6ce07cf9 RW |
7938 | (properties `((upstream-name . "TH.data"))) |
7939 | (build-system r-build-system) | |
7940 | (propagated-inputs | |
7941 | `(("r-mass" ,r-mass) | |
7942 | ("r-survival" ,r-survival))) | |
7943 | (home-page "https://cran.r-project.org/web/packages/TH.data/") | |
7944 | (synopsis "Shared data sets") | |
7945 | (description | |
7946 | "This package contains supporting data sets that are used in other | |
7947 | packages maintained by Torsten Hothorn.") | |
7948 | (license license:gpl3))) | |
7753b543 RW |
7949 | |
7950 | (define-public r-multcomp | |
7951 | (package | |
7952 | (name "r-multcomp") | |
b1f39e8c | 7953 | (version "1.4-10") |
7753b543 RW |
7954 | (source |
7955 | (origin | |
7956 | (method url-fetch) | |
7957 | (uri (cran-uri "multcomp" version)) | |
7958 | (sha256 | |
7959 | (base32 | |
b1f39e8c | 7960 | "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19")))) |
7753b543 RW |
7961 | (build-system r-build-system) |
7962 | (propagated-inputs | |
7963 | `(("r-codetools" ,r-codetools) | |
7964 | ("r-mvtnorm" ,r-mvtnorm) | |
7965 | ("r-sandwich" ,r-sandwich) | |
7966 | ("r-survival" ,r-survival) | |
7967 | ("r-th-data" ,r-th-data))) | |
7968 | (home-page "https://cran.r-project.org/web/packages/multcomp/") | |
7969 | (synopsis "Simultaneous inference in general parametric models") | |
7970 | (description | |
7971 | "Simultaneous tests and confidence intervals for general linear | |
7972 | hypotheses in parametric models, including linear, generalized linear, linear | |
7973 | mixed effects, and survival models. The package includes demos reproducing | |
7974 | analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, | |
7975 | Hothorn, Westfall, 2010, CRC Press).") | |
7976 | (license license:gpl2))) | |
55a08dce RW |
7977 | |
7978 | (define-public r-emmeans | |
7979 | (package | |
7980 | (name "r-emmeans") | |
28110e68 | 7981 | (version "1.4.1") |
55a08dce RW |
7982 | (source |
7983 | (origin | |
7984 | (method url-fetch) | |
7985 | (uri (cran-uri "emmeans" version)) | |
7986 | (sha256 | |
7987 | (base32 | |
28110e68 | 7988 | "1fpawaxnmj67md169a9mzrnnh2d0c973xydfg6hw865933jil9lq")))) |
55a08dce RW |
7989 | (build-system r-build-system) |
7990 | (propagated-inputs | |
7991 | `(("r-estimability" ,r-estimability) | |
7992 | ("r-mvtnorm" ,r-mvtnorm) | |
e0f86164 | 7993 | ("r-numderiv" ,r-numderiv) |
55a08dce RW |
7994 | ("r-plyr" ,r-plyr) |
7995 | ("r-xtable" ,r-xtable))) | |
7996 | (home-page "https://github.com/rvlenth/emmeans") | |
7997 | (synopsis "Estimated marginal means, aka least-squares means") | |
7998 | (description | |
7999 | "This package provides tools to obtain @dfn{estimated marginal | |
8000 | means} (EMMs) for many linear, generalized linear, and mixed models. It can | |
8001 | be used to compute contrasts or linear functions of EMMs, trends, and | |
8002 | comparisons of slopes.") | |
8003 | ;; Either version of the license. | |
8004 | (license (list license:gpl2 license:gpl3)))) | |
63fcb88a RW |
8005 | |
8006 | (define-public r-pwr | |
8007 | (package | |
8008 | (name "r-pwr") | |
8009 | (version "1.2-2") | |
8010 | (source | |
8011 | (origin | |
8012 | (method url-fetch) | |
8013 | (uri (cran-uri "pwr" version)) | |
8014 | (sha256 | |
8015 | (base32 | |
8016 | "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm")))) | |
8017 | (build-system r-build-system) | |
8018 | (native-inputs | |
8019 | `(("r-knitr" ,r-knitr))) | |
8020 | (home-page "https://github.com/heliosdrm/pwr") | |
8021 | (synopsis "Basic functions for power analysis") | |
8022 | (description | |
8023 | "This package provides power analysis functions along the lines of | |
8024 | Cohen (1988).") | |
8025 | (license license:gpl3+))) | |
bd531e83 | 8026 | |
42f344fa RW |
8027 | (define-public r-libcoin |
8028 | (package | |
8029 | (name "r-libcoin") | |
a13f81dd | 8030 | (version "1.0-5") |
42f344fa RW |
8031 | (source |
8032 | (origin | |
8033 | (method url-fetch) | |
8034 | (uri (cran-uri "libcoin" version)) | |
8035 | (sha256 | |
8036 | (base32 | |
a13f81dd | 8037 | "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a")))) |
42f344fa RW |
8038 | (build-system r-build-system) |
8039 | (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) | |
8040 | (home-page "https://cran.r-project.org/web/packages/libcoin") | |
8041 | (synopsis "Linear test statistics for permutation inference") | |
8042 | (description | |
8043 | "This package provides basic infrastructure for linear test statistics | |
8044 | and permutation inference in the framework of Strasser and Weber (1999).") | |
8045 | (license license:gpl2))) | |
8046 | ||
bd531e83 RW |
8047 | (define-public r-coin |
8048 | (package | |
8049 | (name "r-coin") | |
1656a425 | 8050 | (version "1.3-1") |
bd531e83 RW |
8051 | (source |
8052 | (origin | |
8053 | (method url-fetch) | |
8054 | (uri (cran-uri "coin" version)) | |
8055 | (sha256 | |
8056 | (base32 | |
1656a425 | 8057 | "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx")))) |
bd531e83 RW |
8058 | (build-system r-build-system) |
8059 | (propagated-inputs | |
f69ba00f RW |
8060 | `(("r-libcoin" ,r-libcoin) |
8061 | ("r-matrixstats" ,r-matrixstats) | |
8062 | ("r-modeltools" ,r-modeltools) | |
bd531e83 RW |
8063 | ("r-multcomp" ,r-multcomp) |
8064 | ("r-mvtnorm" ,r-mvtnorm) | |
8065 | ("r-survival" ,r-survival))) | |
8066 | (home-page "http://coin.r-forge.r-project.org") | |
8067 | (synopsis "Conditional inference procedures in a permutation test framework") | |
8068 | (description | |
8069 | "This package provides conditional inference procedures for the general | |
8070 | independence problem including two-sample, K-sample (non-parametric ANOVA), | |
8071 | correlation, censored, ordered and multivariate problems.") | |
8072 | (license license:gpl2))) | |
9b3ecb60 RW |
8073 | |
8074 | (define-public r-bayesplot | |
8075 | (package | |
8076 | (name "r-bayesplot") | |
1d7bde78 | 8077 | (version "1.7.0") |
9b3ecb60 RW |
8078 | (source |
8079 | (origin | |
8080 | (method url-fetch) | |
8081 | (uri (cran-uri "bayesplot" version)) | |
8082 | (sha256 | |
8083 | (base32 | |
1d7bde78 | 8084 | "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w")))) |
9b3ecb60 RW |
8085 | (build-system r-build-system) |
8086 | (inputs | |
8087 | `(("pandoc" ,ghc-pandoc) | |
8088 | ("pandoc-citeproc" ,ghc-pandoc-citeproc))) | |
8089 | (propagated-inputs | |
8090 | `(("r-dplyr" ,r-dplyr) | |
8091 | ("r-ggplot2" ,r-ggplot2) | |
8092 | ("r-ggridges" ,r-ggridges) | |
1d7bde78 | 8093 | ("r-glue" ,r-glue) |
9b3ecb60 | 8094 | ("r-reshape2" ,r-reshape2) |
1d7bde78 RW |
8095 | ("r-rlang" ,r-rlang) |
8096 | ("r-tibble" ,r-tibble) | |
8097 | ("r-tidyselect" ,r-tidyselect))) | |
9b3ecb60 RW |
8098 | (home-page "http://mc-stan.org/bayesplot") |
8099 | (synopsis "Plotting for Bayesian models") | |
8100 | (description | |
8101 | "This package provides plotting functions for posterior analysis, model | |
8102 | checking, and MCMC diagnostics. The package is designed not only to provide | |
8103 | convenient functionality for users, but also a common set of functions that | |
8104 | can be easily used by developers working on a variety of R packages for | |
8105 | Bayesian modeling.") | |
8106 | (license license:gpl3+))) | |
3b8a3f55 RW |
8107 | |
8108 | (define-public r-tmb | |
8109 | (package | |
8110 | (name "r-tmb") | |
492ec498 | 8111 | (version "1.7.15") |
3b8a3f55 RW |
8112 | (source |
8113 | (origin | |
8114 | (method url-fetch) | |
8115 | (uri (cran-uri "TMB" version)) | |
8116 | (sha256 | |
8117 | (base32 | |
492ec498 | 8118 | "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs")))) |
3b8a3f55 RW |
8119 | (properties `((upstream-name . "TMB"))) |
8120 | (build-system r-build-system) | |
8121 | (propagated-inputs | |
8122 | `(("r-matrix" ,r-matrix) | |
8123 | ("r-rcppeigen" ,r-rcppeigen))) | |
8124 | (home-page "http://tmb-project.org") | |
8125 | (synopsis "Template model builder: a general random effect tool") | |
8126 | (description | |
8127 | "With this tool, a user should be able to quickly implement complex | |
8128 | random effect models through simple C++ templates. The package combines | |
8129 | @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated | |
8130 | matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available | |
8131 | from R) to obtain an efficient implementation of the applied Laplace | |
8132 | approximation with exact derivatives. Key features are: Automatic sparseness | |
8133 | detection, parallelism through BLAS and parallel user templates.") | |
8134 | (license license:gpl2))) | |
aa4bde0b RW |
8135 | |
8136 | (define-public r-sjstats | |
8137 | (package | |
8138 | (name "r-sjstats") | |
664e15ed | 8139 | (version "0.17.6") |
aa4bde0b RW |
8140 | (source |
8141 | (origin | |
8142 | (method url-fetch) | |
8143 | (uri (cran-uri "sjstats" version)) | |
8144 | (sha256 | |
8145 | (base32 | |
664e15ed | 8146 | "11z1wfi0d74d1rld0320l3vmv6rl41wa0v9bjc44rk06yc90wld2")))) |
aa4bde0b RW |
8147 | (build-system r-build-system) |
8148 | (propagated-inputs | |
a1473cb4 RW |
8149 | `(("r-bayestestr" ,r-bayestestr) |
8150 | ("r-broom" ,r-broom) | |
aa4bde0b RW |
8151 | ("r-dplyr" ,r-dplyr) |
8152 | ("r-emmeans" ,r-emmeans) | |
a7524f70 | 8153 | ("r-insight" ,r-insight) |
aa4bde0b RW |
8154 | ("r-lme4" ,r-lme4) |
8155 | ("r-magrittr" ,r-magrittr) | |
8156 | ("r-mass" ,r-mass) | |
aa4bde0b | 8157 | ("r-modelr" ,r-modelr) |
664e15ed | 8158 | ("r-parameters" ,r-parameters) |
a1473cb4 | 8159 | ("r-performance" ,r-performance) |
aa4bde0b | 8160 | ("r-purrr" ,r-purrr) |
aa4bde0b RW |
8161 | ("r-rlang" ,r-rlang) |
8162 | ("r-sjlabelled" ,r-sjlabelled) | |
8163 | ("r-sjmisc" ,r-sjmisc) | |
8164 | ("r-tidyr" ,r-tidyr))) | |
8165 | (home-page "https://github.com/strengejacke/sjstats") | |
8166 | (synopsis "Functions for common statistical computations") | |
8167 | (description | |
8168 | "This package provides a collection of convenient functions for common | |
8169 | statistical computations, which are not directly provided by R's @code{base} | |
8170 | or @code{stats} packages. This package aims at providing, first, shortcuts | |
8171 | for statistical measures, which otherwise could only be calculated with | |
8172 | additional effort. Second, these shortcut functions are generic, and can be | |
8173 | applied not only to vectors, but also to other objects as well. The focus of | |
8174 | most functions lies on summary statistics or fit measures for regression | |
8175 | models, including generalized linear models, mixed effects models and Bayesian | |
8176 | models.") | |
8177 | (license license:gpl3))) | |
41394423 RW |
8178 | |
8179 | (define-public r-glmmtmb | |
8180 | (package | |
8181 | (name "r-glmmtmb") | |
1afe5644 | 8182 | (version "0.2.3") |
41394423 RW |
8183 | (source |
8184 | (origin | |
8185 | (method url-fetch) | |
8186 | (uri (cran-uri "glmmTMB" version)) | |
8187 | (sha256 | |
8188 | (base32 | |
1afe5644 | 8189 | "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb")))) |
41394423 RW |
8190 | (properties `((upstream-name . "glmmTMB"))) |
8191 | (build-system r-build-system) | |
8192 | (propagated-inputs | |
8193 | `(("r-lme4" ,r-lme4) | |
8194 | ("r-matrix" ,r-matrix) | |
8195 | ("r-nlme" ,r-nlme) | |
8196 | ("r-rcppeigen" ,r-rcppeigen) | |
8197 | ("r-tmb" ,r-tmb))) | |
8198 | (native-inputs | |
1afe5644 | 8199 | `(("r-knitr" ,r-knitr))) ; for vignettes |
41394423 RW |
8200 | (home-page "https://github.com/glmmTMB") |
8201 | (synopsis "Generalized linear mixed models") | |
8202 | (description | |
8203 | "Fit linear and generalized linear mixed models with various extensions, | |
8204 | including zero-inflation. The models are fitted using maximum likelihood | |
8205 | estimation via the Template Model Builder. Random effects are assumed to be | |
8206 | Gaussian on the scale of the linear predictor and are integrated out using the | |
8207 | Laplace approximation. Gradients are calculated using automatic | |
8208 | differentiation.") | |
8209 | (license license:agpl3+))) | |
489a6178 | 8210 | |
c4568c5c RW |
8211 | (define-public r-bayestestr |
8212 | (package | |
8213 | (name "r-bayestestr") | |
f889a157 | 8214 | (version "0.3.0") |
c4568c5c RW |
8215 | (source |
8216 | (origin | |
8217 | (method url-fetch) | |
8218 | (uri (cran-uri "bayestestR" version)) | |
8219 | (sha256 | |
8220 | (base32 | |
f889a157 | 8221 | "0r453zb106hj9w53jjgckxqajjf7shlrgv10gjxsv8if6qybdz5b")))) |
c4568c5c RW |
8222 | (properties `((upstream-name . "bayestestR"))) |
8223 | (build-system r-build-system) | |
8224 | (propagated-inputs | |
8225 | `(("r-insight" ,r-insight))) | |
8226 | (home-page "https://github.com/easystats/bayestestR") | |
8227 | (synopsis "Describe Bayesian models and posterior distributions") | |
8228 | (description | |
8229 | "This package provides utilities to understand and describe posterior | |
8230 | distributions and Bayesian models. It includes point-estimates such as | |
8231 | @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest | |
8232 | Density Interval} (HDI), and indices used for null-hypothesis testing (such as | |
8233 | ROPE percentage and pd).") | |
8234 | (license license:gpl3))) | |
8235 | ||
711a2f06 RW |
8236 | (define-public r-performance |
8237 | (package | |
8238 | (name "r-performance") | |
5ae4cbb6 | 8239 | (version "0.3.0") |
711a2f06 RW |
8240 | (source |
8241 | (origin | |
8242 | (method url-fetch) | |
8243 | (uri (cran-uri "performance" version)) | |
8244 | (sha256 | |
8245 | (base32 | |
5ae4cbb6 | 8246 | "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w")))) |
711a2f06 RW |
8247 | (build-system r-build-system) |
8248 | (propagated-inputs | |
8249 | `(("r-bayestestr" ,r-bayestestr) | |
8250 | ("r-insight" ,r-insight))) | |
8251 | (home-page "https://easystats.github.io/performance/") | |
8252 | (synopsis "Assessment of regression models performance") | |
8253 | (description | |
8254 | "This package provides utilities for computing measures to assess model | |
8255 | quality, which are not directly provided by R's @code{base} or @code{stats} | |
8256 | packages. These include e.g. measures like r-squared, intraclass correlation | |
8257 | coefficient, root mean squared error or functions to check models for | |
8258 | overdispersion, singularity or zero-inflation and more. Functions apply to a | |
8259 | large variety of regression models, including generalized linear models, mixed | |
8260 | effects models and Bayesian models.") | |
8261 | (license license:gpl3))) | |
8262 | ||
489a6178 RW |
8263 | (define-public r-ggeffects |
8264 | (package | |
8265 | (name "r-ggeffects") | |
f396d343 | 8266 | (version "0.12.0") |
489a6178 RW |
8267 | (source |
8268 | (origin | |
8269 | (method url-fetch) | |
8270 | (uri (cran-uri "ggeffects" version)) | |
8271 | (sha256 | |
8272 | (base32 | |
f396d343 | 8273 | "0idfycjk05gyykfp9ibmhxfcjvd01ikh1dl0fb4nqw6znw3ar0xp")))) |
489a6178 RW |
8274 | (build-system r-build-system) |
8275 | (propagated-inputs | |
fef93da8 RW |
8276 | `(("r-dplyr" ,r-dplyr) |
8277 | ("r-insight" ,r-insight) | |
489a6178 RW |
8278 | ("r-magrittr" ,r-magrittr) |
8279 | ("r-mass" ,r-mass) | |
489a6178 RW |
8280 | ("r-purrr" ,r-purrr) |
8281 | ("r-rlang" ,r-rlang) | |
8282 | ("r-scales" ,r-scales) | |
8283 | ("r-sjlabelled" ,r-sjlabelled) | |
fef93da8 | 8284 | ("r-sjmisc" ,r-sjmisc))) |
489a6178 RW |
8285 | (home-page "https://github.com/strengejacke/ggeffects") |
8286 | (synopsis "Create tidy data frames of marginal effects for ggplot") | |
8287 | (description | |
8288 | "This package provides tools to compute marginal effects from statistical | |
8289 | models and return the result as tidy data frames. These data frames are ready | |
8290 | to use with the @code{ggplot2} package. Marginal effects can be calculated | |
8291 | for many different models. Interaction terms, splines and polynomial terms | |
8292 | are also supported. The two main functions are @code{ggpredict()} and | |
8293 | @code{ggeffect()}. There is a generic @code{plot()} method to plot the | |
8294 | results using @code{ggplot2}.") | |
8295 | (license license:gpl3))) | |
7b63047c RW |
8296 | |
8297 | (define-public r-sjplot | |
8298 | (package | |
8299 | (name "r-sjplot") | |
97b44f5e | 8300 | (version "2.7.2") |
7b63047c RW |
8301 | (source |
8302 | (origin | |
8303 | (method url-fetch) | |
8304 | (uri (cran-uri "sjPlot" version)) | |
8305 | (sha256 | |
97b44f5e | 8306 | (base32 "1kx1qqgp4fhwwwpqn9mv8m1pnpjxfs7ww36ns7j1ja4a7ydwn2hp")))) |
7b63047c RW |
8307 | (properties `((upstream-name . "sjPlot"))) |
8308 | (build-system r-build-system) | |
8309 | (propagated-inputs | |
d22d7904 RW |
8310 | `(("r-bayestestr" ,r-bayestestr) |
8311 | ("r-broom" ,r-broom) | |
7b63047c RW |
8312 | ("r-dplyr" ,r-dplyr) |
8313 | ("r-forcats" ,r-forcats) | |
8314 | ("r-ggeffects" ,r-ggeffects) | |
8315 | ("r-ggplot2" ,r-ggplot2) | |
a5a64814 | 8316 | ("r-ggrepel" ,r-ggrepel) |
7b63047c | 8317 | ("r-glmmtmb" ,r-glmmtmb) |
d22d7904 | 8318 | ("r-insight" ,r-insight) |
7b63047c RW |
8319 | ("r-knitr" ,r-knitr) |
8320 | ("r-lme4" ,r-lme4) | |
8321 | ("r-magrittr" ,r-magrittr) | |
8322 | ("r-mass" ,r-mass) | |
8323 | ("r-modelr" ,r-modelr) | |
8324 | ("r-nlme" ,r-nlme) | |
d22d7904 | 8325 | ("r-performance" ,r-performance) |
7b63047c RW |
8326 | ("r-psych" ,r-psych) |
8327 | ("r-purrr" ,r-purrr) | |
8328 | ("r-rlang" ,r-rlang) | |
8329 | ("r-scales" ,r-scales) | |
8330 | ("r-sjlabelled" ,r-sjlabelled) | |
8331 | ("r-sjmisc" ,r-sjmisc) | |
8332 | ("r-sjstats" ,r-sjstats) | |
8333 | ("r-tidyr" ,r-tidyr))) | |
8334 | (home-page "https://strengejacke.github.io/sjPlot/") | |
8335 | (synopsis "Data visualization for statistics in social science") | |
8336 | (description | |
8337 | "This package represents a collection of plotting and table output | |
8338 | functions for data visualization. Results of various statistical | |
8339 | analyses (that are commonly used in social sciences) can be visualized using | |
8340 | this package, including simple and cross tabulated frequencies, histograms, | |
8341 | box plots, (generalized) linear models, mixed effects models, principal | |
8342 | component analysis and correlation matrices, cluster analyses, scatter plots, | |
8343 | stacked scales, effects plots of regression models (including interaction | |
8344 | terms) and much more. This package supports labelled data.") | |
8345 | (license license:gpl3))) | |
03f80112 RW |
8346 | |
8347 | (define-public r-ini | |
8348 | (package | |
8349 | (name "r-ini") | |
8350 | (version "0.3.1") | |
8351 | (source | |
8352 | (origin | |
8353 | (method url-fetch) | |
8354 | (uri (cran-uri "ini" version)) | |
8355 | (sha256 | |
8356 | (base32 | |
8357 | "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) | |
8358 | (build-system r-build-system) | |
8359 | (home-page "https://github.com/dvdscripter/ini") | |
8360 | (synopsis "Read and write configuration files") | |
8361 | (description | |
8362 | "This package provides tools to parse simple @code{.ini} configuration | |
8363 | files to an structured list. Users can manipulate this resulting list with | |
8364 | @code{lapply()} functions. This same structured list can be used to write | |
8365 | back to file after modifications.") | |
8366 | (license license:gpl3))) | |
21405e81 RW |
8367 | |
8368 | (define-public r-gh | |
8369 | (package | |
8370 | (name "r-gh") | |
8371 | (version "1.0.1") | |
8372 | (source | |
8373 | (origin | |
8374 | (method url-fetch) | |
8375 | (uri (cran-uri "gh" version)) | |
8376 | (sha256 | |
8377 | (base32 | |
8378 | "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k")))) | |
8379 | (build-system r-build-system) | |
8380 | (propagated-inputs | |
8381 | `(("r-httr" ,r-httr) | |
8382 | ("r-ini" ,r-ini) | |
8383 | ("r-jsonlite" ,r-jsonlite))) | |
8384 | (home-page "https://github.com/r-lib/gh#readme") | |
8385 | (synopsis "Access the GitHub API via R") | |
8386 | (description | |
8387 | "This package provides a minimal R client to access the GitHub API.") | |
8388 | (license license:expat))) | |
d6871153 RW |
8389 | |
8390 | (define-public r-fs | |
8391 | (package | |
8392 | (name "r-fs") | |
c02f574d | 8393 | (version "1.3.1") |
d6871153 RW |
8394 | (source |
8395 | (origin | |
8396 | (method url-fetch) | |
8397 | (uri (cran-uri "fs" version)) | |
8398 | (sha256 | |
8399 | (base32 | |
c02f574d | 8400 | "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn")))) |
d6871153 RW |
8401 | (build-system r-build-system) |
8402 | (propagated-inputs | |
8403 | `(("r-rcpp" ,r-rcpp))) | |
8404 | (native-inputs | |
8405 | `(("pkg-config" ,pkg-config))) | |
8406 | (home-page "http://fs.r-lib.org") | |
8407 | (synopsis "Cross-platform file system operations based on libuv") | |
8408 | (description | |
8409 | "This package provides a cross-platform interface to file system | |
8410 | operations, built on top of the libuv C library.") | |
8411 | (license license:gpl3))) | |
153e5b2d RW |
8412 | |
8413 | (define-public r-clisymbols | |
8414 | (package | |
8415 | (name "r-clisymbols") | |
8416 | (version "1.2.0") | |
8417 | (source | |
8418 | (origin | |
8419 | (method url-fetch) | |
8420 | (uri (cran-uri "clisymbols" version)) | |
8421 | (sha256 | |
8422 | (base32 | |
8423 | "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86")))) | |
8424 | (build-system r-build-system) | |
8425 | (home-page "https://github.com/gaborcsardi/clisymbols") | |
8426 | (synopsis "Unicode symbols at the R prompt") | |
8427 | (description | |
8428 | "This package provides a small subset of Unicode symbols, that are useful | |
8429 | when building command line applications. They fall back to alternatives on | |
8430 | terminals that do not support Unicode.") | |
8431 | (license license:expat))) | |
efefd3ec RW |
8432 | |
8433 | (define-public r-usethis | |
8434 | (package | |
8435 | (name "r-usethis") | |
99765abb | 8436 | (version "1.5.1") |
efefd3ec RW |
8437 | (source |
8438 | (origin | |
8439 | (method url-fetch) | |
8440 | (uri (cran-uri "usethis" version)) | |
8441 | (sha256 | |
8442 | (base32 | |
99765abb | 8443 | "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy")))) |
efefd3ec RW |
8444 | (build-system r-build-system) |
8445 | (propagated-inputs | |
8446 | `(("r-clipr" ,r-clipr) | |
8447 | ("r-clisymbols" ,r-clisymbols) | |
8448 | ("r-crayon" ,r-crayon) | |
8449 | ("r-curl" ,r-curl) | |
8450 | ("r-desc" ,r-desc) | |
8451 | ("r-fs" ,r-fs) | |
8452 | ("r-gh" ,r-gh) | |
8453 | ("r-git2r" ,r-git2r) | |
8454 | ("r-glue" ,r-glue) | |
35171015 | 8455 | ("r-purrr" ,r-purrr) |
efefd3ec RW |
8456 | ("r-rlang" ,r-rlang) |
8457 | ("r-rprojroot" ,r-rprojroot) | |
8458 | ("r-rstudioapi" ,r-rstudioapi) | |
35171015 RW |
8459 | ("r-whisker" ,r-whisker) |
8460 | ("r-withr" ,r-withr) | |
8461 | ("r-yaml" ,r-yaml))) | |
efefd3ec RW |
8462 | (home-page "https://github.com/r-lib/usethis") |
8463 | (synopsis "Automate R package and project setup") | |
8464 | (description | |
8465 | "This package helps you to automate R package and project setup tasks | |
8466 | that are otherwise performed manually. This includes setting up unit testing, | |
8467 | test coverage, continuous integration, Git, GitHub integration, licenses, | |
8468 | Rcpp, RStudio projects, and more.") | |
8469 | (license license:gpl3))) | |
99342624 RW |
8470 | |
8471 | (define-public r-sessioninfo | |
8472 | (package | |
8473 | (name "r-sessioninfo") | |
3d6fa1a3 | 8474 | (version "1.1.1") |
99342624 RW |
8475 | (source |
8476 | (origin | |
8477 | (method url-fetch) | |
8478 | (uri (cran-uri "sessioninfo" version)) | |
8479 | (sha256 | |
8480 | (base32 | |
3d6fa1a3 | 8481 | "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn")))) |
99342624 RW |
8482 | (build-system r-build-system) |
8483 | (propagated-inputs | |
8484 | `(("r-cli" ,r-cli) | |
8485 | ("r-withr" ,r-withr))) | |
8486 | (home-page "https://github.com/r-lib/sessioninfo#readme") | |
8487 | (synopsis "R session information") | |
8488 | (description | |
8489 | "This package provides tools to query and print information about the | |
8490 | current R session. It is similar to @code{utils::sessionInfo()}, but includes | |
8491 | more information about packages, and where they were installed from.") | |
8492 | (license license:gpl2))) | |
cbc8e6dd RW |
8493 | |
8494 | (define-public r-remotes | |
8495 | (package | |
8496 | (name "r-remotes") | |
da4754a3 | 8497 | (version "2.1.0") |
cbc8e6dd RW |
8498 | (source |
8499 | (origin | |
8500 | (method url-fetch) | |
8501 | (uri (cran-uri "remotes" version)) | |
8502 | (sha256 | |
8503 | (base32 | |
da4754a3 | 8504 | "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49")))) |
cbc8e6dd RW |
8505 | (build-system r-build-system) |
8506 | (home-page "https://github.com/r-lib/remotes#readme") | |
8507 | (synopsis "R package installation from remote repositories") | |
8508 | (description | |
8509 | "Download and install R packages stored in GitHub, BitBucket, or plain | |
8510 | subversion or git repositories. This package is a lightweight replacement of | |
8511 | the @code{install_*} functions in the @code{devtools} package. Indeed most of | |
8512 | the code was copied over from @code{devtools}.") | |
8513 | (license license:gpl2+))) | |
7d8f3470 RW |
8514 | |
8515 | (define-public r-xopen | |
8516 | (package | |
8517 | (name "r-xopen") | |
8518 | (version "1.0.0") | |
8519 | (source | |
8520 | (origin | |
8521 | (method url-fetch) | |
8522 | (uri (cran-uri "xopen" version)) | |
8523 | (sha256 | |
8524 | (base32 | |
8525 | "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) | |
8526 | (build-system r-build-system) | |
8527 | (propagated-inputs | |
8528 | `(("r-processx" ,r-processx))) | |
8529 | (home-page "https://github.com/r-lib/xopen#readme") | |
8530 | (synopsis "Open system files, URLs, anything") | |
8531 | (description | |
8532 | "This package provides a cross-platform solution to open files, | |
8533 | directories or URLs with their associated programs.") | |
8534 | (license license:expat))) | |
5df4e27f RW |
8535 | |
8536 | (define-public r-rcmdcheck | |
8537 | (package | |
8538 | (name "r-rcmdcheck") | |
a75c6d9c | 8539 | (version "1.3.3") |
5df4e27f RW |
8540 | (source |
8541 | (origin | |
8542 | (method url-fetch) | |
8543 | (uri (cran-uri "rcmdcheck" version)) | |
8544 | (sha256 | |
8545 | (base32 | |
a75c6d9c | 8546 | "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs")))) |
5df4e27f RW |
8547 | (build-system r-build-system) |
8548 | (propagated-inputs | |
8549 | `(("r-callr" ,r-callr) | |
8550 | ("r-cli" ,r-cli) | |
8551 | ("r-crayon" ,r-crayon) | |
8552 | ("r-desc" ,r-desc) | |
8553 | ("r-digest" ,r-digest) | |
8554 | ("r-pkgbuild" ,r-pkgbuild) | |
8555 | ("r-prettyunits" ,r-prettyunits) | |
8556 | ("r-r6" ,r-r6) | |
8557 | ("r-rprojroot" ,r-rprojroot) | |
7466c3bb | 8558 | ("r-sessioninfo" ,r-sessioninfo) |
5df4e27f RW |
8559 | ("r-withr" ,r-withr) |
8560 | ("r-xopen" ,r-xopen))) | |
8561 | (home-page "https://github.com/r-Lib/rcmdcheck#readme") | |
8562 | (synopsis "Run R CMD check from R and capture results") | |
8563 | (description | |
8564 | "Run @code{R CMD check} from R programmatically, and capture the results | |
8565 | of the individual checks.") | |
8566 | (license license:expat))) | |
9b02d1a1 RW |
8567 | |
8568 | (define-public r-rapportools | |
8569 | (package | |
8570 | (name "r-rapportools") | |
8571 | (version "1.0") | |
8572 | (source | |
8573 | (origin | |
8574 | (method url-fetch) | |
8575 | (uri (cran-uri "rapportools" version)) | |
8576 | (sha256 | |
8577 | (base32 | |
8578 | "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) | |
8579 | (build-system r-build-system) | |
8580 | (propagated-inputs | |
8581 | `(("r-pander" ,r-pander) | |
8582 | ("r-plyr" ,r-plyr) | |
8583 | ("r-reshape" ,r-reshape))) | |
8584 | (home-page "https://cran.r-project.org/web/packages/rapportools/") | |
8585 | (synopsis "Miscellaneous helper functions with sane defaults for reporting") | |
8586 | (description | |
8587 | "This package provides helper functions that act as wrappers to more | |
8588 | advanced statistical methods with the advantage of having sane defaults for | |
8589 | quick reporting.") | |
8590 | (license license:agpl3+))) | |
319a80ce RW |
8591 | |
8592 | (define-public r-pander | |
8593 | (package | |
8594 | (name "r-pander") | |
a44f8b00 | 8595 | (version "0.6.3") |
319a80ce RW |
8596 | (source |
8597 | (origin | |
8598 | (method url-fetch) | |
8599 | (uri (cran-uri "pander" version)) | |
8600 | (sha256 | |
8601 | (base32 | |
a44f8b00 | 8602 | "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi")))) |
319a80ce RW |
8603 | (build-system r-build-system) |
8604 | (propagated-inputs | |
8605 | `(("r-digest" ,r-digest) | |
8606 | ("r-rcpp" ,r-rcpp))) | |
8607 | (home-page "https://rapporter.github.io/pander") | |
8608 | (synopsis "Render R objects into Pandoc's markdown") | |
8609 | (description | |
8610 | "The main aim of the pander R package is to provide a minimal and easy | |
8611 | tool for rendering R objects into Pandoc's markdown. The package is also | |
8612 | capable of exporting/converting complex Pandoc documents (reports) in various | |
8613 | ways.") | |
8614 | ;; This package is licensed under either the AGPLv3+ or the very rarely | |
8615 | ;; used OSL 3.0. | |
8616 | (license license:agpl3+))) | |
74cc74e4 RW |
8617 | |
8618 | (define-public r-summarytools | |
8619 | (package | |
8620 | (name "r-summarytools") | |
084ea348 | 8621 | (version "0.9.4") |
74cc74e4 RW |
8622 | (source |
8623 | (origin | |
8624 | (method url-fetch) | |
8625 | (uri (cran-uri "summarytools" version)) | |
8626 | (sha256 | |
8627 | (base32 | |
084ea348 | 8628 | "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a")))) |
74cc74e4 RW |
8629 | (build-system r-build-system) |
8630 | (propagated-inputs | |
5093cbdc RW |
8631 | `(("r-checkmate" ,r-checkmate) |
8632 | ("r-dplyr" ,r-dplyr) | |
8633 | ("r-htmltools" ,r-htmltools) | |
74cc74e4 | 8634 | ("r-lubridate" ,r-lubridate) |
5093cbdc | 8635 | ("r-magick" ,r-magick) |
74cc74e4 RW |
8636 | ("r-matrixstats" ,r-matrixstats) |
8637 | ("r-pander" ,r-pander) | |
8638 | ("r-pryr" ,r-pryr) | |
8639 | ("r-rapportools" ,r-rapportools) | |
5093cbdc | 8640 | ("r-rcurl" ,r-rcurl) |
4c920fbb | 8641 | ("r-tibble" ,r-tibble) |
5093cbdc | 8642 | ("r-tidyr" ,r-tidyr))) |
74cc74e4 RW |
8643 | (home-page "https://github.com/dcomtois/summarytools") |
8644 | (synopsis "Tools to quickly and neatly summarize data") | |
8645 | (description | |
8646 | "This package provides tools for data frame summaries, cross-tabulations, | |
8647 | weight-enabled frequency tables and common univariate statistics in concise | |
8648 | tables available in a variety of formats (plain ASCII, Markdown and HTML). A | |
8649 | good point-of-entry for exploring data, both for experienced and new R | |
8650 | users.") | |
8651 | (license license:gpl2))) | |
7c7ee6cf RW |
8652 | |
8653 | (define-public r-lsei | |
8654 | (package | |
8655 | (name "r-lsei") | |
8656 | (version "1.2-0") | |
8657 | (source | |
8658 | (origin | |
8659 | (method url-fetch) | |
8660 | (uri (cran-uri "lsei" version)) | |
8661 | (sha256 | |
8662 | (base32 | |
8663 | "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7")))) | |
8664 | (build-system r-build-system) | |
8665 | (native-inputs | |
8666 | `(("gfortran" ,gfortran))) | |
8667 | (home-page "https://www.stat.auckland.ac.nz/~yongwang") | |
8668 | (synopsis "Solve regression problems under equality/inequality constraints") | |
8669 | (description | |
8670 | "It contains functions that solve least squares linear regression | |
8671 | problems under linear equality/inequality constraints. Functions for solving | |
8672 | quadratic programming problems are also available, which transform such | |
8673 | problems into least squares ones first.") | |
8674 | (license license:gpl2+))) | |
2ea75a83 RW |
8675 | |
8676 | (define-public r-npsurv | |
8677 | (package | |
8678 | (name "r-npsurv") | |
8679 | (version "0.4-0") | |
8680 | (source | |
8681 | (origin | |
8682 | (method url-fetch) | |
8683 | (uri (cran-uri "npsurv" version)) | |
8684 | (sha256 | |
8685 | (base32 | |
8686 | "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20")))) | |
8687 | (build-system r-build-system) | |
8688 | (propagated-inputs | |
8689 | `(("r-lsei" ,r-lsei))) | |
8690 | (home-page "https://www.stat.auckland.ac.nz/~yongwang") | |
8691 | (synopsis "Nonparametric survival analysis") | |
8692 | (description | |
8693 | "This package contains functions for non-parametric survival analysis of | |
8694 | exact and interval-censored observations.") | |
8695 | (license license:gpl2+))) | |
32499b26 RW |
8696 | |
8697 | (define-public r-clusteval | |
8698 | (package | |
8699 | (name "r-clusteval") | |
8700 | (version "0.1") | |
8701 | (source | |
8702 | (origin | |
8703 | (method url-fetch) | |
8704 | (uri (cran-uri "clusteval" version)) | |
8705 | (sha256 | |
8706 | (base32 | |
8707 | "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) | |
8708 | (build-system r-build-system) | |
8709 | (propagated-inputs | |
8710 | `(("r-mvtnorm" ,r-mvtnorm) | |
8711 | ("r-rcpp" ,r-rcpp))) | |
8712 | (home-page "https://cran.r-project.org/web/packages/clusteval/") | |
8713 | (synopsis "Evaluation of clustering algorithms") | |
8714 | (description | |
8715 | "This R package provides a suite of tools to evaluate clustering | |
8716 | algorithms, clusterings, and individual clusters.") | |
8717 | (license license:expat))) | |
373cef0a RW |
8718 | |
8719 | (define-public r-tweedie | |
8720 | (package | |
8721 | (name "r-tweedie") | |
8722 | (version "2.3.2") | |
8723 | (source | |
8724 | (origin | |
8725 | (method url-fetch) | |
8726 | (uri (cran-uri "tweedie" version)) | |
8727 | (sha256 | |
8728 | (base32 | |
8729 | "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls")))) | |
8730 | (build-system r-build-system) | |
8731 | (native-inputs `(("gfortran" ,gfortran))) | |
8732 | (home-page "https://cran.r-project.org/web/packages/tweedie/") | |
8733 | (synopsis "Evaluation of Tweedie exponential family models") | |
8734 | (description | |
8735 | "Maximum likelihood computations for Tweedie families, including the | |
8736 | series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and | |
8737 | the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), | |
8738 | and related methods.") | |
8739 | (license license:gpl2+))) | |
4fb35ebd RW |
8740 | |
8741 | (define-public r-rcppgsl | |
8742 | (package | |
8743 | (name "r-rcppgsl") | |
8744 | (version "0.3.6") | |
8745 | (source | |
8746 | (origin | |
8747 | (method url-fetch) | |
8748 | (uri (cran-uri "RcppGSL" version)) | |
8749 | (sha256 | |
8750 | (base32 | |
8751 | "16pdapq31729db53agnb48jkvdm97167n3bigy5zazc3q3isis1m")))) | |
8752 | (properties `((upstream-name . "RcppGSL"))) | |
8753 | (build-system r-build-system) | |
8754 | (propagated-inputs | |
8755 | `(("r-rcpp" ,r-rcpp) | |
8756 | ("gsl" ,gsl))) | |
8757 | (native-inputs | |
8758 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
8759 | (home-page "https://cran.r-project.org/web/packages/RcppGSL/") | |
8760 | (synopsis "Rcpp integration for GSL vectors and matrices") | |
8761 | (description | |
8762 | "The GNU Scientific Library (or GSL) is a collection of numerical | |
8763 | routines for scientific computing. It is particularly useful for C and C++ | |
8764 | programs as it provides a standard C interface to a wide range of mathematical | |
8765 | routines. There are over 1000 functions in total with an extensive test | |
8766 | suite. The RcppGSL package provides an easy-to-use interface between GSL data | |
8767 | structures and R using concepts from Rcpp which is itself a package that eases | |
8768 | the interfaces between R and C++.") | |
8769 | (license license:gpl2+))) | |
20ff6e3a RW |
8770 | |
8771 | (define-public r-mvabund | |
8772 | (package | |
8773 | (name "r-mvabund") | |
48102ce1 | 8774 | (version "4.0.1") |
20ff6e3a RW |
8775 | (source |
8776 | (origin | |
8777 | (method url-fetch) | |
8778 | (uri (cran-uri "mvabund" version)) | |
8779 | (sha256 | |
8780 | (base32 | |
48102ce1 | 8781 | "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k")))) |
20ff6e3a RW |
8782 | (build-system r-build-system) |
8783 | (propagated-inputs | |
8784 | `(("r-mass" ,r-mass) | |
8785 | ("r-rcpp" ,r-rcpp) | |
8786 | ("r-rcppgsl" ,r-rcppgsl) | |
8787 | ("r-statmod" ,r-statmod) | |
8788 | ("r-tweedie" ,r-tweedie))) | |
8789 | (home-page "https://cran.r-project.org/web/packages/mvabund/") | |
8790 | (synopsis "Statistical methods for analysing multivariate abundance data") | |
8791 | (description | |
8792 | "This package provides a set of tools for displaying, modeling and | |
8793 | analysing multivariate abundance data in community ecology.") | |
8794 | (license license:lgpl2.1+))) | |
49863fd6 RW |
8795 | |
8796 | (define-public r-afex | |
8797 | (package | |
8798 | (name "r-afex") | |
0eb28435 | 8799 | (version "0.25-1") |
49863fd6 RW |
8800 | (source |
8801 | (origin | |
8802 | (method url-fetch) | |
8803 | (uri (cran-uri "afex" version)) | |
8804 | (sha256 | |
8805 | (base32 | |
0eb28435 | 8806 | "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf")))) |
49863fd6 RW |
8807 | (build-system r-build-system) |
8808 | (propagated-inputs | |
8809 | `(("r-car" ,r-car) | |
8810 | ("r-lme4" ,r-lme4) | |
8811 | ("r-lmertest" ,r-lmertest) | |
8812 | ("r-pbkrtest" ,r-pbkrtest) | |
8813 | ("r-reshape2" ,r-reshape2))) | |
8814 | (home-page "https://afex.singmann.science/") | |
8815 | (synopsis "Analysis of factorial experiments") | |
8816 | (description | |
8817 | "This package provides convenience functions for analyzing factorial | |
8818 | experiments using ANOVA or mixed models.") | |
8819 | (license license:gpl2+))) | |
7c02dd62 RW |
8820 | |
8821 | (define-public r-lmertest | |
8822 | (package | |
8823 | (name "r-lmertest") | |
f18ca07e | 8824 | (version "3.1-0") |
7c02dd62 RW |
8825 | (source |
8826 | (origin | |
8827 | (method url-fetch) | |
8828 | (uri (cran-uri "lmerTest" version)) | |
8829 | (sha256 | |
8830 | (base32 | |
f18ca07e | 8831 | "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b")))) |
7c02dd62 RW |
8832 | (properties `((upstream-name . "lmerTest"))) |
8833 | (build-system r-build-system) | |
8834 | (propagated-inputs | |
8835 | `(("r-ggplot2" ,r-ggplot2) | |
8836 | ("r-lme4" ,r-lme4) | |
8837 | ("r-mass" ,r-mass) | |
8838 | ("r-numderiv" ,r-numderiv))) | |
8839 | (home-page "https://github.com/runehaubo/lmerTestR") | |
8840 | (synopsis "Tests in linear mixed effects models") | |
8841 | (description | |
8842 | "This package provides p-values in type I, II or III anova and summary | |
8843 | tables for @code{lmer} model fits via Satterthwaite's degrees of freedom | |
8844 | method. A Kenward-Roger method is also available via the @code{pbkrtest} | |
8845 | package. Model selection methods include step, drop1 and anova-like tables | |
8846 | for random effects (ranova). Methods for Least-Square means (LS-means) and | |
8847 | tests of linear contrasts of fixed effects are also available.") | |
8848 | (license license:gpl2+))) | |
fd649d1e RW |
8849 | |
8850 | (define-public r-r2glmm | |
8851 | (package | |
8852 | (name "r-r2glmm") | |
8853 | (version "0.1.2") | |
8854 | (source | |
8855 | (origin | |
8856 | (method url-fetch) | |
8857 | (uri (cran-uri "r2glmm" version)) | |
8858 | (sha256 | |
8859 | (base32 | |
8860 | "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) | |
8861 | (build-system r-build-system) | |
8862 | (propagated-inputs | |
8863 | `(("r-afex" ,r-afex) | |
8864 | ("r-data-table" ,r-data-table) | |
8865 | ("r-dplyr" ,r-dplyr) | |
8866 | ("r-ggplot2" ,r-ggplot2) | |
8867 | ("r-gridextra" ,r-gridextra) | |
8868 | ("r-lmertest" ,r-lmertest) | |
8869 | ("r-mass" ,r-mass) | |
8870 | ("r-matrix" ,r-matrix) | |
8871 | ("r-mgcv" ,r-mgcv) | |
8872 | ("r-pbkrtest" ,r-pbkrtest))) | |
8873 | (home-page "https://github.com/bcjaeger/r2glmm") | |
8874 | (synopsis "Compute R squared for mixed (multilevel) models") | |
8875 | (description | |
8876 | "This package computes model and semi partial R squared with confidence | |
8877 | limits for the linear and generalized linear mixed model (LMM and GLMM). The | |
8878 | R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM | |
8879 | using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et | |
8880 | al. (2016)).") | |
8881 | (license license:gpl2))) | |
cddc0300 | 8882 | |
8883 | (define-public r-weights | |
8884 | (package | |
8885 | (name "r-weights") | |
8886 | (version "1.0") | |
8887 | (source | |
8888 | (origin | |
8889 | (method url-fetch) | |
8890 | (uri (cran-uri "weights" version)) | |
8891 | (sha256 | |
8892 | (base32 | |
8893 | "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c")))) | |
8894 | (build-system r-build-system) | |
8895 | (propagated-inputs | |
8896 | `(("r-gdata" ,r-gdata) | |
8897 | ("r-hmisc" ,r-hmisc) | |
8898 | ("r-mice" ,r-mice))) | |
8899 | (home-page | |
8900 | "https://cran.r-project.org/web/packages/weights/") | |
8901 | (synopsis "Weighting and weighted statistics") | |
8902 | (description "This package Provides a variety of functions for producing | |
8903 | simple weighted statistics, such as weighted Pearson's correlations, partial | |
8904 | correlations, Chi-Squared statistics, histograms, and t-tests. Also now | |
8905 | includes some software for quickly recoding survey data and plotting point | |
8906 | estimates from interaction terms in regressions (and multiply imputed | |
8907 | regressions). NOTE: Weighted partial correlation calculations pulled to | |
8908 | address a bug.") | |
8909 | (license license:gpl2+))) | |
bfa5662e RW |
8910 | |
8911 | (define-public r-rcppannoy | |
8912 | (package | |
8913 | (name "r-rcppannoy") | |
6b286750 | 8914 | (version "0.0.13") |
bfa5662e RW |
8915 | (source |
8916 | (origin | |
8917 | (method url-fetch) | |
8918 | (uri (cran-uri "RcppAnnoy" version)) | |
8919 | (sha256 | |
8920 | (base32 | |
6b286750 | 8921 | "1jibp9b07c5ka1kif0nl7f168hxfvysj32wnmnxg85l663hmvm8j")))) |
bfa5662e RW |
8922 | (properties `((upstream-name . "RcppAnnoy"))) |
8923 | (build-system r-build-system) | |
8924 | (propagated-inputs | |
8925 | `(("r-rcpp" ,r-rcpp))) | |
8926 | (native-inputs | |
8927 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
8928 | (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") | |
8929 | (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") | |
8930 | (description | |
8931 | "Annoy is a small C++ library for Approximate Nearest Neighbors written | |
8932 | for efficient memory usage as well an ability to load from and save to disk. | |
8933 | This package provides an R interface.") | |
8934 | ;; Annoy is released under ASL 2.0, but this wrapper is released under | |
8935 | ;; GPLv2+. | |
8936 | (license (list license:gpl2+ license:asl2.0)))) | |
b58940cb | 8937 | |
81281899 RW |
8938 | (define-public r-rcpphnsw |
8939 | (package | |
8940 | (name "r-rcpphnsw") | |
7c27558a | 8941 | (version "0.2.0") |
81281899 RW |
8942 | (source |
8943 | (origin | |
8944 | (method url-fetch) | |
8945 | (uri (cran-uri "RcppHNSW" version)) | |
8946 | (sha256 | |
8947 | (base32 | |
7c27558a | 8948 | "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv")))) |
81281899 RW |
8949 | (properties `((upstream-name . "RcppHNSW"))) |
8950 | (build-system r-build-system) | |
8951 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
8952 | (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") | |
8953 | (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") | |
8954 | (description | |
8955 | "Hnswlib is a C++ library for approximate nearest neighbors. This | |
8956 | package provides a minimal R interface by relying on the Rcpp package.") | |
8957 | ;; hnswlib is released under Version 2.0 of the Apache License. | |
8958 | (license (list license:gpl3 license:asl2.0)))) | |
8959 | ||
c4a5ce46 RW |
8960 | (define-public r-rcppparallel |
8961 | (package | |
8962 | (name "r-rcppparallel") | |
8963 | (version "4.4.3") | |
8964 | (source | |
8965 | (origin | |
8966 | (method url-fetch) | |
8967 | (uri (cran-uri "RcppParallel" version)) | |
8968 | (sha256 | |
8969 | (base32 | |
8970 | "1ym0bzs9g6bsg2lz24fisxxa3gypr6xcvrczn304czmrrag9413s")))) | |
8971 | (properties `((upstream-name . "RcppParallel"))) | |
8972 | (build-system r-build-system) | |
8973 | (home-page "http://rcppcore.github.io/RcppParallel") | |
8974 | (synopsis "Parallel programming tools for Rcpp") | |
8975 | (description | |
8976 | "This package provides high level functions for parallel programming with | |
8977 | Rcpp. For example, the @code{parallelFor()} function can be used to convert | |
8978 | the work of a standard serial @code{for} loop into a parallel one and the | |
8979 | @code{parallelReduce()} function can be used for accumulating aggregates or | |
8980 | other values.") | |
8981 | (license license:gpl2))) | |
8982 | ||
b58940cb RW |
8983 | (define-public r-ncdf4 |
8984 | (package | |
8985 | (name "r-ncdf4") | |
1adcbeda | 8986 | (version "1.16.1") |
b58940cb RW |
8987 | (source |
8988 | (origin | |
8989 | (method url-fetch) | |
8990 | (uri (cran-uri "ncdf4" version)) | |
8991 | (sha256 | |
8992 | (base32 | |
1adcbeda | 8993 | "083sb24anyd4sw0il3x07pqn9rbx5y5ayqass6mz8x443rnjvphd")))) |
b58940cb RW |
8994 | (build-system r-build-system) |
8995 | (inputs | |
8996 | `(("netcdf" ,netcdf) | |
8997 | ("zlib" ,zlib))) | |
8998 | (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") | |
8999 | (synopsis "R interface to Unidata netCDF format data files") | |
9000 | (description | |
9001 | "This package provides a high-level R interface to data files written | |
9002 | using Unidata's netCDF library (version 4 or earlier), which are binary data | |
9003 | files that are portable across platforms and include metadata information in | |
9004 | addition to the data sets. Using this package, netCDF files can be opened and | |
9005 | data sets read in easily. It is also easy to create new netCDF dimensions, | |
9006 | variables, and files, in either version 3 or 4 format, and manipulate existing | |
9007 | netCDF files.") | |
9008 | (license license:gpl3+))) | |
1e605c03 RW |
9009 | |
9010 | (define-public r-biocmanager | |
9011 | (package | |
9012 | (name "r-biocmanager") | |
749872a5 | 9013 | (version "1.30.4") |
1e605c03 RW |
9014 | (source |
9015 | (origin | |
9016 | (method url-fetch) | |
9017 | (uri (cran-uri "BiocManager" version)) | |
9018 | (sha256 | |
9019 | (base32 | |
749872a5 | 9020 | "0kxs76pixk1d2lpvkyrq6nnvv1rqf55ph5f7igkadyyqirf3y2ah")))) |
1e605c03 RW |
9021 | (properties `((upstream-name . "BiocManager"))) |
9022 | (build-system r-build-system) | |
9023 | (home-page "https://cran.r-project.org/web/packages/BiocManager/") | |
9024 | (synopsis "Access the Bioconductor project package repository") | |
9025 | (description | |
9026 | "This package provides a convenient tool to install and update | |
9027 | Bioconductor packages.") | |
9028 | (license license:artistic2.0))) | |
f338e480 RW |
9029 | |
9030 | (define-public r-rgl | |
9031 | (package | |
9032 | (name "r-rgl") | |
4f1c668d | 9033 | (version "0.100.30") |
f338e480 RW |
9034 | (source |
9035 | (origin | |
9036 | (method url-fetch) | |
9037 | (uri (cran-uri "rgl" version)) | |
9038 | (sha256 | |
9039 | (base32 | |
4f1c668d | 9040 | "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5")))) |
f338e480 RW |
9041 | (build-system r-build-system) |
9042 | (native-inputs | |
9043 | `(("pkg-config" ,pkg-config))) | |
9044 | (inputs | |
9045 | `(("freetype" ,freetype) | |
9046 | ("libpng" ,libpng) | |
9047 | ("glu" ,glu) | |
9048 | ("libx11" ,libx11) | |
9049 | ("ghc-pandoc" ,ghc-pandoc) | |
9050 | ("zlib" ,zlib))) | |
9051 | (propagated-inputs | |
9052 | `(("r-crosstalk" ,r-crosstalk) | |
9053 | ("r-htmltools" ,r-htmltools) | |
9054 | ("r-htmlwidgets" ,r-htmlwidgets) | |
9055 | ("r-jsonlite" ,r-jsonlite) | |
9056 | ("r-knitr" ,r-knitr) | |
9057 | ("r-magrittr" ,r-magrittr) | |
9058 | ("r-manipulatewidget" ,r-manipulatewidget) | |
9059 | ("r-shiny" ,r-shiny))) | |
9060 | (home-page "https://r-forge.r-project.org/projects/rgl/") | |
9061 | (synopsis "3D visualization using OpenGL") | |
9062 | (description | |
9063 | "This package provides medium to high level functions for 3D interactive graphics, | |
9064 | including functions modelled on base graphics (@code{plot3d()}, etc.) as well | |
9065 | as functions for constructing representations of geometric | |
9066 | objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to | |
9067 | various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D | |
9068 | image formats, including PNG, Postscript, SVG, PGF.") | |
9069 | ;; Any version of the GPL. | |
9070 | (license (list license:gpl2+ license:gpl3+)))) | |
213e72a1 RW |
9071 | |
9072 | (define-public r-multicool | |
9073 | (package | |
9074 | (name "r-multicool") | |
9075 | (version "0.1-10") | |
9076 | (source | |
9077 | (origin | |
9078 | (method url-fetch) | |
9079 | (uri (cran-uri "multicool" version)) | |
9080 | (sha256 | |
9081 | (base32 | |
9082 | "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v")))) | |
9083 | (build-system r-build-system) | |
9084 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
9085 | (home-page "https://cran.r-project.org/web/packages/multicool/") | |
9086 | (synopsis "Permutations of multisets in cool-lex order") | |
9087 | (description | |
9088 | "This package provides a set of tools to permute multisets without loops | |
9089 | or hash tables and to generate integer partitions. Cool-lex order is similar | |
9090 | to colexicographical order.") | |
9091 | (license license:gpl2))) | |
4106e6ad RW |
9092 | |
9093 | (define-public r-misc3d | |
9094 | (package | |
9095 | (name "r-misc3d") | |
9096 | (version "0.8-4") | |
9097 | (source | |
9098 | (origin | |
9099 | (method url-fetch) | |
9100 | (uri (cran-uri "misc3d" version)) | |
9101 | (sha256 | |
9102 | (base32 | |
9103 | "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) | |
9104 | (build-system r-build-system) | |
9105 | (home-page "https://cran.r-project.org/web/packages/misc3d/") | |
9106 | (synopsis "Miscellaneous 3D Plots") | |
9107 | (description | |
9108 | "This package provides a collection of miscellaneous 3d plots, including | |
9109 | isosurfaces.") | |
9110 | ;; Any version of the GPL. | |
9111 | (license (list license:gpl2+ license:gpl3+)))) | |
da256afb RW |
9112 | |
9113 | (define-public r-ks | |
9114 | (package | |
9115 | (name "r-ks") | |
fa10f0d3 | 9116 | (version "1.11.5") |
da256afb RW |
9117 | (source |
9118 | (origin | |
9119 | (method url-fetch) | |
9120 | (uri (cran-uri "ks" version)) | |
9121 | (sha256 | |
9122 | (base32 | |
fa10f0d3 | 9123 | "06ymx244yknmpl6935l4pafqbm4gcbpnhqg7rinql6rrfr9mcrag")))) |
da256afb RW |
9124 | (build-system r-build-system) |
9125 | (propagated-inputs | |
9126 | `(("r-fnn" ,r-fnn) | |
9127 | ("r-kernlab" ,r-kernlab) | |
9128 | ("r-kernsmooth" ,r-kernsmooth) | |
9129 | ("r-matrix" ,r-matrix) | |
9130 | ("r-mclust" ,r-mclust) | |
9131 | ("r-mgcv" ,r-mgcv) | |
da256afb RW |
9132 | ("r-multicool" ,r-multicool) |
9133 | ("r-mvtnorm" ,r-mvtnorm))) | |
9134 | (home-page "http://www.mvstat.net/tduong/") | |
9135 | (synopsis "Kernel smoothing") | |
9136 | (description | |
9137 | "This package provides kernel smoothers for univariate and multivariate | |
9138 | data, including density functions, density derivatives, cumulative | |
9139 | distributions, modal clustering, discriminant analysis, and two-sample | |
9140 | hypothesis testing.") | |
9141 | ;; Either version of the GPL. | |
9142 | (license (list license:gpl2 license:gpl3)))) | |
cf383cf0 RW |
9143 | |
9144 | (define-public r-feature | |
9145 | (package | |
9146 | (name "r-feature") | |
9147 | (version "1.2.13") | |
9148 | (source | |
9149 | (origin | |
9150 | (method url-fetch) | |
9151 | (uri (cran-uri "feature" version)) | |
9152 | (sha256 | |
9153 | (base32 | |
9154 | "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra")))) | |
9155 | (build-system r-build-system) | |
9156 | (propagated-inputs | |
9157 | `(("r-ks" ,r-ks) | |
9158 | ("r-misc3d" ,r-misc3d) | |
9159 | ("r-rgl" ,r-rgl))) | |
9160 | (home-page "http://www.mvstat.net/tduong/") | |
9161 | (synopsis "Inferential feature significance for kernel density estimation") | |
9162 | (description | |
9163 | "The feature package contains functions to display and compute kernel | |
9164 | density estimates, significant gradient and significant curvature regions. | |
9165 | Significant gradient and/or curvature regions often correspond to significant | |
9166 | features (e.g. local modes).") | |
9167 | ;; Either version of the GPL. | |
9168 | (license (list license:gpl2 license:gpl3)))) | |
06bc7b82 RW |
9169 | |
9170 | (define-public r-arm | |
9171 | (package | |
9172 | (name "r-arm") | |
9173 | (version "1.10-1") | |
9174 | (source | |
9175 | (origin | |
9176 | (method url-fetch) | |
9177 | (uri (cran-uri "arm" version)) | |
9178 | (sha256 | |
9179 | (base32 | |
9180 | "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg")))) | |
9181 | (build-system r-build-system) | |
9182 | (propagated-inputs | |
9183 | `(("r-abind" ,r-abind) | |
9184 | ("r-coda" ,r-coda) | |
9185 | ("r-lme4" ,r-lme4) | |
9186 | ("r-mass" ,r-mass) | |
9187 | ("r-matrix" ,r-matrix) | |
9188 | ("r-nlme" ,r-nlme))) | |
9189 | (home-page "https://cran.r-project.org/web/packages/arm/") | |
9190 | (synopsis "Data analysis using regression and multilevel/hierarchical models") | |
9191 | (description | |
9192 | "This package provides functions to accompany A. Gelman and J. Hill, | |
9193 | Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge | |
9194 | University Press, 2007.") | |
9195 | (license license:gpl3+))) | |
3cef715a RW |
9196 | |
9197 | (define-public r-circular | |
9198 | (package | |
9199 | (name "r-circular") | |
9200 | (version "0.4-93") | |
9201 | (source | |
9202 | (origin | |
9203 | (method url-fetch) | |
9204 | (uri (cran-uri "circular" version)) | |
9205 | (sha256 | |
9206 | (base32 | |
9207 | "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) | |
9208 | (build-system r-build-system) | |
9209 | (propagated-inputs | |
9210 | `(("r-boot" ,r-boot) | |
9211 | ("r-mvtnorm" ,r-mvtnorm))) | |
9212 | (native-inputs | |
9213 | `(("gfortran" ,gfortran))) | |
9214 | (home-page "https://cran.r-project.org/web/packages/circular/") | |
9215 | (synopsis "Circular statistics") | |
9216 | (description | |
9217 | "This package provides tools for circular statistics, from \"Topics in | |
9218 | circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World | |
9219 | Scientific.") | |
9220 | (license license:gpl2+))) | |
10483a64 RW |
9221 | |
9222 | (define-public r-activity | |
9223 | (package | |
9224 | (name "r-activity") | |
aef5e2aa | 9225 | (version "1.3") |
10483a64 RW |
9226 | (source |
9227 | (origin | |
9228 | (method url-fetch) | |
9229 | (uri (cran-uri "activity" version)) | |
9230 | (sha256 | |
9231 | (base32 | |
aef5e2aa | 9232 | "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92")))) |
10483a64 RW |
9233 | (build-system r-build-system) |
9234 | (propagated-inputs | |
9235 | `(("r-circular" ,r-circular) | |
aef5e2aa | 9236 | ("r-insol" ,r-insol) |
10483a64 RW |
9237 | ("r-pbapply" ,r-pbapply))) |
9238 | (home-page "https://cran.r-project.org/web/packages/activity/") | |
9239 | (synopsis "Animal activity statistics") | |
9240 | (description | |
9241 | "This package provides functions to fit kernel density functions to | |
9242 | animal activity time data; plot activity distributions; quantify overall | |
9243 | levels of activity; statistically compare activity metrics through | |
9244 | bootstrapping; and evaluate variation in linear variables with time (or other | |
9245 | circular variables).") | |
9246 | (license license:gpl3))) | |
e4f4a04a RW |
9247 | |
9248 | (define-public r-ouch | |
9249 | (package | |
9250 | (name "r-ouch") | |
27b4bfbe | 9251 | (version "2.14-1") |
e4f4a04a RW |
9252 | (source |
9253 | (origin | |
9254 | (method url-fetch) | |
9255 | (uri (cran-uri "ouch" version)) | |
9256 | (sha256 | |
9257 | (base32 | |
27b4bfbe | 9258 | "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b")))) |
e4f4a04a RW |
9259 | (build-system r-build-system) |
9260 | (propagated-inputs `(("r-subplex" ,r-subplex))) | |
9261 | (home-page "http://kingaa.github.io/ouch/") | |
9262 | (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") | |
9263 | (description | |
9264 | "This package provides tools to fit and compare Ornstein-Uhlenbeck models | |
9265 | for evolution along a phylogenetic tree.") | |
9266 | (license license:gpl2+))) | |
705ea5bf RW |
9267 | |
9268 | (define-public r-fmsb | |
9269 | (package | |
9270 | (name "r-fmsb") | |
9271 | (version "0.6.3") | |
9272 | (source | |
9273 | (origin | |
9274 | (method url-fetch) | |
9275 | (uri (cran-uri "fmsb" version)) | |
9276 | (sha256 | |
9277 | (base32 | |
9278 | "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5")))) | |
9279 | (build-system r-build-system) | |
9280 | (home-page "http://minato.sip21c.org/msb/") | |
9281 | (synopsis "Functions for medical statistics book with demographic data") | |
9282 | (description | |
9283 | "This package provides several utility functions for the book entitled | |
9284 | \"Practices of Medical and Health Data Analysis using R\" (Pearson Education | |
9285 | Japan, 2007) with Japanese demographic data and some demographic analysis | |
9286 | related functions.") | |
9287 | (license license:gpl2+))) | |
ced51a20 RW |
9288 | |
9289 | (define-public r-stabledist | |
9290 | (package | |
9291 | (name "r-stabledist") | |
9292 | (version "0.7-1") | |
9293 | (source | |
9294 | (origin | |
9295 | (method url-fetch) | |
9296 | (uri (cran-uri "stabledist" version)) | |
9297 | (sha256 | |
9298 | (base32 | |
9299 | "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86")))) | |
9300 | (build-system r-build-system) | |
9301 | (home-page "http://www.rmetrics.org") | |
9302 | (synopsis "Stable distribution functions") | |
9303 | (description | |
9304 | "This package provides density, probability and quantile functions, and | |
9305 | random number generation for (skew) stable distributions, using the | |
9306 | parametrizations of Nolan.") | |
9307 | (license license:gpl2+))) | |
a50abb36 RW |
9308 | |
9309 | (define-public r-gsl | |
9310 | (package | |
9311 | (name "r-gsl") | |
6bdce94f | 9312 | (version "2.1-6") |
a50abb36 RW |
9313 | (source |
9314 | (origin | |
9315 | (method url-fetch) | |
9316 | (uri (cran-uri "gsl" version)) | |
9317 | (sha256 | |
9318 | (base32 | |
6bdce94f | 9319 | "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m")))) |
a50abb36 RW |
9320 | (build-system r-build-system) |
9321 | (inputs | |
9322 | `(("gsl" ,gsl))) | |
9323 | (home-page "https://cran.r-project.org/web/packages/gsl") | |
9324 | (synopsis "Wrapper for the GNU Scientific Library") | |
9325 | (description | |
9326 | "This package provides an R wrapper for the special functions and quasi | |
9327 | random number generators of the GNU Scientific Library.") | |
9328 | (license license:gpl2+))) | |
03a3ec5e RW |
9329 | |
9330 | (define-public r-adgoftest | |
9331 | (package | |
9332 | (name "r-adgoftest") | |
9333 | (version "0.3") | |
9334 | (source | |
9335 | (origin | |
9336 | (method url-fetch) | |
9337 | (uri (cran-uri "ADGofTest" version)) | |
9338 | (sha256 | |
9339 | (base32 | |
9340 | "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) | |
9341 | (properties `((upstream-name . "ADGofTest"))) | |
9342 | (build-system r-build-system) | |
9343 | (home-page "https://cran.r-project.org/web/packages/ADGofTest") | |
9344 | (synopsis "Anderson-Darling GoF test") | |
9345 | (description | |
9346 | "This package provides an implementation of the Anderson-Darling GoF test | |
9347 | with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the | |
9348 | Anderson-Darling Distribution\".") | |
9349 | ;; Any version of the GPL. | |
9350 | (license license:gpl3+))) | |
71601a5d RW |
9351 | |
9352 | (define-public r-softimpute | |
9353 | (package | |
9354 | (name "r-softimpute") | |
9355 | (version "1.4") | |
9356 | (source | |
9357 | (origin | |
9358 | (method url-fetch) | |
9359 | (uri (cran-uri "softImpute" version)) | |
9360 | (sha256 | |
9361 | (base32 | |
9362 | "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq")))) | |
9363 | (properties `((upstream-name . "softImpute"))) | |
9364 | (build-system r-build-system) | |
9365 | (propagated-inputs | |
9366 | `(("r-matrix" ,r-matrix))) | |
9367 | (native-inputs | |
9368 | `(("gfortran" ,gfortran))) | |
9369 | (home-page "https://cran.r-project.org/web/packages/softImpute") | |
9370 | (synopsis "Matrix completion via iterative soft-thresholded SVD") | |
9371 | (description | |
9372 | "This package provides iterative methods for matrix completion that use | |
9373 | nuclear-norm regularization. The package includes procedures for centering | |
9374 | and scaling rows, columns or both, and for computing low-rank @dfn{single | |
9375 | value decompositions} (SVDs) on large sparse centered matrices (i.e. principal | |
9376 | components).") | |
9377 | (license license:gpl2))) | |
44b0c5b5 RW |
9378 | |
9379 | (define-public r-fftwtools | |
9380 | (package | |
9381 | (name "r-fftwtools") | |
9382 | (version "0.9-8") | |
9383 | (source | |
9384 | (origin | |
9385 | (method url-fetch) | |
9386 | (uri (cran-uri "fftwtools" version)) | |
9387 | (sha256 | |
9388 | (base32 | |
9389 | "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6")))) | |
9390 | (build-system r-build-system) | |
9391 | (inputs `(("fftw" ,fftw))) | |
9392 | (home-page "https://github.com/krahim/fftwtools") | |
9393 | (synopsis "Wrapper for FFTW3") | |
9394 | (description | |
9395 | "This package provides a wrapper for several FFTW functions. It provides | |
9396 | access to the two-dimensional FFT, the multivariate FFT, and the | |
9397 | one-dimensional real to complex FFT using the FFTW3 library. The package | |
9398 | includes the functions @code{fftw()} and @code{mvfftw()} which are designed to | |
9399 | mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. | |
9400 | The FFT functions have a parameter that allows them to not return the | |
9401 | redundant complex conjugate when the input is real data.") | |
9402 | (license license:gpl2+))) | |
db084d79 RW |
9403 | |
9404 | (define-public r-tiff | |
9405 | (package | |
9406 | (name "r-tiff") | |
9407 | (version "0.1-5") | |
9408 | (source | |
9409 | (origin | |
9410 | (method url-fetch) | |
9411 | (uri (cran-uri "tiff" version)) | |
9412 | (sha256 | |
9413 | (base32 | |
9414 | "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) | |
9415 | (build-system r-build-system) | |
9416 | (inputs | |
9417 | `(("libtiff" ,libtiff) | |
9418 | ("libjpeg" ,libjpeg) | |
9419 | ("zlib" ,zlib))) | |
9420 | (home-page "http://www.rforge.net/tiff/") | |
9421 | (synopsis "Read and write TIFF images") | |
9422 | (description | |
9423 | "This package provides an easy and simple way to read, write and display | |
9424 | bitmap images stored in the TIFF format. It can read and write both files and | |
9425 | in-memory raw vectors.") | |
9426 | ;; Either of these two license versions. | |
9427 | (license (list license:gpl2 license:gpl3)))) | |
f3949fec | 9428 | |
53bd3ab3 RW |
9429 | (define-public r-nlp |
9430 | (package | |
9431 | (name "r-nlp") | |
9432 | (version "0.2-0") | |
9433 | (source | |
9434 | (origin | |
9435 | (method url-fetch) | |
9436 | (uri (cran-uri "NLP" version)) | |
9437 | (sha256 | |
9438 | (base32 | |
9439 | "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w")))) | |
9440 | (properties `((upstream-name . "NLP"))) | |
9441 | (build-system r-build-system) | |
9442 | (home-page "https://cran.r-project.org/web/packages/NLP/") | |
9443 | (synopsis "Natural language processing infrastructure") | |
9444 | (description | |
9445 | "This package provides basic classes and methods for Natural Language | |
9446 | Processing.") | |
9447 | (license license:gpl3))) | |
9448 | ||
f785d546 RW |
9449 | (define-public r-tm |
9450 | (package | |
9451 | (name "r-tm") | |
9452 | (version "0.7-6") | |
9453 | (source | |
9454 | (origin | |
9455 | (method url-fetch) | |
9456 | (uri (cran-uri "tm" version)) | |
9457 | (sha256 | |
9458 | (base32 | |
9459 | "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r")))) | |
9460 | (properties `((upstream-name . "tm"))) | |
9461 | (build-system r-build-system) | |
9462 | (propagated-inputs | |
9463 | `(("r-bh" ,r-bh) | |
9464 | ("r-nlp" ,r-nlp) | |
9465 | ("r-rcpp" ,r-rcpp) | |
9466 | ("r-slam" ,r-slam) | |
9467 | ("r-xml2" ,r-xml2))) | |
9468 | (home-page "http://tm.r-forge.r-project.org/") | |
9469 | (synopsis "Text mining package") | |
9470 | (description | |
9471 | "This package provides a framework for text mining applications within R.") | |
9472 | (license license:gpl3))) | |
9473 | ||
f3949fec RW |
9474 | (define-public r-waveslim |
9475 | (package | |
9476 | (name "r-waveslim") | |
61cb2e31 | 9477 | (version "1.7.5.1") |
f3949fec RW |
9478 | (source |
9479 | (origin | |
9480 | (method url-fetch) | |
9481 | (uri (cran-uri "waveslim" version)) | |
9482 | (sha256 | |
9483 | (base32 | |
61cb2e31 | 9484 | "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk")))) |
f3949fec RW |
9485 | (build-system r-build-system) |
9486 | (native-inputs | |
9487 | `(("gfortran" ,gfortran))) | |
9488 | (home-page "http://waveslim.blogspot.com") | |
9489 | (synopsis "Basic wavelet routines for signal processing") | |
9490 | (description | |
9491 | "This package provides basic wavelet routines for time series (1D), | |
9492 | image (2D) and array (3D) analysis. The code provided here is based on | |
9493 | wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk | |
9494 | and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from | |
9495 | Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet | |
9496 | pairs (Selesnick 2001, 2002).") | |
9497 | (license license:bsd-3))) | |
e37935e4 RW |
9498 | |
9499 | (define-public r-wordcloud | |
9500 | (package | |
9501 | (name "r-wordcloud") | |
9502 | (version "2.6") | |
9503 | (source | |
9504 | (origin | |
9505 | (method url-fetch) | |
9506 | (uri (cran-uri "wordcloud" version)) | |
9507 | (sha256 | |
9508 | (base32 | |
9509 | "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) | |
9510 | (build-system r-build-system) | |
9511 | (propagated-inputs | |
9512 | `(("r-rcolorbrewer" ,r-rcolorbrewer) | |
f847b659 RW |
9513 | ("r-rcpp" ,r-rcpp) |
9514 | ;; The "tm" package is only "suggested" according to CRAN, but the | |
9515 | ;; wordcloud package cannot be loaded without it. | |
9516 | ("r-tm" ,r-tm))) | |
e37935e4 RW |
9517 | (home-page "https://cran.r-project.org/web/packages/wordcloud") |
9518 | (synopsis "Word clouds") | |
9519 | (description | |
9520 | "This package provides functionality to create pretty word clouds, | |
9521 | visualize differences and similarity between documents, and avoid | |
9522 | over-plotting in scatter plots with text.") | |
9523 | (license license:lgpl2.1))) | |
a6e4413d RW |
9524 | |
9525 | (define-public r-colorramps | |
9526 | (package | |
9527 | (name "r-colorramps") | |
9528 | (version "2.3") | |
9529 | (source | |
9530 | (origin | |
9531 | (method url-fetch) | |
9532 | (uri (cran-uri "colorRamps" version)) | |
9533 | (sha256 | |
9534 | (base32 | |
9535 | "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z")))) | |
9536 | (properties `((upstream-name . "colorRamps"))) | |
9537 | (build-system r-build-system) | |
9538 | (home-page "https://cran.r-project.org/web/packages/colorRamps") | |
9539 | (synopsis "Build color tables") | |
9540 | (description "This package provides features to build gradient color | |
9541 | maps.") | |
9542 | ;; Any version of the GPL | |
9543 | (license license:gpl3+))) | |
61d73349 RW |
9544 | |
9545 | (define-public r-tidytree | |
9546 | (package | |
9547 | (name "r-tidytree") | |
194c6826 | 9548 | (version "0.2.8") |
61d73349 RW |
9549 | (source |
9550 | (origin | |
9551 | (method url-fetch) | |
9552 | (uri (cran-uri "tidytree" version)) | |
9553 | (sha256 | |
9554 | (base32 | |
194c6826 | 9555 | "1hkddl8kj1g01dy7xiracx81f6b405b3ga2qp4wlrl552b9xxpby")))) |
61d73349 RW |
9556 | (build-system r-build-system) |
9557 | (propagated-inputs | |
9558 | `(("r-ape" ,r-ape) | |
9559 | ("r-dplyr" ,r-dplyr) | |
9560 | ("r-lazyeval" ,r-lazyeval) | |
9561 | ("r-magrittr" ,r-magrittr) | |
9562 | ("r-rlang" ,r-rlang) | |
9563 | ("r-tibble" ,r-tibble))) | |
9564 | (home-page "https://github.com/GuangchuangYu/tidytree") | |
9565 | (synopsis "Tidy tool for phylogenetic tree data manipulation") | |
9566 | (description | |
9567 | "Phylogenetic trees generally contain multiple components including nodes, | |
9568 | edges, branches and associated data. This package provides an approach to | |
9569 | convert tree objects to tidy data frames. It also provides tidy interfaces to | |
9570 | manipulate tree data.") | |
9571 | (license license:artistic2.0))) | |
45b469a4 RW |
9572 | |
9573 | (define-public r-rvcheck | |
9574 | (package | |
9575 | (name "r-rvcheck") | |
9bcd8b68 | 9576 | (version "0.1.5") |
45b469a4 RW |
9577 | (source |
9578 | (origin | |
9579 | (method url-fetch) | |
9580 | (uri (cran-uri "rvcheck" version)) | |
9581 | (sha256 | |
9bcd8b68 | 9582 | (base32 "15222q3sglq0mad5q806p99fhrb96qizmpqw35fa1rb148f95paf")))) |
45b469a4 RW |
9583 | (build-system r-build-system) |
9584 | (propagated-inputs | |
9bcd8b68 TGR |
9585 | `(("r-biocmanager" ,r-biocmanager) |
9586 | ("r-rlang" ,r-rlang))) | |
45b469a4 RW |
9587 | (home-page "https://cran.r-project.org/web/packages/rvcheck") |
9588 | (synopsis "R package version check") | |
9589 | (description | |
9590 | "This package provides tools to check the latest release version of R and | |
9591 | R packages (on CRAN, Bioconductor or Github).") | |
9592 | (license license:artistic2.0))) | |
fbebccf7 RW |
9593 | |
9594 | (define-public r-docopt | |
9595 | (package | |
9596 | (name "r-docopt") | |
9597 | (version "0.6.1") | |
9598 | (source | |
9599 | (origin | |
9600 | (method url-fetch) | |
9601 | (uri (cran-uri "docopt" version)) | |
9602 | (sha256 | |
9603 | (base32 | |
9604 | "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068")))) | |
9605 | (build-system r-build-system) | |
9606 | (home-page "https://github.com/docopt/docopt.R") | |
9607 | (synopsis "Command-line interface specification language") | |
9608 | (description | |
9609 | "This package enables you to define a command-line interface by just | |
9610 | giving it a description in the specific format.") | |
9611 | (license license:expat))) | |
b614009e RW |
9612 | |
9613 | (define-public r-sparsesvd | |
9614 | (package | |
9615 | (name "r-sparsesvd") | |
e0f20dce | 9616 | (version "0.2") |
b614009e RW |
9617 | (source |
9618 | (origin | |
9619 | (method url-fetch) | |
9620 | (uri (cran-uri "sparsesvd" version)) | |
9621 | (sha256 | |
9622 | (base32 | |
e0f20dce | 9623 | "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs")))) |
b614009e RW |
9624 | (build-system r-build-system) |
9625 | (propagated-inputs `(("r-matrix" ,r-matrix))) | |
9626 | (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") | |
9627 | (synopsis "Sparse truncated singular value decomposition") | |
9628 | (description | |
9629 | "This package provides a Wrapper around the SVDLIBC library | |
9630 | for (truncated) singular value decomposition of a sparse matrix. Currently, | |
9631 | only sparse real matrices in Matrix package format are supported.") | |
9632 | ;; SVDLIBC is released under BSD-2. The R interface is released under | |
9633 | ;; BSD-3. | |
9634 | (license (list license:bsd-3 license:bsd-2)))) | |
13f5837b | 9635 | |
8f7d7cd0 RW |
9636 | (define-public r-speedglm |
9637 | (package | |
9638 | (name "r-speedglm") | |
9639 | (version "0.3-2") | |
9640 | (source | |
9641 | (origin | |
9642 | (method url-fetch) | |
9643 | (uri (cran-uri "speedglm" version)) | |
9644 | (sha256 | |
9645 | (base32 | |
9646 | "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz")))) | |
9647 | (build-system r-build-system) | |
9648 | (propagated-inputs | |
9649 | `(("r-mass" ,r-mass) | |
9650 | ("r-matrix" ,r-matrix))) | |
9651 | (home-page "https://cran.r-project.org/web/packages/speedglm") | |
9652 | (synopsis "Fit linear and generalized linear models to large data sets") | |
9653 | (description | |
9654 | "This package provides tools for fitting linear models and generalized | |
9655 | linear models to large data sets by updating algorithms.") | |
9656 | ;; Any version of the GPL | |
9657 | (license license:gpl2+))) | |
9658 | ||
13f5837b RW |
9659 | (define-public r-densityclust |
9660 | (package | |
9661 | (name "r-densityclust") | |
9662 | (version "0.3") | |
9663 | (source | |
9664 | (origin | |
9665 | (method url-fetch) | |
9666 | (uri (cran-uri "densityClust" version)) | |
9667 | (sha256 | |
9668 | (base32 | |
9669 | "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13")))) | |
9670 | (properties `((upstream-name . "densityClust"))) | |
9671 | (build-system r-build-system) | |
9672 | (propagated-inputs | |
9673 | `(("r-fnn" ,r-fnn) | |
9674 | ("r-ggplot2" ,r-ggplot2) | |
9675 | ("r-ggrepel" ,r-ggrepel) | |
9676 | ("r-gridextra" ,r-gridextra) | |
9677 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9678 | ("r-rcpp" ,r-rcpp) | |
9679 | ("r-rtsne" ,r-rtsne))) | |
9680 | (home-page "https://cran.r-project.org/web/packages/densityClust") | |
9681 | (synopsis "Clustering by fast search and find of density peaks") | |
9682 | (description | |
9683 | "This package provides an improved implementation (based on k-nearest | |
9684 | neighbors) of the density peak clustering algorithm, originally described by | |
9685 | Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle | |
9686 | large datasets (> 100,000 samples) very efficiently.") | |
9687 | (license license:gpl2+))) | |
58bc8857 RW |
9688 | |
9689 | (define-public r-combinat | |
9690 | (package | |
9691 | (name "r-combinat") | |
9692 | (version "0.0-8") | |
9693 | (source | |
9694 | (origin | |
9695 | (method url-fetch) | |
9696 | (uri (cran-uri "combinat" version)) | |
9697 | (sha256 | |
9698 | (base32 | |
9699 | "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) | |
9700 | (build-system r-build-system) | |
9701 | (home-page "https://cran.r-project.org/web/packages/combinat") | |
9702 | (synopsis "Combinatorics utilities") | |
9703 | (description "This package provides assorted routines for combinatorics.") | |
9704 | (license license:gpl2))) | |
9f33d76c RW |
9705 | |
9706 | (define-public r-qlcmatrix | |
9707 | (package | |
9708 | (name "r-qlcmatrix") | |
9709 | (version "0.9.7") | |
9710 | (source | |
9711 | (origin | |
9712 | (method url-fetch) | |
9713 | (uri (cran-uri "qlcMatrix" version)) | |
9714 | (sha256 | |
9715 | (base32 | |
9716 | "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) | |
9717 | (properties `((upstream-name . "qlcMatrix"))) | |
9718 | (build-system r-build-system) | |
9719 | (propagated-inputs | |
9720 | `(("r-docopt" ,r-docopt) | |
9721 | ("r-matrix" ,r-matrix) | |
9722 | ("r-slam" ,r-slam) | |
9723 | ("r-sparsesvd" ,r-sparsesvd))) | |
9724 | (home-page "https://cran.r-project.org/web/packages/qlcMatrix") | |
9725 | (synopsis "Sparse matrix functions for quantitative language comparison") | |
9726 | (description | |
9727 | "This package provides an extension of the functionality of the Matrix | |
9728 | package for using sparse matrices. Some of the functions are very general, | |
9729 | while other are highly specific for the special data format used for | |
9730 | @dfn{quantitative language comparison} (QLC).") | |
9731 | (license license:gpl3))) | |
e3bb0766 RW |
9732 | |
9733 | (define-public r-ddrtree | |
9734 | (package | |
9735 | (name "r-ddrtree") | |
9736 | (version "0.1.5") | |
9737 | (source | |
9738 | (origin | |
9739 | (method url-fetch) | |
9740 | (uri (cran-uri "DDRTree" version)) | |
9741 | (sha256 | |
9742 | (base32 | |
9743 | "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) | |
9744 | (properties `((upstream-name . "DDRTree"))) | |
9745 | (build-system r-build-system) | |
9746 | (propagated-inputs | |
9747 | `(("r-bh" ,r-bh) | |
9748 | ("r-irlba" ,r-irlba) | |
9749 | ("r-rcpp" ,r-rcpp) | |
9750 | ("r-rcppeigen" ,r-rcppeigen))) | |
9751 | (home-page "https://cran.r-project.org/web/packages/DDRTree") | |
9752 | (synopsis "Learning principal graphs with DDRTree") | |
9753 | (description | |
9754 | "This package provides an implementation of the framework of | |
9755 | @dfn{reversed graph embedding} (RGE) which projects data into a reduced | |
9756 | dimensional space while constructs a principal tree which passes through the | |
9757 | middle of the data simultaneously. DDRTree shows superiority to | |
9758 | alternatives (Wishbone, DPT) for inferring the ordering as well as the | |
9759 | intrinsic structure of single cell genomics data. In general, it could be | |
9760 | used to reconstruct the temporal progression as well as the bifurcation | |
9761 | structure of any data type.") | |
9762 | (license license:asl2.0))) | |
d53b2317 RW |
9763 | |
9764 | (define-public r-corpcor | |
9765 | (package | |
9766 | (name "r-corpcor") | |
9767 | (version "1.6.9") | |
9768 | (source | |
9769 | (origin | |
9770 | (method url-fetch) | |
9771 | (uri (cran-uri "corpcor" version)) | |
9772 | (sha256 | |
9773 | (base32 | |
9774 | "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf")))) | |
9775 | (build-system r-build-system) | |
9776 | (home-page "http://strimmerlab.org/software/corpcor/") | |
9777 | (synopsis "Efficient estimation of covariance and (partial) correlation") | |
9778 | (description | |
9779 | "This package implements a James-Stein-type shrinkage estimator for the | |
9780 | covariance matrix, with separate shrinkage for variances and correlations. | |
9781 | Furthermore, functions are available for fast singular value decomposition, | |
9782 | for computing the pseudoinverse, and for checking the rank and positive | |
9783 | definiteness of a matrix.") | |
9784 | (license license:gpl3+))) | |
3088b3fc RW |
9785 | |
9786 | (define-public r-rspectra | |
9787 | (package | |
9788 | (name "r-rspectra") | |
935c6532 | 9789 | (version "0.15-0") |
3088b3fc RW |
9790 | (source |
9791 | (origin | |
9792 | (method url-fetch) | |
9793 | (uri (cran-uri "RSpectra" version)) | |
9794 | (sha256 | |
9795 | (base32 | |
935c6532 | 9796 | "1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s")))) |
3088b3fc RW |
9797 | (properties `((upstream-name . "RSpectra"))) |
9798 | (build-system r-build-system) | |
9799 | (propagated-inputs | |
9800 | `(("r-matrix" ,r-matrix) | |
9801 | ("r-rcpp" ,r-rcpp) | |
9802 | ("r-rcppeigen" ,r-rcppeigen))) | |
9803 | (home-page "https://github.com/yixuan/RSpectra") | |
9804 | (synopsis "Solvers for large-scale Eigenvalue and SVD problems") | |
9805 | (description | |
9806 | "This package provides an R interface to the Spectra library for | |
9807 | large-scale eigenvalue and SVD problems. It is typically used to compute a | |
9808 | few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, | |
9809 | which is usually more efficient than @code{eigen()} if k << n.") | |
9810 | ;; MPL 2 or later. | |
9811 | (license license:mpl2.0))) | |
029425cb RW |
9812 | |
9813 | (define-public r-vbsr | |
9814 | (package | |
9815 | (name "r-vbsr") | |
9816 | (version "0.0.5") | |
9817 | (source | |
9818 | (origin | |
9819 | (method url-fetch) | |
9820 | (uri (cran-uri "vbsr" version)) | |
9821 | (sha256 | |
9822 | (base32 | |
9823 | "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) | |
9824 | (build-system r-build-system) | |
9825 | (home-page "https://cran.r-project.org/web/packages/vbsr") | |
9826 | (synopsis "Variational Bayes spike regression regularized linear models") | |
9827 | (description | |
9828 | "This package provides an efficient algorithm for solving ultra-sparse | |
9829 | regularized regression models using a variational Bayes algorithm with a spike | |
9830 | prior. The algorithm is solved on a path, with coordinate updates, and is | |
9831 | capable of generating very sparse models. Very general model | |
9832 | diagnostics for controlling type-1 errors are also provided.") | |
9833 | (license license:gpl2))) | |
3d62d98e RW |
9834 | |
9835 | (define-public r-flare | |
9836 | (package | |
9837 | (name "r-flare") | |
b154b026 | 9838 | (version "1.6.0.2") |
3d62d98e RW |
9839 | (source |
9840 | (origin | |
9841 | (method url-fetch) | |
9842 | (uri (cran-uri "flare" version)) | |
9843 | (sha256 | |
9844 | (base32 | |
b154b026 | 9845 | "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5")))) |
3d62d98e RW |
9846 | (build-system r-build-system) |
9847 | (propagated-inputs | |
9848 | `(("r-igraph" ,r-igraph) | |
9849 | ("r-lattice" ,r-lattice) | |
9850 | ("r-mass" ,r-mass) | |
9851 | ("r-matrix" ,r-matrix))) | |
9852 | (home-page "https://cran.r-project.org/web/packages/flare") | |
9853 | (synopsis "Family of Lasso regression implementations") | |
9854 | (description | |
6a0c3e03 | 9855 | "This package provides implementations of a family of Lasso variants |
3d62d98e RW |
9856 | including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating |
9857 | high dimensional sparse linear models.") | |
9858 | (license license:gpl2))) | |
5f0fbfc0 RW |
9859 | |
9860 | (define-public r-lassopv | |
9861 | (package | |
9862 | (name "r-lassopv") | |
9863 | (version "0.2.0") | |
9864 | (source | |
9865 | (origin | |
9866 | (method url-fetch) | |
9867 | (uri (cran-uri "lassopv" version)) | |
9868 | (sha256 | |
9869 | (base32 | |
9870 | "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) | |
9871 | (build-system r-build-system) | |
9872 | (propagated-inputs `(("r-lars" ,r-lars))) | |
9873 | (home-page "https://github.com/lingfeiwang/lassopv") | |
9874 | (synopsis "Non-parametric p-value estimation for predictors in Lasso") | |
9875 | (description | |
9876 | "This package enables you to estimate the p-values for predictors x | |
9877 | against target variable y in Lasso regression, using the regularization | |
9878 | strength when each predictor enters the active set of regularization path for | |
9879 | the first time as the statistic.") | |
9880 | (license license:gpl3))) | |
adcd0cc8 RW |
9881 | |
9882 | (define-public r-splitstackshape | |
9883 | (package | |
9884 | (name "r-splitstackshape") | |
90325bb1 | 9885 | (version "1.4.8") |
adcd0cc8 RW |
9886 | (source |
9887 | (origin | |
9888 | (method url-fetch) | |
9889 | (uri (cran-uri "splitstackshape" version)) | |
9890 | (sha256 | |
9891 | (base32 | |
90325bb1 | 9892 | "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) |
adcd0cc8 RW |
9893 | (build-system r-build-system) |
9894 | (propagated-inputs | |
9895 | `(("r-data-table" ,r-data-table))) | |
9896 | (home-page "https://github.com/mrdwab/splitstackshape") | |
9897 | (synopsis "Stack and reshape datasets after splitting concatenated values") | |
9898 | (description | |
9899 | "Online data collection tools like Google Forms often export | |
9900 | multiple-response questions with data concatenated in cells. The | |
9901 | @code{concat.split} (cSplit) family of functions provided by this package | |
9902 | splits such data into separate cells. This package also includes functions to | |
9903 | stack groups of columns and to reshape wide data, even when the data are | |
9904 | \"unbalanced\"---something which @code{reshape} (from base R) does not handle, | |
9905 | and which @code{melt} and @code{dcast} from @code{reshape2} do not easily | |
9906 | handle.") | |
9907 | (license license:gpl3))) | |
b2e777b2 RW |
9908 | |
9909 | (define-public r-tfmpvalue | |
9910 | (package | |
9911 | (name "r-tfmpvalue") | |
9912 | (version "0.0.8") | |
9913 | (source | |
9914 | (origin | |
9915 | (method url-fetch) | |
9916 | (uri (cran-uri "TFMPvalue" version)) | |
9917 | (sha256 | |
9918 | (base32 | |
9919 | "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) | |
9920 | (properties `((upstream-name . "TFMPvalue"))) | |
9921 | (build-system r-build-system) | |
9922 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
9923 | (home-page "https://github.com/ge11232002/TFMPvalue") | |
9924 | (synopsis "P-value computation for position weight matrices") | |
9925 | (description | |
9926 | "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) | |
9927 | identification from sequence/alignments, we are interested in the significance | |
9928 | of certain match scores. TFMPvalue provides the accurate calculation of a | |
9929 | p-value with a score threshold for position weight matrices, or the score with | |
9930 | a given p-value. It is an interface to code originally made available by | |
9931 | Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. | |
9932 | Touzet and Varre (2007).") | |
9933 | (license license:gpl2))) | |
f79e63a5 RW |
9934 | |
9935 | (define-public r-rnifti | |
9936 | (package | |
9937 | (name "r-rnifti") | |
12618b50 | 9938 | (version "0.11.1") |
f79e63a5 RW |
9939 | (source |
9940 | (origin | |
9941 | (method url-fetch) | |
9942 | (uri (cran-uri "RNifti" version)) | |
9943 | (sha256 | |
9944 | (base32 | |
12618b50 | 9945 | "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg")))) |
f79e63a5 RW |
9946 | (properties `((upstream-name . "RNifti"))) |
9947 | (build-system r-build-system) | |
9948 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
9949 | (home-page "https://github.com/jonclayden/RNifti") | |
9950 | (synopsis "Fast R and C++ access to NIfTI images") | |
9951 | (description | |
9952 | "This package provides very fast read and write access to images stored | |
9953 | in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between | |
9954 | compiled C and interpreted R code. It also provides a C/C++ API that can be | |
9955 | used by other packages.") | |
9956 | (license license:gpl2))) | |
6e09f506 RW |
9957 | |
9958 | (define-public r-shades | |
9959 | (package | |
9960 | (name "r-shades") | |
031afc48 | 9961 | (version "1.4.0") |
6e09f506 RW |
9962 | (source |
9963 | (origin | |
9964 | (method url-fetch) | |
9965 | (uri (cran-uri "shades" version)) | |
9966 | (sha256 | |
9967 | (base32 | |
031afc48 | 9968 | "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) |
6e09f506 RW |
9969 | (build-system r-build-system) |
9970 | (home-page "https://github.com/jonclayden/shades") | |
9971 | (synopsis "Simple color manipulation") | |
9972 | (description | |
9973 | "This package provides functions for easily manipulating colors, | |
9974 | creating color scales and calculating color distances.") | |
9975 | (license license:bsd-3))) | |
cb03d6c6 RW |
9976 | |
9977 | (define-public r-ore | |
9978 | (package | |
9979 | (name "r-ore") | |
9980 | (version "1.6.2") | |
9981 | (source | |
9982 | (origin | |
9983 | (method url-fetch) | |
9984 | (uri (cran-uri "ore" version)) | |
9985 | (sha256 | |
9986 | (base32 | |
9987 | "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m")))) | |
9988 | (build-system r-build-system) | |
9989 | (home-page "https://github.com/jonclayden/ore") | |
9990 | (synopsis "R interface to the Onigmo regular expression library") | |
9991 | (description | |
9992 | "This package provides an alternative to R's built-in functionality for | |
9993 | handling regular expressions, based on the Onigmo library. It offers | |
9994 | first-class compiled regex objects, partial matching and function-based | |
9995 | substitutions, amongst other features.") | |
9996 | (license license:bsd-3))) | |
b98662c5 RW |
9997 | |
9998 | (define-public r-reportr | |
9999 | (package | |
10000 | (name "r-reportr") | |
10001 | (version "1.3.0") | |
10002 | (source | |
10003 | (origin | |
10004 | (method url-fetch) | |
10005 | (uri (cran-uri "reportr" version)) | |
10006 | (sha256 | |
10007 | (base32 | |
10008 | "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) | |
10009 | (build-system r-build-system) | |
10010 | (propagated-inputs `(("r-ore" ,r-ore))) | |
10011 | (home-page "https://github.com/jonclayden/reportr") | |
10012 | (synopsis "General message and error reporting system") | |
10013 | (description | |
10014 | "This package provides a system for reporting messages, which offers | |
10015 | certain useful features over the standard R system, such as the incorporation | |
10016 | of output consolidation, message filtering, assertions, expression | |
10017 | substitution, automatic generation of stack traces for debugging, and | |
10018 | conditional reporting based on the current \"output level\".") | |
10019 | (license license:gpl2))) | |
7eec973e RW |
10020 | |
10021 | (define-public r-tractor-base | |
10022 | (package | |
10023 | (name "r-tractor-base") | |
5cc89654 | 10024 | (version "3.3.2") |
7eec973e RW |
10025 | (source |
10026 | (origin | |
10027 | (method url-fetch) | |
10028 | (uri (cran-uri "tractor.base" version)) | |
10029 | (sha256 | |
10030 | (base32 | |
5cc89654 | 10031 | "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i")))) |
7eec973e RW |
10032 | (properties `((upstream-name . "tractor.base"))) |
10033 | (build-system r-build-system) | |
10034 | (propagated-inputs | |
10035 | `(("r-ore" ,r-ore) | |
10036 | ("r-reportr" ,r-reportr) | |
10037 | ("r-rnifti" ,r-rnifti) | |
10038 | ("r-shades" ,r-shades))) | |
10039 | (home-page "http://www.tractor-mri.org.uk") | |
10040 | (synopsis "Read, manipulate and visualize magnetic resonance images") | |
10041 | (description | |
10042 | "This package provides functions for working with magnetic resonance | |
10043 | images. It supports reading and writing of popular file formats (DICOM, | |
10044 | Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive | |
10045 | visualization; flexible image manipulation; metadata and sparse image | |
10046 | handling.") | |
10047 | (license license:gpl2))) | |
d0eb09a1 RW |
10048 | |
10049 | (define-public r-grimport | |
10050 | (package | |
10051 | (name "r-grimport") | |
cb4a6e67 | 10052 | (version "0.9-2") |
d0eb09a1 RW |
10053 | (source |
10054 | (origin | |
10055 | (method url-fetch) | |
10056 | (uri (cran-uri "grImport" version)) | |
10057 | (sha256 | |
10058 | (base32 | |
cb4a6e67 | 10059 | "0n3y6dzy8s0ifvyrgwbly6cl14lmgd54dyi74s5i984apszpsp16")))) |
d0eb09a1 RW |
10060 | (properties `((upstream-name . "grImport"))) |
10061 | (build-system r-build-system) | |
10062 | (inputs | |
10063 | `(("ghostscript" ,ghostscript))) | |
10064 | (propagated-inputs | |
10065 | `(("r-xml" ,r-xml))) | |
10066 | (home-page "https://cran.r-project.org/web/packages/grImport") | |
10067 | (synopsis "Convert, import, and draw PostScript pictures") | |
10068 | (description | |
10069 | "This package provides functions for converting, importing, and drawing | |
10070 | PostScript pictures in R plots.") | |
10071 | (license license:gpl2+))) | |
78735b9f RW |
10072 | |
10073 | (define-public r-grimport2 | |
10074 | (package | |
10075 | (name "r-grimport2") | |
407a04fa | 10076 | (version "0.1-5") |
78735b9f RW |
10077 | (source |
10078 | (origin | |
10079 | (method url-fetch) | |
10080 | (uri (cran-uri "grImport2" version)) | |
10081 | (sha256 | |
10082 | (base32 | |
407a04fa | 10083 | "0dyb3nrrvxnkk9q5b136bdivcz1jj3ajx1kscm3k0kkpqjif0pls")))) |
78735b9f RW |
10084 | (properties `((upstream-name . "grImport2"))) |
10085 | (build-system r-build-system) | |
10086 | (propagated-inputs | |
10087 | `(("r-base64enc" ,r-base64enc) | |
10088 | ("r-jpeg" ,r-jpeg) | |
10089 | ("r-png" ,r-png) | |
10090 | ("r-xml" ,r-xml))) | |
10091 | (home-page "https://cran.r-project.org/web/packages/grImport2/") | |
10092 | (synopsis "Import SVG graphics") | |
10093 | (description | |
10094 | "This package provides functions for importing external vector images and | |
10095 | drawing them as part of R plots. This package is different from the | |
10096 | @code{grImport} package because, where that package imports PostScript format | |
10097 | images, this package imports SVG format images. Furthermore, this package | |
10098 | imports a specific subset of SVG, so external images must be preprocessed | |
10099 | using a package like @code{rsvg} to produce SVG that this package can import. | |
10100 | SVG features that are not supported by R graphics, such as gradient fills, can | |
10101 | be imported and then exported via the @code{gridSVG} package.") | |
10102 | (license license:gpl2+))) | |
2871b670 RW |
10103 | |
10104 | (define-public r-kohonen | |
10105 | (package | |
10106 | (name "r-kohonen") | |
10107 | (version "3.0.8") | |
10108 | (source | |
10109 | (origin | |
10110 | (method url-fetch) | |
10111 | (uri (cran-uri "kohonen" version)) | |
10112 | (sha256 | |
10113 | (base32 | |
10114 | "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q")))) | |
10115 | (build-system r-build-system) | |
10116 | (propagated-inputs | |
10117 | `(("r-mass" ,r-mass) | |
10118 | ("r-rcpp" ,r-rcpp))) | |
10119 | (home-page "https://cran.r-project.org/web/packages/kohonen") | |
10120 | (synopsis "Supervised and unsupervised self-organising maps") | |
10121 | (description | |
10122 | "This package provides functions to train @dfn{self-organising | |
10123 | maps} (SOMs). Also interrogation of the maps and prediction using trained | |
10124 | maps are supported. The name of the package refers to Teuvo Kohonen, the | |
10125 | inventor of the SOM.") | |
10126 | (license license:gpl2+))) | |
00436e2c RW |
10127 | |
10128 | (define-public r-nnls | |
10129 | (package | |
10130 | (name "r-nnls") | |
10131 | (version "1.4") | |
10132 | (source | |
10133 | (origin | |
10134 | (method url-fetch) | |
10135 | (uri (cran-uri "nnls" version)) | |
10136 | (sha256 | |
10137 | (base32 | |
10138 | "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) | |
10139 | (build-system r-build-system) | |
10140 | (native-inputs `(("gfortran" ,gfortran))) | |
10141 | (home-page "https://cran.r-project.org/web/packages/nnls") | |
10142 | (synopsis "Lawson-Hanson algorithm for non-negative least squares") | |
10143 | (description | |
10144 | "This package provides an R interface to the Lawson-Hanson implementation | |
10145 | of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows | |
10146 | the combination of non-negative and non-positive constraints.") | |
10147 | (license license:gpl2+))) | |
25861356 RW |
10148 | |
10149 | (define-public r-iso | |
10150 | (package | |
10151 | (name "r-iso") | |
85f3ec6a | 10152 | (version "0.0-18") |
25861356 RW |
10153 | (source |
10154 | (origin | |
10155 | (method url-fetch) | |
10156 | (uri (cran-uri "Iso" version)) | |
10157 | (sha256 | |
10158 | (base32 | |
85f3ec6a | 10159 | "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid")))) |
25861356 RW |
10160 | (properties `((upstream-name . "Iso"))) |
10161 | (build-system r-build-system) | |
10162 | (native-inputs `(("gfortran" ,gfortran))) | |
10163 | (home-page "http://www.stat.auckland.ac.nz/~rolf/") | |
10164 | (synopsis "Functions to perform isotonic regression") | |
10165 | (description | |
10166 | "This package provides support for linear order and unimodal | |
10167 | order (univariate) isotonic regression and bivariate isotonic regression with | |
10168 | linear order on both variables.") | |
10169 | (license license:gpl2+))) | |
9401f56b RW |
10170 | |
10171 | (define-public r-chemometricswithr | |
10172 | (package | |
10173 | (name "r-chemometricswithr") | |
e0417402 | 10174 | (version "0.1.13") |
9401f56b RW |
10175 | (source |
10176 | (origin | |
10177 | (method url-fetch) | |
10178 | (uri (cran-uri "ChemometricsWithR" version)) | |
10179 | (sha256 | |
10180 | (base32 | |
e0417402 | 10181 | "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) |
9401f56b RW |
10182 | (properties |
10183 | `((upstream-name . "ChemometricsWithR"))) | |
10184 | (build-system r-build-system) | |
10185 | (propagated-inputs | |
10186 | `(("r-devtools" ,r-devtools) | |
10187 | ("r-kohonen" ,r-kohonen) | |
10188 | ("r-mass" ,r-mass) | |
10189 | ("r-pls" ,r-pls))) | |
10190 | (home-page "https://github.com/rwehrens/CWR") | |
10191 | (synopsis "Chemometrics with R") | |
10192 | (description | |
10193 | "This package provides functions and scripts used in the book | |
10194 | \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and | |
10195 | Life Sciences\" by Ron Wehrens, Springer (2011).") | |
10196 | (license license:gpl2+))) | |
d28be7b7 RW |
10197 | |
10198 | (define-public r-als | |
10199 | (package | |
10200 | (name "r-als") | |
10201 | (version "0.0.6") | |
10202 | (source | |
10203 | (origin | |
10204 | (method url-fetch) | |
10205 | (uri (cran-uri "ALS" version)) | |
10206 | (sha256 | |
10207 | (base32 | |
10208 | "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) | |
10209 | (properties `((upstream-name . "ALS"))) | |
10210 | (build-system r-build-system) | |
10211 | (propagated-inputs | |
10212 | `(("r-iso" ,r-iso) | |
10213 | ("r-nnls" ,r-nnls))) | |
10214 | (home-page "https://cran.r-project.org/web/packages/ALS") | |
10215 | (synopsis "Multivariate curve resolution alternating least squares") | |
10216 | (description | |
10217 | "Alternating least squares is often used to resolve components | |
10218 | contributing to data with a bilinear structure; the basic technique may be | |
10219 | extended to alternating constrained least squares. This package provides an | |
10220 | implementation of @dfn{multivariate curve resolution alternating least | |
10221 | squares} (MCR-ALS). | |
10222 | ||
10223 | Commonly applied constraints include unimodality, non-negativity, and | |
10224 | normalization of components. Several data matrices may be decomposed | |
10225 | simultaneously by assuming that one of the two matrices in the bilinear | |
10226 | decomposition is shared between datasets.") | |
10227 | (license license:gpl2+))) | |
895efece RW |
10228 | |
10229 | (define-public r-strucchange | |
10230 | (package | |
10231 | (name "r-strucchange") | |
10232 | (version "1.5-1") | |
10233 | (source | |
10234 | (origin | |
10235 | (method url-fetch) | |
10236 | (uri (cran-uri "strucchange" version)) | |
10237 | (sha256 | |
10238 | (base32 | |
10239 | "0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl")))) | |
10240 | (build-system r-build-system) | |
10241 | (propagated-inputs | |
10242 | `(("r-sandwich" ,r-sandwich) | |
10243 | ("r-zoo" ,r-zoo))) | |
10244 | (home-page "https://cran.r-project.org/web/packages/strucchange") | |
10245 | (synopsis "Testing, monitoring, and dating structural changes") | |
10246 | (description | |
10247 | "This package provides tools for testing, monitoring and dating | |
10248 | structural changes in (linear) regression models. It features tests/methods | |
10249 | from the generalized fluctuation test framework as well as from the F | |
10250 | test (Chow test) framework. This includes methods to fit, plot and test | |
10251 | fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F | |
10252 | statistics, respectively. It is possible to monitor incoming data online | |
10253 | using fluctuation processes. Finally, the breakpoints in regression models | |
10254 | with structural changes can be estimated together with confidence intervals. | |
10255 | Emphasis is always given to methods for visualizing the data.") | |
10256 | ;; Either of these two GPL versions | |
10257 | (license (list license:gpl2 license:gpl3)))) | |
e7176ac5 RW |
10258 | |
10259 | (define-public r-pixmap | |
10260 | (package | |
10261 | (name "r-pixmap") | |
10262 | (version "0.4-11") | |
10263 | (source | |
10264 | (origin | |
10265 | (method url-fetch) | |
10266 | (uri (cran-uri "pixmap" version)) | |
10267 | (sha256 | |
10268 | (base32 | |
10269 | "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) | |
10270 | (build-system r-build-system) | |
10271 | (home-page "https://cran.r-project.org/web/packages/pixmap") | |
10272 | (synopsis "Tools for bitmap images") | |
10273 | (description | |
10274 | "This package provides functions for importing, exporting, plotting and | |
10275 | other manipulations of bitmapped images.") | |
10276 | (license license:gpl2))) | |
9170eb7f RW |
10277 | |
10278 | (define-public r-rapidjsonr | |
10279 | (package | |
10280 | (name "r-rapidjsonr") | |
10281 | (version "1.1") | |
10282 | (source | |
10283 | (origin | |
10284 | (method url-fetch) | |
10285 | (uri (cran-uri "rapidjsonr" version)) | |
10286 | (sha256 | |
10287 | (base32 | |
10288 | "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd")))) | |
10289 | (build-system r-build-system) | |
10290 | (home-page "https://cran.r-project.org/web/packages/rapidjsonr") | |
10291 | (synopsis "JSON parser") | |
10292 | (description | |
10293 | "This package provides JSON parsing capability through the Rapidjson | |
10294 | library.") | |
10295 | (license license:expat))) | |
ad6fea16 RW |
10296 | |
10297 | (define-public r-ontologyindex | |
10298 | (package | |
10299 | (name "r-ontologyindex") | |
209e504b | 10300 | (version "2.5") |
ad6fea16 RW |
10301 | (source |
10302 | (origin | |
10303 | (method url-fetch) | |
10304 | (uri (cran-uri "ontologyIndex" version)) | |
10305 | (sha256 | |
10306 | (base32 | |
209e504b | 10307 | "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) |
ad6fea16 RW |
10308 | (properties `((upstream-name . "ontologyIndex"))) |
10309 | (build-system r-build-system) | |
10310 | (home-page "https://cran.r-project.org/web/packages/ontologyIndex") | |
10311 | (synopsis "Functions for processing ontologies in R") | |
10312 | (description | |
10313 | "This package provides functions for reading ontologies into R as lists | |
10314 | and manipulating sets of ontological terms.") | |
10315 | (license license:gpl2+))) | |
dfd09f7b | 10316 | |
6275418b RW |
10317 | (define-public r-gargle |
10318 | (package | |
10319 | (name "r-gargle") | |
10320 | (version "0.3.1") | |
10321 | (source | |
10322 | (origin | |
10323 | (method url-fetch) | |
10324 | (uri (cran-uri "gargle" version)) | |
10325 | (sha256 | |
10326 | (base32 | |
10327 | "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v")))) | |
10328 | (build-system r-build-system) | |
10329 | (propagated-inputs | |
10330 | `(("r-fs" ,r-fs) | |
10331 | ("r-glue" ,r-glue) | |
10332 | ("r-httr" ,r-httr) | |
10333 | ("r-jsonlite" ,r-jsonlite) | |
10334 | ("r-rlang" ,r-rlang) | |
10335 | ("r-withr" ,r-withr))) | |
10336 | (home-page "https://gargle.r-lib.org") | |
10337 | (synopsis "Utilities for working with Google APIs") | |
10338 | (description | |
10339 | "This package provides utilities for working with Google APIs. This | |
10340 | includes functions and classes for handling common credential types and for | |
10341 | preparing, executing, and processing HTTP requests.") | |
10342 | (license license:expat))) | |
10343 | ||
dfd09f7b RW |
10344 | (define-public r-bigrquery |
10345 | (package | |
10346 | (name "r-bigrquery") | |
504a5136 | 10347 | (version "1.2.0") |
dfd09f7b RW |
10348 | (source |
10349 | (origin | |
10350 | (method url-fetch) | |
10351 | (uri (cran-uri "bigrquery" version)) | |
10352 | (sha256 | |
10353 | (base32 | |
504a5136 | 10354 | "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb")))) |
dfd09f7b RW |
10355 | (build-system r-build-system) |
10356 | (propagated-inputs | |
10357 | `(("r-assertthat" ,r-assertthat) | |
4bc5d451 | 10358 | ("r-bit64" ,r-bit64) |
dfd09f7b RW |
10359 | ("r-curl" ,r-curl) |
10360 | ("r-dbi" ,r-dbi) | |
504a5136 | 10361 | ("r-gargle" ,r-gargle) |
dfd09f7b RW |
10362 | ("r-glue" ,r-glue) |
10363 | ("r-httr" ,r-httr) | |
10364 | ("r-jsonlite" ,r-jsonlite) | |
10365 | ("r-prettyunits" ,r-prettyunits) | |
10366 | ("r-progress" ,r-progress) | |
10367 | ("r-rapidjsonr" ,r-rapidjsonr) | |
10368 | ("r-rcpp" ,r-rcpp) | |
504a5136 | 10369 | ("r-rlang" ,r-rlang) |
dfd09f7b RW |
10370 | ("r-tibble" ,r-tibble))) |
10371 | (home-page "https://github.com/rstats-db/bigrquery") | |
10372 | (synopsis "R interface to Google's BigQuery API") | |
10373 | (description | |
10374 | "This package provides an R interface to Google's BigQuery database.") | |
10375 | (license license:gpl3))) | |
1ab51604 RW |
10376 | |
10377 | (define-public r-gmp | |
10378 | (package | |
10379 | (name "r-gmp") | |
83bfddd1 | 10380 | (version "0.5-13.5") |
1ab51604 RW |
10381 | (source |
10382 | (origin | |
10383 | (method url-fetch) | |
10384 | (uri (cran-uri "gmp" version)) | |
10385 | (sha256 | |
10386 | (base32 | |
83bfddd1 | 10387 | "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn")))) |
1ab51604 RW |
10388 | (build-system r-build-system) |
10389 | (arguments | |
10390 | '(#:phases | |
10391 | (modify-phases %standard-phases | |
10392 | (add-after 'unpack 'set-CC | |
10393 | (lambda _ (setenv "CC" "gcc") #t))))) | |
10394 | (inputs `(("gmp" ,gmp))) | |
10395 | (home-page "https://cran.r-project.org/web/packages/gmp") | |
10396 | (synopsis "Multiple precision arithmetic") | |
10397 | (description | |
10398 | "This package supports multiple precision arithmetic (big integers and | |
10399 | rationals, prime number tests, matrix computation), \"arithmetic without | |
10400 | limitations\" using the GNU Multiple Precision library.") | |
10401 | ;; Any version of the GPL. | |
10402 | (license license:gpl3+))) | |
a536c7c9 RW |
10403 | |
10404 | (define-public r-rmpfr | |
10405 | (package | |
10406 | (name "r-rmpfr") | |
df00ca25 | 10407 | (version "0.7-2") |
a536c7c9 RW |
10408 | (source |
10409 | (origin | |
10410 | (method url-fetch) | |
10411 | (uri (cran-uri "Rmpfr" version)) | |
10412 | (sha256 | |
10413 | (base32 | |
df00ca25 | 10414 | "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc")))) |
a536c7c9 RW |
10415 | (properties `((upstream-name . "Rmpfr"))) |
10416 | (build-system r-build-system) | |
10417 | (inputs | |
10418 | `(("mpfr" ,mpfr))) | |
10419 | (propagated-inputs | |
10420 | `(("r-gmp" ,r-gmp))) | |
10421 | (home-page "http://rmpfr.r-forge.r-project.org/") | |
10422 | (synopsis "R bindings to the MPFR library") | |
10423 | (description | |
10424 | "This package supports arithmetic (via S4 classes and methods) for | |
10425 | arbitrary precision floating point numbers, including transcendental | |
10426 | functions. To this end, the package interfaces with the @dfn{Multiple | |
10427 | Precision Floating-Point Reliable} (MPFR) library.") | |
10428 | (license license:gpl2+))) | |
8004bb24 RW |
10429 | |
10430 | (define-public r-assertive-base | |
10431 | (package | |
10432 | (name "r-assertive-base") | |
10433 | (version "0.0-7") | |
10434 | (source | |
10435 | (origin | |
10436 | (method url-fetch) | |
10437 | (uri (cran-uri "assertive.base" version)) | |
10438 | (sha256 | |
10439 | (base32 | |
10440 | "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh")))) | |
10441 | (properties | |
10442 | `((upstream-name . "assertive.base"))) | |
10443 | (build-system r-build-system) | |
10444 | (home-page "https://bitbucket.org/richierocks/assertive.base") | |
10445 | (synopsis "Core of the assertive package") | |
10446 | (description | |
10447 | "This package provides a minimal set of predicates and assertions used by | |
10448 | the assertive package. This is mainly for use by other package developers who | |
10449 | want to include run-time testing features in their own packages.") | |
10450 | (license license:gpl3+))) | |
4b2d17ed RW |
10451 | |
10452 | (define-public r-assertive-properties | |
10453 | (package | |
10454 | (name "r-assertive-properties") | |
10455 | (version "0.0-4") | |
10456 | (source | |
10457 | (origin | |
10458 | (method url-fetch) | |
10459 | (uri (cran-uri "assertive.properties" version)) | |
10460 | (sha256 | |
10461 | (base32 | |
10462 | "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw")))) | |
10463 | (properties | |
10464 | `((upstream-name . "assertive.properties"))) | |
10465 | (build-system r-build-system) | |
10466 | (propagated-inputs | |
10467 | `(("r-assertive-base" ,r-assertive-base))) | |
10468 | (home-page "https://bitbucket.org/richierocks/assertive.properties") | |
10469 | (synopsis "Assertions to check properties of variables") | |
10470 | (description | |
10471 | "This package provides a set of predicates and assertions for checking | |
10472 | the properties of variables, such as length, names and attributes. This is | |
10473 | mainly for use by other package developers who want to include run-time | |
10474 | testing features in their own packages.") | |
10475 | (license license:gpl3+))) | |
dac9c1f6 RW |
10476 | |
10477 | (define-public r-assertive-numbers | |
10478 | (package | |
10479 | (name "r-assertive-numbers") | |
10480 | (version "0.0-2") | |
10481 | (source | |
10482 | (origin | |
10483 | (method url-fetch) | |
10484 | (uri (cran-uri "assertive.numbers" version)) | |
10485 | (sha256 | |
10486 | (base32 | |
10487 | "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds")))) | |
10488 | (properties | |
10489 | `((upstream-name . "assertive.numbers"))) | |
10490 | (build-system r-build-system) | |
10491 | (propagated-inputs | |
10492 | `(("r-assertive-base" ,r-assertive-base))) | |
10493 | (home-page "https://bitbucket.org/richierocks/assertive.numbers") | |
10494 | (synopsis "Assertions to check properties of numbers") | |
10495 | (description | |
10496 | "This package provides a set of predicates and assertions for checking | |
10497 | the properties of numbers. This is mainly for use by other package developers | |
10498 | who want to include run-time testing features in their own packages.") | |
10499 | (license license:gpl3+))) | |
2da2d2f6 RW |
10500 | |
10501 | (define-public r-assertive-sets | |
10502 | (package | |
10503 | (name "r-assertive-sets") | |
10504 | (version "0.0-3") | |
10505 | (source | |
10506 | (origin | |
10507 | (method url-fetch) | |
10508 | (uri (cran-uri "assertive.sets" version)) | |
10509 | (sha256 | |
10510 | (base32 | |
10511 | "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7")))) | |
10512 | (properties | |
10513 | `((upstream-name . "assertive.sets"))) | |
10514 | (build-system r-build-system) | |
10515 | (propagated-inputs | |
10516 | `(("r-assertive-base" ,r-assertive-base))) | |
10517 | (home-page "https://bitbucket.org/richierocks/assertive.sets") | |
10518 | (synopsis "Assertions to check properties of sets") | |
10519 | (description | |
10520 | "This package provides a set of predicates and assertions for checking | |
10521 | the properties of sets. This is mainly for use by other package developers | |
10522 | who want to include run-time testing features in their own packages.") | |
10523 | (license license:gpl3+))) | |
905aa46a RW |
10524 | |
10525 | (define-public r-assertive-matrices | |
10526 | (package | |
10527 | (name "r-assertive-matrices") | |
10528 | (version "0.0-2") | |
10529 | (source | |
10530 | (origin | |
10531 | (method url-fetch) | |
10532 | (uri (cran-uri "assertive.matrices" version)) | |
10533 | (sha256 | |
10534 | (base32 | |
10535 | "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil")))) | |
10536 | (properties | |
10537 | `((upstream-name . "assertive.matrices"))) | |
10538 | (build-system r-build-system) | |
10539 | (propagated-inputs | |
10540 | `(("r-assertive-base" ,r-assertive-base))) | |
10541 | (home-page "https://bitbucket.org/richierocks/assertive.matrices") | |
10542 | (synopsis "Assertions to check properties of matrices") | |
10543 | (description | |
10544 | "This package provides a set of predicates and assertions for checking | |
10545 | the properties of matrices. This is mainly for use by other package | |
10546 | developers who want to include run-time testing features in their own | |
10547 | packages.") | |
10548 | (license license:gpl3+))) | |
c358b5d4 RW |
10549 | |
10550 | (define-public r-assertive-models | |
10551 | (package | |
10552 | (name "r-assertive-models") | |
10553 | (version "0.0-2") | |
10554 | (source | |
10555 | (origin | |
10556 | (method url-fetch) | |
10557 | (uri (cran-uri "assertive.models" version)) | |
10558 | (sha256 | |
10559 | (base32 | |
10560 | "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr")))) | |
10561 | (properties | |
10562 | `((upstream-name . "assertive.models"))) | |
10563 | (build-system r-build-system) | |
10564 | (propagated-inputs | |
10565 | `(("r-assertive-base" ,r-assertive-base))) | |
10566 | (home-page "https://bitbucket.org/richierocks/assertive.models") | |
10567 | (synopsis "Assertions to check properties of models") | |
10568 | (description | |
10569 | "This package provides a set of predicates and assertions for checking | |
10570 | the properties of models. This is mainly for use by other package developers | |
10571 | who want to include run-time testing features in their own packages.") | |
10572 | (license license:gpl3+))) | |
dcafcfb4 RW |
10573 | |
10574 | (define-public r-assertive-reflection | |
10575 | (package | |
10576 | (name "r-assertive-reflection") | |
10577 | (version "0.0-4") | |
10578 | (source | |
10579 | (origin | |
10580 | (method url-fetch) | |
10581 | (uri (cran-uri "assertive.reflection" version)) | |
10582 | (sha256 | |
10583 | (base32 | |
10584 | "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj")))) | |
10585 | (properties | |
10586 | `((upstream-name . "assertive.reflection"))) | |
10587 | (build-system r-build-system) | |
10588 | (propagated-inputs | |
10589 | `(("r-assertive-base" ,r-assertive-base))) | |
10590 | (home-page "https://bitbucket.org/richierocks/assertive.reflection") | |
10591 | (synopsis "Assertions for checking the state of R") | |
10592 | (description | |
10593 | "This package provides a set of predicates and assertions for checking | |
10594 | the state and capabilities of R, the operating system it is running on, and | |
10595 | the IDE being used. This is mainly for use by other package developers who | |
10596 | want to include run-time testing features in their own packages.") | |
10597 | (license license:gpl3+))) | |
5e3bd355 RW |
10598 | |
10599 | (define-public r-assertive-types | |
10600 | (package | |
10601 | (name "r-assertive-types") | |
10602 | (version "0.0-3") | |
10603 | (source | |
10604 | (origin | |
10605 | (method url-fetch) | |
10606 | (uri (cran-uri "assertive.types" version)) | |
10607 | (sha256 | |
10608 | (base32 | |
10609 | "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb")))) | |
10610 | (properties | |
10611 | `((upstream-name . "assertive.types"))) | |
10612 | (build-system r-build-system) | |
10613 | (propagated-inputs | |
10614 | `(("r-assertive-base" ,r-assertive-base) | |
10615 | ("r-assertive-properties" ,r-assertive-properties) | |
10616 | ("r-codetools" ,r-codetools))) | |
10617 | (home-page "https://bitbucket.org/richierocks/assertive.types") | |
10618 | (synopsis "Assertions to check types of variables") | |
10619 | (description | |
10620 | "This package provides a set of predicates and assertions for checking | |
10621 | the types of variables. This is mainly for use by other package developers | |
10622 | who want to include run-time testing features in their own packages.") | |
10623 | (license license:gpl3+))) | |
1f0a761a RW |
10624 | |
10625 | (define-public r-assertive-files | |
10626 | (package | |
10627 | (name "r-assertive-files") | |
10628 | (version "0.0-2") | |
10629 | (source | |
10630 | (origin | |
10631 | (method url-fetch) | |
10632 | (uri (cran-uri "assertive.files" version)) | |
10633 | (sha256 | |
10634 | (base32 | |
10635 | "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy")))) | |
10636 | (properties | |
10637 | `((upstream-name . "assertive.files"))) | |
10638 | (build-system r-build-system) | |
10639 | (propagated-inputs | |
10640 | `(("r-assertive-base" ,r-assertive-base) | |
10641 | ("r-assertive-numbers" ,r-assertive-numbers))) | |
10642 | (home-page "https://bitbucket.org/richierocks/assertive.files") | |
10643 | (synopsis "Assertions to check properties of files") | |
10644 | (description | |
10645 | "This package provides a set of predicates and assertions for checking | |
10646 | the properties of files and connections. This is mainly for use by other | |
10647 | package developers who want to include run-time testing features in their own | |
10648 | packages.") | |
10649 | (license license:gpl3+))) | |
50ce8b1e RW |
10650 | |
10651 | (define-public r-assertive-code | |
10652 | (package | |
10653 | (name "r-assertive-code") | |
10654 | (version "0.0-3") | |
10655 | (source | |
10656 | (origin | |
10657 | (method url-fetch) | |
10658 | (uri (cran-uri "assertive.code" version)) | |
10659 | (sha256 | |
10660 | (base32 | |
10661 | "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) | |
10662 | (properties | |
10663 | `((upstream-name . "assertive.code"))) | |
10664 | (build-system r-build-system) | |
10665 | (propagated-inputs | |
10666 | `(("r-assertive-base" ,r-assertive-base) | |
10667 | ("r-assertive-properties" ,r-assertive-properties) | |
10668 | ("r-assertive-types" ,r-assertive-types))) | |
10669 | (home-page "https://bitbucket.org/richierocks/assertive.code") | |
10670 | (synopsis "Assertions to check properties of code") | |
10671 | (description | |
10672 | "This package provides a set of predicates and assertions for checking | |
10673 | the properties of code. This is mainly for use by other package developers | |
10674 | who want to include run-time testing features in their own packages.") | |
10675 | (license license:gpl3+))) | |
29d9a2af RW |
10676 | |
10677 | (define-public r-assertive-datetimes | |
10678 | (package | |
10679 | (name "r-assertive-datetimes") | |
10680 | (version "0.0-2") | |
10681 | (source | |
10682 | (origin | |
10683 | (method url-fetch) | |
10684 | (uri (cran-uri "assertive.datetimes" version)) | |
10685 | (sha256 | |
10686 | (base32 | |
10687 | "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78")))) | |
10688 | (properties | |
10689 | `((upstream-name . "assertive.datetimes"))) | |
10690 | (build-system r-build-system) | |
10691 | (propagated-inputs | |
10692 | `(("r-assertive-base" ,r-assertive-base) | |
10693 | ("r-assertive-types" ,r-assertive-types))) | |
10694 | (home-page "https://bitbucket.org/richierocks/assertive.datetimes") | |
10695 | (synopsis "Assertions to check properties of dates and times") | |
10696 | (description | |
10697 | "This package provides a set of predicates and assertions for checking | |
10698 | the properties of dates and times. This is mainly for use by other package | |
10699 | developers who want to include run-time testing features in their own | |
10700 | packages.") | |
10701 | (license license:gpl3+))) | |
66d0a0a7 RW |
10702 | |
10703 | (define-public r-assertive-strings | |
10704 | (package | |
10705 | (name "r-assertive-strings") | |
10706 | (version "0.0-3") | |
10707 | (source | |
10708 | (origin | |
10709 | (method url-fetch) | |
10710 | (uri (cran-uri "assertive.strings" version)) | |
10711 | (sha256 | |
10712 | (base32 | |
10713 | "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm")))) | |
10714 | (properties | |
10715 | `((upstream-name . "assertive.strings"))) | |
10716 | (build-system r-build-system) | |
10717 | (propagated-inputs | |
10718 | `(("r-assertive-base" ,r-assertive-base) | |
10719 | ("r-assertive-types" ,r-assertive-types) | |
10720 | ("r-stringi" ,r-stringi))) | |
10721 | (home-page "https://bitbucket.org/richierocks/assertive.strings") | |
10722 | (synopsis "Assertions to check properties of strings") | |
10723 | (description | |
10724 | "This package provides a set of predicates and assertions for checking | |
10725 | the properties of strings. This is mainly for use by other package developers | |
10726 | who want to include run-time testing features in their own packages.") | |
10727 | (license license:gpl3+))) | |
6d3702e5 RW |
10728 | |
10729 | (define-public r-assertive-data-us | |
10730 | (package | |
10731 | (name "r-assertive-data-us") | |
10732 | (version "0.0-2") | |
10733 | (source | |
10734 | (origin | |
10735 | (method url-fetch) | |
10736 | (uri (cran-uri "assertive.data.us" version)) | |
10737 | (sha256 | |
10738 | (base32 | |
10739 | "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq")))) | |
10740 | (properties | |
10741 | `((upstream-name . "assertive.data.us"))) | |
10742 | (build-system r-build-system) | |
10743 | (propagated-inputs | |
10744 | `(("r-assertive-base" ,r-assertive-base) | |
10745 | ("r-assertive-strings" ,r-assertive-strings))) | |
10746 | (home-page "https://bitbucket.org/richierocks/assertive.data.us") | |
10747 | (synopsis "Assertions to check properties of strings") | |
10748 | (description | |
10749 | "This package provides a set of predicates and assertions for checking | |
10750 | the properties of US-specific complex data types. This is mainly for use by | |
10751 | other package developers who want to include run-time testing features in | |
10752 | their own packages.") | |
10753 | (license license:gpl3+))) | |
39ef8e09 RW |
10754 | |
10755 | (define-public r-assertive-data-uk | |
10756 | (package | |
10757 | (name "r-assertive-data-uk") | |
10758 | (version "0.0-2") | |
10759 | (source | |
10760 | (origin | |
10761 | (method url-fetch) | |
10762 | (uri (cran-uri "assertive.data.uk" version)) | |
10763 | (sha256 | |
10764 | (base32 | |
10765 | "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b")))) | |
10766 | (properties | |
10767 | `((upstream-name . "assertive.data.uk"))) | |
10768 | (build-system r-build-system) | |
10769 | (propagated-inputs | |
10770 | `(("r-assertive-base" ,r-assertive-base) | |
10771 | ("r-assertive-strings" ,r-assertive-strings))) | |
10772 | (home-page "https://bitbucket.org/richierocks/assertive.data.uk") | |
10773 | (synopsis "Assertions to check properties of strings") | |
10774 | (description | |
10775 | "This package provides a set of predicates and assertions for checking | |
10776 | the properties of UK-specific complex data types. This is mainly for use by | |
10777 | other package developers who want to include run-time testing features in | |
10778 | their own packages.") | |
10779 | (license license:gpl3+))) | |
39231abf RW |
10780 | |
10781 | (define-public r-assertive-data | |
10782 | (package | |
10783 | (name "r-assertive-data") | |
10784 | (version "0.0-3") | |
10785 | (source | |
10786 | (origin | |
10787 | (method url-fetch) | |
10788 | (uri (cran-uri "assertive.data" version)) | |
10789 | (sha256 | |
10790 | (base32 | |
10791 | "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s")))) | |
10792 | (properties | |
10793 | `((upstream-name . "assertive.data"))) | |
10794 | (build-system r-build-system) | |
10795 | (propagated-inputs | |
10796 | `(("r-assertive-base" ,r-assertive-base) | |
10797 | ("r-assertive-strings" ,r-assertive-strings))) | |
10798 | (home-page "https://bitbucket.org/richierocks/assertive.data") | |
10799 | (synopsis "Assertions to check properties of data") | |
10800 | (description | |
10801 | "This package provides a set of predicates and assertions for checking | |
10802 | the properties of (country independent) complex data types. This is mainly | |
10803 | for use by other package developers who want to include run-time testing | |
10804 | features in their own packages.") | |
10805 | (license license:gpl3+))) | |
658b2b62 RW |
10806 | |
10807 | (define-public r-assertive | |
10808 | (package | |
10809 | (name "r-assertive") | |
10810 | (version "0.3-5") | |
10811 | (source | |
10812 | (origin | |
10813 | (method url-fetch) | |
10814 | (uri (cran-uri "assertive" version)) | |
10815 | (sha256 | |
10816 | (base32 | |
10817 | "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3")))) | |
10818 | (build-system r-build-system) | |
10819 | (propagated-inputs | |
10820 | `(("r-assertive-base" ,r-assertive-base) | |
10821 | ("r-assertive-code" ,r-assertive-code) | |
10822 | ("r-assertive-data" ,r-assertive-data) | |
10823 | ("r-assertive-data-uk" ,r-assertive-data-uk) | |
10824 | ("r-assertive-data-us" ,r-assertive-data-us) | |
10825 | ("r-assertive-datetimes" ,r-assertive-datetimes) | |
10826 | ("r-assertive-files" ,r-assertive-files) | |
10827 | ("r-assertive-matrices" ,r-assertive-matrices) | |
10828 | ("r-assertive-models" ,r-assertive-models) | |
10829 | ("r-assertive-numbers" ,r-assertive-numbers) | |
10830 | ("r-assertive-properties" ,r-assertive-properties) | |
10831 | ("r-assertive-reflection" ,r-assertive-reflection) | |
10832 | ("r-assertive-sets" ,r-assertive-sets) | |
10833 | ("r-assertive-strings" ,r-assertive-strings) | |
10834 | ("r-assertive-types" ,r-assertive-types) | |
10835 | ("r-knitr" ,r-knitr))) | |
10836 | (home-page "https://bitbucket.org/richierocks/assertive") | |
10837 | (synopsis "Readable check functions to ensure code integrity") | |
10838 | (description | |
10839 | "This package provides lots of predicates (@code{is_*} functions) to | |
10840 | check the state of your variables, and assertions (@code{assert_*} functions) | |
10841 | to throw errors if they aren't in the right form.") | |
10842 | (license license:gpl3+))) | |
f51dcc27 RW |
10843 | |
10844 | (define-public r-dotcall64 | |
10845 | (package | |
10846 | (name "r-dotcall64") | |
10847 | (version "1.0-0") | |
10848 | (source | |
10849 | (origin | |
10850 | (method url-fetch) | |
10851 | (uri (cran-uri "dotCall64" version)) | |
10852 | (sha256 | |
10853 | (base32 | |
10854 | "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) | |
10855 | (properties `((upstream-name . "dotCall64"))) | |
10856 | (build-system r-build-system) | |
10857 | (native-inputs `(("gfortran" ,gfortran))) | |
10858 | (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") | |
10859 | (synopsis "Enhanced foreign function interface supporting long vectors") | |
10860 | (description | |
10861 | "This package provides @code{.C64()}, an enhanced version of @code{.C()} | |
10862 | and @code{.Fortran()} from the R foreign function interface. @code{.C64()} | |
10863 | supports long vectors, arguments of type 64-bit integer, and provides a | |
10864 | mechanism to avoid unnecessary copies of read-only and write-only arguments. | |
10865 | This makes it a convenient and fast interface to C/C++ and Fortran code.") | |
10866 | (license license:gpl2+))) | |
90104ecd RW |
10867 | |
10868 | (define-public r-spam | |
10869 | (package | |
10870 | (name "r-spam") | |
d77e69e9 | 10871 | (version "2.3-0") |
90104ecd RW |
10872 | (source |
10873 | (origin | |
10874 | (method url-fetch) | |
10875 | (uri (cran-uri "spam" version)) | |
10876 | (sha256 | |
10877 | (base32 | |
d77e69e9 | 10878 | "194n5mgvyms9ckjqixl3h33apii8h9kqspqg2si9k741k578qb3w")))) |
90104ecd RW |
10879 | (build-system r-build-system) |
10880 | (propagated-inputs | |
10881 | `(("r-dotcall64" ,r-dotcall64))) | |
10882 | (native-inputs `(("gfortran" ,gfortran))) | |
10883 | (home-page "https://www.math.uzh.ch/pages/spam/") | |
10884 | (synopsis "Sparse matrix algebra") | |
10885 | (description | |
10886 | "This package provides a set of functions for sparse matrix algebra. | |
10887 | Differences with other sparse matrix packages are: | |
10888 | ||
10889 | @enumerate | |
10890 | @item it only supports (essentially) one sparse matrix format; | |
10891 | @item it is based on transparent and simple structure(s); | |
10892 | @item it is tailored for MCMC calculations within G(M)RF; | |
10893 | @item and it is fast and scalable (with the extension package @code{spam64}). | |
10894 | @end enumerate\n") | |
10895 | ;; Either of these licenses | |
10896 | (license (list license:bsd-3 license:lgpl2.0)))) | |
32725458 RW |
10897 | |
10898 | (define-public r-fields | |
10899 | (package | |
10900 | (name "r-fields") | |
6c81cc88 | 10901 | (version "9.8-6") |
32725458 RW |
10902 | (source |
10903 | (origin | |
10904 | (method url-fetch) | |
10905 | (uri (cran-uri "fields" version)) | |
10906 | (sha256 | |
10907 | (base32 | |
6c81cc88 | 10908 | "07x95vk1idjfzi5ikn0ijal754mssdmgr1p4nswmx9w3i5ndcqaz")))) |
32725458 RW |
10909 | (build-system r-build-system) |
10910 | (propagated-inputs | |
10911 | `(("r-maps" ,r-maps) | |
10912 | ("r-spam" ,r-spam))) | |
10913 | (native-inputs | |
10914 | `(("gfortran" ,gfortran))) | |
10915 | (home-page "http://www.image.ucar.edu/fields") | |
10916 | (synopsis "Tools for spatial data") | |
10917 | (description | |
10918 | "This is a package for curve, surface and function fitting with an | |
10919 | emphasis on splines, spatial data and spatial statistics. The major methods | |
10920 | include cubic, and thin plate splines, Kriging, and compactly supported | |
10921 | covariance functions for large data sets.") | |
10922 | (license license:gpl2+))) | |
99c164a5 RW |
10923 | |
10924 | (define-public r-spatialextremes | |
10925 | (package | |
10926 | (name "r-spatialextremes") | |
ffb97e69 | 10927 | (version "2.0-7.2") |
99c164a5 RW |
10928 | (source |
10929 | (origin | |
10930 | (method url-fetch) | |
10931 | (uri (cran-uri "SpatialExtremes" version)) | |
10932 | (sha256 | |
10933 | (base32 | |
ffb97e69 | 10934 | "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8")))) |
99c164a5 RW |
10935 | (properties |
10936 | `((upstream-name . "SpatialExtremes"))) | |
10937 | (build-system r-build-system) | |
10938 | (propagated-inputs | |
10939 | `(("r-fields" ,r-fields) | |
10940 | ("r-maps" ,r-maps))) | |
10941 | (home-page "http://spatialextremes.r-forge.r-project.org/") | |
10942 | (synopsis "Modelling spatial extremes") | |
10943 | (description | |
10944 | "This package provides tools for the statistical modelling of spatial | |
10945 | extremes using max-stable processes, copula or Bayesian hierarchical models. | |
10946 | More precisely, this package allows (conditional) simulations from various | |
10947 | parametric max-stable models, analysis of the extremal spatial dependence, the | |
10948 | fitting of such processes using composite likelihoods or least square (simple | |
10949 | max-stable processes only), model checking and selection and prediction.") | |
10950 | (license license:gpl2+))) | |
c2d6e866 RW |
10951 | |
10952 | (define-public r-drc | |
10953 | (package | |
10954 | (name "r-drc") | |
10955 | (version "3.0-1") | |
10956 | (source | |
10957 | (origin | |
10958 | (method url-fetch) | |
10959 | (uri (cran-uri "drc" version)) | |
10960 | (sha256 | |
10961 | (base32 | |
10962 | "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) | |
10963 | (build-system r-build-system) | |
10964 | (propagated-inputs | |
10965 | `(("r-car" ,r-car) | |
10966 | ("r-gtools" ,r-gtools) | |
10967 | ("r-mass" ,r-mass) | |
10968 | ("r-multcomp" ,r-multcomp) | |
10969 | ("r-plotrix" ,r-plotrix) | |
10970 | ("r-scales" ,r-scales))) | |
10971 | (home-page "https://cran.r-project.org/web/packages/drc") | |
10972 | (synopsis "Analysis of dose-response curves") | |
10973 | (description | |
10974 | "This package provides a suite of flexible and versatile model fitting | |
10975 | and after-fitting functions for the analysis of dose-response data.") | |
10976 | (license license:gpl2+))) | |
4fcbd7ea RW |
10977 | |
10978 | (define-public r-rmeta | |
10979 | (package | |
10980 | (name "r-rmeta") | |
10981 | (version "3.0") | |
10982 | (source | |
10983 | (origin | |
10984 | (method url-fetch) | |
10985 | (uri (cran-uri "rmeta" version)) | |
10986 | (sha256 | |
10987 | (base32 | |
10988 | "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) | |
10989 | (build-system r-build-system) | |
10990 | (home-page "https://cran.r-project.org/web/packages/rmeta") | |
10991 | (synopsis "Tools for meta-analysis") | |
10992 | (description | |
10993 | "This package provides functions for simple fixed and random effects | |
10994 | meta-analysis for two-sample comparisons and cumulative meta-analyses. It | |
10995 | draws standard summary plots, funnel plots, and computes summaries and tests | |
10996 | for association and heterogeneity.") | |
10997 | (license license:gpl2))) | |
afc0d815 RW |
10998 | |
10999 | (define-public r-bootstrap | |
11000 | (package | |
11001 | (name "r-bootstrap") | |
36ff60f5 | 11002 | (version "2019.6") |
afc0d815 RW |
11003 | (source |
11004 | (origin | |
11005 | (method url-fetch) | |
11006 | (uri (cran-uri "bootstrap" version)) | |
11007 | (sha256 | |
11008 | (base32 | |
36ff60f5 | 11009 | "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj")))) |
afc0d815 RW |
11010 | (build-system r-build-system) |
11011 | (native-inputs `(("gfortran" ,gfortran))) | |
11012 | (home-page "https://cran.r-project.org/web/packages/bootstrap") | |
11013 | (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") | |
11014 | (description | |
11015 | "This package provides software and data for the book \"An Introduction | |
11016 | to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. | |
11017 | This package is primarily provided for projects already based on it, and for | |
11018 | support of the book. New projects should preferentially use the recommended | |
11019 | package \"boot\".") | |
11020 | (license license:bsd-3))) | |
1ea708af RW |
11021 | |
11022 | (define-public r-survivalroc | |
11023 | (package | |
11024 | (name "r-survivalroc") | |
11025 | (version "1.0.3") | |
11026 | (source | |
11027 | (origin | |
11028 | (method url-fetch) | |
11029 | (uri (cran-uri "survivalROC" version)) | |
11030 | (sha256 | |
11031 | (base32 | |
11032 | "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) | |
11033 | (properties `((upstream-name . "survivalROC"))) | |
11034 | (build-system r-build-system) | |
11035 | (home-page "https://cran.r-project.org/web/packages/survivalROC") | |
11036 | (synopsis "Time-dependent ROC curve estimation from censored survival data") | |
11037 | (description | |
11038 | "Compute time-dependent ROC curve from censored survival data using | |
11039 | Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, | |
11040 | Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") | |
11041 | (license license:gpl2+))) | |
6a5bfe09 RW |
11042 | |
11043 | (define-public r-longitudinal | |
11044 | (package | |
11045 | (name "r-longitudinal") | |
11046 | (version "1.1.12") | |
11047 | (source | |
11048 | (origin | |
11049 | (method url-fetch) | |
11050 | (uri (cran-uri "longitudinal" version)) | |
11051 | (sha256 | |
11052 | (base32 | |
11053 | "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l")))) | |
11054 | (build-system r-build-system) | |
11055 | (propagated-inputs `(("r-corpcor" ,r-corpcor))) | |
11056 | (home-page "http://strimmerlab.org/software/longitudinal/") | |
11057 | (synopsis "Analysis of multiple time course data") | |
11058 | (description | |
11059 | "This package contains general data structures and functions for | |
11060 | longitudinal data with multiple variables, repeated measurements, and | |
11061 | irregularly spaced time points. It also implements a shrinkage estimator of | |
11062 | dynamical correlation and dynamical covariance.") | |
11063 | (license license:gpl3+))) | |
e50722c8 RW |
11064 | |
11065 | (define-public r-genenet | |
11066 | (package | |
11067 | (name "r-genenet") | |
11068 | (version "1.2.13") | |
11069 | (source | |
11070 | (origin | |
11071 | (method url-fetch) | |
11072 | (uri (cran-uri "GeneNet" version)) | |
11073 | (sha256 | |
11074 | (base32 | |
11075 | "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p")))) | |
11076 | (properties `((upstream-name . "GeneNet"))) | |
11077 | (build-system r-build-system) | |
11078 | (propagated-inputs | |
11079 | `(("r-corpcor" ,r-corpcor) | |
11080 | ("r-fdrtool" ,r-fdrtool) | |
11081 | ("r-longitudinal" ,r-longitudinal))) | |
11082 | (home-page "http://strimmerlab.org/software/genenet/") | |
11083 | (synopsis "Modeling and inferring gene networks") | |
11084 | (description | |
11085 | "This package analyzes gene expression (time series) data with focus on | |
11086 | the inference of gene networks. In particular, GeneNet implements the methods | |
11087 | of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) | |
11088 | for learning large-scale gene association networks (including assignment of | |
11089 | putative directions).") | |
11090 | (license license:gpl3+))) | |
fe4e9f03 RW |
11091 | |
11092 | (define-public r-rbamtools | |
11093 | (package | |
11094 | (name "r-rbamtools") | |
11095 | (version "2.16.11.2") | |
11096 | (source | |
11097 | (origin | |
11098 | (method url-fetch) | |
11099 | (uri (cran-uri "rbamtools" version)) | |
11100 | (sha256 | |
11101 | (base32 | |
11102 | "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj")))) | |
11103 | (build-system r-build-system) | |
11104 | (inputs `(("zlib" ,zlib))) | |
11105 | (propagated-inputs | |
11106 | `(("r-refgenome" ,r-refgenome))) | |
11107 | (home-page "https://cran.r-project.org/web/packages/rbamtools") | |
11108 | (synopsis "Read and write BAM (binary alignment) files") | |
11109 | (description | |
11110 | "This package provides an R interface to functions of the SAMtools | |
11111 | library.") | |
11112 | (license license:artistic2.0))) | |
e3c0e3e3 RW |
11113 | |
11114 | (define-public r-protviz | |
11115 | (package | |
11116 | (name "r-protviz") | |
c3e5b456 | 11117 | (version "0.4.0") |
e3c0e3e3 RW |
11118 | (source |
11119 | (origin | |
11120 | (method url-fetch) | |
11121 | (uri (cran-uri "protViz" version)) | |
11122 | (sha256 | |
11123 | (base32 | |
c3e5b456 | 11124 | "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1")))) |
e3c0e3e3 RW |
11125 | (properties `((upstream-name . "protViz"))) |
11126 | (build-system r-build-system) | |
11127 | (inputs | |
11128 | `(("perl" ,perl) | |
11129 | ("python-2" ,python-2))) | |
11130 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
11131 | (home-page "https://github.com/protViz/protViz/") | |
11132 | (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") | |
11133 | (description | |
11134 | "This package helps with quality checks, visualizations and analysis of | |
11135 | mass spectrometry data, coming from proteomics experiments. The package is | |
11136 | developed, tested and used at the Functional Genomics Center Zurich, where it | |
11137 | is used mainly for prototyping, teaching, and having fun with proteomics data. | |
11138 | But it can also be used to do data analysis for small scale data sets.") | |
11139 | (license license:gpl3))) | |
7aeec0cf RW |
11140 | |
11141 | (define-public r-cmprsk | |
11142 | (package | |
11143 | (name "r-cmprsk") | |
10dbc3fc | 11144 | (version "2.2-8") |
7aeec0cf RW |
11145 | (source |
11146 | (origin | |
11147 | (method url-fetch) | |
11148 | (uri (cran-uri "cmprsk" version)) | |
11149 | (sha256 | |
11150 | (base32 | |
10dbc3fc | 11151 | "1nacbzx950ygaqgnj0949skhwpzar5i3xlscd44jsimk2gsppx6z")))) |
7aeec0cf RW |
11152 | (build-system r-build-system) |
11153 | (propagated-inputs | |
11154 | `(("r-survival" ,r-survival))) | |
11155 | (native-inputs | |
11156 | `(("gfortran" ,gfortran))) | |
11157 | (home-page "https://cran.r-project.org/web/packages/cmprsk") | |
11158 | (synopsis "Subdistribution analysis of competing risks") | |
11159 | (description | |
11160 | "This package provides tool for estimation, testing and regression | |
11161 | modeling of subdistribution functions in competing risks, as described in | |
11162 | Gray (1988), A class of K-sample tests for comparing the cumulative incidence | |
11163 | of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), | |
11164 | A proportional hazards model for the subdistribution of a competing risk, | |
11165 | JASA, 94:496-509.") | |
11166 | (license license:gpl2+))) | |
728012da RW |
11167 | |
11168 | (define-public r-etm | |
11169 | (package | |
11170 | (name "r-etm") | |
9a749cad | 11171 | (version "1.0.5") |
728012da RW |
11172 | (source |
11173 | (origin | |
11174 | (method url-fetch) | |
11175 | (uri (cran-uri "etm" version)) | |
11176 | (sha256 | |
11177 | (base32 | |
9a749cad | 11178 | "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677")))) |
728012da RW |
11179 | (build-system r-build-system) |
11180 | (propagated-inputs | |
11181 | `(("r-data-table" ,r-data-table) | |
11182 | ("r-lattice" ,r-lattice) | |
11183 | ("r-rcpp" ,r-rcpp) | |
11184 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
11185 | ("r-survival" ,r-survival))) | |
11186 | (home-page "https://cran.r-project.org/web/packages/etm") | |
11187 | (synopsis "Empirical transition matrix") | |
11188 | (description | |
11189 | "The @dfn{empirical transition matrix} (etm) package permits to estimate | |
11190 | the matrix of transition probabilities for any time-inhomogeneous multistate | |
11191 | model with finite state space using the Aalen-Johansen estimator.") | |
11192 | (license license:expat))) | |
17932a0f RW |
11193 | |
11194 | (define-public r-epi | |
11195 | (package | |
11196 | (name "r-epi") | |
42a8b01d | 11197 | (version "2.38") |
17932a0f RW |
11198 | (source |
11199 | (origin | |
11200 | (method url-fetch) | |
11201 | (uri (cran-uri "Epi" version)) | |
11202 | (sha256 | |
11203 | (base32 | |
42a8b01d | 11204 | "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd")))) |
17932a0f RW |
11205 | (properties `((upstream-name . "Epi"))) |
11206 | (build-system r-build-system) | |
11207 | (propagated-inputs | |
11208 | `(("r-cmprsk" ,r-cmprsk) | |
11209 | ("r-data-table" ,r-data-table) | |
11210 | ("r-etm" ,r-etm) | |
11211 | ("r-mass" ,r-mass) | |
11212 | ("r-matrix" ,r-matrix) | |
11213 | ("r-mgcv" ,r-mgcv) | |
11214 | ("r-numderiv" ,r-numderiv) | |
11215 | ("r-plyr" ,r-plyr) | |
11216 | ("r-survival" ,r-survival) | |
11217 | ("r-zoo" ,r-zoo))) | |
11218 | (home-page "http://BendixCarstensen.com/Epi/") | |
11219 | (synopsis "Statistical analysis in epidemiology") | |
11220 | (description | |
11221 | "This package provides functions for demographic and epidemiological | |
11222 | analysis in the Lexis diagram, i.e. register and cohort follow-up data, in | |
11223 | particular representation, manipulation and simulation of multistate data - | |
11224 | the Lexis suite of functions, which includes interfaces to the @code{mstate}, | |
11225 | @code{etm} and @code{cmprsk} packages. It also contains functions for | |
11226 | Age-Period-Cohort and Lee-Carter modeling and a function for interval censored | |
11227 | data and some useful functions for tabulation and plotting, as well as a | |
11228 | number of epidemiological data sets.") | |
11229 | (license license:gpl2))) | |
879a1520 RW |
11230 | |
11231 | (define-public r-ppls | |
11232 | (package | |
11233 | (name "r-ppls") | |
11234 | (version "1.6-1.1") | |
11235 | (source | |
11236 | (origin | |
11237 | (method url-fetch) | |
11238 | (uri (cran-uri "ppls" version)) | |
11239 | (sha256 | |
11240 | (base32 | |
11241 | "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) | |
11242 | (build-system r-build-system) | |
11243 | (propagated-inputs `(("r-mass" ,r-mass))) | |
11244 | (home-page "https://cran.r-project.org/web/packages/ppls") | |
11245 | (synopsis "Penalized partial least squares") | |
11246 | (description | |
11247 | "This package contains linear and nonlinear regression methods based on | |
11248 | partial least squares and penalization techniques. Model parameters are | |
11249 | selected via cross-validation, and confidence intervals ans tests for the | |
11250 | regression coefficients can be conducted via jackknifing.") | |
11251 | (license license:gpl2+))) | |
0af9616d RW |
11252 | |
11253 | (define-public r-huge | |
11254 | (package | |
11255 | (name "r-huge") | |
cd3ba9c8 | 11256 | (version "1.3.3") |
0af9616d RW |
11257 | (source |
11258 | (origin | |
11259 | (method url-fetch) | |
11260 | (uri (cran-uri "huge" version)) | |
11261 | (sha256 | |
11262 | (base32 | |
cd3ba9c8 | 11263 | "18f8w4hdp9fdi2k5ip6fnrn5z47w4ybgxs2m6a7jdvd2v4wfdr69")))) |
0af9616d RW |
11264 | (build-system r-build-system) |
11265 | (propagated-inputs | |
11266 | `(("r-igraph" ,r-igraph) | |
0af9616d | 11267 | ("r-mass" ,r-mass) |
7706a98c RW |
11268 | ("r-matrix" ,r-matrix) |
11269 | ("r-rcpp" ,r-rcpp) | |
11270 | ("r-rcppeigen" ,r-rcppeigen))) | |
0af9616d RW |
11271 | (home-page "https://cran.r-project.org/web/packages/huge") |
11272 | (synopsis "High-dimensional undirected graph estimation") | |
11273 | (description | |
11274 | "This package provides a general framework for high-dimensional | |
11275 | undirected graph estimation. It integrates data preprocessing, neighborhood | |
11276 | screening, graph estimation, and model selection techniques into a pipeline.") | |
11277 | (license license:gpl2))) | |
39274ab4 RW |
11278 | |
11279 | (define-public r-parcor | |
11280 | (package | |
11281 | (name "r-parcor") | |
11282 | (version "0.2-6") | |
11283 | (source | |
11284 | (origin | |
11285 | (method url-fetch) | |
11286 | (uri (cran-uri "parcor" version)) | |
11287 | (sha256 | |
11288 | (base32 | |
11289 | "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) | |
11290 | (build-system r-build-system) | |
11291 | (propagated-inputs | |
11292 | `(("r-epi" ,r-epi) | |
11293 | ("r-genenet" ,r-genenet) | |
11294 | ("r-glmnet" ,r-glmnet) | |
11295 | ("r-mass" ,r-mass) | |
11296 | ("r-ppls" ,r-ppls))) | |
11297 | (home-page "https://cran.r-project.org/web/packages/parcor") | |
11298 | (synopsis "Regularized estimation of partial correlation matrices") | |
11299 | (description | |
11300 | "This package estimates the matrix of partial correlations based on | |
11301 | different regularized regression methods: lasso, adaptive lasso, PLS, and | |
11302 | Ridge Regression. In addition, the package provides model selection for | |
11303 | lasso, adaptive lasso and Ridge regression based on cross-validation.") | |
11304 | (license license:gpl2+))) | |
cba08f60 RW |
11305 | |
11306 | (define-public r-mcmc | |
11307 | (package | |
11308 | (name "r-mcmc") | |
ae7e6f06 | 11309 | (version "0.9-6") |
cba08f60 RW |
11310 | (source |
11311 | (origin | |
11312 | (method url-fetch) | |
11313 | (uri (cran-uri "mcmc" version)) | |
11314 | (sha256 | |
11315 | (base32 | |
ae7e6f06 | 11316 | "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4")))) |
cba08f60 RW |
11317 | (build-system r-build-system) |
11318 | (home-page "http://www.stat.umn.edu/geyer/mcmc/") | |
11319 | (synopsis "Markov chain Monte Carlo") | |
11320 | (description | |
11321 | "This package simulates continuous distributions of random vectors using | |
11322 | @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R | |
11323 | function that evaluates the log unnormalized density. Algorithms are random | |
11324 | walk Metropolis algorithm (function @code{metrop}), simulated | |
11325 | tempering (function @code{temper}), and morphometric random walk | |
11326 | Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity | |
11327 | by change of variable.") | |
11328 | (license license:expat))) | |
cf4cd8bc RW |
11329 | |
11330 | (define-public r-listenv | |
11331 | (package | |
11332 | (name "r-listenv") | |
11333 | (version "0.7.0") | |
11334 | (source | |
11335 | (origin | |
11336 | (method url-fetch) | |
11337 | (uri (cran-uri "listenv" version)) | |
11338 | (sha256 | |
11339 | (base32 | |
11340 | "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1")))) | |
11341 | (build-system r-build-system) | |
11342 | (native-inputs | |
11343 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
11344 | (home-page "https://github.com/HenrikBengtsson/listenv") | |
11345 | (synopsis "Environments behaving (almost) as lists") | |
11346 | (description | |
11347 | "This package implements list environments. List environments are | |
11348 | environments that have list-like properties. For instance, the elements of a | |
11349 | list environment are ordered and can be accessed and iterated over using index | |
11350 | subsetting.") | |
11351 | (license license:lgpl2.1+))) | |
226294a4 RW |
11352 | |
11353 | (define-public r-globals | |
11354 | (package | |
11355 | (name "r-globals") | |
11356 | (version "0.12.4") | |
11357 | (source | |
11358 | (origin | |
11359 | (method url-fetch) | |
11360 | (uri (cran-uri "globals" version)) | |
11361 | (sha256 | |
11362 | (base32 | |
11363 | "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br")))) | |
11364 | (build-system r-build-system) | |
11365 | (propagated-inputs | |
11366 | `(("r-codetools" ,r-codetools))) | |
11367 | (home-page "https://github.com/HenrikBengtsson/globals") | |
11368 | (synopsis "Identify global objects in R expressions") | |
11369 | (description | |
11370 | "This package provides tools to identify global (\"unknown\" or \"free\") | |
11371 | objects in R expressions by code inspection using various strategies, e.g. | |
11372 | conservative or liberal. The objective of this package is to make it as | |
11373 | simple as possible to identify global objects for the purpose of exporting | |
11374 | them in distributed compute environments.") | |
11375 | (license license:lgpl2.1+))) | |
b3080cdd RW |
11376 | |
11377 | (define-public r-future | |
11378 | (package | |
11379 | (name "r-future") | |
d5d631b6 | 11380 | (version "1.14.0") |
b3080cdd RW |
11381 | (source |
11382 | (origin | |
11383 | (method url-fetch) | |
11384 | (uri (cran-uri "future" version)) | |
11385 | (sha256 | |
11386 | (base32 | |
d5d631b6 | 11387 | "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa")))) |
b3080cdd RW |
11388 | (build-system r-build-system) |
11389 | (propagated-inputs | |
11390 | `(("r-digest" ,r-digest) | |
11391 | ("r-globals" ,r-globals) | |
11392 | ("r-listenv" ,r-listenv))) | |
11393 | (native-inputs | |
11394 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
11395 | (home-page "https://github.com/HenrikBengtsson/future") | |
11396 | (synopsis "Unified parallel and distributed processing in R") | |
11397 | (description | |
11398 | "The purpose of this package is to provide a lightweight and unified | |
11399 | Future API for sequential and parallel processing of R expression via futures. | |
11400 | This package implements sequential, multicore, multisession, and cluster | |
11401 | futures. With these, R expressions can be evaluated on the local machine, in | |
11402 | parallel a set of local machines, or distributed on a mix of local and remote | |
11403 | machines. Extensions to this package implement additional backends for | |
11404 | processing futures via compute cluster schedulers etc. Because of its unified | |
11405 | API, there is no need to modify any code in order to switch from sequential on | |
11406 | the local machine to, say, distributed processing on a remote compute cluster.") | |
11407 | (license license:lgpl2.1+))) | |
9680047c RW |
11408 | |
11409 | (define-public r-future-apply | |
11410 | (package | |
11411 | (name "r-future-apply") | |
d42fb7d2 | 11412 | (version "1.3.0") |
9680047c RW |
11413 | (source |
11414 | (origin | |
11415 | (method url-fetch) | |
11416 | (uri (cran-uri "future.apply" version)) | |
11417 | (sha256 | |
11418 | (base32 | |
d42fb7d2 | 11419 | "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33")))) |
9680047c RW |
11420 | (properties `((upstream-name . "future.apply"))) |
11421 | (build-system r-build-system) | |
11422 | (propagated-inputs | |
11423 | `(("r-future" ,r-future) | |
11424 | ("r-globals" ,r-globals))) | |
11425 | (native-inputs | |
11426 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
11427 | (home-page "https://github.com/HenrikBengtsson/future.apply") | |
11428 | (synopsis "Apply function to elements in parallel using futures") | |
11429 | (description | |
11430 | "This package provides implementations of @code{apply()}, | |
11431 | @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()}, | |
11432 | @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that | |
11433 | can be resolved using any future-supported backend, e.g. parallel on the local | |
11434 | machine or distributed on a compute cluster.") | |
11435 | (license license:gpl2+))) | |
867e2b1b RW |
11436 | |
11437 | (define-public r-rsvd | |
11438 | (package | |
11439 | (name "r-rsvd") | |
eebd93eb | 11440 | (version "1.0.2") |
867e2b1b RW |
11441 | (source |
11442 | (origin | |
11443 | (method url-fetch) | |
11444 | (uri (cran-uri "rsvd" version)) | |
11445 | (sha256 | |
11446 | (base32 | |
eebd93eb | 11447 | "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8")))) |
867e2b1b RW |
11448 | (build-system r-build-system) |
11449 | (propagated-inputs | |
11450 | `(("r-matrix" ,r-matrix))) | |
11451 | (home-page "https://github.com/erichson/rSVD") | |
11452 | (synopsis "Randomized singular value decomposition") | |
11453 | (description | |
11454 | "Low-rank matrix decompositions are fundamental tools and widely used for | |
11455 | data analysis, dimension reduction, and data compression. Classically, highly | |
11456 | accurate deterministic matrix algorithms are used for this task. However, the | |
11457 | emergence of large-scale data has severely challenged our computational | |
11458 | ability to analyze big data. The concept of randomness has been demonstrated | |
11459 | as an effective strategy to quickly produce approximate answers to familiar | |
11460 | problems such as the @dfn{singular value decomposition} (SVD). This package | |
11461 | provides several randomized matrix algorithms such as the randomized singular | |
11462 | value decomposition (@code{rsvd}), randomized principal component | |
11463 | analysis (@code{rpca}), randomized robust principal component | |
11464 | analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}), | |
11465 | and the randomized CUR decomposition (@code{rcur}). In addition several plot | |
11466 | functions are provided.") | |
11467 | (license license:gpl3+))) | |
14afee3e BG |
11468 | |
11469 | (define-public r-sloop | |
11470 | (package | |
11471 | (name "r-sloop") | |
11472 | (version "1.0.1") | |
11473 | (source | |
11474 | (origin | |
11475 | (method url-fetch) | |
11476 | (uri (cran-uri "sloop" version)) | |
11477 | (sha256 | |
11478 | (base32 | |
11479 | "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j")))) | |
11480 | (build-system r-build-system) | |
11481 | (propagated-inputs | |
11482 | `(("r-codetools" ,r-codetools) | |
11483 | ("r-crayon" ,r-crayon) | |
11484 | ("r-purrr" ,r-purrr) | |
11485 | ("r-rlang" ,r-rlang) | |
11486 | ("r-tibble" ,r-tibble))) | |
11487 | (home-page "https://github.com/r-lib/sloop") | |
11488 | (synopsis "Helpers for object-oriented programming in R") | |
11489 | (description | |
11490 | "This package provides a collection of helper functions designed to | |
11491 | help you to better understand object oriented programming in R, particularly | |
11492 | using @code{S3}.") | |
11493 | (license license:gpl3))) | |
4254b480 RW |
11494 | |
11495 | (define-public r-capushe | |
11496 | (package | |
11497 | (name "r-capushe") | |
11498 | (version "1.1.1") | |
11499 | (source | |
11500 | (origin | |
11501 | (method url-fetch) | |
11502 | (uri (cran-uri "capushe" version)) | |
11503 | (sha256 | |
11504 | (base32 | |
11505 | "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc")))) | |
11506 | (build-system r-build-system) | |
11507 | (propagated-inputs `(("r-mass" ,r-mass))) | |
11508 | (home-page "https://cran.r-project.org/web/packages/capushe/index.html") | |
49369a01 | 11509 | (synopsis "Calibrating penalties using slope heuristics") |
4254b480 RW |
11510 | (description |
11511 | "This package provides tools for the calibration of penalized criteria | |
11512 | for model selection. The calibration methods available are based on the slope | |
11513 | heuristics.") | |
11514 | (license license:gpl2+))) | |
c691c607 RW |
11515 | |
11516 | (define-public r-dorng | |
11517 | (package | |
11518 | (name "r-dorng") | |
11519 | (version "1.7.1") | |
11520 | (source | |
11521 | (origin | |
11522 | (method url-fetch) | |
11523 | (uri (cran-uri "doRNG" version)) | |
11524 | (sha256 | |
11525 | (base32 | |
11526 | "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7")))) | |
11527 | (properties `((upstream-name . "doRNG"))) | |
11528 | (build-system r-build-system) | |
11529 | (propagated-inputs | |
11530 | `(("r-foreach" ,r-foreach) | |
11531 | ("r-iterators" ,r-iterators) | |
11532 | ("r-pkgmaker" ,r-pkgmaker) | |
11533 | ("r-rngtools" ,r-rngtools))) | |
11534 | (home-page "https://renozao.github.io/doRNG/") | |
11535 | (synopsis "Generic reproducible parallel backend for foreach loops") | |
11536 | (description | |
11537 | "This package provides functions to perform reproducible parallel | |
11538 | @code{foreach} loops, using independent random streams as generated by | |
11539 | L'Ecuyer's combined multiple-recursive generator. It enables to easily | |
11540 | convert standard @code{%dopar%} loops into fully reproducible loops, | |
11541 | independently of the number of workers, the task scheduling strategy, or the | |
11542 | chosen parallel environment and associated foreach backend.") | |
11543 | (license license:gpl2+))) | |
f3233bee RW |
11544 | |
11545 | (define-public r-blockmodeling | |
11546 | (package | |
11547 | (name "r-blockmodeling") | |
11548 | (version "0.3.4") | |
11549 | (source | |
11550 | (origin | |
11551 | (method url-fetch) | |
11552 | (uri (cran-uri "blockmodeling" version)) | |
11553 | (sha256 | |
11554 | (base32 | |
11555 | "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2")))) | |
11556 | (build-system r-build-system) | |
11557 | (propagated-inputs | |
11558 | `(("r-doparallel" ,r-doparallel) | |
11559 | ("r-dorng" ,r-dorng) | |
11560 | ("r-foreach" ,r-foreach) | |
11561 | ("r-matrix" ,r-matrix))) | |
11562 | (native-inputs `(("gfortran" ,gfortran))) | |
11563 | (home-page "https://cran.r-project.org/web/packages/blockmodeling") | |
11564 | (synopsis "Generalized and classical blockmodeling of valued networks") | |
11565 | (description | |
11566 | "This package is primarily meant as an implementation of generalized | |
11567 | blockmodeling for valued networks. In addition, measures of similarity or | |
11568 | dissimilarity based on structural equivalence and regular equivalence (REGE | |
11569 | algorithms) can be computed and partitioned matrices can be plotted.") | |
11570 | (license license:gpl2+))) | |
4af186a9 RW |
11571 | |
11572 | (define-public r-upsetr | |
11573 | (package | |
11574 | (name "r-upsetr") | |
20656a02 | 11575 | (version "1.4.0") |
4af186a9 RW |
11576 | (source |
11577 | (origin | |
11578 | (method url-fetch) | |
11579 | (uri (cran-uri "UpSetR" version)) | |
11580 | (sha256 | |
11581 | (base32 | |
20656a02 | 11582 | "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im")))) |
4af186a9 RW |
11583 | (properties `((upstream-name . "UpSetR"))) |
11584 | (build-system r-build-system) | |
11585 | (propagated-inputs | |
11586 | `(("r-ggplot2" ,r-ggplot2) | |
11587 | ("r-gridextra" ,r-gridextra) | |
11588 | ("r-plyr" ,r-plyr) | |
11589 | ("r-scales" ,r-scales))) | |
11590 | (home-page "https://github.com/hms-dbmi/UpSetR") | |
11591 | (synopsis "Visualize intersecting sets") | |
11592 | (description | |
11593 | "This package provides a more scalable alternative to Venn and Euler | |
11594 | diagrams for visualizing intersecting sets. Create visualizations of | |
11595 | intersecting sets using a novel matrix design, along with visualizations of | |
11596 | several common set, element and attribute related tasks.") | |
11597 | (license license:expat))) | |
1901a532 | 11598 | |
849350fb RW |
11599 | ;; This package includes a JavaScript file, which is not minified. When |
11600 | ;; upgrading please check that there are no new minified JavaScript files. | |
11601 | (define-public r-shinybs | |
11602 | (package | |
11603 | (name "r-shinybs") | |
11604 | (version "0.61") | |
11605 | (source | |
11606 | (origin | |
11607 | (method url-fetch) | |
11608 | (uri (cran-uri "shinyBS" version)) | |
11609 | (sha256 | |
11610 | (base32 | |
11611 | "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji")))) | |
11612 | (properties `((upstream-name . "shinyBS"))) | |
11613 | (build-system r-build-system) | |
11614 | ;; The tests spawn Shiny browser apps. They cannot be run | |
11615 | ;; non-interactively. | |
11616 | (arguments '(#:tests? #f)) | |
11617 | (propagated-inputs | |
11618 | `(("r-htmltools" ,r-htmltools) | |
11619 | ("r-shiny" ,r-shiny))) | |
11620 | (home-page "https://ebailey78.github.io/shinyBS/") | |
11621 | (synopsis "Twitter Bootstrap components for Shiny") | |
11622 | (description | |
11623 | "This package adds additional Twitter Bootstrap components to Shiny.") | |
11624 | (license license:gpl3))) | |
11625 | ||
1901a532 RW |
11626 | (define-public r-outliers |
11627 | (package | |
11628 | (name "r-outliers") | |
11629 | (version "0.14") | |
11630 | (source | |
11631 | (origin | |
11632 | (method url-fetch) | |
11633 | (uri (cran-uri "outliers" version)) | |
11634 | (sha256 | |
11635 | (base32 | |
11636 | "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn")))) | |
11637 | (build-system r-build-system) | |
11638 | (home-page "https://cran.r-project.org/web/packages/outliers/index.html") | |
11639 | (synopsis "Tests for outliers") | |
11640 | (description | |
11641 | "This package provides a collection of some tests commonly used for | |
11642 | identifying outliers.") | |
11643 | (license license:gpl2+))) | |
8cd3f49d RW |
11644 | |
11645 | (define-public r-bayesm | |
11646 | (package | |
11647 | (name "r-bayesm") | |
01629c66 | 11648 | (version "3.1-3") |
8cd3f49d RW |
11649 | (source |
11650 | (origin | |
11651 | (method url-fetch) | |
11652 | (uri (cran-uri "bayesm" version)) | |
11653 | (sha256 | |
11654 | (base32 | |
01629c66 | 11655 | "041ach2f2vrqzd5kz17v7wmkjz6z8cjjihpk4qvczm4cr9z85r2i")))) |
8cd3f49d RW |
11656 | (build-system r-build-system) |
11657 | (propagated-inputs | |
11658 | `(("r-rcpp" ,r-rcpp) | |
11659 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
11660 | (home-page "http://www.perossi.org/home/bsm-1") | |
11661 | (synopsis "Bayesian inference for marketing/micro-econometrics") | |
11662 | (description | |
11663 | "This package covers many important models used in marketing and | |
11664 | micro-econometrics applications, including Bayes Regression (univariate or | |
11665 | multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and | |
11666 | Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), | |
11667 | Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate | |
11668 | Mixtures of Normals (including clustering), Dirichlet Process Prior Density | |
11669 | Estimation with normal base, Hierarchical Linear Models with normal prior and | |
11670 | covariates, Hierarchical Linear Models with a mixture of normals prior and | |
11671 | covariates, Hierarchical Multinomial Logits with a mixture of normals prior | |
11672 | and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior | |
11673 | and covariates, Hierarchical Negative Binomial Regression Models, Bayesian | |
11674 | analysis of choice-based conjoint data, Bayesian treatment of linear | |
11675 | instrumental variables models, Analysis of Multivariate Ordinal survey data | |
11676 | with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random | |
11677 | Coefficient Logit Models.") | |
11678 | (license license:gpl2+))) | |
262ab4b1 RW |
11679 | |
11680 | (define-public r-tensora | |
11681 | (package | |
11682 | (name "r-tensora") | |
11683 | (version "0.36.1") | |
11684 | (source | |
11685 | (origin | |
11686 | (method url-fetch) | |
11687 | (uri (cran-uri "tensorA" version)) | |
11688 | (sha256 | |
11689 | (base32 | |
11690 | "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7")))) | |
11691 | (properties `((upstream-name . "tensorA"))) | |
11692 | (build-system r-build-system) | |
11693 | (home-page "http://www.stat.boogaart.de/tensorA") | |
11694 | (synopsis "Advanced tensor arithmetic with named indices") | |
11695 | (description | |
11696 | "This package provides convenience functions for advanced linear algebra | |
11697 | with tensors and computation with datasets of tensors on a higher level | |
11698 | abstraction. It includes Einstein and Riemann summing conventions, dragging, | |
11699 | co- and contravariate indices, and parallel computations on sequences of | |
11700 | tensors.") | |
11701 | (license license:gpl2+))) | |
7d779142 RW |
11702 | |
11703 | (define-public r-rarpack | |
11704 | (package | |
11705 | (name "r-rarpack") | |
11706 | (version "0.11-0") | |
11707 | (source | |
11708 | (origin | |
11709 | (method url-fetch) | |
11710 | (uri (cran-uri "rARPACK" version)) | |
11711 | (sha256 | |
11712 | (base32 | |
11713 | "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) | |
11714 | (properties `((upstream-name . "rARPACK"))) | |
11715 | (build-system r-build-system) | |
11716 | (propagated-inputs `(("r-rspectra" ,r-rspectra))) | |
11717 | (home-page "https://github.com/yixuan/rARPACK") | |
11718 | (synopsis "Solvers for large scale eigenvalue and SVD problems") | |
11719 | (description | |
11720 | "This package was previously an R wrapper of the ARPACK library, and now | |
11721 | a shell of the R package RSpectra, an R interface to the Spectra library for | |
11722 | solving large scale eigenvalue/vector problems. The current version of | |
11723 | rARPACK simply imports and exports the functions provided by RSpectra. New | |
11724 | users of rARPACK are advised to switch to the RSpectra package.") | |
11725 | (license license:bsd-3))) | |
5fde35b3 RW |
11726 | |
11727 | (define-public r-compositions | |
11728 | (package | |
11729 | (name "r-compositions") | |
11730 | (version "1.40-2") | |
11731 | (source | |
11732 | (origin | |
11733 | (method url-fetch) | |
11734 | (uri (cran-uri "compositions" version)) | |
11735 | (sha256 | |
11736 | (base32 | |
11737 | "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i")))) | |
11738 | (build-system r-build-system) | |
11739 | (propagated-inputs | |
11740 | `(("r-bayesm" ,r-bayesm) | |
11741 | ("r-energy" ,r-energy) | |
11742 | ("r-robustbase" ,r-robustbase) | |
11743 | ("r-tensora" ,r-tensora))) | |
11744 | (home-page "http://www.stat.boogaart.de/compositions") | |
11745 | (synopsis "Compositional data analysis") | |
11746 | (description | |
11747 | "This package provides functions for the consistent analysis of | |
11748 | compositional data (e.g. portions of substances) and positive | |
11749 | numbers (e.g. concentrations).") | |
11750 | (license license:gpl2+))) | |
5f673e2c RW |
11751 | |
11752 | (define-public r-cobs | |
11753 | (package | |
11754 | (name "r-cobs") | |
11755 | (version "1.3-3") | |
11756 | (source | |
11757 | (origin | |
11758 | (method url-fetch) | |
11759 | (uri (cran-uri "cobs" version)) | |
11760 | (sha256 | |
11761 | (base32 | |
11762 | "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb")))) | |
11763 | (build-system r-build-system) | |
11764 | (propagated-inputs | |
11765 | `(("r-quantreg" ,r-quantreg) | |
11766 | ("r-sparsem" ,r-sparsem))) | |
11767 | (home-page "https://cran.r-project.org/web/packages/cobs") | |
11768 | (synopsis "Constrained B-Splines (sparse matrix based)") | |
11769 | (description | |
11770 | "This package provides qualitatively constrained (regression) smoothing | |
11771 | splines via linear programming and sparse matrices.") | |
11772 | (license license:gpl2+))) | |
c60e3e10 RW |
11773 | |
11774 | (define-public r-drimpute | |
11775 | (package | |
11776 | (name "r-drimpute") | |
11777 | (version "1.0") | |
11778 | (source | |
11779 | (origin | |
11780 | (method url-fetch) | |
11781 | (uri (cran-uri "DrImpute" version)) | |
11782 | (sha256 | |
11783 | (base32 | |
11784 | "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b")))) | |
11785 | (properties `((upstream-name . "DrImpute"))) | |
11786 | (build-system r-build-system) | |
11787 | (propagated-inputs | |
11788 | `(("r-rcpp" ,r-rcpp) | |
11789 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
11790 | (home-page "https://github.com/ikwak2/DrImpute") | |
11791 | (synopsis "Imputing dropout events in single-cell RNA-Seq data") | |
11792 | (description | |
11793 | "This is an R package for imputing dropout events. Many statistical | |
11794 | methods in cell type identification, visualization and lineage reconstruction | |
11795 | do not account for dropout events. DrImpute can improve the performance of | |
11796 | such software by imputing dropout events.") | |
11797 | (license license:gpl3))) | |
061a4b68 RW |
11798 | |
11799 | (define-public r-gamlss-dist | |
11800 | (package | |
11801 | (name "r-gamlss-dist") | |
ecf4ccb9 | 11802 | (version "5.1-4") |
061a4b68 RW |
11803 | (source |
11804 | (origin | |
11805 | (method url-fetch) | |
11806 | (uri (cran-uri "gamlss.dist" version)) | |
11807 | (sha256 | |
11808 | (base32 | |
ecf4ccb9 | 11809 | "0zi87lgigr83l35zqq1y1g4cdq6ssjamripzz7yis74aznh6qg1l")))) |
061a4b68 RW |
11810 | (properties `((upstream-name . "gamlss.dist"))) |
11811 | (build-system r-build-system) | |
11812 | (propagated-inputs `(("r-mass" ,r-mass))) | |
11813 | (home-page "http://www.gamlss.org/") | |
11814 | (synopsis "Distributions for Generalized Additive Models for location scale and shape") | |
11815 | (description | |
11816 | "This package provides a set of distributions which can be used for | |
11817 | modelling the response variables in Generalized Additive Models for Location | |
11818 | Scale and Shape. The distributions can be continuous, discrete or mixed | |
11819 | distributions. Extra distributions can be created, by transforming, any | |
11820 | continuous distribution defined on the real line, to a distribution defined on | |
11821 | ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} | |
11822 | transformation, respectively.") | |
11823 | ;; Either version of the GPL. | |
11824 | (license (list license:gpl2 license:gpl3)))) | |
4fd99443 | 11825 | |
5146a24e RW |
11826 | ;; This package includes JavaScript files, which are not minified. When |
11827 | ;; upgrading please check that there are no new minified JavaScript files. | |
11828 | (define-public r-shinyjs | |
11829 | (package | |
11830 | (name "r-shinyjs") | |
11831 | (version "1.0") | |
11832 | (source | |
11833 | (origin | |
11834 | (method url-fetch) | |
11835 | (uri (cran-uri "shinyjs" version)) | |
11836 | (sha256 | |
11837 | (base32 | |
11838 | "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8")))) | |
11839 | (build-system r-build-system) | |
11840 | (propagated-inputs | |
11841 | `(("r-digest" ,r-digest) | |
11842 | ("r-htmltools" ,r-htmltools) | |
11843 | ("r-jsonlite" ,r-jsonlite) | |
11844 | ("r-shiny" ,r-shiny))) | |
11845 | (home-page "https://deanattali.com/shinyjs") | |
11846 | (synopsis "Improve the user experience of your Shiny apps") | |
11847 | (description | |
11848 | "Perform common useful JavaScript operations in Shiny apps that will | |
11849 | greatly improve your apps without having to know any JavaScript. Examples | |
11850 | include: hiding an element, disabling an input, resetting an input back to its | |
11851 | original value, delaying code execution by a few seconds, and many more useful | |
11852 | functions for both the end user and the developer. Shinyjs can also be used | |
11853 | to easily call your own custom JavaScript functions from R.") | |
11854 | (license license:agpl3+))) | |
11855 | ||
c27927db RW |
11856 | ;; This package includes minified JavaScript files. When upgrading please |
11857 | ;; check that there are no new minified JavaScript files. | |
11858 | (define-public r-colourpicker | |
11859 | (package | |
11860 | (name "r-colourpicker") | |
11861 | (version "1.0") | |
11862 | (source | |
11863 | (origin | |
11864 | (method url-fetch) | |
11865 | (uri (cran-uri "colourpicker" version)) | |
11866 | (sha256 | |
11867 | (base32 | |
11868 | "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi")))) | |
11869 | (build-system r-build-system) | |
11870 | (arguments | |
11871 | `(#:modules ((guix build utils) | |
11872 | (guix build r-build-system) | |
11873 | (srfi srfi-1) | |
11874 | (ice-9 popen)) | |
11875 | #:phases | |
11876 | (modify-phases %standard-phases | |
11877 | (add-after 'unpack 'process-javascript | |
11878 | (lambda* (#:key inputs #:allow-other-keys) | |
11879 | (with-directory-excursion "inst" | |
11880 | (call-with-values | |
11881 | (lambda () | |
11882 | (unzip2 | |
11883 | `((,(assoc-ref inputs "js-salvattore") | |
11884 | "examples/colourInput/www/salvattore.min.js") | |
11885 | (,(assoc-ref inputs "js-jquery") | |
11886 | "htmlwidgets/lib/jquery/jquery.min.js") | |
11887 | ("www/shared/colourpicker/js/colourpicker.js" | |
11888 | "www/shared/colourpicker/js/colourpicker.min.js")))) | |
11889 | (lambda (sources targets) | |
11890 | (for-each (lambda (source target) | |
11891 | (format #t "Processing ~a --> ~a~%" | |
11892 | source target) | |
11893 | (delete-file target) | |
11894 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
11895 | (call-with-output-file target | |
11896 | (lambda (port) | |
11897 | (dump-port minified port))))) | |
11898 | sources targets)))) | |
11899 | #t))))) | |
11900 | (propagated-inputs | |
11901 | `(("r-ggplot2" ,r-ggplot2) | |
11902 | ("r-htmltools" ,r-htmltools) | |
11903 | ("r-htmlwidgets" ,r-htmlwidgets) | |
11904 | ("r-jsonlite" ,r-jsonlite) | |
11905 | ("r-miniui" ,r-miniui) | |
11906 | ("r-shiny" ,r-shiny) | |
11907 | ("r-shinyjs" ,r-shinyjs))) | |
11908 | (native-inputs | |
11909 | `(("uglify-js" ,uglify-js) | |
11910 | ("js-jquery" | |
11911 | ,(origin | |
11912 | (method url-fetch) | |
11913 | (uri "https://code.jquery.com/jquery-3.3.1.js") | |
11914 | (sha256 | |
11915 | (base32 | |
11916 | "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) | |
11917 | ("js-salvattore" | |
11918 | ,(origin | |
11919 | (method url-fetch) | |
11920 | (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js") | |
11921 | (sha256 | |
11922 | (base32 | |
11923 | "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5")))))) | |
11924 | (home-page "https://github.com/daattali/colourpicker") | |
11925 | (synopsis "Color picker tool for Shiny and for selecting colors in plots") | |
11926 | (description | |
11927 | "This package provides a color picker that can be used as an input in | |
11928 | Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, | |
11929 | custom color palettes, and many more options. A plot color helper tool is | |
11930 | available as an RStudio Addin, which helps you pick colors to use in your | |
11931 | plots. A more generic color picker RStudio Addin is also provided to let you | |
11932 | select colors to use in your R code.") | |
11933 | (license license:expat))) | |
11934 | ||
30f53ec8 RW |
11935 | (define-public r-ggextra |
11936 | (package | |
11937 | (name "r-ggextra") | |
e31eb738 | 11938 | (version "0.9") |
30f53ec8 RW |
11939 | (source |
11940 | (origin | |
11941 | (method url-fetch) | |
11942 | (uri (cran-uri "ggExtra" version)) | |
11943 | (sha256 | |
11944 | (base32 | |
e31eb738 | 11945 | "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj")))) |
30f53ec8 RW |
11946 | (properties `((upstream-name . "ggExtra"))) |
11947 | (build-system r-build-system) | |
11948 | (propagated-inputs | |
11949 | `(("r-colourpicker" ,r-colourpicker) | |
11950 | ("r-ggplot2" ,r-ggplot2) | |
11951 | ("r-gtable" ,r-gtable) | |
11952 | ("r-miniui" ,r-miniui) | |
e31eb738 | 11953 | ("r-r6" ,r-r6) |
30f53ec8 RW |
11954 | ("r-scales" ,r-scales) |
11955 | ("r-shiny" ,r-shiny) | |
11956 | ("r-shinyjs" ,r-shinyjs))) | |
11957 | (home-page "https://github.com/daattali/ggExtra") | |
11958 | (synopsis "Marginal histograms for ggplot2 and other enhancements") | |
11959 | (description | |
11960 | "This package is a collection of functions and layers to enhance ggplot2. | |
11961 | The flagship function is @code{ggMarginal()}, which can be used to add | |
11962 | marginal histograms/boxplots/density plots to ggplot2 scatterplots.") | |
11963 | (license license:expat))) | |
11964 | ||
4fd99443 RW |
11965 | (define-public r-minpack-lm |
11966 | (package | |
11967 | (name "r-minpack-lm") | |
11968 | (version "1.2-1") | |
11969 | (source | |
11970 | (origin | |
11971 | (method url-fetch) | |
11972 | (uri (cran-uri "minpack.lm" version)) | |
11973 | (sha256 | |
11974 | (base32 | |
11975 | "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) | |
11976 | (properties `((upstream-name . "minpack.lm"))) | |
11977 | (build-system r-build-system) | |
11978 | (native-inputs `(("gfortran" ,gfortran))) | |
11979 | (home-page "https://cran.r-project.org/web/packages/minpack.lm") | |
11980 | (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") | |
11981 | (description | |
11982 | "The @code{nls.lm} function provides an R interface to @code{lmder} and | |
11983 | @code{lmdif} from the MINPACK library, for solving nonlinear least-squares | |
11984 | problems by a modification of the Levenberg-Marquardt algorithm, with support | |
11985 | for lower and upper parameter bounds. The implementation can be used via | |
2f041a4c | 11986 | @code{nls}-like calls using the @code{nlsLM} function.") |
4fd99443 | 11987 | (license license:gpl3))) |
01fe44cb RW |
11988 | |
11989 | (define-public r-moments | |
11990 | (package | |
11991 | (name "r-moments") | |
11992 | (version "0.14") | |
11993 | (source | |
11994 | (origin | |
11995 | (method url-fetch) | |
11996 | (uri (cran-uri "moments" version)) | |
11997 | (sha256 | |
11998 | (base32 | |
11999 | "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra")))) | |
12000 | (build-system r-build-system) | |
12001 | (home-page "https://cran.r-project.org/web/packages/moments") | |
12002 | (synopsis "Moments, cumulants, skewness, kurtosis and related tests") | |
12003 | (description | |
12004 | "This package provides functions to calculate: moments, Pearson's | |
12005 | kurtosis, Geary's kurtosis and skewness; it also includes tests related to | |
12006 | them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") | |
12007 | (license license:gpl2+))) | |
9e2ff342 RW |
12008 | |
12009 | (define-public r-msir | |
12010 | (package | |
12011 | (name "r-msir") | |
5ccf16c7 | 12012 | (version "1.3.2") |
9e2ff342 RW |
12013 | (source |
12014 | (origin | |
12015 | (method url-fetch) | |
12016 | (uri (cran-uri "msir" version)) | |
12017 | (sha256 | |
12018 | (base32 | |
5ccf16c7 | 12019 | "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb")))) |
9e2ff342 RW |
12020 | (build-system r-build-system) |
12021 | (propagated-inputs | |
5ccf16c7 | 12022 | `(("r-mclust" ,r-mclust))) |
9e2ff342 RW |
12023 | (home-page "https://cran.r-project.org/web/packages/msir") |
12024 | (synopsis "Model-based sliced inverse regression") | |
12025 | (description | |
12026 | "This is an R package for dimension reduction based on finite Gaussian | |
12027 | mixture modeling of inverse regression.") | |
12028 | (license license:gpl2+))) | |
e8be5a00 RW |
12029 | |
12030 | (define-public r-pbivnorm | |
12031 | (package | |
12032 | (name "r-pbivnorm") | |
12033 | (version "0.6.0") | |
12034 | (source | |
12035 | (origin | |
12036 | (method url-fetch) | |
12037 | (uri (cran-uri "pbivnorm" version)) | |
12038 | (sha256 | |
12039 | (base32 | |
12040 | "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) | |
12041 | (build-system r-build-system) | |
12042 | (native-inputs `(("gfortran" ,gfortran))) | |
12043 | (home-page "https://github.com/brentonk/pbivnorm") | |
12044 | (synopsis "Vectorized bivariate normal CDF") | |
12045 | (description | |
12046 | "This package provides a vectorized R function for calculating | |
12047 | probabilities from a standard bivariate normal CDF.") | |
12048 | (license license:gpl2+))) | |
ca3f1370 RW |
12049 | |
12050 | (define-public r-lavaan | |
12051 | (package | |
12052 | (name "r-lavaan") | |
553742fa | 12053 | (version "0.6-5") |
ca3f1370 RW |
12054 | (source |
12055 | (origin | |
12056 | (method url-fetch) | |
12057 | (uri (cran-uri "lavaan" version)) | |
12058 | (sha256 | |
12059 | (base32 | |
553742fa | 12060 | "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy")))) |
ca3f1370 RW |
12061 | (build-system r-build-system) |
12062 | (propagated-inputs | |
12063 | `(("r-mass" ,r-mass) | |
12064 | ("r-mnormt" ,r-mnormt) | |
12065 | ("r-numderiv" ,r-numderiv) | |
12066 | ("r-pbivnorm" ,r-pbivnorm))) | |
12067 | (home-page "http://lavaan.ugent.be") | |
12068 | (synopsis "Latent variable analysis") | |
12069 | (description | |
12070 | "This package provides tools to fit a variety of latent variable models, | |
12071 | including confirmatory factor analysis, structural equation modeling and | |
12072 | latent growth curve models.") | |
12073 | (license license:gpl2+))) | |
4d1f19e0 RW |
12074 | |
12075 | (define-public r-nonnest2 | |
12076 | (package | |
12077 | (name "r-nonnest2") | |
12078 | (version "0.5-2") | |
12079 | (source | |
12080 | (origin | |
12081 | (method url-fetch) | |
12082 | (uri (cran-uri "nonnest2" version)) | |
12083 | (sha256 | |
12084 | (base32 | |
12085 | "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6")))) | |
12086 | (build-system r-build-system) | |
12087 | (propagated-inputs | |
12088 | `(("r-compquadform" ,r-compquadform) | |
12089 | ("r-lavaan" ,r-lavaan) | |
12090 | ("r-mvtnorm" ,r-mvtnorm) | |
12091 | ("r-sandwich" ,r-sandwich))) | |
12092 | (home-page "https://cran.r-project.org/web/packages/nonnest2/") | |
12093 | (synopsis "Tests of non-nested models") | |
12094 | (description | |
12095 | "This package allows for testing of non-nested models. It includes tests | |
12096 | of model distinguishability and of model fit that can be applied to both | |
12097 | nested and non-nested models. The package also includes functionality to | |
12098 | obtain confidence intervals associated with AIC and BIC.") | |
12099 | ;; Either version of the GPL. | |
12100 | (license (list license:gpl2 license:gpl3)))) | |
be0777ba RW |
12101 | |
12102 | (define-public r-penalized | |
12103 | (package | |
12104 | (name "r-penalized") | |
12105 | (version "0.9-51") | |
12106 | (source | |
12107 | (origin | |
12108 | (method url-fetch) | |
12109 | (uri (cran-uri "penalized" version)) | |
12110 | (sha256 | |
12111 | (base32 | |
12112 | "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) | |
12113 | (build-system r-build-system) | |
12114 | (propagated-inputs | |
12115 | `(("r-rcpp" ,r-rcpp) | |
12116 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
12117 | ("r-survival" ,r-survival))) | |
12118 | (home-page "https://cran.r-project.org/web/packages/penalized/") | |
12119 | (synopsis "Penalized estimation in GLMs and in the Cox model") | |
12120 | (description | |
12121 | "This package provides tools for fitting possibly high dimensional | |
12122 | penalized regression models. The penalty structure can be any combination of | |
12123 | an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity | |
12124 | constraint on the regression coefficients. The supported regression models | |
12125 | are linear, logistic and Poisson regression and the Cox Proportional Hazards | |
12126 | model. Cross-validation routines allow optimization of the tuning | |
12127 | parameters.") | |
12128 | (license license:gpl2+))) | |
5570804a RW |
12129 | |
12130 | (define-public r-zim | |
12131 | (package | |
12132 | (name "r-zim") | |
12133 | (version "1.1.0") | |
12134 | (source | |
12135 | (origin | |
12136 | (method url-fetch) | |
12137 | (uri (cran-uri "ZIM" version)) | |
12138 | (sha256 | |
12139 | (base32 | |
12140 | "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) | |
12141 | (properties `((upstream-name . "ZIM"))) | |
12142 | (build-system r-build-system) | |
12143 | (propagated-inputs `(("r-mass" ,r-mass))) | |
12144 | (home-page "https://github.com/biostatstudio/ZIM") | |
12145 | (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") | |
12146 | (description | |
12147 | "Analyze count time series with excess zeros. Two types of statistical | |
12148 | models are supported: Markov regression and state-space models. They are also | |
12149 | known as observation-driven and parameter-driven models respectively in the | |
12150 | time series literature. The functions used for Markov regression or | |
12151 | observation-driven models can also be used to fit ordinary regression models | |
12152 | with independent data under the zero-inflated Poisson (ZIP) or zero-inflated | |
12153 | negative binomial (ZINB) assumption. The package also contains miscellaneous | |
12154 | functions to compute density, distribution, quantile, and generate random | |
12155 | numbers from ZIP and ZINB distributions.") | |
12156 | (license license:gpl3))) | |
026dd77c RW |
12157 | |
12158 | (define-public r-nor1mix | |
12159 | (package | |
12160 | (name "r-nor1mix") | |
776c62d1 | 12161 | (version "1.3-0") |
026dd77c RW |
12162 | (source |
12163 | (origin | |
12164 | (method url-fetch) | |
12165 | (uri (cran-uri "nor1mix" version)) | |
12166 | (sha256 | |
12167 | (base32 | |
776c62d1 | 12168 | "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w")))) |
026dd77c RW |
12169 | (build-system r-build-system) |
12170 | (home-page "https://cran.r-project.org/web/packages/nor1mix/") | |
12171 | (synopsis "Normal (1-d) mixture models") | |
12172 | (description | |
12173 | "This package provides S3 classes and methods for one-dimensional normal | |
12174 | mixture models, for, e.g., density estimation or clustering algorithms | |
12175 | research and teaching; it provides the widely used Marron-Wand densities. It | |
12176 | also provides tools for efficient random number generation and graphics.") | |
12177 | (license license:gpl2+))) | |
648dbd27 RW |
12178 | |
12179 | (define-public r-beanplot | |
12180 | (package | |
12181 | (name "r-beanplot") | |
12182 | (version "1.2") | |
12183 | (source | |
12184 | (origin | |
12185 | (method url-fetch) | |
12186 | (uri (cran-uri "beanplot" version)) | |
12187 | (sha256 | |
12188 | (base32 | |
12189 | "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9")))) | |
12190 | (build-system r-build-system) | |
12191 | (home-page "https://cran.r-project.org/web/packages/beanplot/") | |
12192 | (synopsis "Visualization via beanplots") | |
12193 | (description | |
12194 | "This package provides beanplots, an alternative to | |
12195 | boxplot/stripchart/violin plots. It can be used to plot univariate comparison | |
12196 | graphs.") | |
12197 | (license license:gpl2))) | |
f313baf0 RW |
12198 | |
12199 | (define-public r-pbdzmq | |
12200 | (package | |
12201 | (name "r-pbdzmq") | |
12202 | (version "0.3-3") | |
12203 | (source | |
12204 | (origin | |
12205 | (method url-fetch) | |
12206 | (uri (cran-uri "pbdZMQ" version)) | |
12207 | (sha256 | |
12208 | (base32 | |
12209 | "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf")))) | |
12210 | (properties `((upstream-name . "pbdZMQ"))) | |
12211 | (build-system r-build-system) | |
12212 | (inputs | |
12213 | `(("zeromq" ,zeromq) | |
12214 | ("zlib" ,zlib))) | |
12215 | (native-inputs | |
12216 | `(("pkg-config" ,pkg-config))) | |
12217 | (home-page "https://pbdr.org/") | |
12218 | (synopsis "R interface to ZeroMQ") | |
12219 | (description | |
12220 | "ZeroMQ is a well-known library for high-performance asynchronous | |
12221 | messaging in scalable, distributed applications. This package provides high | |
12222 | level R wrapper functions to easily utilize ZeroMQ. The main focus is on | |
12223 | interactive client/server programming frameworks. A few wrapper functions | |
12224 | compatible with @code{rzmq} are also provided.") | |
12225 | (license license:gpl3))) | |
d17186d6 RW |
12226 | |
12227 | (define-public r-repr | |
12228 | (package | |
12229 | (name "r-repr") | |
2785e615 | 12230 | (version "1.0.1") |
d17186d6 RW |
12231 | (source |
12232 | (origin | |
12233 | (method url-fetch) | |
12234 | (uri (cran-uri "repr" version)) | |
12235 | (sha256 | |
12236 | (base32 | |
2785e615 | 12237 | "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc")))) |
d17186d6 RW |
12238 | (build-system r-build-system) |
12239 | (propagated-inputs | |
12240 | `(("r-base64enc" ,r-base64enc) | |
12241 | ("r-htmltools" ,r-htmltools) | |
8b96b860 RW |
12242 | ("r-jsonlite" ,r-jsonlite) |
12243 | ("r-pillar" ,r-pillar))) | |
d17186d6 RW |
12244 | (home-page "https://cran.r-project.org/web/packages/repr/") |
12245 | (synopsis "Serializable representations") | |
12246 | (description | |
12247 | "This package provides string and binary representations of objects for | |
12248 | several formats and MIME types.") | |
12249 | (license license:gpl3))) | |
664dedd5 RW |
12250 | |
12251 | (define-public r-irdisplay | |
12252 | (package | |
12253 | (name "r-irdisplay") | |
12254 | (version "0.7.0") | |
12255 | (source | |
12256 | (origin | |
12257 | (method url-fetch) | |
12258 | (uri (cran-uri "IRdisplay" version)) | |
12259 | (sha256 | |
12260 | (base32 | |
12261 | "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli")))) | |
12262 | (properties `((upstream-name . "IRdisplay"))) | |
12263 | (build-system r-build-system) | |
12264 | (propagated-inputs | |
12265 | `(("r-repr" ,r-repr))) | |
12266 | (home-page "https://cran.r-project.org/web/packages/IRdisplay/") | |
12267 | (synopsis "Jupyter display machinery") | |
12268 | (description | |
12269 | "This package provides an interface to the rich display capabilities of | |
12270 | Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a | |
12271 | running IRkernel session.") | |
12272 | (license license:expat))) | |
984a8aa6 RW |
12273 | |
12274 | (define-public r-irkernel | |
12275 | (package | |
12276 | (name "r-irkernel") | |
bd008356 | 12277 | (version "1.0.2") |
984a8aa6 RW |
12278 | (source |
12279 | (origin | |
12280 | (method url-fetch) | |
12281 | (uri (cran-uri "IRkernel" version)) | |
12282 | (sha256 | |
12283 | (base32 | |
bd008356 | 12284 | "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp")))) |
984a8aa6 RW |
12285 | (properties `((upstream-name . "IRkernel"))) |
12286 | (build-system r-build-system) | |
12287 | (arguments | |
12288 | `(#:phases | |
12289 | (modify-phases %standard-phases | |
12290 | (add-after 'install 'install-kernelspec | |
12291 | (lambda* (#:key outputs #:allow-other-keys) | |
12292 | (let ((out (assoc-ref outputs "out"))) | |
12293 | (setenv "HOME" "/tmp") | |
12294 | (invoke "jupyter" "kernelspec" "install" | |
12295 | "--name" "ir" | |
12296 | "--prefix" out | |
12297 | (string-append out "/site-library/IRkernel/kernelspec")) | |
12298 | #t)))))) | |
12299 | (inputs | |
12300 | `(("jupyter" ,jupyter))) | |
12301 | (propagated-inputs | |
12302 | `(("r-crayon" ,r-crayon) | |
12303 | ("r-digest" ,r-digest) | |
12304 | ("r-evaluate" ,r-evaluate) | |
12305 | ("r-irdisplay" ,r-irdisplay) | |
12306 | ("r-jsonlite" ,r-jsonlite) | |
12307 | ("r-pbdzmq" ,r-pbdzmq) | |
12308 | ("r-repr" ,r-repr) | |
12309 | ("r-uuid" ,r-uuid))) | |
12310 | (home-page "https://cran.r-project.org/web/packages/IRkernel/") | |
12311 | (synopsis "Native R kernel for Jupyter") | |
12312 | (description | |
12313 | "The R kernel for the Jupyter environment executes R code which the | |
12314 | front-end (Jupyter Notebook or other front-ends) submits to the kernel via the | |
12315 | network.") | |
12316 | (license license:expat))) | |
51df4340 RW |
12317 | |
12318 | (define-public r-gmodels | |
12319 | (package | |
12320 | (name "r-gmodels") | |
12321 | (version "2.18.1") | |
12322 | (source | |
12323 | (origin | |
12324 | (method url-fetch) | |
12325 | (uri (cran-uri "gmodels" version)) | |
12326 | (sha256 | |
12327 | (base32 | |
12328 | "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) | |
12329 | (build-system r-build-system) | |
12330 | (propagated-inputs | |
12331 | `(("r-gdata" ,r-gdata) | |
12332 | ("r-mass" ,r-mass))) | |
12333 | (home-page "https://cran.r-project.org/web/packages/gmodels/") | |
12334 | (synopsis "Various R programming tools for model fitting") | |
12335 | (description | |
12336 | "This package provides various R programming tools for model fitting.") | |
12337 | (license license:gpl2))) | |
3942bf5e RW |
12338 | |
12339 | (define-public r-apcluster | |
12340 | (package | |
12341 | (name "r-apcluster") | |
53040408 | 12342 | (version "1.4.8") |
3942bf5e RW |
12343 | (source |
12344 | (origin | |
12345 | (method url-fetch) | |
12346 | (uri (cran-uri "apcluster" version)) | |
12347 | (sha256 | |
12348 | (base32 | |
53040408 | 12349 | "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj")))) |
3942bf5e RW |
12350 | (build-system r-build-system) |
12351 | (propagated-inputs | |
12352 | `(("r-matrix" ,r-matrix) | |
12353 | ("r-rcpp" ,r-rcpp))) | |
12354 | (home-page "https://cran.r-project.org/web/packages/apcluster/") | |
12355 | (synopsis "Affinity propagation clustering") | |
12356 | (description | |
12357 | "This package implements affinity propagation clustering introduced by | |
12358 | Frey and Dueck (2007). The package further provides leveraged affinity | |
12359 | propagation and an algorithm for exemplar-based agglomerative clustering that | |
12360 | can also be used to join clusters obtained from affinity propagation. Various | |
12361 | plotting functions are available for analyzing clustering results.") | |
12362 | (license license:gpl2+))) | |
a97796cd RW |
12363 | |
12364 | (define-public r-valr | |
12365 | (package | |
12366 | (name "r-valr") | |
12367 | (version "0.5.0") | |
12368 | (source | |
12369 | (origin | |
12370 | (method url-fetch) | |
12371 | (uri (cran-uri "valr" version)) | |
12372 | (sha256 | |
12373 | (base32 | |
12374 | "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika")))) | |
12375 | (build-system r-build-system) | |
12376 | (propagated-inputs | |
12377 | `(("r-broom" ,r-broom) | |
12378 | ("r-dplyr" ,r-dplyr) | |
12379 | ("r-ggplot2" ,r-ggplot2) | |
12380 | ("r-rcpp" ,r-rcpp) | |
12381 | ("r-readr" ,r-readr) | |
12382 | ("r-rlang" ,r-rlang) | |
12383 | ("r-stringr" ,r-stringr) | |
12384 | ("r-tibble" ,r-tibble))) | |
12385 | (home-page "http://github.com/rnabioco/valr") | |
12386 | (synopsis "Genome interval arithmetic in R") | |
12387 | (description | |
12388 | "This package enables you to read and manipulate genome intervals and | |
12389 | signals. It provides functionality similar to command-line tool suites within | |
12390 | R, enabling interactive analysis and visualization of genome-scale data.") | |
12391 | (license license:expat))) | |
100f5602 NB |
12392 | |
12393 | (define-public r-rematch2 | |
12394 | (package | |
12395 | (name "r-rematch2") | |
8518744e | 12396 | (version "2.1.0") |
100f5602 NB |
12397 | (source |
12398 | (origin | |
12399 | (method url-fetch) | |
12400 | (uri (cran-uri "rematch2" version)) | |
12401 | (sha256 | |
12402 | (base32 | |
8518744e | 12403 | "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq")))) |
100f5602 NB |
12404 | (build-system r-build-system) |
12405 | (propagated-inputs | |
12406 | `(("r-tibble" ,r-tibble))) | |
12407 | (home-page "https://github.com/r-lib/rematch2") | |
12408 | (synopsis "Tidy output from regular expression matching") | |
12409 | (description | |
12410 | "This package provides wrappers on @code{regexpr} and @code{gregexpr} to | |
12411 | return the match results in tidy data frames.") | |
12412 | (license license:expat))) | |
0c02f94f RW |
12413 | |
12414 | (define-public r-picante | |
12415 | (package | |
12416 | (name "r-picante") | |
12417 | (version "1.8") | |
12418 | (source | |
12419 | (origin | |
12420 | (method url-fetch) | |
12421 | (uri (cran-uri "picante" version)) | |
12422 | (sha256 | |
12423 | (base32 | |
12424 | "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1")))) | |
12425 | (build-system r-build-system) | |
12426 | (propagated-inputs | |
12427 | `(("r-ape" ,r-ape) | |
12428 | ("r-nlme" ,r-nlme) | |
12429 | ("r-vegan" ,r-vegan))) | |
12430 | (home-page "https://cran.r-project.org/web/packages/picante/") | |
12431 | (synopsis "Integrating phylogenies and ecology") | |
12432 | (description | |
12433 | "This package provides functions for phylocom integration, community | |
12434 | analyses, null-models, traits and evolution. It implements numerous | |
12435 | ecophylogenetic approaches including measures of community phylogenetic and | |
12436 | trait diversity, phylogenetic signal, estimation of trait values for | |
12437 | unobserved taxa, null models for community and phylogeny randomizations, and | |
12438 | utility functions for data input/output and phylogeny plotting. A full | |
12439 | description of package functionality and methods are provided by Kembel et | |
12440 | al. (2010).") | |
12441 | (license license:gpl2))) | |
93f178b5 RW |
12442 | |
12443 | (define-public r-reinforcelearn | |
12444 | (package | |
12445 | (name "r-reinforcelearn") | |
d1ed092e | 12446 | (version "0.2.1") |
93f178b5 RW |
12447 | (source |
12448 | (origin | |
12449 | (method url-fetch) | |
12450 | (uri (cran-uri "reinforcelearn" version)) | |
12451 | (sha256 | |
12452 | (base32 | |
d1ed092e | 12453 | "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b")))) |
93f178b5 RW |
12454 | (build-system r-build-system) |
12455 | (propagated-inputs | |
12456 | `(("r-checkmate" ,r-checkmate) | |
12457 | ("r-nnet" ,r-nnet) | |
12458 | ("r-purrr" ,r-purrr) | |
12459 | ("r-r6" ,r-r6))) | |
12460 | (home-page "https://markusdumke.github.io/reinforcelearn") | |
12461 | (synopsis "Reinforcement learning") | |
12462 | (description | |
12463 | "This package implements reinforcement learning environments and | |
12464 | algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm | |
12465 | can be used with function approximation, eligibility traces (Singh & Sutton, | |
12466 | 1996) and experience replay (Mnih et al., 2013).") | |
12467 | (license license:expat))) | |
f98d97c6 RW |
12468 | |
12469 | (define-public r-lemon | |
12470 | (package | |
12471 | (name "r-lemon") | |
12472 | (version "0.4.3") | |
12473 | (source | |
12474 | (origin | |
12475 | (method url-fetch) | |
12476 | (uri (cran-uri "lemon" version)) | |
12477 | (sha256 | |
12478 | (base32 | |
12479 | "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw")))) | |
12480 | (build-system r-build-system) | |
12481 | (propagated-inputs | |
12482 | `(("r-ggplot2" ,r-ggplot2) | |
12483 | ("r-gridextra" ,r-gridextra) | |
12484 | ("r-gtable" ,r-gtable) | |
12485 | ("r-knitr" ,r-knitr) | |
12486 | ("r-lattice" ,r-lattice) | |
12487 | ("r-plyr" ,r-plyr) | |
12488 | ("r-scales" ,r-scales))) | |
12489 | (home-page "https://github.com/stefanedwards/lemon") | |
12490 | (synopsis "Freshen up your ggplot2 plots") | |
12491 | (description | |
12492 | "This package provides functions for working with legends and axis lines | |
12493 | of ggplot2, facets that repeat axis lines on all panels, and some knitr | |
12494 | extensions.") | |
12495 | (license license:gpl3))) | |
79db3a1a RW |
12496 | |
12497 | (define-public r-wgaim | |
12498 | (package | |
12499 | (name "r-wgaim") | |
5feaa775 | 12500 | (version "2.0-0") |
79db3a1a RW |
12501 | (source |
12502 | (origin | |
12503 | (method url-fetch) | |
12504 | (uri (cran-uri "wgaim" version)) | |
12505 | (sha256 | |
12506 | (base32 | |
5feaa775 | 12507 | "0wnb10vibgq8h1ly6lq8kzymf30vx0j0g8fc2zidblbvwag9ka1g")))) |
79db3a1a RW |
12508 | (build-system r-build-system) |
12509 | (propagated-inputs | |
5feaa775 | 12510 | `(("r-ggplot2" ,r-ggplot2) |
79db3a1a RW |
12511 | ("r-qtl" ,r-qtl))) |
12512 | (home-page "https://cran.r-project.org/web/packages/wgaim") | |
12513 | (synopsis "Whole genome average interval mapping for QTL detection") | |
12514 | (description | |
12515 | "This package integrates sophisticated mixed modelling methods with a | |
12516 | whole genome approach to detecting significant QTL in linkage maps.") | |
12517 | (license license:gpl2+))) | |
f33cb7ab RW |
12518 | |
12519 | (define-public r-bedr | |
12520 | (package | |
12521 | (name "r-bedr") | |
3c18fb13 | 12522 | (version "1.0.7") |
f33cb7ab RW |
12523 | (source |
12524 | (origin | |
12525 | (method url-fetch) | |
12526 | (uri (cran-uri "bedr" version)) | |
12527 | (sha256 | |
12528 | (base32 | |
3c18fb13 | 12529 | "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) |
f33cb7ab RW |
12530 | (build-system r-build-system) |
12531 | (propagated-inputs | |
12532 | `(("r-data-table" ,r-data-table) | |
12533 | ("r-r-utils" ,r-r-utils) | |
12534 | ("r-testthat" ,r-testthat) | |
12535 | ("r-venndiagram" ,r-venndiagram) | |
12536 | ("r-yaml" ,r-yaml) | |
12537 | ("bedops" ,bedops) | |
12538 | ("bedtools" ,bedtools) | |
12539 | ("htslib" ,htslib))) ; for tabix | |
12540 | (native-inputs | |
12541 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
12542 | (home-page "https://cran.r-project.org/web/packages/bedr") | |
12543 | (synopsis "Genomic region processing") | |
12544 | (description | |
12545 | "This package is for genomic regions processing using command line tools | |
12546 | such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient | |
12547 | utilities to perform genome arithmetic e.g indexing, formatting and merging. | |
12548 | The bedr package's API enhances access to these tools as well as offers | |
12549 | additional utilities for genomic regions processing.") | |
12550 | (license license:gpl2))) | |
459dcb95 RW |
12551 | |
12552 | (define-public r-partitions | |
12553 | (package | |
12554 | (name "r-partitions") | |
12555 | (version "1.9-19") | |
12556 | (source | |
12557 | (origin | |
12558 | (method url-fetch) | |
12559 | (uri (cran-uri "partitions" version)) | |
12560 | (sha256 | |
12561 | (base32 | |
12562 | "1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx")))) | |
12563 | (build-system r-build-system) | |
12564 | (propagated-inputs | |
12565 | `(("r-gmp" ,r-gmp) | |
12566 | ("r-polynom" ,r-polynom))) | |
12567 | (home-page "https://cran.r-project.org/web/packages/partitions") | |
12568 | (synopsis "Additive partitions of integers") | |
12569 | (description | |
12570 | "This package provides tools to enumerates the partitions, unequal | |
12571 | partitions, and restricted partitions of an integer; the three corresponding | |
12572 | partition functions are also given.") | |
12573 | ;; Any version of the GPL | |
12574 | (license license:gpl2+))) | |
761c097f RW |
12575 | |
12576 | (define-public r-brobdingnag | |
12577 | (package | |
12578 | (name "r-brobdingnag") | |
12579 | (version "1.2-6") | |
12580 | (source | |
12581 | (origin | |
12582 | (method url-fetch) | |
12583 | (uri (cran-uri "Brobdingnag" version)) | |
12584 | (sha256 | |
12585 | (base32 | |
12586 | "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r")))) | |
12587 | (properties `((upstream-name . "Brobdingnag"))) | |
12588 | (build-system r-build-system) | |
12589 | (home-page "https://github.com/RobinHankin/Brobdingnag.git") | |
12590 | (synopsis "Very large numbers in R") | |
12591 | (description | |
12592 | "This package handles very large numbers in R. Real numbers are held | |
12593 | using their natural logarithms, plus a logical flag indicating sign. The | |
12594 | package includes a vignette that gives a step-by-step introduction to using S4 | |
12595 | methods.") | |
12596 | ;; Any version of the GPL | |
12597 | (license license:gpl2+))) | |
c30be23a RW |
12598 | |
12599 | (define-public r-untb | |
12600 | (package | |
12601 | (name "r-untb") | |
12602 | (version "1.7-4") | |
12603 | (source | |
12604 | (origin | |
12605 | (method url-fetch) | |
12606 | (uri (cran-uri "untb" version)) | |
12607 | (sha256 | |
12608 | (base32 | |
12609 | "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6")))) | |
12610 | (build-system r-build-system) | |
12611 | (propagated-inputs | |
12612 | `(("r-brobdingnag" ,r-brobdingnag) | |
12613 | ("r-partitions" ,r-partitions) | |
12614 | ("r-polynom" ,r-polynom))) | |
12615 | (home-page "https://github.com/RobinHankin/untb.git") | |
12616 | (synopsis "Ecological drift under the UNTB") | |
12617 | (description | |
12618 | "This package provides numerical simulations, and visualizations, of | |
12619 | Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).") | |
12620 | (license license:gpl2+))) | |
ea87b4e3 RW |
12621 | |
12622 | (define-public r-stepwise | |
12623 | (package | |
12624 | (name "r-stepwise") | |
12625 | (version "0.3") | |
12626 | (source | |
12627 | (origin | |
12628 | (method url-fetch) | |
12629 | (uri (cran-uri "stepwise" version)) | |
12630 | (sha256 | |
12631 | (base32 | |
12632 | "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2")))) | |
12633 | (build-system r-build-system) | |
12634 | (home-page "http://stat.sfu.ca/statgen/research/stepwise.html") | |
12635 | (synopsis "Stepwise detection of recombination breakpoints") | |
12636 | (description | |
12637 | "This package provides a stepwise approach to identifying recombination | |
12638 | breakpoints in a genomic sequence alignment.") | |
12639 | (license license:gpl2+))) | |
2a35bb15 RW |
12640 | |
12641 | (define-public r-snpmaxsel | |
12642 | (package | |
12643 | (name "r-snpmaxsel") | |
12644 | (version "1.0-3") | |
12645 | (source | |
12646 | (origin | |
12647 | (method url-fetch) | |
12648 | (uri (cran-uri "SNPmaxsel" version)) | |
12649 | (sha256 | |
12650 | (base32 | |
12651 | "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z")))) | |
12652 | (properties `((upstream-name . "SNPmaxsel"))) | |
12653 | (build-system r-build-system) | |
12654 | (propagated-inputs | |
12655 | `(("r-combinat" ,r-combinat) | |
12656 | ("r-mvtnorm" ,r-mvtnorm))) | |
12657 | (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") | |
12658 | (synopsis "Maximally selected statistics for SNP data") | |
12659 | (description | |
12660 | "This package implements asymptotic methods related to maximally selected | |
12661 | statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP) | |
12662 | data.") | |
12663 | (license license:gpl2+))) | |
7002c44f | 12664 | |
49a48c49 RW |
12665 | (define-public r-acsnminer |
12666 | (package | |
12667 | (name "r-acsnminer") | |
12668 | (version "0.16.8.25") | |
12669 | (source (origin | |
12670 | (method url-fetch) | |
12671 | (uri (cran-uri "ACSNMineR" version)) | |
12672 | (sha256 | |
12673 | (base32 | |
12674 | "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) | |
12675 | (properties `((upstream-name . "ACSNMineR"))) | |
12676 | (build-system r-build-system) | |
12677 | (propagated-inputs | |
12678 | `(("r-ggplot2" ,r-ggplot2) | |
12679 | ("r-gridextra" ,r-gridextra))) | |
12680 | (home-page "https://cran.r-project.org/web/packages/ACSNMineR") | |
12681 | (synopsis "Gene enrichment analysis") | |
12682 | (description | |
12683 | "This package provides tools to compute and represent gene set enrichment | |
12684 | or depletion from your data based on pre-saved maps from the @dfn{Atlas of | |
12685 | Cancer Signalling Networks} (ACSN) or user imported maps. The gene set | |
12686 | enrichment can be run with hypergeometric test or Fisher exact test, and can | |
12687 | use multiple corrections. Visualization of data can be done either by | |
12688 | barplots or heatmaps.") | |
12689 | (license license:gpl2+))) | |
12690 | ||
c4d521ba RW |
12691 | (define-public r-seqinr |
12692 | (package | |
12693 | (name "r-seqinr") | |
fd399b7a | 12694 | (version "3.6-1") |
c4d521ba RW |
12695 | (source |
12696 | (origin | |
12697 | (method url-fetch) | |
12698 | (uri (cran-uri "seqinr" version)) | |
12699 | (sha256 | |
12700 | (base32 | |
fd399b7a | 12701 | "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4")))) |
c4d521ba RW |
12702 | (build-system r-build-system) |
12703 | (propagated-inputs | |
12704 | `(("r-ade4" ,r-ade4) | |
12705 | ("r-segmented" ,r-segmented))) | |
12706 | (inputs | |
12707 | `(("zlib" ,zlib))) | |
12708 | (home-page "http://seqinr.r-forge.r-project.org/") | |
12709 | (synopsis "Biological sequences retrieval and analysis") | |
12710 | (description | |
12711 | "This package provides tools for exploratory data analysis and data | |
12712 | visualization of biological sequence (DNA and protein) data. It also includes | |
12713 | utilities for sequence data management under the ACNUC system.") | |
12714 | (license license:gpl2+))) | |
12715 | ||
7002c44f RW |
12716 | (define-public r-units |
12717 | (package | |
12718 | (name "r-units") | |
dfe4c8c4 | 12719 | (version "0.6-4") |
7002c44f RW |
12720 | (source |
12721 | (origin | |
12722 | (method url-fetch) | |
12723 | (uri (cran-uri "units" version)) | |
12724 | (sha256 | |
12725 | (base32 | |
dfe4c8c4 | 12726 | "1jz0mzd78sdfxkhqw041ji50hmhjk2ha55i31yjvz35nsw30lwi5")))) |
7002c44f RW |
12727 | (build-system r-build-system) |
12728 | (inputs | |
12729 | `(("udunits" ,udunits))) | |
12730 | (propagated-inputs | |
12731 | `(("r-rcpp" ,r-rcpp))) | |
12732 | (home-page "https://github.com/r-quantities/units/") | |
12733 | (synopsis "Measurement Units for R Vectors") | |
12734 | (description | |
12735 | "This package provides support for measurement units in R vectors, | |
12736 | matrices and arrays: automatic propagation, conversion, derivation and | |
12737 | simplification of units; raising errors in case of unit incompatibility. It | |
12738 | is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} | |
12739 | classes.") | |
12740 | (license license:gpl2))) | |
518c1dea RW |
12741 | |
12742 | (define-public r-classint | |
12743 | (package | |
12744 | (name "r-classint") | |
24d43986 | 12745 | (version "0.4-1") |
518c1dea RW |
12746 | (source |
12747 | (origin | |
12748 | (method url-fetch) | |
12749 | (uri (cran-uri "classInt" version)) | |
12750 | (sha256 | |
12751 | (base32 | |
24d43986 | 12752 | "00q1bpgblrldckn1rk166q1b0hgap2sjjyfmfcyh6ydk6y73ziir")))) |
518c1dea RW |
12753 | (properties `((upstream-name . "classInt"))) |
12754 | (build-system r-build-system) | |
12755 | (propagated-inputs | |
12756 | `(("r-class" ,r-class) | |
1bbfca18 RW |
12757 | ("r-e1071" ,r-e1071) |
12758 | ("r-kernsmooth" ,r-kernsmooth))) | |
518c1dea RW |
12759 | (native-inputs `(("gfortran" ,gfortran))) |
12760 | (home-page "https://github.com/r-spatial/classInt/") | |
12761 | (synopsis "Choose univariate class intervals") | |
12762 | (description | |
12763 | "This package provides selected commonly used methods for choosing | |
12764 | univariate class intervals for mapping or other graphics purposes.") | |
12765 | (license license:gpl2+))) | |
66c08ff4 RW |
12766 | |
12767 | (define-public r-spdata | |
12768 | (package | |
12769 | (name "r-spdata") | |
b9d9bc66 | 12770 | (version "0.3.2") |
66c08ff4 RW |
12771 | (source |
12772 | (origin | |
12773 | (method url-fetch) | |
12774 | (uri (cran-uri "spData" version)) | |
12775 | (sha256 | |
12776 | (base32 | |
b9d9bc66 | 12777 | "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw")))) |
66c08ff4 RW |
12778 | (properties `((upstream-name . "spData"))) |
12779 | (build-system r-build-system) | |
12780 | (home-page "https://github.com/Nowosad/spData") | |
12781 | (synopsis "Datasets for spatial analysis") | |
12782 | (description | |
12783 | "This a package containing diverse spatial datasets for demonstrating, | |
12784 | benchmarking and teaching spatial data analysis. It includes R data of class | |
12785 | @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a | |
12786 | range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some | |
12787 | of the datasets are designed to illustrate specific analysis techniques. | |
12788 | @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to | |
12789 | illustrate point pattern analysis techniques.") | |
12790 | (license license:cc0))) | |
e5228273 RW |
12791 | |
12792 | (define-public r-learnbayes | |
12793 | (package | |
12794 | (name "r-learnbayes") | |
12795 | (version "2.15.1") | |
12796 | (source | |
12797 | (origin | |
12798 | (method url-fetch) | |
12799 | (uri (cran-uri "LearnBayes" version)) | |
12800 | (sha256 | |
12801 | (base32 | |
12802 | "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv")))) | |
12803 | (properties `((upstream-name . "LearnBayes"))) | |
12804 | (build-system r-build-system) | |
12805 | (home-page "https://cran.r-project.org/web/packages/LearnBayes") | |
12806 | (synopsis "Functions for learning Bayesian inference") | |
12807 | (description | |
12808 | "This package provides a collection of functions helpful in learning the | |
12809 | basic tenets of Bayesian statistical inference. It contains functions for | |
12810 | summarizing basic one and two parameter posterior distributions and predictive | |
12811 | distributions. It contains MCMC algorithms for summarizing posterior | |
12812 | distributions defined by the user. It also contains functions for regression | |
12813 | models, hierarchical models, Bayesian tests, and illustrations of Gibbs | |
12814 | sampling.") | |
12815 | (license license:gpl2+))) | |
dcc50286 RW |
12816 | |
12817 | (define-public r-deldir | |
12818 | (package | |
12819 | (name "r-deldir") | |
4eed03ea | 12820 | (version "0.1-23") |
dcc50286 RW |
12821 | (source |
12822 | (origin | |
12823 | (method url-fetch) | |
12824 | (uri (cran-uri "deldir" version)) | |
12825 | (sha256 | |
12826 | (base32 | |
4eed03ea | 12827 | "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0")))) |
dcc50286 RW |
12828 | (build-system r-build-system) |
12829 | (native-inputs `(("gfortran" ,gfortran))) | |
12830 | (home-page "https://cran.r-project.org/web/packages/deldir") | |
12831 | (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") | |
12832 | (description | |
12833 | "This package provides tools for calculating the Delaunay triangulation | |
12834 | and the Dirichlet or Voronoi tessellation (with respect to the entire plane) | |
12835 | of a planar point set. It plots triangulations and tessellations in various | |
12836 | ways, clips tessellations to sub-windows, calculates perimeters of | |
12837 | tessellations, and summarizes information about the tiles of the | |
12838 | tessellation.") | |
12839 | (license license:gpl2+))) | |
d884e407 RW |
12840 | |
12841 | (define-public r-sf | |
12842 | (package | |
12843 | (name "r-sf") | |
bc9a839f | 12844 | (version "0.8-0") |
d884e407 RW |
12845 | (source |
12846 | (origin | |
12847 | (method url-fetch) | |
12848 | (uri (cran-uri "sf" version)) | |
12849 | (sha256 | |
12850 | (base32 | |
bc9a839f | 12851 | "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf")))) |
d884e407 RW |
12852 | (build-system r-build-system) |
12853 | (inputs | |
12854 | `(("gdal" ,gdal) | |
12855 | ("geos" ,geos) | |
12856 | ("proj" ,proj.4) | |
12857 | ("zlib" ,zlib))) | |
12858 | (propagated-inputs | |
12859 | `(("r-classint" ,r-classint) | |
12860 | ("r-dbi" ,r-dbi) | |
12861 | ("r-magrittr" ,r-magrittr) | |
12862 | ("r-rcpp" ,r-rcpp) | |
12863 | ("r-units" ,r-units))) | |
12864 | (native-inputs `(("pkg-config" ,pkg-config))) | |
12865 | (home-page "https://github.com/r-spatial/sf/") | |
12866 | (synopsis "Simple features for R") | |
12867 | (description | |
12868 | "This package provides support for simple features, a standardized way to | |
12869 | encode spatial vector data. It binds to GDAL for reading and writing data, to | |
12870 | GEOS for geometrical operations, and to PROJ for projection conversions and | |
12871 | datum transformations.") | |
12872 | ;; Either of these licenses | |
12873 | (license (list license:gpl2 license:expat)))) | |
e371e534 RW |
12874 | |
12875 | (define-public r-spdep | |
12876 | (package | |
12877 | (name "r-spdep") | |
4978222a | 12878 | (version "1.1-3") |
e371e534 RW |
12879 | (source |
12880 | (origin | |
12881 | (method url-fetch) | |
12882 | (uri (cran-uri "spdep" version)) | |
12883 | (sha256 | |
12884 | (base32 | |
4978222a | 12885 | "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk")))) |
e371e534 RW |
12886 | (build-system r-build-system) |
12887 | (propagated-inputs | |
12888 | `(("r-boot" ,r-boot) | |
12889 | ("r-coda" ,r-coda) | |
12890 | ("r-deldir" ,r-deldir) | |
12891 | ("r-expm" ,r-expm) | |
12892 | ("r-gmodels" ,r-gmodels) | |
12893 | ("r-learnbayes" ,r-learnbayes) | |
12894 | ("r-mass" ,r-mass) | |
12895 | ("r-matrix" ,r-matrix) | |
12896 | ("r-nlme" ,r-nlme) | |
12897 | ("r-sf" ,r-sf) | |
12898 | ("r-sp" ,r-sp) | |
12899 | ("r-spdata" ,r-spdata))) | |
12900 | (home-page "https://github.com/r-spatial/spdep/") | |
12901 | (synopsis "Spatial dependence: weighting schemes, statistics and models") | |
12902 | (description | |
12903 | "This package provides a collection of functions to create spatial | |
12904 | weights matrix objects from polygon contiguities, from point patterns by | |
12905 | distance and tessellations, for summarizing these objects, and for permitting | |
12906 | their use in spatial data analysis, including regional aggregation by minimum | |
12907 | spanning tree.") | |
12908 | (license license:gpl2+))) | |
91c1fbdf RW |
12909 | |
12910 | (define-public r-adegenet | |
12911 | (package | |
12912 | (name "r-adegenet") | |
12913 | (version "2.1.1") | |
12914 | (source | |
12915 | (origin | |
12916 | (method url-fetch) | |
12917 | (uri (cran-uri "adegenet" version)) | |
12918 | (sha256 | |
12919 | (base32 | |
12920 | "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh")))) | |
12921 | (build-system r-build-system) | |
12922 | (propagated-inputs | |
12923 | `(("r-ade4" ,r-ade4) | |
12924 | ("r-ape" ,r-ape) | |
12925 | ("r-boot" ,r-boot) | |
12926 | ("r-dplyr" ,r-dplyr) | |
12927 | ("r-ggplot2" ,r-ggplot2) | |
12928 | ("r-igraph" ,r-igraph) | |
12929 | ("r-mass" ,r-mass) | |
12930 | ("r-reshape2" ,r-reshape2) | |
12931 | ("r-seqinr" ,r-seqinr) | |
12932 | ("r-shiny" ,r-shiny) | |
12933 | ("r-spdep" ,r-spdep) | |
12934 | ("r-vegan" ,r-vegan))) | |
12935 | (home-page "https://github.com/thibautjombart/adegenet") | |
12936 | (synopsis "Exploratory analysis of genetic and genomic data") | |
12937 | (description | |
12938 | "This package provides a toolset for the exploration of genetic and | |
12939 | genomic data. Adegenet provides formal (S4) classes for storing and handling | |
12940 | various genetic data, including genetic markers with varying ploidy and | |
12941 | hierarchical population structure (@code{genind} class), alleles counts by | |
12942 | populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It | |
12943 | also implements original multivariate methods (DAPC, sPCA), graphics, | |
12944 | statistical tests, simulation tools, distance and similarity measures, and | |
12945 | several spatial methods. A range of both empirical and simulated datasets is | |
12946 | also provided to illustrate various methods.") | |
12947 | (license license:gpl2+))) | |
3d2bc817 RW |
12948 | |
12949 | (define-public r-pegas | |
12950 | (package | |
12951 | (name "r-pegas") | |
12952 | (version "0.11") | |
12953 | (source | |
12954 | (origin | |
12955 | (method url-fetch) | |
12956 | (uri (cran-uri "pegas" version)) | |
12957 | (sha256 | |
12958 | (base32 | |
12959 | "0l21bapzbjcvblbvks3jh9rpy9hng1ccd7f0glhqw695lc737bpx")))) | |
12960 | (build-system r-build-system) | |
12961 | (propagated-inputs | |
12962 | `(("r-adegenet" ,r-adegenet) | |
12963 | ("r-ape" ,r-ape))) | |
12964 | (home-page "http://ape-package.ird.fr/pegas.html") | |
12965 | (synopsis "Population and evolutionary genetics analysis system") | |
12966 | (description | |
12967 | "This package provides functions for reading, writing, plotting, | |
12968 | analysing, and manipulating allelic and haplotypic data, including from VCF | |
12969 | files, and for the analysis of population nucleotide sequences and | |
12970 | micro-satellites including coalescent analyses, linkage disequilibrium, | |
12971 | population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, | |
12972 | minimum spanning tree and network, and median-joining networks.") | |
12973 | (license license:gpl2+))) | |
cd977b35 RW |
12974 | |
12975 | (define-public r-rmetasim | |
12976 | (package | |
12977 | (name "r-rmetasim") | |
12978 | (version "3.1.7") | |
12979 | (source | |
12980 | (origin | |
12981 | (method url-fetch) | |
12982 | (uri (cran-uri "rmetasim" version)) | |
12983 | (sha256 | |
12984 | (base32 | |
12985 | "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r")))) | |
12986 | (build-system r-build-system) | |
12987 | (propagated-inputs | |
12988 | `(("r-ade4" ,r-ade4) | |
12989 | ("r-adegenet" ,r-adegenet) | |
12990 | ("r-gtools" ,r-gtools) | |
12991 | ("r-pegas" ,r-pegas))) | |
12992 | (home-page "https://cran.r-project.org/web/packages/rmetasim") | |
12993 | (synopsis "Individual-based population genetic simulation environment") | |
12994 | (description | |
12995 | "This package provides an interface between R and the metasim simulation | |
12996 | engine. The simulation environment is documented in: Strand, A.(2002), | |
12997 | Metasim 1.0: an individual-based environment for simulating population | |
12998 | genetics of complex population dynamics.") | |
12999 | ;; Any GPL version | |
13000 | (license license:gpl2+))) | |
601ddf02 RW |
13001 | |
13002 | (define-public r-genetics | |
13003 | (package | |
13004 | (name "r-genetics") | |
f1c1bbc1 | 13005 | (version "1.3.8.1.2") |
601ddf02 RW |
13006 | (source |
13007 | (origin | |
13008 | (method url-fetch) | |
13009 | (uri (cran-uri "genetics" version)) | |
13010 | (sha256 | |
13011 | (base32 | |
f1c1bbc1 | 13012 | "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh")))) |
601ddf02 RW |
13013 | (build-system r-build-system) |
13014 | (propagated-inputs | |
13015 | `(("r-combinat" ,r-combinat) | |
13016 | ("r-gdata" ,r-gdata) | |
13017 | ("r-gtools" ,r-gtools) | |
13018 | ("r-mass" ,r-mass) | |
13019 | ("r-mvtnorm" ,r-mvtnorm))) | |
13020 | (home-page "https://cran.r-project.org/web/packages/genetics/") | |
13021 | (synopsis "Population genetics") | |
13022 | (description | |
13023 | "This package provides classes and methods for handling genetic data. | |
13024 | It includes classes to represent genotypes and haplotypes at single markers up | |
13025 | to multiple markers on multiple chromosomes. Function include allele | |
13026 | frequencies, flagging homo/heterozygotes, flagging carriers of certain | |
13027 | alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating | |
13028 | and testing for linkage disequilibrium, ...") | |
13029 | ;; Any GPL version. | |
13030 | (license license:gpl2+))) | |
5ef7d057 RW |
13031 | |
13032 | (define-public r-snp-plotter | |
13033 | (package | |
13034 | (name "r-snp-plotter") | |
13035 | (version "0.5.1") | |
13036 | (source | |
13037 | (origin | |
13038 | (method url-fetch) | |
13039 | (uri (cran-uri "snp.plotter" version)) | |
13040 | (sha256 | |
13041 | (base32 | |
13042 | "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) | |
13043 | (properties `((upstream-name . "snp.plotter"))) | |
13044 | (build-system r-build-system) | |
13045 | (propagated-inputs `(("r-genetics" ,r-genetics))) | |
13046 | (home-page "https://cran.r-project.org/web/packages/snp.plotter/") | |
13047 | (synopsis "Plot p-values using single SNP and/or haplotype data") | |
13048 | (description | |
13049 | "This package helps you create plots of p-values using single SNP and/or | |
13050 | haplotype data. Main features of the package include options to display a | |
13051 | @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple | |
13052 | datasets simultaneously. Plots can be created using global and/or individual | |
13053 | haplotype p-values along with single SNP p-values. Images are created as | |
13054 | either PDF/EPS files.") | |
13055 | (license license:gpl2+))) | |
6a472af3 RW |
13056 | |
13057 | (define-public r-polspline | |
13058 | (package | |
13059 | (name "r-polspline") | |
9fea25cf | 13060 | (version "1.1.15") |
6a472af3 RW |
13061 | (source |
13062 | (origin | |
13063 | (method url-fetch) | |
13064 | (uri (cran-uri "polspline" version)) | |
13065 | (sha256 | |
13066 | (base32 | |
9fea25cf | 13067 | "19zs4kpagsrzhng1byjbz1c4jxnfk58h4rgr096ml1bjwrgamnwc")))) |
6a472af3 RW |
13068 | (build-system r-build-system) |
13069 | (native-inputs `(("gfortran" ,gfortran))) | |
13070 | (home-page "https://cran.r-project.org/web/packages/polspline/") | |
13071 | (synopsis "Polynomial spline routines") | |
13072 | (description | |
13073 | "This package provides routines for the polynomial spline fitting | |
13074 | routines hazard regression, hazard estimation with flexible tails, logspline, | |
13075 | lspec, polyclass, and polymars.") | |
13076 | (license license:gpl2+))) | |
a8c965cf RW |
13077 | |
13078 | (define-public r-rms | |
13079 | (package | |
13080 | (name "r-rms") | |
88a39cc6 | 13081 | (version "5.1-3.1") |
a8c965cf RW |
13082 | (source |
13083 | (origin | |
13084 | (method url-fetch) | |
13085 | (uri (cran-uri "rms" version)) | |
13086 | (sha256 | |
13087 | (base32 | |
88a39cc6 | 13088 | "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9")))) |
a8c965cf RW |
13089 | (build-system r-build-system) |
13090 | (propagated-inputs | |
13091 | `(("r-ggplot2" ,r-ggplot2) | |
13092 | ("r-hmisc" ,r-hmisc) | |
13093 | ("r-htmltable" ,r-htmltable) | |
13094 | ("r-htmltools" ,r-htmltools) | |
13095 | ("r-lattice" ,r-lattice) | |
13096 | ("r-multcomp" ,r-multcomp) | |
13097 | ("r-nlme" ,r-nlme) | |
13098 | ("r-polspline" ,r-polspline) | |
13099 | ("r-quantreg" ,r-quantreg) | |
13100 | ("r-rpart" ,r-rpart) | |
13101 | ("r-sparsem" ,r-sparsem) | |
13102 | ("r-survival" ,r-survival))) | |
13103 | (native-inputs `(("gfortran" ,gfortran))) | |
13104 | (home-page "http://biostat.mc.vanderbilt.edu/rms") | |
13105 | (synopsis "Regression modeling strategies") | |
13106 | (description | |
13107 | "This is a package for regression modeling, testing, estimation, | |
13108 | validation, graphics, prediction, and typesetting by storing enhanced model | |
13109 | design attributes in the fit. The rms package is a collection of functions | |
13110 | that assist with and streamline modeling. It also contains functions for | |
13111 | binary and ordinal logistic regression models, ordinal models for continuous Y | |
13112 | with a variety of distribution families, and the Buckley-James multiple | |
13113 | regression model for right-censored responses, and implements penalized | |
13114 | maximum likelihood estimation for logistic and ordinary linear models. The | |
13115 | package works with almost any regression model, but it was especially written | |
13116 | to work with binary or ordinal regression models, Cox regression, accelerated | |
13117 | failure time models, ordinary linear models, the Buckley-James model, | |
13118 | generalized least squares for serially or spatially correlated observations, | |
13119 | generalized linear models, and quantile regression.") | |
13120 | (license license:gpl2+))) | |
cd47dcf6 RW |
13121 | |
13122 | (define-public r-haplo-stats | |
13123 | (package | |
13124 | (name "r-haplo-stats") | |
13125 | (version "1.7.9") | |
13126 | (source | |
13127 | (origin | |
13128 | (method url-fetch) | |
13129 | (uri (cran-uri "haplo.stats" version)) | |
13130 | (sha256 | |
13131 | (base32 | |
13132 | "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx")))) | |
13133 | (properties `((upstream-name . "haplo.stats"))) | |
13134 | (build-system r-build-system) | |
13135 | (propagated-inputs | |
13136 | `(("r-rms" ,r-rms))) | |
13137 | (native-inputs | |
13138 | `(("r-r-rsp" ,r-r-rsp))) ; for vignettes | |
13139 | (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") | |
13140 | (synopsis "Analysis of haplotypes when linkage phase is ambiguous") | |
13141 | (description | |
13142 | "This package provides routines for the analysis of indirectly measured | |
13143 | haplotypes. The statistical methods assume that all subjects are unrelated | |
13144 | and that haplotypes are ambiguous (due to unknown linkage phase of the genetic | |
13145 | markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()}, | |
13146 | @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed | |
13147 | examples in the vignette.") | |
13148 | (license license:gpl2+))) | |
bffb5826 RW |
13149 | |
13150 | (define-public r-bqtl | |
13151 | (package | |
13152 | (name "r-bqtl") | |
13153 | (version "1.0-32") | |
13154 | (source | |
13155 | (origin | |
13156 | (method url-fetch) | |
13157 | (uri (cran-uri "bqtl" version)) | |
13158 | (sha256 | |
13159 | (base32 | |
13160 | "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci")))) | |
13161 | (build-system r-build-system) | |
13162 | (native-inputs `(("gfortran" ,gfortran))) | |
13163 | (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") | |
13164 | (synopsis "Bayesian QTL mapping toolkit") | |
13165 | (description | |
13166 | "This is a QTL mapping toolkit for inbred crosses and recombinant inbred | |
13167 | lines. It includes maximum likelihood and Bayesian tools.") | |
13168 | (license license:gpl2+))) | |
73fcd222 RW |
13169 | |
13170 | (define-public r-ibdreg | |
13171 | (package | |
13172 | (name "r-ibdreg") | |
13173 | (version "0.2.5") | |
13174 | (source | |
13175 | (origin | |
13176 | (method url-fetch) | |
13177 | (uri (cran-uri "ibdreg" version)) | |
13178 | (sha256 | |
13179 | (base32 | |
13180 | "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g")))) | |
13181 | (build-system r-build-system) | |
13182 | (home-page "https://www.mayo.edu/research/labs/\ | |
13183 | statistical-genetics-genetic-epidemiology/software") | |
13184 | (synopsis "Regression methods for IBD linkage with covariates") | |
13185 | (description | |
13186 | "This package provides a method to test genetic linkage with covariates | |
13187 | by regression methods with response IBD sharing for relative pairs. Account | |
13188 | for correlations of IBD statistics and covariates for relative pairs within | |
13189 | the same pedigree.") | |
13190 | (license license:gpl2+))) | |
d4a255a4 RW |
13191 | |
13192 | (define-public r-dlmap | |
13193 | (package | |
13194 | (name "r-dlmap") | |
13195 | (version "1.13") | |
13196 | (source | |
13197 | (origin | |
13198 | (method url-fetch) | |
13199 | (uri (cran-uri "dlmap" version)) | |
13200 | (sha256 | |
13201 | (base32 | |
13202 | "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) | |
13203 | (build-system r-build-system) | |
13204 | (propagated-inputs | |
13205 | `(("r-ibdreg" ,r-ibdreg) | |
13206 | ("r-mgcv" ,r-mgcv) | |
13207 | ("r-nlme" ,r-nlme) | |
13208 | ("r-qtl" ,r-qtl) | |
13209 | ("r-wgaim" ,r-wgaim))) | |
13210 | (home-page "https://cran.r-project.org/web/packages/dlmap/") | |
13211 | (synopsis "Detection localization mapping for QTL") | |
13212 | (description | |
13213 | "This is package for QTL mapping in a mixed model framework with separate | |
13214 | detection and localization stages. The first stage detects the number of QTL | |
13215 | on each chromosome based on the genetic variation due to grouped markers on | |
13216 | the chromosome; the second stage uses this information to determine the most | |
13217 | likely QTL positions. The mixed model can accommodate general fixed and | |
13218 | random effects, including spatial effects in field trials and pedigree | |
13219 | effects. It is applicable to backcrosses, doubled haploids, recombinant | |
13220 | inbred lines, F2 intercrosses, and association mapping populations.") | |
13221 | (license license:gpl2))) | |
1cdd9f0e RW |
13222 | |
13223 | (define-public r-ldheatmap | |
13224 | (package | |
13225 | (name "r-ldheatmap") | |
1a88de18 | 13226 | (version "0.99-7") |
1cdd9f0e RW |
13227 | (source |
13228 | (origin | |
13229 | (method url-fetch) | |
13230 | (uri (cran-uri "LDheatmap" version)) | |
13231 | (sha256 | |
13232 | (base32 | |
1a88de18 | 13233 | "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc")))) |
1cdd9f0e RW |
13234 | (properties `((upstream-name . "LDheatmap"))) |
13235 | (build-system r-build-system) | |
13236 | (propagated-inputs | |
13237 | `(("r-genetics" ,r-genetics) | |
1a88de18 | 13238 | ("r-rcpp" ,r-rcpp) |
1cdd9f0e RW |
13239 | ("r-snpstats" ,r-snpstats))) |
13240 | (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html") | |
13241 | (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") | |
13242 | (description | |
13243 | "This package provides tools to produce a graphical display, as a heat | |
13244 | map, of measures of pairwise linkage disequilibria between SNPs. Users may | |
13245 | optionally include the physical locations or genetic map distances of each SNP | |
13246 | on the plot.") | |
13247 | (license license:gpl3))) | |
b8fea3c8 RW |
13248 | |
13249 | (define-public r-hwde | |
13250 | (package | |
13251 | (name "r-hwde") | |
13252 | (version "0.67") | |
13253 | (source | |
13254 | (origin | |
13255 | (method url-fetch) | |
13256 | (uri (cran-uri "hwde" version)) | |
13257 | (sha256 | |
13258 | (base32 | |
13259 | "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy")))) | |
13260 | (build-system r-build-system) | |
13261 | (home-page "https://cran.r-project.org/web/packages/hwde/") | |
13262 | (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium") | |
13263 | (description | |
13264 | "This package fits models for genotypic disequilibria, as described in | |
13265 | Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast | |
13266 | terms are available that account for first order interactions between loci. | |
13267 | It also implements, for a single locus in a single population, a conditional | |
13268 | exact test for Hardy-Weinberg equilibrium.") | |
13269 | (license license:gpl2+))) | |
7cd4ff2f RW |
13270 | |
13271 | (define-public r-tdthap | |
13272 | (package | |
13273 | (name "r-tdthap") | |
87b43815 | 13274 | (version "1.1-11") |
7cd4ff2f RW |
13275 | (source |
13276 | (origin | |
13277 | (method url-fetch) | |
13278 | (uri (cran-uri "tdthap" version)) | |
13279 | (sha256 | |
13280 | (base32 | |
87b43815 | 13281 | "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k")))) |
7cd4ff2f RW |
13282 | (build-system r-build-system) |
13283 | (home-page "https://cran.r-project.org/web/packages/tdthap/") | |
13284 | (synopsis "TDT tests for extended haplotypes") | |
13285 | (description | |
13286 | "Functions and examples are provided for transmission/disequilibrium | |
13287 | tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) | |
13288 | \"Transmission/disequilibrium tests for extended marker haplotypes\".") | |
13289 | (license license:artistic2.0))) | |
469fb438 RW |
13290 | |
13291 | (define-public r-sparql | |
13292 | (package | |
13293 | (name "r-sparql") | |
13294 | (version "1.16") | |
13295 | (source (origin | |
13296 | (method url-fetch) | |
13297 | (uri (cran-uri "SPARQL" version)) | |
13298 | (sha256 | |
13299 | (base32 | |
13300 | "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) | |
13301 | (properties `((upstream-name . "SPARQL"))) | |
13302 | (build-system r-build-system) | |
13303 | (propagated-inputs | |
13304 | `(("r-rcurl" ,r-rcurl) | |
13305 | ("r-xml" ,r-xml))) | |
13306 | (home-page "https://cran.r-project.org/web/packages/SPARQL") | |
13307 | (synopsis "SPARQL client for R") | |
13308 | (description "This package provides an interface to use SPARQL to pose | |
13309 | SELECT or UPDATE queries to an end-point.") | |
13310 | ;; The only license indication is found in the DESCRIPTION file, | |
13311 | ;; which states GPL-3. So we cannot assume GPLv3+. | |
13312 | (license license:gpl3))) | |
0ef062b3 RW |
13313 | |
13314 | (define-public r-bookdown | |
13315 | (package | |
13316 | (name "r-bookdown") | |
dcb45ce5 | 13317 | (version "0.14") |
0ef062b3 RW |
13318 | (source (origin |
13319 | (method url-fetch) | |
13320 | (uri (cran-uri "bookdown" version)) | |
13321 | (sha256 | |
13322 | (base32 | |
dcb45ce5 | 13323 | "1jiq2d292y0l3f4npyfzfpnmb0sqxsl212kkjfbjg5301h0na762")))) |
0ef062b3 RW |
13324 | (build-system r-build-system) |
13325 | (propagated-inputs | |
13326 | `(("r-htmltools" ,r-htmltools) | |
13327 | ("r-knitr" ,r-knitr) | |
13328 | ("r-rmarkdown" ,r-rmarkdown) | |
13329 | ("r-tinytex" ,r-tinytex) | |
650e8def RW |
13330 | ("r-xfun" ,r-xfun) |
13331 | ("pandoc" ,ghc-pandoc))) | |
0ef062b3 RW |
13332 | (home-page "https://github.com/rstudio/bookdown") |
13333 | (synopsis "Authoring books and technical documents with R markdown") | |
13334 | (description "This package provides output formats and utilities for | |
13335 | authoring books and technical documents with R Markdown.") | |
13336 | (license license:gpl3))) | |
72a216a9 RW |
13337 | |
13338 | (define-public r-optparse | |
13339 | (package | |
13340 | (name "r-optparse") | |
cbe42da2 | 13341 | (version "1.6.4") |
72a216a9 RW |
13342 | (source |
13343 | (origin | |
13344 | (method url-fetch) | |
13345 | (uri (cran-uri "optparse" version)) | |
13346 | (sha256 | |
13347 | (base32 | |
cbe42da2 | 13348 | "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d")))) |
72a216a9 RW |
13349 | (build-system r-build-system) |
13350 | (propagated-inputs | |
13351 | `(("r-getopt" ,r-getopt))) | |
13352 | (home-page "https://github.com/trevorld/optparse") | |
13353 | (synopsis "Command line option parser") | |
13354 | (description | |
13355 | "This package provides a command line parser inspired by Python's | |
13356 | @code{optparse} library to be used with Rscript to write shebang scripts | |
13357 | that accept short and long options.") | |
13358 | (license license:gpl2+))) | |
c5a2b518 RW |
13359 | |
13360 | (define-public r-wgcna | |
13361 | (package | |
13362 | (name "r-wgcna") | |
7a857771 | 13363 | (version "1.68") |
c5a2b518 RW |
13364 | (source |
13365 | (origin | |
13366 | (method url-fetch) | |
13367 | (uri (cran-uri "WGCNA" version)) | |
13368 | (sha256 | |
13369 | (base32 | |
7a857771 | 13370 | "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a")))) |
c5a2b518 RW |
13371 | (properties `((upstream-name . "WGCNA"))) |
13372 | (build-system r-build-system) | |
13373 | (propagated-inputs | |
13374 | `(("r-annotationdbi" ,r-annotationdbi) | |
13375 | ("r-doparallel" ,r-doparallel) | |
13376 | ("r-dynamictreecut" ,r-dynamictreecut) | |
13377 | ("r-fastcluster" ,r-fastcluster) | |
13378 | ("r-foreach" ,r-foreach) | |
13379 | ("r-go-db" ,r-go-db) | |
13380 | ("r-hmisc" ,r-hmisc) | |
13381 | ("r-impute" ,r-impute) | |
13382 | ("r-rcpp" ,r-rcpp) | |
13383 | ("r-robust" ,r-robust) | |
13384 | ("r-survival" ,r-survival) | |
13385 | ("r-matrixstats" ,r-matrixstats) | |
13386 | ("r-preprocesscore" ,r-preprocesscore))) | |
13387 | (home-page | |
13388 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
13389 | (synopsis "Weighted correlation network analysis") | |
13390 | (description | |
13391 | "This package provides functions necessary to perform Weighted | |
13392 | Correlation Network Analysis on high-dimensional data. It includes functions | |
13393 | for rudimentary data cleaning, construction and summarization of correlation | |
13394 | networks, module identification and functions for relating both variables and | |
13395 | modules to sample traits. It also includes a number of utility functions for | |
13396 | data manipulation and visualization.") | |
13397 | (license license:gpl2+))) | |
bac0ca32 RW |
13398 | |
13399 | (define-public r-kernlab | |
13400 | (package | |
13401 | (name "r-kernlab") | |
13402 | (version "0.9-27") | |
13403 | (source | |
13404 | (origin | |
13405 | (method url-fetch) | |
13406 | (uri (cran-uri "kernlab" version)) | |
13407 | (sha256 | |
13408 | (base32 | |
13409 | "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn")))) | |
13410 | (build-system r-build-system) | |
13411 | (home-page "https://cran.r-project.org/web/packages/kernlab") | |
13412 | (synopsis "Kernel-based machine learning tools") | |
13413 | (description | |
13414 | "This package provides kernel-based machine learning methods for | |
13415 | classification, regression, clustering, novelty detection, quantile regression | |
13416 | and dimensionality reduction. Among other methods @code{kernlab} includes | |
13417 | Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes | |
13418 | and a QP solver.") | |
13419 | (license license:gpl2))) | |
a0583c0d RW |
13420 | |
13421 | (define-public r-hierfstat | |
13422 | (package | |
13423 | (name "r-hierfstat") | |
13424 | (version "0.04-22") | |
13425 | (source | |
13426 | (origin | |
13427 | (method url-fetch) | |
13428 | (uri (cran-uri "hierfstat" version)) | |
13429 | (sha256 | |
13430 | (base32 | |
13431 | "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx")))) | |
13432 | (build-system r-build-system) | |
13433 | (propagated-inputs | |
13434 | `(("r-ade4" ,r-ade4) | |
13435 | ("r-adegenet" ,r-adegenet) | |
13436 | ("r-gtools" ,r-gtools))) | |
13437 | (home-page "https://cran.r-project.org/web/packages/hierfstat/") | |
13438 | (synopsis "Estimation and tests of hierarchical F-statistics") | |
13439 | (description | |
13440 | "This package allows the estimation of hierarchical F-statistics from | |
13441 | haploid or diploid genetic data with any numbers of levels in the hierarchy, | |
13442 | following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions | |
13443 | are also given to test via randomisations the significance of each F and | |
13444 | variance components, using the likelihood-ratio statistics G.") | |
13445 | (license license:gpl2+))) | |
3080b81a RW |
13446 | |
13447 | (define-public r-hapassoc | |
13448 | (package | |
13449 | (name "r-hapassoc") | |
13450 | (version "1.2-8") | |
13451 | (source | |
13452 | (origin | |
13453 | (method url-fetch) | |
13454 | (uri (cran-uri "hapassoc" version)) | |
13455 | (sha256 | |
13456 | (base32 | |
13457 | "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s")))) | |
13458 | (build-system r-build-system) | |
13459 | (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html") | |
13460 | (synopsis "Inference of trait associations with SNP haplotypes") | |
13461 | (description | |
13462 | "Hapassoc performs likelihood inference of trait associations with | |
13463 | haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The | |
13464 | functions are developed primarily for data collected in cohort or | |
13465 | cross-sectional studies. They can accommodate uncertain haplotype phase and | |
13466 | handle missing genotypes at some SNPs.") | |
13467 | (license license:gpl2))) | |
7166b77a RW |
13468 | |
13469 | (define-public r-sampling | |
13470 | (package | |
13471 | (name "r-sampling") | |
13472 | (version "2.8") | |
13473 | (source | |
13474 | (origin | |
13475 | (method url-fetch) | |
13476 | (uri (cran-uri "sampling" version)) | |
13477 | (sha256 | |
13478 | (base32 | |
13479 | "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m")))) | |
13480 | (build-system r-build-system) | |
13481 | (propagated-inputs | |
13482 | `(("r-lpsolve" ,r-lpsolve) | |
13483 | ("r-mass" ,r-mass))) | |
13484 | (home-page "https://cran.r-project.org/web/packages/sampling/") | |
13485 | (synopsis "Survey sampling") | |
13486 | (description | |
13487 | "This package provides functions for drawing and calibrating samples.") | |
13488 | (license license:gpl2+))) | |
4f8b1fb3 RW |
13489 | |
13490 | (define-public r-r2html | |
13491 | (package | |
13492 | (name "r-r2html") | |
13493 | (version "2.3.2") | |
13494 | (source | |
13495 | (origin | |
13496 | (method url-fetch) | |
13497 | (uri (cran-uri "R2HTML" version)) | |
13498 | (sha256 | |
13499 | (base32 | |
13500 | "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9")))) | |
13501 | (properties `((upstream-name . "R2HTML"))) | |
13502 | (build-system r-build-system) | |
13503 | (home-page "https://github.com/nalimilan/R2HTML") | |
13504 | (synopsis "HTML export for R objects") | |
13505 | (description | |
13506 | "This package includes HTML functions and methods to write in an HTML | |
13507 | file. Thus, making HTML reports is easy. It includes a function that allows | |
13508 | redirection on the fly, which appears to be very useful for teaching purposes, | |
13509 | as the student can keep a copy of the produced output to keep all that they | |
13510 | did during the course. The package comes with a vignette describing how to | |
13511 | write HTML reports for statistical analysis. Finally, a driver for Sweave | |
13512 | allows to parse HTML flat files containing R code and to automatically write | |
13513 | the corresponding outputs (tables and graphs).") | |
13514 | (license license:gpl2+))) | |
3f6e6e98 RW |
13515 | |
13516 | (define-public r-rjava | |
13517 | (package | |
13518 | (name "r-rjava") | |
f2f89e9a | 13519 | (version "0.9-11") |
3f6e6e98 RW |
13520 | (source |
13521 | (origin | |
13522 | (method url-fetch) | |
13523 | (uri (cran-uri "rJava" version)) | |
13524 | (sha256 | |
13525 | (base32 | |
f2f89e9a | 13526 | "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2")))) |
3f6e6e98 RW |
13527 | (properties `((upstream-name . "rJava"))) |
13528 | (build-system r-build-system) | |
13529 | (arguments | |
13530 | `(#:modules ((guix build utils) | |
13531 | (guix build r-build-system) | |
13532 | (ice-9 match)) | |
13533 | #:phases | |
13534 | (modify-phases %standard-phases | |
13535 | (add-after 'unpack 'set-JAVA_HOME | |
13536 | (lambda* (#:key inputs #:allow-other-keys) | |
13537 | (let ((jdk (assoc-ref inputs "jdk"))) | |
13538 | (setenv "JAVA_HOME" jdk) | |
13539 | (setenv "JAVA" (which "java")) | |
13540 | (setenv "JAR" (which "jar")) | |
13541 | (setenv "JAVAC" (which "javac")) | |
13542 | (setenv "JAVAH" (which "javah")) | |
13543 | (setenv "JAVA_CPPFLAGS" | |
13544 | (string-append "-I" jdk "/include " | |
13545 | "-I" jdk "/include/linux")) | |
13546 | (match (find-files (string-append jdk "/jre/lib/") "libjvm.so") | |
13547 | ((lib) (setenv "JAVA_LIBS" lib)) | |
13548 | (_ (error "Could not find libjvm.so")))) | |
13549 | #t))))) | |
13550 | (inputs | |
13551 | `(("icu4c" ,icu4c) | |
13552 | ("jdk" ,icedtea-8 "jdk") | |
13553 | ("pcre" ,pcre) | |
13554 | ("zlib" ,zlib))) | |
13555 | (home-page "http://www.rforge.net/rJava/") | |
13556 | (synopsis "Low-Level R to Java interface") | |
13557 | (description | |
13558 | "This package provides a low-level interface to the Java VM very much | |
13559 | like .C/.Call and friends. It allows the creation of objects, calling methods | |
13560 | and accessing fields.") | |
13561 | (license license:gpl2))) | |
b9b177b3 RW |
13562 | |
13563 | (define-public r-svmisc | |
13564 | (package | |
13565 | (name "r-svmisc") | |
13566 | (version "1.1.0") | |
13567 | (source | |
13568 | (origin | |
13569 | (method url-fetch) | |
13570 | (uri (cran-uri "svMisc" version)) | |
13571 | (sha256 | |
13572 | (base32 | |
13573 | "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2")))) | |
13574 | (properties `((upstream-name . "svMisc"))) | |
13575 | (build-system r-build-system) | |
13576 | (home-page "https://github.com/SciViews/svMisc") | |
13577 | (synopsis "Miscellaneous functions for SciViews") | |
13578 | (description | |
13579 | "This package provides miscellaneous functions for SciViews or general | |
13580 | use, including tools to manage a temporary environment attached to the search | |
13581 | path for temporary variables you do not want to @code{save()} or | |
13582 | @code{load()}; test the current platform; showing progress bars, etc.") | |
13583 | (license license:gpl2))) | |
18c51cf3 RW |
13584 | |
13585 | (define-public r-xyz | |
13586 | (package | |
13587 | (name "r-xyz") | |
13588 | (version "0.2") | |
13589 | (source | |
13590 | (origin | |
13591 | (method url-fetch) | |
13592 | (uri (cran-uri "xyz" version)) | |
13593 | (sha256 | |
13594 | (base32 | |
13595 | "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) | |
13596 | (build-system r-build-system) | |
13597 | (propagated-inputs | |
13598 | `(("r-rcpp" ,r-rcpp))) | |
13599 | (home-page "https://cran.r-project.org/web/packages/xyz/") | |
13600 | (synopsis "Algorithm for fast interaction search in high-dimensional data") | |
13601 | (description | |
13602 | "High dimensional interaction search by brute force requires a quadratic | |
13603 | computational cost in the number of variables. The xyz algorithm provably | |
13604 | finds strong interactions in almost linear time. For details of the algorithm | |
13605 | see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast | |
13606 | interaction search in high-dimensional data.") | |
13607 | ;; Any version of the GPL. | |
13608 | (license license:gpl2+))) | |
81df4e1e RW |
13609 | |
13610 | (define-public r-rttf2pt1 | |
13611 | (package | |
13612 | (name "r-rttf2pt1") | |
13613 | (version "1.3.7") | |
13614 | (source | |
13615 | (origin | |
13616 | (method url-fetch) | |
13617 | (uri (cran-uri "Rttf2pt1" version)) | |
13618 | (sha256 | |
13619 | (base32 | |
13620 | "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja")))) | |
13621 | (properties `((upstream-name . "Rttf2pt1"))) | |
13622 | (build-system r-build-system) | |
13623 | (home-page "https://github.com/wch/Rttf2pt1") | |
13624 | (synopsis "Font conversion utility") | |
13625 | (description | |
13626 | "This package contains the program @code{ttf2pt1}, for use with the | |
13627 | @code{extrafont} package.") | |
13628 | ;; Most of the files are covered under the Expat license. Some files are | |
13629 | ;; covered under BSD-3. Deviations for individual files are recorded in | |
13630 | ;; the LICENSE file. | |
13631 | (license (list license:bsd-3 license:expat | |
13632 | (license:non-copyleft "file://LICENSE"))))) | |
b6933ea6 RW |
13633 | |
13634 | (define-public r-extrafontdb | |
13635 | (package | |
13636 | (name "r-extrafontdb") | |
13637 | (version "1.0") | |
13638 | (source | |
13639 | (origin | |
13640 | (method url-fetch) | |
13641 | (uri (cran-uri "extrafontdb" version)) | |
13642 | (sha256 | |
13643 | (base32 | |
13644 | "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs")))) | |
13645 | (build-system r-build-system) | |
13646 | (home-page "https://github.com/wch/extrafontdb") | |
13647 | (synopsis "Database for the extrafont package") | |
13648 | (description | |
13649 | "This package holds the database for the @code{extrafont} package.") | |
13650 | (license license:gpl2))) | |
2331bf2a RW |
13651 | |
13652 | (define-public r-extrafont | |
13653 | (package | |
13654 | (name "r-extrafont") | |
13655 | (version "0.17") | |
13656 | (source | |
13657 | (origin | |
13658 | (method url-fetch) | |
13659 | (uri (cran-uri "extrafont" version)) | |
13660 | (sha256 | |
13661 | (base32 | |
13662 | "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g")))) | |
13663 | (build-system r-build-system) | |
13664 | (propagated-inputs | |
13665 | `(("r-extrafontdb" ,r-extrafontdb) | |
13666 | ("r-rttf2pt1" ,r-rttf2pt1))) | |
13667 | (home-page "https://github.com/wch/extrafont") | |
13668 | (synopsis "Tools for using fonts in R") | |
13669 | (description | |
13670 | "The extrafont package makes it easier to use fonts other than the basic | |
13671 | PostScript fonts that R uses. Fonts that are imported into extrafont can be | |
13672 | used with PDF or PostScript output files. There are two hurdles for using | |
13673 | fonts in PDF (or Postscript) output files: | |
13674 | ||
13675 | @enumerate | |
13676 | @item Making R aware of the font and the dimensions of the characters. | |
13677 | @item Embedding the fonts in the PDF file so that the PDF can be displayed | |
13678 | properly on a device that doesn't have the font. This is usually needed if | |
13679 | you want to print the PDF file or share it with others. | |
13680 | @end enumerate | |
13681 | ||
13682 | The extrafont package makes both of these things easier.") | |
13683 | (license license:gpl2))) | |
2d704608 RW |
13684 | |
13685 | (define-public r-xkcd | |
13686 | (package | |
13687 | (name "r-xkcd") | |
13688 | (version "0.0.6") | |
13689 | (source | |
13690 | (origin | |
13691 | (method url-fetch) | |
13692 | (uri (cran-uri "xkcd" version)) | |
13693 | (sha256 | |
13694 | (base32 | |
13695 | "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) | |
13696 | (build-system r-build-system) | |
13697 | (propagated-inputs | |
13698 | `(("r-extrafont" ,r-extrafont) | |
13699 | ("r-ggplot2" ,r-ggplot2) | |
13700 | ("r-hmisc" ,r-hmisc))) | |
13701 | (home-page "https://cran.r-project.org/web/packages/xkcd/") | |
13702 | (synopsis "Plot ggplot2 graphics in the XKCD style") | |
13703 | (description | |
13704 | "This package provides the means to plot ggplot2 graphs in the style of | |
13705 | the XKCD web comic.") | |
13706 | (license license:gpl3))) | |
0d50d0df RW |
13707 | |
13708 | (define-public r-msigdbr | |
13709 | (package | |
13710 | (name "r-msigdbr") | |
995a20e8 | 13711 | (version "7.0.1") |
0d50d0df RW |
13712 | (source |
13713 | (origin | |
13714 | (method url-fetch) | |
13715 | (uri (cran-uri "msigdbr" version)) | |
13716 | (sha256 | |
13717 | (base32 | |
995a20e8 | 13718 | "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd")))) |
0d50d0df RW |
13719 | (build-system r-build-system) |
13720 | (propagated-inputs | |
13721 | `(("r-dplyr" ,r-dplyr) | |
13722 | ("r-magrittr" ,r-magrittr) | |
13723 | ("r-rlang" ,r-rlang) | |
13724 | ("r-tibble" ,r-tibble))) | |
13725 | (home-page "https://github.com/igordot/msigdbr") | |
13726 | (synopsis "MSigDB gene sets for multiple organisms") | |
13727 | (description | |
13728 | "This package provides the @dfn{Molecular Signatures Database} (MSigDB) | |
13729 | gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA) | |
13730 | software in a standard R data frame with key-value pairs. Included are the | |
13731 | original human gene symbols and Entrez IDs as well as the equivalents for | |
13732 | various frequently studied model organisms such as mouse, rat, pig, fly, and | |
13733 | yeast.") | |
13734 | ;; The package is covered under the Expat license, but the upstream MSigDB | |
13735 | ;; files are made available under the Creative Commons Attribution 4.0 | |
13736 | ;; International license. | |
13737 | (license (list license:expat license:cc-by4.0)))) | |
585d5ae0 RW |
13738 | |
13739 | (define-public r-gridgraphics | |
13740 | (package | |
13741 | (name "r-gridgraphics") | |
b985cc35 | 13742 | (version "0.4-1") |
585d5ae0 RW |
13743 | (source |
13744 | (origin | |
13745 | (method url-fetch) | |
13746 | (uri (cran-uri "gridGraphics" version)) | |
13747 | (sha256 | |
13748 | (base32 | |
b985cc35 | 13749 | "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p")))) |
585d5ae0 RW |
13750 | (properties `((upstream-name . "gridGraphics"))) |
13751 | (build-system r-build-system) | |
13752 | (home-page "https://github.com/pmur002/gridgraphics") | |
13753 | (synopsis "Redraw base graphics using @code{grid} graphics") | |
13754 | (description | |
13755 | "This package provides functions to convert a page of plots drawn with | |
13756 | the @code{graphics} package into identical output drawn with the @code{grid} | |
13757 | package. The result looks like the original @code{graphics}-based plot, but | |
13758 | consists of @code{grid} grobs and viewports that can then be manipulated with | |
13759 | @code{grid} functions (e.g., edit grobs and revisit viewports).") | |
13760 | (license license:gpl2+))) | |
1c59ec70 RW |
13761 | |
13762 | (define-public r-farver | |
13763 | (package | |
13764 | (name "r-farver") | |
13765 | (version "1.1.0") | |
13766 | (source | |
13767 | (origin | |
13768 | (method url-fetch) | |
13769 | (uri (cran-uri "farver" version)) | |
13770 | (sha256 | |
13771 | (base32 | |
13772 | "1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0")))) | |
13773 | (build-system r-build-system) | |
13774 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
13775 | (home-page "https://github.com/thomasp85/farver") | |
13776 | (synopsis "Vectorized color conversion and comparison") | |
13777 | (description | |
13778 | "The encoding of color can be handled in many different ways, using | |
13779 | different color spaces. As different color spaces have different uses, | |
13780 | efficient conversion between these representations are important. This | |
13781 | package provides a set of functions that gives access to very fast color space | |
13782 | conversion and comparisons implemented in C++, and offers 100-fold speed | |
13783 | improvements over the @code{convertColor} function in the @code{grDevices} | |
13784 | package.") | |
13785 | (license license:expat))) | |
e2582883 RW |
13786 | |
13787 | (define-public r-ggplotify | |
13788 | (package | |
13789 | (name "r-ggplotify") | |
f2758945 | 13790 | (version "0.0.4") |
e2582883 RW |
13791 | (source |
13792 | (origin | |
13793 | (method url-fetch) | |
13794 | (uri (cran-uri "ggplotify" version)) | |
13795 | (sha256 | |
13796 | (base32 | |
f2758945 | 13797 | "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg")))) |
e2582883 RW |
13798 | (build-system r-build-system) |
13799 | (propagated-inputs | |
13800 | `(("r-ggplot2" ,r-ggplot2) | |
13801 | ("r-gridgraphics" ,r-gridgraphics) | |
13802 | ("r-rvcheck" ,r-rvcheck))) | |
13803 | (home-page "https://github.com/GuangchuangYu/ggplotify") | |
13804 | (synopsis "Convert plots to @code{grob} or @code{ggplot} object") | |
13805 | (description | |
13806 | "This package provides tools to convert plot function calls (using | |
13807 | expression or formula) to @code{grob} or @code{ggplot} objects that are | |
13808 | compatible with the @code{grid} and @code{ggplot2} environment. With this | |
13809 | package, we are able to e.g. use @code{cowplot} to align plots produced by | |
13810 | @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by | |
13811 | converting them to @code{ggplot} objects.") | |
13812 | (license license:artistic2.0))) | |
85431ca3 RW |
13813 | |
13814 | (define-public r-triebeard | |
13815 | (package | |
13816 | (name "r-triebeard") | |
13817 | (version "0.3.0") | |
13818 | (source | |
13819 | (origin | |
13820 | (method url-fetch) | |
13821 | (uri (cran-uri "triebeard" version)) | |
13822 | (sha256 | |
13823 | (base32 | |
13824 | "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) | |
13825 | (build-system r-build-system) | |
13826 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
13827 | (home-page "https://github.com/Ironholds/triebeard/") | |
13828 | (synopsis "Radix trees in Rcpp") | |
13829 | (description | |
13830 | "Radix trees, or tries, are key-value data structures optimized for | |
13831 | efficient lookups, similar in purpose to hash tables. This package provides | |
13832 | an implementation of radix trees for use in R programming and in developing | |
13833 | packages with Rcpp.") | |
13834 | (license license:expat))) | |
91e06bed RW |
13835 | |
13836 | (define-public r-tweenr | |
13837 | (package | |
13838 | (name "r-tweenr") | |
13839 | (version "1.0.1") | |
13840 | (source | |
13841 | (origin | |
13842 | (method url-fetch) | |
13843 | (uri (cran-uri "tweenr" version)) | |
13844 | (sha256 | |
13845 | (base32 | |
13846 | "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg")))) | |
13847 | (build-system r-build-system) | |
13848 | (propagated-inputs | |
13849 | `(("r-farver" ,r-farver) | |
13850 | ("r-magrittr" ,r-magrittr) | |
13851 | ("r-rcpp" ,r-rcpp) | |
13852 | ("r-rlang" ,r-rlang))) | |
13853 | (home-page "https://github.com/thomasp85/tweenr") | |
13854 | (synopsis "Interpolate data for smooth animations") | |
13855 | (description | |
13856 | "In order to create smooth animation between states of data, tweening is | |
13857 | necessary. This package provides a range of functions for creating tweened | |
13858 | data that can be used as basis for animation. Furthermore it adds a number of | |
13859 | vectorized interpolaters for common R data types such as numeric, date and | |
13860 | color.") | |
13861 | (license license:expat))) | |
09dde7fb RW |
13862 | |
13863 | (define-public r-polyclip | |
13864 | (package | |
13865 | (name "r-polyclip") | |
13866 | (version "1.10-0") | |
13867 | (source | |
13868 | (origin | |
13869 | (method url-fetch) | |
13870 | (uri (cran-uri "polyclip" version)) | |
13871 | (sha256 | |
13872 | (base32 | |
13873 | "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl")))) | |
13874 | (build-system r-build-system) | |
13875 | (native-inputs `(("pkg-config" ,pkg-config))) | |
13876 | (home-page "http://www.angusj.com/delphi/clipper.php") | |
13877 | (synopsis "Polygon clipping") | |
13878 | (description | |
13879 | "This package provides an R port of the library Clipper. It performs | |
13880 | polygon clipping operations (intersection, union, set minus, set difference) | |
13881 | for polygonal regions of arbitrary complexity, including holes. It computes | |
13882 | offset polygons (spatial buffer zones, morphological dilations, Minkowski | |
13883 | dilations) for polygonal regions and polygonal lines. It computes the | |
13884 | Minkowski Sum of general polygons. There is a function for removing | |
13885 | self-intersections from polygon data.") | |
13886 | (license license:boost1.0))) | |
d4ff09af RW |
13887 | |
13888 | (define-public r-urltools | |
13889 | (package | |
13890 | (name "r-urltools") | |
7015ae68 | 13891 | (version "1.7.3") |
d4ff09af RW |
13892 | (source |
13893 | (origin | |
13894 | (method url-fetch) | |
13895 | (uri (cran-uri "urltools" version)) | |
13896 | (sha256 | |
13897 | (base32 | |
7015ae68 | 13898 | "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830")))) |
d4ff09af RW |
13899 | (build-system r-build-system) |
13900 | (propagated-inputs | |
13901 | `(("r-rcpp" ,r-rcpp) | |
13902 | ("r-triebeard" ,r-triebeard))) | |
13903 | (home-page "https://github.com/Ironholds/urltools/") | |
13904 | (synopsis "Vectorized tools for URL handling and parsing") | |
13905 | (description | |
13906 | "This package provides a toolkit for all URL-handling needs, including | |
13907 | encoding and decoding, parsing, parameter extraction and modification. All | |
13908 | functions are designed to be both fast and entirely vectorized. It is | |
13909 | intended to be useful for people dealing with web-related datasets, such as | |
13910 | server-side logs, although may be useful for other situations involving large | |
13911 | sets of URLs.") | |
13912 | (license license:expat))) | |
83f43284 RW |
13913 | |
13914 | (define-public r-ggforce | |
13915 | (package | |
13916 | (name "r-ggforce") | |
466e68b4 | 13917 | (version "0.3.1") |
83f43284 RW |
13918 | (source |
13919 | (origin | |
13920 | (method url-fetch) | |
13921 | (uri (cran-uri "ggforce" version)) | |
13922 | (sha256 | |
13923 | (base32 | |
466e68b4 | 13924 | "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0")))) |
83f43284 RW |
13925 | (build-system r-build-system) |
13926 | (propagated-inputs | |
13927 | `(("r-ggplot2" ,r-ggplot2) | |
13928 | ("r-gtable" ,r-gtable) | |
13929 | ("r-mass" ,r-mass) | |
13930 | ("r-polyclip" ,r-polyclip) | |
13931 | ("r-rcpp" ,r-rcpp) | |
13932 | ("r-rcppeigen" ,r-rcppeigen) | |
13933 | ("r-rlang" ,r-rlang) | |
13934 | ("r-scales" ,r-scales) | |
3ea54829 RW |
13935 | ("r-tidyselect" ,r-tidyselect) |
13936 | ("r-tweenr" ,r-tweenr) | |
13937 | ("r-withr" ,r-withr))) | |
83f43284 RW |
13938 | (home-page "https://ggforce.data-imaginist.com") |
13939 | (synopsis "Accelerating ggplot2") | |
13940 | (description | |
13941 | "The aim of the ggplot2 package is to aid in visual data investigations. | |
13942 | This focus has led to a lack of facilities for composing specialized plots. | |
13943 | Thi package aims to be a collection of mainly new statistics and geometries | |
13944 | that fills this gap.") | |
13945 | (license license:expat))) | |
b5b0a2ff RW |
13946 | |
13947 | (define-public r-europepmc | |
13948 | (package | |
13949 | (name "r-europepmc") | |
13950 | (version "0.3") | |
13951 | (source | |
13952 | (origin | |
13953 | (method url-fetch) | |
13954 | (uri (cran-uri "europepmc" version)) | |
13955 | (sha256 | |
13956 | (base32 | |
13957 | "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h")))) | |
13958 | (build-system r-build-system) | |
13959 | (propagated-inputs | |
13960 | `(("r-dplyr" ,r-dplyr) | |
13961 | ("r-httr" ,r-httr) | |
13962 | ("r-jsonlite" ,r-jsonlite) | |
13963 | ("r-plyr" ,r-plyr) | |
13964 | ("r-progress" ,r-progress) | |
13965 | ("r-purrr" ,r-purrr) | |
13966 | ("r-urltools" ,r-urltools) | |
13967 | ("r-xml2" ,r-xml2))) | |
13968 | (home-page "https://github.com/ropensci/europepmc/") | |
13969 | (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") | |
13970 | (description | |
13971 | "This package provides an R Client for the | |
13972 | @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web | |
13973 | Service}. It gives access to both metadata on life science literature and | |
13974 | open access full texts. Europe PMC indexes all PubMed content and other | |
13975 | literature sources including Agricola, a bibliographic database of citations | |
13976 | to the agricultural literature, or Biological Patents. In addition to | |
13977 | bibliographic metadata, the client allows users to fetch citations and | |
13978 | reference lists. Links between life-science literature and other EBI | |
13979 | databases, including ENA, PDB or ChEMBL are also accessible.") | |
13980 | (license license:gpl3))) | |
11f226e1 RW |
13981 | |
13982 | (define-public r-ggraph | |
13983 | (package | |
13984 | (name "r-ggraph") | |
801dc98f | 13985 | (version "2.0.0") |
11f226e1 RW |
13986 | (source |
13987 | (origin | |
13988 | (method url-fetch) | |
13989 | (uri (cran-uri "ggraph" version)) | |
13990 | (sha256 | |
13991 | (base32 | |
801dc98f | 13992 | "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3")))) |
11f226e1 RW |
13993 | (build-system r-build-system) |
13994 | (propagated-inputs | |
13995 | `(("r-digest" ,r-digest) | |
13996 | ("r-dplyr" ,r-dplyr) | |
13997 | ("r-ggforce" ,r-ggforce) | |
13998 | ("r-ggplot2" ,r-ggplot2) | |
13999 | ("r-ggrepel" ,r-ggrepel) | |
801dc98f | 14000 | ("r-graphlayouts" ,r-graphlayouts) |
11f226e1 RW |
14001 | ("r-gtable" ,r-gtable) |
14002 | ("r-igraph" ,r-igraph) | |
14003 | ("r-mass" ,r-mass) | |
11f226e1 | 14004 | ("r-rcpp" ,r-rcpp) |
801dc98f | 14005 | ("r-rlang" ,r-rlang) |
11f226e1 | 14006 | ("r-scales" ,r-scales) |
801dc98f | 14007 | ("r-tidygraph" ,r-tidygraph) |
11f226e1 RW |
14008 | ("r-viridis" ,r-viridis))) |
14009 | (home-page "https://cran.r-project.org/web/packages/ggraph/") | |
14010 | (synopsis "Implementation of grammar of graphics for graphs and networks") | |
14011 | (description | |
14012 | "The grammar of graphics as implemented in ggplot2 is a poor fit for | |
14013 | graph and network visualizations due to its reliance on tabular data input. | |
14014 | The ggraph package is an extension of the ggplot2 API tailored to graph | |
14015 | visualizations and provides the same flexible approach to building up plots | |
14016 | layer by layer.") | |
14017 | (license license:gpl3))) | |
1c0c4b54 RW |
14018 | |
14019 | (define-public r-varselrf | |
14020 | (package | |
14021 | (name "r-varselrf") | |
14022 | (version "0.7-8") | |
14023 | (source | |
14024 | (origin | |
14025 | (method url-fetch) | |
14026 | (uri (cran-uri "varSelRF" version)) | |
14027 | (sha256 | |
14028 | (base32 | |
14029 | "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i")))) | |
14030 | (properties `((upstream-name . "varSelRF"))) | |
14031 | (build-system r-build-system) | |
14032 | (propagated-inputs | |
14033 | `(("r-randomforest" ,r-randomforest))) | |
14034 | (home-page "http://ligarto.org/rdiaz/Software/Software.html") | |
14035 | (synopsis "Variable selection using random forests") | |
14036 | (description | |
14037 | "This package provides tools for the variable selection from random | |
14038 | forests using both backwards variable elimination (for the selection of small | |
14039 | sets of non-redundant variables) and selection based on the importance | |
14040 | spectrum (somewhat similar to scree plots; for the selection of large, | |
14041 | potentially highly-correlated variables). The main applications are in | |
14042 | high-dimensional data (e.g., microarray data, and other genomics and | |
14043 | proteomics applications).") | |
14044 | (license license:gpl2+))) | |
aae0b86d RW |
14045 | |
14046 | (define-public r-pamr | |
14047 | (package | |
14048 | (name "r-pamr") | |
8fc6188e | 14049 | (version "1.56.1") |
aae0b86d RW |
14050 | (source |
14051 | (origin | |
14052 | (method url-fetch) | |
14053 | (uri (cran-uri "pamr" version)) | |
14054 | (sha256 | |
14055 | (base32 | |
8fc6188e | 14056 | "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) |
aae0b86d RW |
14057 | (build-system r-build-system) |
14058 | (propagated-inputs | |
14059 | `(("r-cluster" ,r-cluster) | |
14060 | ("r-survival" ,r-survival))) | |
14061 | (native-inputs `(("gfortran" ,gfortran))) | |
14062 | (home-page "https://cran.r-project.org/web/packages/pamr/") | |
14063 | (synopsis "Prediction Analysis for Microarrays") | |
14064 | (description | |
14065 | "This package provides some functions for sample classification in | |
14066 | microarrays.") | |
14067 | (license license:gpl2))) | |
fe3fb4e7 RW |
14068 | |
14069 | (define-public r-rda | |
14070 | (package | |
14071 | (name "r-rda") | |
14072 | (version "1.0.2-2.1") | |
14073 | (source | |
14074 | (origin | |
14075 | (method url-fetch) | |
14076 | (uri (cran-uri "rda" version)) | |
14077 | (sha256 | |
14078 | (base32 | |
14079 | "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639")))) | |
14080 | (build-system r-build-system) | |
14081 | (home-page "https://cran.r-project.org/web/packages/rda/") | |
14082 | (synopsis "Shrunken centroids regularized discriminant analysis") | |
14083 | (description | |
14084 | "This package provides tools for shrunken centroids regularized | |
14085 | discriminant analysis for the purpose of classifying high dimensional data.") | |
14086 | (license license:gpl2+))) | |
8473597f RW |
14087 | |
14088 | (define-public r-ggvis | |
14089 | (package | |
14090 | (name "r-ggvis") | |
14091 | (version "0.4.4") | |
14092 | (source | |
14093 | (origin | |
14094 | (method url-fetch) | |
14095 | (uri (cran-uri "ggvis" version)) | |
14096 | (sha256 | |
14097 | (base32 | |
14098 | "1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk")))) | |
14099 | (build-system r-build-system) | |
14100 | (propagated-inputs | |
14101 | `(("r-assertthat" ,r-assertthat) | |
14102 | ("r-dplyr" ,r-dplyr) | |
14103 | ("r-htmltools" ,r-htmltools) | |
14104 | ("r-jsonlite" ,r-jsonlite) | |
14105 | ("r-lazyeval" ,r-lazyeval) | |
14106 | ("r-magrittr" ,r-magrittr) | |
14107 | ("r-shiny" ,r-shiny))) | |
14108 | (home-page "https://ggvis.rstudio.com/") | |
14109 | (synopsis "Interactive grammar of graphics") | |
14110 | (description | |
14111 | "This package is a data visualization package for R providing an | |
14112 | implementation of an interactive grammar of graphics, taking the best parts of | |
14113 | ggplot2, combining them with the reactive framework of Shiny and drawing web | |
14114 | graphics using Vega.") | |
14115 | (license license:gpl2))) | |
d59df334 RW |
14116 | |
14117 | (define-public r-gbm | |
14118 | (package | |
14119 | (name "r-gbm") | |
14120 | (version "2.1.5") | |
14121 | (source | |
14122 | (origin | |
14123 | (method url-fetch) | |
14124 | (uri (cran-uri "gbm" version)) | |
14125 | (sha256 | |
14126 | (base32 | |
14127 | "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6")))) | |
14128 | (build-system r-build-system) | |
14129 | (propagated-inputs | |
14130 | `(("r-gridextra" ,r-gridextra) | |
14131 | ("r-lattice" ,r-lattice) | |
14132 | ("r-survival" ,r-survival))) | |
14133 | (home-page "https://github.com/gbm-developers/gbm") | |
14134 | (synopsis "Generalized boosted regression models") | |
14135 | (description | |
14136 | "This package is an implementation of extensions to Freund and Schapire's | |
14137 | AdaBoost algorithm and Friedman's gradient boosting machine. It includes | |
14138 | regression methods for least squares, absolute loss, t-distribution loss, | |
14139 | quantile regression, logistic, multinomial logistic, Poisson, Cox proportional | |
14140 | hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, | |
14141 | and Learning to Rank measures (LambdaMart).") | |
14142 | (license license:gpl2+))) | |
efba5613 RW |
14143 | |
14144 | (define-public r-threejs | |
14145 | (package | |
14146 | (name "r-threejs") | |
14147 | (version "0.3.1") | |
14148 | (source | |
14149 | (origin | |
14150 | (method url-fetch) | |
14151 | (uri (cran-uri "threejs" version)) | |
14152 | (sha256 | |
14153 | (base32 | |
14154 | "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi")))) | |
14155 | (build-system r-build-system) | |
14156 | (arguments | |
14157 | `(#:modules ((guix build utils) | |
14158 | (guix build r-build-system) | |
14159 | (srfi srfi-1) | |
14160 | (ice-9 popen)) | |
14161 | #:phases | |
14162 | (modify-phases %standard-phases | |
14163 | (add-after 'unpack 'process-javascript | |
14164 | (lambda* (#:key inputs #:allow-other-keys) | |
14165 | (with-directory-excursion "inst" | |
14166 | (call-with-values | |
14167 | (lambda () | |
14168 | (unzip2 | |
14169 | `((,(assoc-ref inputs "js-jquery") | |
14170 | "htmlwidgets/lib/jquery/jquery.min.js") | |
14171 | (,(assoc-ref inputs "js-threejs-85") | |
14172 | "htmlwidgets/lib/threejs-85/three.min.js")))) | |
14173 | (lambda (sources targets) | |
14174 | (for-each (lambda (source target) | |
14175 | (format #t "Processing ~a --> ~a~%" | |
14176 | source target) | |
14177 | (delete-file target) | |
14178 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
14179 | (call-with-output-file target | |
14180 | (lambda (port) | |
14181 | (dump-port minified port))))) | |
14182 | sources targets)))) | |
14183 | #t))))) | |
14184 | (propagated-inputs | |
14185 | `(("r-base64enc" ,r-base64enc) | |
14186 | ("r-crosstalk" ,r-crosstalk) | |
14187 | ("r-htmlwidgets" ,r-htmlwidgets) | |
14188 | ("r-igraph" ,r-igraph))) | |
14189 | (native-inputs | |
14190 | `(("uglify-js" ,uglify-js) | |
14191 | ("js-jquery" | |
14192 | ,(origin | |
14193 | (method url-fetch) | |
14194 | (uri "https://code.jquery.com/jquery-3.3.1.js") | |
14195 | (sha256 | |
14196 | (base32 | |
14197 | "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) | |
14198 | ("js-threejs-85" | |
14199 | ,(origin | |
14200 | (method url-fetch) | |
14201 | (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js") | |
14202 | (sha256 | |
14203 | (base32 | |
14204 | "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl")))))) | |
14205 | (home-page "https://bwlewis.github.io/rthreejs") | |
14206 | (synopsis "Interactive 3D scatter plots, networks and globes") | |
14207 | (description | |
14208 | "Create interactive 3D scatter plots, network plots, and globes in R | |
14209 | using the three.js visualization library.") | |
14210 | (license license:expat))) | |
74cada8e RW |
14211 | |
14212 | (define-public r-mlbench | |
14213 | (package | |
14214 | (name "r-mlbench") | |
14215 | (version "2.1-1") | |
14216 | (source | |
14217 | (origin | |
14218 | (method url-fetch) | |
14219 | (uri (cran-uri "mlbench" version)) | |
14220 | (sha256 | |
14221 | (base32 | |
14222 | "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl")))) | |
14223 | (build-system r-build-system) | |
14224 | (home-page "https://cran.r-project.org/web/packages/mlbench/") | |
14225 | (synopsis "Machine learning benchmark problems") | |
14226 | (description | |
14227 | "This package provides a collection of artificial and real-world machine | |
14228 | learning benchmark problems, including, e.g., several data sets from the UCI | |
14229 | repository.") | |
14230 | (license license:gpl2))) | |
409a13fe RW |
14231 | |
14232 | (define-public r-mpm | |
14233 | (package | |
14234 | (name "r-mpm") | |
14235 | (version "1.0-22") | |
14236 | (source | |
14237 | (origin | |
14238 | (method url-fetch) | |
14239 | (uri (cran-uri "mpm" version)) | |
14240 | (sha256 | |
14241 | (base32 | |
14242 | "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk")))) | |
14243 | (build-system r-build-system) | |
14244 | (propagated-inputs | |
14245 | `(("r-kernsmooth" ,r-kernsmooth) | |
14246 | ("r-mass" ,r-mass))) | |
14247 | (home-page "http://mpm.r-forge.r-project.org") | |
14248 | (synopsis "Multivariate projection methods") | |
14249 | (description | |
14250 | "This is a package for exploratory graphical analysis of multivariate | |
14251 | data, specifically gene expression data with different projection methods: | |
14252 | principal component analysis, correspondence analysis, spectral map | |
14253 | analysis.") | |
14254 | (license license:gpl2+))) | |
d8a28332 | 14255 | |
d2aa2d24 RW |
14256 | (define-public r-png |
14257 | (package | |
14258 | (name "r-png") | |
14259 | (version "0.1-7") | |
14260 | (source (origin | |
14261 | (method url-fetch) | |
14262 | (uri (cran-uri "png" version)) | |
14263 | (sha256 | |
14264 | (base32 | |
14265 | "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) | |
14266 | (build-system r-build-system) | |
14267 | (inputs | |
14268 | `(("libpng" ,libpng) | |
14269 | ("zlib" ,zlib))) | |
14270 | (home-page "http://www.rforge.net/png/") | |
14271 | (synopsis "Read and write PNG images") | |
14272 | (description | |
14273 | "This package provides an easy and simple way to read, write and display | |
14274 | bitmap images stored in the PNG format. It can read and write both files and | |
14275 | in-memory raw vectors.") | |
14276 | ;; Any of these GPL versions. | |
14277 | (license (list license:gpl2 license:gpl3)))) | |
14278 | ||
d8a28332 RW |
14279 | (define-public r-ggcorrplot |
14280 | (package | |
14281 | (name "r-ggcorrplot") | |
e9c526be | 14282 | (version "0.1.3") |
d8a28332 RW |
14283 | (source |
14284 | (origin | |
14285 | (method url-fetch) | |
14286 | (uri (cran-uri "ggcorrplot" version)) | |
14287 | (sha256 | |
14288 | (base32 | |
e9c526be | 14289 | "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b")))) |
d8a28332 RW |
14290 | (build-system r-build-system) |
14291 | (propagated-inputs | |
14292 | `(("r-ggplot2" ,r-ggplot2) | |
14293 | ("r-reshape2" ,r-reshape2))) | |
14294 | (home-page "http://www.sthda.com/english/wiki/ggcorrplot") | |
14295 | (synopsis "Visualization of a correlation matrix using ggplot2") | |
14296 | (description | |
14297 | "The ggcorrplot package can be used to visualize easily a correlation | |
14298 | matrix using ggplot2. It provides a solution for reordering the correlation | |
14299 | matrix and displays the significance level on the plot. It also includes a | |
14300 | function for computing a matrix of correlation p-values.") | |
14301 | (license license:gpl2))) | |
f084e41e RW |
14302 | |
14303 | (define-public r-flexdashboard | |
14304 | (package | |
14305 | (name "r-flexdashboard") | |
14306 | (version "0.5.1.1") | |
14307 | (source | |
14308 | (origin | |
14309 | (method url-fetch) | |
14310 | (uri (cran-uri "flexdashboard" version)) | |
14311 | (sha256 | |
14312 | (base32 | |
14313 | "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x")))) | |
14314 | (build-system r-build-system) | |
14315 | (arguments | |
14316 | `(#:modules ((guix build utils) | |
14317 | (guix build r-build-system) | |
14318 | (srfi srfi-1) | |
14319 | (srfi srfi-26) | |
14320 | (ice-9 popen) | |
14321 | (ice-9 textual-ports)) | |
14322 | #:phases | |
14323 | (modify-phases %standard-phases | |
14324 | (add-after 'unpack 'process-javascript | |
14325 | (lambda* (#:key inputs #:allow-other-keys) | |
14326 | (with-directory-excursion "inst" | |
14327 | ;; Concatenate all components of prism.js | |
14328 | (let ((contents (string-join | |
14329 | (map (lambda (name) | |
14330 | (call-with-input-file | |
14331 | (assoc-ref inputs name) | |
14332 | get-string-all)) | |
14333 | (list "js-prism" | |
14334 | "js-prism-r" | |
14335 | "js-prism-line-numbers")) | |
14336 | "\n"))) | |
14337 | (call-with-output-file "prism-src.js" | |
14338 | (cut display contents <>))) | |
14339 | (call-with-values | |
14340 | (lambda () | |
14341 | (unzip2 | |
14342 | `(("www/stickytableheaders/jquery.stickytableheaders.js" | |
14343 | "www/stickytableheaders/jquery.stickytableheaders.min.js") | |
14344 | ("www/sly/sly.js" | |
14345 | "www/sly/sly.min.js") | |
14346 | ("prism-src.js" | |
14347 | "www/prism/prism.js") | |
14348 | (,(assoc-ref inputs "js-raphael") | |
14349 | "htmlwidgets/lib/raphael/raphael-2.1.4.min.js") | |
14350 | (,(assoc-ref inputs "js-featherlight") | |
14351 | "www/featherlight/featherlight.min.js")))) | |
14352 | (lambda (sources targets) | |
14353 | (for-each (lambda (source target) | |
14354 | (format #t "Processing ~a --> ~a~%" | |
14355 | source target) | |
14356 | (delete-file target) | |
14357 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
14358 | (call-with-output-file target | |
14359 | (lambda (port) | |
14360 | (dump-port minified port))))) | |
14361 | sources targets)))) | |
14362 | #t))))) | |
14363 | (propagated-inputs | |
14364 | `(("r-htmltools" ,r-htmltools) | |
14365 | ("r-htmlwidgets" ,r-htmlwidgets) | |
14366 | ("r-jsonlite" ,r-jsonlite) | |
14367 | ("r-knitr" ,r-knitr) | |
14368 | ("r-rmarkdown" ,r-rmarkdown) | |
14369 | ("r-shiny" ,r-shiny))) | |
14370 | (native-inputs | |
14371 | `(("uglify-js" ,uglify-js) | |
14372 | ("js-raphael" | |
14373 | ,(origin | |
14374 | (method url-fetch) | |
14375 | (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js") | |
14376 | (sha256 | |
14377 | (base32 | |
14378 | "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x")))) | |
14379 | ("js-prism" | |
14380 | ,(origin | |
14381 | (method url-fetch) | |
14382 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js") | |
14383 | (sha256 | |
14384 | (base32 | |
14385 | "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c")))) | |
14386 | ("js-prism-r" | |
14387 | ,(origin | |
14388 | (method url-fetch) | |
14389 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js") | |
14390 | (sha256 | |
14391 | (base32 | |
14392 | "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki")))) | |
14393 | ("js-prism-line-numbers" | |
14394 | ,(origin | |
14395 | (method url-fetch) | |
14396 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js") | |
14397 | (sha256 | |
14398 | (base32 | |
14399 | "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991")))) | |
14400 | ("js-featherlight" | |
14401 | ,(origin | |
14402 | (method url-fetch) | |
14403 | (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js") | |
14404 | (sha256 | |
14405 | (base32 | |
14406 | "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb")))))) | |
14407 | (home-page "https://rmarkdown.rstudio.com/flexdashboard") | |
14408 | (synopsis "R Markdown format for flexible dashboards") | |
14409 | (description | |
14410 | "This package provides an R Markdown format for converting an R Markdown | |
14411 | document to a grid-oriented dashboard. The dashboard flexibly adapts the size | |
14412 | of its components to the containing web page.") | |
14413 | (license license:expat))) | |
c54ab337 RW |
14414 | |
14415 | (define-public r-preseqr | |
14416 | (package | |
14417 | (name "r-preseqr") | |
14418 | (version "4.0.0") | |
14419 | (source | |
14420 | (origin | |
14421 | (method url-fetch) | |
14422 | (uri (cran-uri "preseqR" version)) | |
14423 | (sha256 | |
14424 | (base32 | |
14425 | "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1")))) | |
14426 | (properties `((upstream-name . "preseqR"))) | |
14427 | (build-system r-build-system) | |
14428 | (propagated-inputs | |
14429 | `(("r-polynom" ,r-polynom))) | |
14430 | (home-page "https://cran.r-project.org/web/packages/preseqR/") | |
14431 | (synopsis "Predicting species accumulation curves") | |
14432 | (description | |
14433 | "This package can be used to predict the r-species accumulation | |
14434 | curve (r-SAC), which is the number of species represented at least r times as | |
14435 | a function of the sampling effort. When r = 1, the curve is known as the | |
14436 | species accumulation curve, or the library complexity curve in high-throughput | |
14437 | genomic sequencing. The package includes both parametric and nonparametric | |
14438 | methods, as described by Deng C, et al. (2018).") | |
14439 | (license license:gpl3))) | |
1fab2cf8 RW |
14440 | |
14441 | (define-public r-mapplots | |
14442 | (package | |
14443 | (name "r-mapplots") | |
14444 | (version "1.5.1") | |
14445 | (source | |
14446 | (origin | |
14447 | (method url-fetch) | |
14448 | (uri (cran-uri "mapplots" version)) | |
14449 | (sha256 | |
14450 | (base32 | |
14451 | "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p")))) | |
14452 | (build-system r-build-system) | |
14453 | (home-page "https://cran.r-project.org/web/packages/mapplots/") | |
14454 | (synopsis "Data visualization on maps") | |
14455 | (description | |
14456 | "This package helps you create simple maps; add sub-plots like pie plots | |
14457 | to a map or any other plot; format, plot and export gridded data. The package | |
14458 | was developed for displaying fisheries data but most functions can be used for | |
14459 | more generic data visualisation.") | |
14460 | (license license:gpl2+))) | |
9563dd55 RW |
14461 | |
14462 | (define-public r-pmcmr | |
14463 | (package | |
14464 | (name "r-pmcmr") | |
14465 | (version "4.3") | |
14466 | (source | |
14467 | (origin | |
14468 | (method url-fetch) | |
14469 | (uri (cran-uri "PMCMR" version)) | |
14470 | (sha256 | |
14471 | (base32 | |
14472 | "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij")))) | |
14473 | (properties `((upstream-name . "PMCMR"))) | |
14474 | (build-system r-build-system) | |
14475 | (home-page "https://cran.r-project.org/web/packages/PMCMR/") | |
14476 | (synopsis "Calculate pairwise multiple comparisons of mean rank sums") | |
14477 | (description | |
14478 | "This is a deprecated package for calculating pairwise multiple | |
14479 | comparisons of mean rank sums. This package is superseded by the novel | |
14480 | PMCMRplus package. The PMCMR package is no longer maintained, but kept for | |
c8ae38d3 | 14481 | compatibility of dependent packages for some time.") |
9563dd55 | 14482 | (license license:gpl3+))) |
8d1990d4 RW |
14483 | |
14484 | (define-public r-downloader | |
14485 | (package | |
14486 | (name "r-downloader") | |
14487 | (version "0.4") | |
14488 | (source | |
14489 | (origin | |
14490 | (method url-fetch) | |
14491 | (uri (cran-uri "downloader" version)) | |
14492 | (sha256 | |
14493 | (base32 | |
14494 | "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q")))) | |
14495 | (build-system r-build-system) | |
14496 | (propagated-inputs | |
14497 | `(("r-digest" ,r-digest))) | |
14498 | (home-page "https://github.com/wch/downloader") | |
14499 | (synopsis "Download files over HTTP and HTTPS") | |
14500 | (description | |
14501 | "This package provides a wrapper for the @code{download.file} function, | |
14502 | making it possible to download files over HTTPS across platforms. The | |
14503 | @code{RCurl} package provides this functionality (and much more) but has | |
14504 | external dependencies. This package has is implemented purely in R.") | |
14505 | (license license:gpl2))) | |
296ea15c NB |
14506 | |
14507 | (define-public r-rex | |
14508 | (package | |
14509 | (name "r-rex") | |
14510 | (version "1.1.2") | |
14511 | (source | |
14512 | (origin | |
14513 | (method url-fetch) | |
14514 | (uri (cran-uri "rex" version)) | |
14515 | (sha256 | |
14516 | (base32 | |
14517 | "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x")))) | |
14518 | (build-system r-build-system) | |
14519 | (propagated-inputs | |
14520 | `(("r-lazyeval" ,r-lazyeval) | |
14521 | ("r-magrittr" ,r-magrittr))) | |
14522 | (home-page "https://github.com/kevinushey/rex") | |
14523 | (synopsis "Friendly regular expressions") | |
14524 | (description | |
14525 | "This package provides a friendly interface for the construction of | |
14526 | regular expressions. Regular expressions are a very powerful feature, however | |
14527 | they are often difficult to interpret. Rex allows you to build complex | |
14528 | regular expressions from human readable expressions") | |
14529 | (license license:expat))) | |
9b86fea0 RW |
14530 | |
14531 | (define-public r-sctransform | |
14532 | (package | |
14533 | (name "r-sctransform") | |
14534 | (version "0.2.0") | |
14535 | (source | |
14536 | (origin | |
14537 | (method url-fetch) | |
14538 | (uri (cran-uri "sctransform" version)) | |
14539 | (sha256 | |
14540 | (base32 | |
14541 | "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p")))) | |
14542 | (build-system r-build-system) | |
14543 | (propagated-inputs | |
14544 | `(("r-future" ,r-future) | |
14545 | ("r-future-apply" ,r-future-apply) | |
14546 | ("r-ggplot2" ,r-ggplot2) | |
14547 | ("r-gridextra" ,r-gridextra) | |
14548 | ("r-mass" ,r-mass) | |
14549 | ("r-matrix" ,r-matrix) | |
14550 | ("r-rcpp" ,r-rcpp) | |
14551 | ("r-rcppeigen" ,r-rcppeigen) | |
14552 | ("r-reshape2" ,r-reshape2))) | |
14553 | (home-page "https://github.com/ChristophH/sctransform") | |
14554 | (synopsis "Variance stabilizing transformations for Single Cell UMI Data") | |
14555 | (description | |
14556 | "This package provides a normalization method for single-cell UMI count | |
14557 | data using a variance stabilizing transformation. The transformation is based | |
14558 | on a negative binomial regression model with regularized parameters. As part | |
14559 | of the same regression framework, this package also provides functions for | |
14560 | batch correction, and data correction.") | |
14561 | (license license:gpl3))) | |
107850b3 NB |
14562 | |
14563 | (define-public r-styler | |
14564 | (package | |
14565 | (name "r-styler") | |
4238c3ee | 14566 | (version "1.1.1") |
107850b3 NB |
14567 | (source |
14568 | (origin | |
14569 | (method url-fetch) | |
14570 | (uri (cran-uri "styler" version)) | |
14571 | (sha256 | |
14572 | (base32 | |
4238c3ee | 14573 | "1k660lpjvd64gnf6bndcb1cq3qxsvik928kcn6271zmkhja5rgyb")))) |
107850b3 NB |
14574 | (build-system r-build-system) |
14575 | (propagated-inputs | |
14576 | `(("r-backports" ,r-backports) | |
14577 | ("r-cli" ,r-cli) | |
14578 | ("r-magrittr" ,r-magrittr) | |
14579 | ("r-purrr" ,r-purrr) | |
14580 | ("r-rematch2" ,r-rematch2) | |
14581 | ("r-rlang" ,r-rlang) | |
14582 | ("r-rprojroot" ,r-rprojroot) | |
14583 | ("r-tibble" ,r-tibble) | |
14584 | ("r-withr" ,r-withr) | |
14585 | ("r-xfun" ,r-xfun))) | |
14586 | (home-page "https://github.com/r-lib/styler") | |
14587 | (synopsis "Non-invasive pretty printing of R code") | |
14588 | (description | |
14589 | "This is a package for pretty-printing R code without changing the user's | |
14590 | formatting intent.") | |
14591 | (license license:gpl3))) | |
2b9d4f58 RW |
14592 | |
14593 | (define-public r-scrime | |
14594 | (package | |
14595 | (name "r-scrime") | |
14596 | (version "1.3.5") | |
14597 | (source | |
14598 | (origin | |
14599 | (method url-fetch) | |
14600 | (uri (cran-uri "scrime" version)) | |
14601 | (sha256 | |
14602 | (base32 | |
14603 | "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx")))) | |
14604 | (build-system r-build-system) | |
14605 | (home-page "https://cran.r-project.org/web/packages/scrime/") | |
14606 | (synopsis "Analysis of high-dimensional categorical data such as SNP data") | |
14607 | (description | |
14608 | "This package provides tools for the analysis of high-dimensional data | |
14609 | developed/implemented at the group \"Statistical Complexity Reduction In | |
14610 | Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of | |
14611 | the functions can also be applied to other types of categorical data.") | |
14612 | (license license:gpl2))) | |
04bf86ba | 14613 | |
3e63f078 RW |
14614 | (define-public r-pbmcapply |
14615 | (package | |
14616 | (name "r-pbmcapply") | |
14617 | (version "1.5.0") | |
14618 | (source | |
14619 | (origin | |
14620 | (method url-fetch) | |
14621 | (uri (cran-uri "pbmcapply" version)) | |
14622 | (sha256 | |
14623 | (base32 | |
14624 | "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz")))) | |
14625 | (build-system r-build-system) | |
14626 | (home-page "https://github.com/kvnkuang/pbmcapply") | |
14627 | (synopsis "Track the progress of apply procedures with a progress bar") | |
14628 | (description | |
14629 | "This light-weight package helps you track and visualize the progress of | |
14630 | parallel versions of vectorized R functions of the @code{mc*apply} family.") | |
14631 | (license license:expat))) | |
14632 | ||
04bf86ba RW |
14633 | (define-public r-blme |
14634 | (package | |
14635 | (name "r-blme") | |
14636 | (version "1.0-4") | |
14637 | (source | |
14638 | (origin | |
14639 | (method url-fetch) | |
14640 | (uri (cran-uri "blme" version)) | |
14641 | (sha256 | |
14642 | (base32 | |
14643 | "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2")))) | |
14644 | (build-system r-build-system) | |
14645 | (propagated-inputs `(("r-lme4" ,r-lme4))) | |
14646 | (home-page "https://github.com/vdorie/blme") | |
14647 | (synopsis "Bayesian linear mixed-effects models") | |
14648 | (description | |
14649 | "This package provides tools for maximum a posteriori estimation for | |
14650 | linear and generalized linear mixed-effects models in a Bayesian setting. It | |
14651 | extends the lme4 package.") | |
14652 | (license license:gpl2+))) | |
be23c491 RW |
14653 | |
14654 | (define-public r-batchtools | |
14655 | (package | |
14656 | (name "r-batchtools") | |
14657 | (version "0.9.11") | |
14658 | (source | |
14659 | (origin | |
14660 | (method url-fetch) | |
14661 | (uri (cran-uri "batchtools" version)) | |
14662 | (sha256 | |
14663 | (base32 | |
14664 | "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v")))) | |
14665 | (build-system r-build-system) | |
14666 | (propagated-inputs | |
14667 | `(("r-backports" ,r-backports) | |
14668 | ("r-base64url" ,r-base64url) | |
14669 | ("r-brew" ,r-brew) | |
14670 | ("r-checkmate" ,r-checkmate) | |
14671 | ("r-data-table" ,r-data-table) | |
14672 | ("r-digest" ,r-digest) | |
14673 | ("r-fs" ,r-fs) | |
14674 | ("r-progress" ,r-progress) | |
14675 | ("r-r6" ,r-r6) | |
14676 | ("r-rappdirs" ,r-rappdirs) | |
14677 | ("r-stringi" ,r-stringi) | |
14678 | ("r-withr" ,r-withr))) | |
14679 | (home-page "https://github.com/mllg/batchtools") | |
14680 | (synopsis "Tools for computation on batch systems") | |
14681 | (description | |
14682 | "As a successor of the packages BatchJobs and BatchExperiments, this | |
14683 | package provides a parallel implementation of the Map function for high | |
14684 | performance computing systems managed by various schedulers. A multicore and | |
14685 | socket mode allow the parallelization on a local machines, and multiple | |
14686 | machines can be hooked up via SSH to create a makeshift cluster. Moreover, | |
14687 | the package provides an abstraction mechanism to define large-scale computer | |
14688 | experiments in a well-organized and reproducible way.") | |
14689 | (license license:lgpl3))) | |
0c8960df RW |
14690 | |
14691 | (define-public r-clue | |
14692 | (package | |
14693 | (name "r-clue") | |
14694 | (version "0.3-57") | |
14695 | (source | |
14696 | (origin | |
14697 | (method url-fetch) | |
14698 | (uri (cran-uri "clue" version)) | |
14699 | (sha256 | |
14700 | (base32 | |
14701 | "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf")))) | |
14702 | (build-system r-build-system) | |
14703 | (propagated-inputs `(("r-cluster" ,r-cluster))) | |
14704 | (home-page "https://cran.r-project.org/web/packages/clue/") | |
14705 | (synopsis "Tools for analyzing cluster ensembles") | |
14706 | (description "Cluster ensembles are collections of individual solutions to | |
14707 | a given clustering problem which are useful or necessary to consider in a wide | |
14708 | range of applications. This R package provides an extensible computational | |
14709 | environment for creating and analyzing cluster ensembles, with basic data | |
14710 | structures for representing partitions and hierarchies, and facilities for | |
14711 | computing on them, including methods for measuring proximity and obtaining | |
14712 | consensus and secondary clusterings.") | |
14713 | (license license:gpl2))) | |
b8d6dffb RW |
14714 | |
14715 | (define-public r-sitmo | |
14716 | (package | |
14717 | (name "r-sitmo") | |
14718 | (version "2.0.1") | |
14719 | (source | |
14720 | (origin | |
14721 | (method url-fetch) | |
14722 | (uri (cran-uri "sitmo" version)) | |
14723 | (sha256 | |
14724 | (base32 | |
14725 | "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c")))) | |
14726 | (build-system r-build-system) | |
14727 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
14728 | (home-page "https://github.com/coatless/sitmo/") | |
14729 | (synopsis "Parallel pseudo random number generator header files") | |
14730 | (description | |
14731 | "This package provides two high quality and fast PPRNGs that may be used | |
14732 | in an OpenMP parallel environment. In addition, there is a generator for one | |
14733 | dimensional low-discrepancy sequence.") | |
14734 | (license license:expat))) | |
3961b3b9 RW |
14735 | |
14736 | (define-public r-dqrng | |
14737 | (package | |
14738 | (name "r-dqrng") | |
12242ffb | 14739 | (version "0.2.1") |
3961b3b9 RW |
14740 | (source |
14741 | (origin | |
14742 | (method url-fetch) | |
14743 | (uri (cran-uri "dqrng" version)) | |
14744 | (sha256 | |
14745 | (base32 | |
12242ffb | 14746 | "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1")))) |
3961b3b9 RW |
14747 | (build-system r-build-system) |
14748 | (propagated-inputs | |
14749 | `(("r-bh" ,r-bh) | |
14750 | ("r-rcpp" ,r-rcpp) | |
14751 | ("r-sitmo" ,r-sitmo))) | |
14752 | (home-page "https://www.daqana.org/dqrng") | |
14753 | (synopsis "Fast pseudo random number generators") | |
14754 | (description | |
14755 | "Several fast random number generators are provided as C++ header-only | |
14756 | libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+. | |
14757 | Additionally, fast functions for generating random numbers according to a | |
14758 | uniform, normal and exponential distribution are included. The latter two use | |
14759 | the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These | |
14760 | functions are exported to R and as a C++ interface and are enabled for use | |
14761 | with the default 64 bit generator from the PCG family, Xoroshiro128+ and | |
14762 | Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry | |
14763 | engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") | |
14764 | ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a | |
14765 | ;; whole is distributed under the terms of the AGPL 3. | |
14766 | (license license:agpl3))) | |
5bea832f RW |
14767 | |
14768 | (define-public r-dalex | |
14769 | (package | |
14770 | (name "r-dalex") | |
d64ac92f | 14771 | (version "0.4.7") |
5bea832f RW |
14772 | (source |
14773 | (origin | |
14774 | (method url-fetch) | |
14775 | (uri (cran-uri "DALEX" version)) | |
14776 | (sha256 | |
14777 | (base32 | |
d64ac92f | 14778 | "0iiwkf0pfdb90lf1xhv43qd32z3cjmkmf0ly9841n5lldkjazy3h")))) |
5bea832f RW |
14779 | (properties `((upstream-name . "DALEX"))) |
14780 | (build-system r-build-system) | |
14781 | (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) | |
14782 | (home-page "https://pbiecek.github.io/DALEX/") | |
14783 | (synopsis "Descriptive machine learning explanations") | |
14784 | (description | |
14785 | "Machine Learning models are widely used and have various applications in | |
14786 | classification or regression. Models created with boosting, bagging, stacking | |
14787 | or similar techniques are often used due to their high performance, but such | |
14788 | black-box models usually lack interpretability. The DALEX package contains | |
14789 | various explainers that help to understand the link between input variables | |
14790 | and model output.") | |
14791 | ;; Any version of the GPL | |
14792 | (license license:gpl3+))) | |
70debac5 RW |
14793 | |
14794 | (define-public r-enrichr | |
14795 | (package | |
14796 | (name "r-enrichr") | |
7a90573f | 14797 | (version "2.1") |
70debac5 RW |
14798 | (source |
14799 | (origin | |
14800 | (method url-fetch) | |
14801 | (uri (cran-uri "enrichR" version)) | |
14802 | (sha256 | |
14803 | (base32 | |
7a90573f | 14804 | "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1")))) |
70debac5 RW |
14805 | (properties `((upstream-name . "enrichR"))) |
14806 | (build-system r-build-system) | |
14807 | (propagated-inputs | |
14808 | `(("r-httr" ,r-httr) | |
14809 | ("r-rjson" ,r-rjson))) | |
14810 | (home-page "https://cran.r-project.org/web/packages/enrichR/") | |
14811 | (synopsis "R Interface to Enrichr database for analyzing gene sets") | |
14812 | (description | |
14813 | "This package provides an R interface to all Enrichr databases, a | |
14814 | web-based tool for analyzing gene sets and returns any enrichment of common | |
14815 | annotated biological functions.") | |
14816 | (license license:gpl2+))) | |
c9487dfa RW |
14817 | |
14818 | (define-public r-plot3d | |
14819 | (package | |
14820 | (name "r-plot3d") | |
14821 | (version "1.1.1") | |
14822 | (source | |
14823 | (origin | |
14824 | (method url-fetch) | |
14825 | (uri (cran-uri "plot3D" version)) | |
14826 | (sha256 | |
14827 | (base32 | |
14828 | "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn")))) | |
14829 | (properties `((upstream-name . "plot3D"))) | |
14830 | (build-system r-build-system) | |
14831 | (propagated-inputs `(("r-misc3d" ,r-misc3d))) | |
14832 | (home-page "https://cran.r-project.org/web/packages/plot3D") | |
14833 | (synopsis "Plot multi-dimensional data") | |
14834 | (description | |
14835 | "This package provides functions for viewing 2D and 3D data, including | |
14836 | perspective plots, slice plots, surface plots, scatter plots, etc. It | |
14837 | includes data sets from oceanography.") | |
14838 | (license license:gpl3+))) | |
85625cae RW |
14839 | |
14840 | (define-public r-ggfortify | |
14841 | (package | |
14842 | (name "r-ggfortify") | |
0fe52daa | 14843 | (version "0.4.7") |
85625cae RW |
14844 | (source |
14845 | (origin | |
14846 | (method url-fetch) | |
14847 | (uri (cran-uri "ggfortify" version)) | |
14848 | (sha256 | |
14849 | (base32 | |
0fe52daa | 14850 | "1wk9j0xg5hj9i1vf62qjiphv8cbsgq7y6baay3pfl3wyb2dwgci0")))) |
85625cae RW |
14851 | (build-system r-build-system) |
14852 | (propagated-inputs | |
14853 | `(("r-dplyr" ,r-dplyr) | |
14854 | ("r-ggplot2" ,r-ggplot2) | |
14855 | ("r-gridextra" ,r-gridextra) | |
14856 | ("r-scales" ,r-scales) | |
14857 | ("r-stringr" ,r-stringr) | |
14858 | ("r-tibble" ,r-tibble) | |
14859 | ("r-tidyr" ,r-tidyr))) | |
14860 | (home-page "https://github.com/sinhrks/ggfortify") | |
14861 | (synopsis "Data visualization tools for statistical analysis results") | |
14862 | (description | |
14863 | "This package provides unified plotting tools for statistics commonly | |
14864 | used, such as GLM, time series, PCA families, clustering and survival | |
14865 | analysis. The package offers a single plotting interface for these analysis | |
14866 | results and plots in a unified style using the @code{ggplot2} package.") | |
14867 | (license license:gpl2))) | |
afc4370d RW |
14868 | |
14869 | (define-public r-refmanager | |
14870 | (package | |
14871 | (name "r-refmanager") | |
14872 | (version "1.2.12") | |
14873 | (source | |
14874 | (origin | |
14875 | (method url-fetch) | |
14876 | (uri (cran-uri "RefManageR" version)) | |
14877 | (sha256 | |
14878 | (base32 | |
14879 | "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp")))) | |
14880 | (properties `((upstream-name . "RefManageR"))) | |
14881 | (build-system r-build-system) | |
14882 | (propagated-inputs | |
14883 | `(("r-bibtex" ,r-bibtex) | |
14884 | ("r-httr" ,r-httr) | |
14885 | ("r-jsonlite" ,r-jsonlite) | |
14886 | ("r-lubridate" ,r-lubridate) | |
14887 | ("r-plyr" ,r-plyr) | |
14888 | ("r-stringr" ,r-stringr) | |
14889 | ("r-xml2" ,r-xml2))) | |
14890 | (home-page "https://github.com/ropensci/RefManageR/") | |
14891 | (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") | |
14892 | (description | |
14893 | "This package provides tools for importing and working with bibliographic | |
14894 | references. It greatly enhances the @code{bibentry} class by providing a | |
14895 | class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports | |
14896 | UTF-8 encoding, and can be easily searched by any field, by date ranges, and | |
14897 | by various formats for name lists (author by last names, translator by full | |
14898 | names, etc.). Entries can be updated, combined, sorted, printed in a number | |
14899 | of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read | |
14900 | into R and converted to @code{BibEntry} objects.") | |
14901 | ;; Any of these licenses may be picked. | |
14902 | (license (list license:gpl2 license:gpl3 license:bsd-3)))) | |
29591ca6 RW |
14903 | |
14904 | (define-public r-citr | |
14905 | (package | |
14906 | (name "r-citr") | |
6b28386d | 14907 | (version "0.3.2") |
29591ca6 RW |
14908 | (source |
14909 | (origin | |
14910 | (method url-fetch) | |
14911 | (uri (cran-uri "citr" version)) | |
14912 | (sha256 | |
14913 | (base32 | |
6b28386d | 14914 | "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las")))) |
29591ca6 RW |
14915 | (build-system r-build-system) |
14916 | (propagated-inputs | |
14917 | `(("r-assertthat" ,r-assertthat) | |
29591ca6 RW |
14918 | ("r-curl" ,r-curl) |
14919 | ("r-httr" ,r-httr) | |
14920 | ("r-miniui" ,r-miniui) | |
14921 | ("r-refmanager" ,r-refmanager) | |
14922 | ("r-rstudioapi" ,r-rstudioapi) | |
14923 | ("r-shiny" ,r-shiny) | |
14924 | ("r-shinyjs" ,r-shinyjs) | |
14925 | ("r-yaml" ,r-yaml))) | |
14926 | (home-page "https://github.com/crsh/citr") | |
14927 | (synopsis "RStudio add-in to insert Markdown citations") | |
14928 | (description | |
14929 | "This package provides functions and an RStudio add-in that search a | |
14930 | BibTeX or BibLaTeX file to create and insert formatted Markdown citations into | |
14931 | the current document.") | |
14932 | (license license:expat))) | |
30f1029f RW |
14933 | |
14934 | (define-public r-xgboost | |
14935 | (package | |
14936 | (name "r-xgboost") | |
00300de5 | 14937 | (version "0.90.0.2") |
30f1029f RW |
14938 | (source |
14939 | (origin | |
14940 | (method url-fetch) | |
14941 | (uri (cran-uri "xgboost" version)) | |
14942 | (sha256 | |
14943 | (base32 | |
00300de5 | 14944 | "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194")))) |
30f1029f RW |
14945 | (build-system r-build-system) |
14946 | (propagated-inputs | |
14947 | `(("r-data-table" ,r-data-table) | |
14948 | ("r-magrittr" ,r-magrittr) | |
14949 | ("r-matrix" ,r-matrix) | |
14950 | ("r-stringi" ,r-stringi))) | |
14951 | (home-page "https://github.com/dmlc/xgboost") | |
14952 | (synopsis "Extreme gradient boosting") | |
14953 | (description | |
14954 | "This package provides an R interface to Extreme Gradient Boosting, which | |
14955 | is an efficient implementation of the gradient boosting framework from Chen | |
14956 | and Guestrin (2016). The package includes efficient linear model solver and | |
14957 | tree learning algorithms. The package can automatically do parallel | |
14958 | computation on a single machine. It supports various objective functions, | |
14959 | including regression, classification and ranking. The package is made to be | |
14960 | extensible, so that users are also allowed to define their own objectives | |
14961 | easily.") | |
14962 | (license license:asl2.0))) | |
1c0b2e74 | 14963 | |
14964 | (define-public r-umap | |
14965 | (package | |
14966 | (name "r-umap") | |
8bcd6c95 | 14967 | (version "0.2.3.1") |
1c0b2e74 | 14968 | (source |
14969 | (origin | |
14970 | (method url-fetch) | |
14971 | (uri (cran-uri "umap" version)) | |
14972 | (sha256 | |
14973 | (base32 | |
8bcd6c95 | 14974 | "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d")))) |
1c0b2e74 | 14975 | (build-system r-build-system) |
14976 | (propagated-inputs | |
8bcd6c95 RW |
14977 | `(("r-openssl" ,r-openssl) |
14978 | ("r-rcpp" ,r-rcpp) | |
1c0b2e74 | 14979 | ("r-reticulate" ,r-reticulate) |
14980 | ("r-rspectra" ,r-rspectra))) | |
14981 | (home-page "https://github.com/tkonopka/umap") | |
14982 | (synopsis "Uniform manifold approximation and projection") | |
14983 | (description | |
14984 | "Uniform manifold approximation and projection is a technique for | |
14985 | dimension reduction. This package provides an interface to the UMAP algorithm | |
14986 | in R, including a translation of the original algorithm into R.") | |
14987 | (license license:expat))) | |
6deb08a3 | 14988 | |
86c46d71 RW |
14989 | (define-public r-uwot |
14990 | (package | |
14991 | (name "r-uwot") | |
4d86ea4a | 14992 | (version "0.1.4") |
86c46d71 RW |
14993 | (source |
14994 | (origin | |
14995 | (method url-fetch) | |
14996 | (uri (cran-uri "uwot" version)) | |
14997 | (sha256 | |
14998 | (base32 | |
4d86ea4a | 14999 | "1y9wpzs92d1fl2x5figfywd48lkyhwx37j542z0rf6ckrl46n89n")))) |
86c46d71 RW |
15000 | (build-system r-build-system) |
15001 | (propagated-inputs | |
15002 | `(("r-dqrng" ,r-dqrng) | |
15003 | ("r-fnn" ,r-fnn) | |
15004 | ("r-irlba" ,r-irlba) | |
15005 | ("r-matrix" ,r-matrix) | |
15006 | ("r-rcpp" ,r-rcpp) | |
15007 | ("r-rcppannoy" ,r-rcppannoy) | |
15008 | ("r-rcppparallel" ,r-rcppparallel) | |
15009 | ("r-rcppprogress" ,r-rcppprogress) | |
15010 | ("r-rspectra" ,r-rspectra))) | |
15011 | (home-page "https://github.com/jlmelville/uwot") | |
15012 | (synopsis "Uniform manifold approximation and projection") | |
15013 | (description | |
15014 | "This package provides an implementation of the Uniform Manifold | |
15015 | Approximation and Projection dimensionality reduction by McInnes et | |
15016 | al. (2018). It also provides means to transform new data and to carry out | |
15017 | supervised dimensionality reduction. An implementation of the related | |
15018 | LargeVis method of Tang et al. (2016) is also provided.") | |
15019 | (license license:gpl3))) | |
15020 | ||
6deb08a3 | 15021 | (define-public r-kableextra |
15022 | (package | |
15023 | (name "r-kableextra") | |
15024 | (version "1.1.0") | |
15025 | (source | |
15026 | (origin | |
15027 | (method url-fetch) | |
15028 | (uri (cran-uri "kableExtra" version)) | |
15029 | (sha256 | |
15030 | (base32 | |
15031 | "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i")))) | |
15032 | (properties `((upstream-name . "kableExtra"))) | |
15033 | (build-system r-build-system) | |
15034 | (propagated-inputs | |
15035 | `(("r-digest" ,r-digest) | |
15036 | ("r-glue" ,r-glue) | |
15037 | ("r-htmltools" ,r-htmltools) | |
15038 | ("r-knitr" ,r-knitr) | |
15039 | ("r-magrittr" ,r-magrittr) | |
15040 | ("r-readr" ,r-readr) | |
15041 | ("r-rmarkdown" ,r-rmarkdown) | |
15042 | ("r-rstudioapi" ,r-rstudioapi) | |
15043 | ("r-rvest" ,r-rvest) | |
15044 | ("r-scales" ,r-scales) | |
15045 | ("r-stringr" ,r-stringr) | |
15046 | ("r-viridislite" ,r-viridislite) | |
15047 | ("r-webshot" ,r-webshot) | |
15048 | ("r-xml2" ,r-xml2))) | |
15049 | (home-page "https://haozhu233.github.io/kableExtra/") | |
15050 | (synopsis "Construct complex tables with pipe syntax") | |
15051 | (description | |
15052 | "Build complex HTML or LaTeX tables using @code{kable()} from | |
15053 | @code{knitr} and the piping syntax from @code{magrittr}. The function | |
15054 | @code{kable()} is a light weight table generator coming from @code{knitr}. | |
15055 | This package simplifies the way to manipulate the HTML or LaTeX codes | |
15056 | generated by @code{kable()} and allows users to construct complex tables and | |
15057 | customize styles using a readable syntax.") | |
15058 | (license license:expat))) | |
79f04920 RW |
15059 | |
15060 | (define-public r-glasso | |
15061 | (package | |
15062 | (name "r-glasso") | |
afbc3a87 | 15063 | (version "1.11") |
79f04920 RW |
15064 | (source |
15065 | (origin | |
15066 | (method url-fetch) | |
15067 | (uri (cran-uri "glasso" version)) | |
15068 | (sha256 | |
afbc3a87 | 15069 | (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc")))) |
79f04920 RW |
15070 | (build-system r-build-system) |
15071 | (native-inputs `(("gfortran" ,gfortran))) | |
15072 | (home-page "http://www-stat.stanford.edu/~tibs/glasso") | |
15073 | (synopsis "Graphical Lasso: estimation of Gaussian graphical models") | |
15074 | (description | |
15075 | "This is a package for estimation of a sparse inverse covariance matrix | |
15076 | using a lasso (L1) penalty. Facilities are provided for estimates along a | |
15077 | path of values for the regularization parameter.") | |
15078 | (license license:gpl2))) | |
37120e7a RW |
15079 | |
15080 | (define-public r-rhpcblasctl | |
15081 | (package | |
15082 | (name "r-rhpcblasctl") | |
15083 | (version "0.18-205") | |
15084 | (source | |
15085 | (origin | |
15086 | (method url-fetch) | |
15087 | (uri (cran-uri "RhpcBLASctl" version)) | |
15088 | (sha256 | |
15089 | (base32 | |
15090 | "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp")))) | |
15091 | (properties `((upstream-name . "RhpcBLASctl"))) | |
15092 | (build-system r-build-system) | |
15093 | (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/") | |
15094 | (synopsis "Control the number of threads on BLAS") | |
15095 | (description | |
15096 | "This package allows you to control the number of threads the BLAS | |
15097 | library uses. It is also possible to control the number of threads in | |
15098 | OpenMP.") | |
15099 | (license license:agpl3+))) | |
6e7553ff | 15100 | |
19f1aac0 RW |
15101 | (define-public r-lda |
15102 | (package | |
15103 | (name "r-lda") | |
15104 | (version "1.4.2") | |
15105 | (source | |
15106 | (origin | |
15107 | (method url-fetch) | |
15108 | (uri (cran-uri "lda" version)) | |
15109 | (sha256 | |
15110 | (base32 | |
15111 | "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn")))) | |
15112 | (build-system r-build-system) | |
15113 | (home-page "https://cran.r-project.org/web/packages/lda/") | |
15114 | (synopsis "Collapsed Gibbs sampling methods for topic models") | |
15115 | (description | |
15116 | "This package implements @dfn{latent Dirichlet allocation} (LDA) and | |
15117 | related models. This includes (but is not limited to) sLDA, corrLDA, and the | |
15118 | mixed-membership stochastic blockmodel. Inference for all of these models is | |
15119 | implemented via a fast collapsed Gibbs sampler written in C. Utility | |
15120 | functions for reading/writing data typically used in topic models, as well as | |
15121 | tools for examining posterior distributions are also included.") | |
15122 | ;; Any version of the LGPL | |
15123 | (license license:lgpl3+))) | |
15124 | ||
6e7553ff RW |
15125 | (define-public r-rann-l1 |
15126 | (package | |
15127 | (name "r-rann-l1") | |
15128 | (version "2.5.2") | |
15129 | (source | |
15130 | (origin | |
15131 | (method url-fetch) | |
15132 | (uri (cran-uri "RANN.L1" version)) | |
15133 | (sha256 | |
15134 | (base32 | |
15135 | "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44")))) | |
15136 | (properties `((upstream-name . "RANN.L1"))) | |
15137 | (build-system r-build-system) | |
15138 | (home-page "https://github.com/jefferis/RANN/tree/master-L1") | |
15139 | (synopsis "Fast nearest neighbour search using L1 metric") | |
15140 | (description | |
15141 | "This package provides tools to find the k nearest neighbours for every | |
15142 | point in a given dataset in O(N log N) time using Arya and Mount's ANN | |
15143 | library. There is support for approximate as well as exact searches, fixed | |
15144 | radius searches and @code{bd} as well as @code{kd} trees. The distance is | |
15145 | computed using the L1 (Manhattan, taxicab) metric.") | |
15146 | (license license:gpl3+))) | |
9c3bfea6 | 15147 | |
8e28535d RW |
15148 | (define-public r-leiden |
15149 | (package | |
15150 | (name "r-leiden") | |
15151 | (version "0.3.1") | |
15152 | (source | |
15153 | (origin | |
15154 | (method url-fetch) | |
15155 | (uri (cran-uri "leiden" version)) | |
15156 | (sha256 | |
15157 | (base32 | |
15158 | "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp")))) | |
15159 | (properties `((upstream-name . "leiden"))) | |
15160 | (build-system r-build-system) | |
15161 | (propagated-inputs | |
15162 | `(("r-igraph" ,r-igraph) | |
15163 | ("r-matrix" ,r-matrix) | |
15164 | ("r-reticulate" ,r-reticulate))) | |
15165 | (home-page "https://github.com/TomKellyGenetics/leiden") | |
15166 | (synopsis "R implementation of Leiden clustering algorithm") | |
15167 | (description | |
15168 | "This package implements the Python @code{leidenalg} module to be called | |
15169 | in R. It enables clustering using the Leiden algorithm for partitioning a | |
15170 | graph into communities. See also Traag et al (2018) \"From Louvain to Leiden: | |
15171 | guaranteeing well-connected communities.\" <arXiv:1810.08473>.") | |
15172 | (license license:gpl3))) | |
15173 | ||
9c3bfea6 RW |
15174 | (define-public r-patchwork |
15175 | ;; There has been no public release yet. | |
15176 | (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242") | |
15177 | (revision "1")) | |
15178 | (package | |
15179 | (name "r-patchwork") | |
15180 | (version (git-version "0.0.1" revision commit)) | |
15181 | (source | |
15182 | (origin | |
15183 | (method git-fetch) | |
15184 | (uri (git-reference | |
15185 | (url "https://github.com/thomasp85/patchwork.git") | |
15186 | (commit commit))) | |
15187 | (file-name (git-file-name name version)) | |
15188 | (sha256 | |
15189 | (base32 | |
15190 | "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4")))) | |
15191 | (build-system r-build-system) | |
15192 | (propagated-inputs | |
15193 | `(("r-ggplot2" ,r-ggplot2) | |
15194 | ("r-gtable" ,r-gtable))) | |
15195 | (home-page "https://github.com/thomasp85/patchwork") | |
15196 | (synopsis "Compose ggplot2 plots") | |
15197 | (description | |
15198 | "The @code{ggplot2} package provides a strong API for sequentially | |
15199 | building up a plot, but does not concern itself with composition of multiple | |
15200 | plots. Patchwork is a package that expands the API to allow for arbitrarily | |
15201 | complex composition of plots by providing mathmatical operators for combining | |
15202 | multiple plots.") | |
15203 | (license license:expat)))) | |
86d38228 RW |
15204 | |
15205 | (define-public r-liger | |
15206 | (package | |
15207 | (name "r-liger") | |
15208 | (version "0.4.2") | |
15209 | (source | |
15210 | (origin | |
15211 | (method git-fetch) | |
15212 | (uri (git-reference | |
15213 | (url "https://github.com/MacoskoLab/liger.git") | |
15214 | (commit (string-append "v" version)))) | |
15215 | (file-name (git-file-name name version)) | |
15216 | (sha256 | |
15217 | (base32 | |
15218 | "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx")) | |
15219 | (modules '((guix build utils))) | |
15220 | (snippet | |
15221 | '(begin | |
15222 | (delete-file "inst/java/ModularityOptimizer.jar") | |
15223 | #t)))) | |
15224 | (build-system r-build-system) | |
15225 | (arguments | |
15226 | `(#:phases | |
15227 | (modify-phases %standard-phases | |
15228 | (add-after 'unpack 'build-java-part | |
15229 | (lambda* (#:key inputs #:allow-other-keys) | |
15230 | (invoke "unzip" (assoc-ref inputs "optimizer-src")) | |
15231 | (for-each (lambda (file) (invoke "javac" file)) | |
15232 | (find-files "." "\\.java$")) | |
15233 | (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar" | |
15234 | (find-files "." "\\.class$")) | |
15235 | #t))))) | |
15236 | (propagated-inputs | |
15237 | `(("r-cowplot" ,r-cowplot) | |
15238 | ("r-dosnow" ,r-dosnow) | |
15239 | ("r-dplyr" ,r-dplyr) | |
15240 | ("r-fnn" ,r-fnn) | |
15241 | ("r-foreach" ,r-foreach) | |
15242 | ("r-ggplot2" ,r-ggplot2) | |
15243 | ("r-ggrepel" ,r-ggrepel) | |
15244 | ("r-hmisc" ,r-hmisc) | |
15245 | ("r-ica" ,r-ica) | |
15246 | ("r-irlba" ,r-irlba) | |
15247 | ("r-matrix" ,r-matrix) | |
15248 | ("r-mclust" ,r-mclust) | |
15249 | ("r-patchwork" ,r-patchwork) | |
15250 | ("r-plyr" ,r-plyr) | |
15251 | ("r-rann-l1" ,r-rann-l1) | |
15252 | ("r-rcpp" ,r-rcpp) | |
15253 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
15254 | ("r-riverplot" ,r-riverplot) | |
15255 | ("r-rtsne" ,r-rtsne) | |
15256 | ("r-snow" ,r-snow))) | |
15257 | (native-inputs | |
15258 | `(("jdk" ,icedtea "jdk") | |
15259 | ;; See https://github.com/MacoskoLab/liger/issues/96 | |
15260 | ;; The optimizer is released under the Expat license. | |
15261 | ("optimizer-src" | |
15262 | ,(origin | |
15263 | (method url-fetch) | |
15264 | (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip") | |
15265 | (sha256 | |
15266 | (base32 | |
15267 | "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18")))) | |
15268 | ("unzip" ,unzip) | |
15269 | ("r-knitr" ,r-knitr))) ; for vignettes | |
15270 | (home-page "https://github.com/MacoskoLab/liger") | |
15271 | (synopsis "Integrate and analyze multiple single-cell datasets") | |
15272 | (description | |
15273 | "LIGER is a package for integrating and analyzing multiple single-cell | |
15274 | datasets, developed and maintained by the Macosko lab. It relies on | |
15275 | integrative non-negative matrix factorization to identify shared and | |
15276 | dataset-specific factors.") | |
15277 | (license license:gpl3))) | |
711cec9d RW |
15278 | |
15279 | (define-public r-harmony | |
15280 | ;; There are no tagged commits | |
15281 | (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a") | |
15282 | (revision "1")) | |
15283 | (package | |
15284 | (name "r-harmony") | |
15285 | (version (git-version "1.0" revision commit)) | |
15286 | (source | |
15287 | (origin | |
15288 | (method git-fetch) | |
15289 | (uri (git-reference | |
15290 | (url "https://github.com/immunogenomics/harmony") | |
15291 | (commit commit))) | |
15292 | (file-name (git-file-name name version)) | |
15293 | (sha256 | |
15294 | (base32 | |
15295 | "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85")))) | |
15296 | (build-system r-build-system) | |
15297 | (propagated-inputs | |
15298 | `(("r-cowplot" ,r-cowplot) | |
15299 | ("r-dplyr" ,r-dplyr) | |
15300 | ("r-ggplot2" ,r-ggplot2) | |
15301 | ("r-irlba" ,r-irlba) | |
15302 | ("r-matrix" ,r-matrix) | |
15303 | ("r-rcpp" ,r-rcpp) | |
15304 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
15305 | ("r-rcppprogress" ,r-rcppprogress) | |
15306 | ("r-rlang" ,r-rlang) | |
15307 | ("r-tibble" ,r-tibble) | |
15308 | ("r-tidyr" ,r-tidyr))) | |
15309 | (home-page "https://github.com/immunogenomics/harmony") | |
15310 | (synopsis "Integration of single cell sequencing data") | |
15311 | (description | |
15312 | "This package provides an implementation of the Harmony algorithm for | |
15313 | single cell integration, described in Korsunsky et al | |
15314 | @url{doi.org/10.1101/461954}. The package includes a standalone Harmony | |
15315 | function and interfaces to external frameworks.") | |
15316 | (license license:gpl3)))) | |
7a5ed348 RW |
15317 | |
15318 | (define-public r-covr | |
15319 | (package | |
15320 | (name "r-covr") | |
15321 | (version "3.3.1") | |
15322 | (source | |
15323 | (origin | |
15324 | (method url-fetch) | |
15325 | (uri (cran-uri "covr" version)) | |
15326 | (sha256 | |
15327 | (base32 | |
15328 | "0fvd7v53w11x6kaw61hbml8n1j2ck9l2fv2wvqdsg689xic9rqcs")))) | |
15329 | (properties `((upstream-name . "covr"))) | |
15330 | (build-system r-build-system) | |
15331 | (propagated-inputs | |
15332 | `(("r-crayon" ,r-crayon) | |
15333 | ("r-digest" ,r-digest) | |
15334 | ("r-httr" ,r-httr) | |
15335 | ("r-jsonlite" ,r-jsonlite) | |
15336 | ("r-rex" ,r-rex) | |
15337 | ("r-withr" ,r-withr) | |
15338 | ("r-yaml" ,r-yaml))) | |
15339 | (home-page "https://github.com/r-lib/covr") | |
15340 | (synopsis "Test coverage for R packages") | |
15341 | (description | |
15342 | "Thisp package enables you to track and report code coverage for your | |
15343 | package and (optionally) upload the results to a coverage service. Code | |
15344 | coverage is a measure of the amount of code being exercised by a set of tests. | |
15345 | It is an indirect measure of test quality and completeness. This package is | |
15346 | compatible with any testing methodology or framework and tracks coverage of | |
15347 | both R code and compiled C/C++/FORTRAN code.") | |
15348 | (license license:gpl3))) | |
6983178b RW |
15349 | |
15350 | (define-public r-systemfonts | |
15351 | (package | |
15352 | (name "r-systemfonts") | |
15353 | (version "0.1.1") | |
15354 | (source | |
15355 | (origin | |
15356 | (method url-fetch) | |
15357 | (uri (cran-uri "systemfonts" version)) | |
15358 | (sha256 | |
15359 | (base32 | |
15360 | "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z")))) | |
15361 | (properties `((upstream-name . "systemfonts"))) | |
15362 | (build-system r-build-system) | |
15363 | (inputs | |
15364 | `(("fontconfig" ,fontconfig) | |
15365 | ("freetype" ,freetype) | |
15366 | ("zlib" ,zlib))) | |
15367 | (native-inputs | |
15368 | `(("pkg-config" ,pkg-config))) | |
15369 | (home-page "https://github.com/r-lib/systemfonts") | |
15370 | (synopsis "System native font finding") | |
15371 | (description | |
15372 | "This package provides system native access to the font catalogue. As | |
15373 | font handling varies between systems it is difficult to correctly locate | |
15374 | installed fonts across different operating systems. The 'systemfonts' package | |
15375 | provides bindings to the native libraries for finding font files that can then | |
15376 | be used further by e.g. graphic devices.") | |
15377 | (license license:expat))) | |
93903009 RW |
15378 | |
15379 | (define-public r-graphlayouts | |
15380 | (package | |
15381 | (name "r-graphlayouts") | |
15382 | (version "0.5.0") | |
15383 | (source | |
15384 | (origin | |
15385 | (method url-fetch) | |
15386 | (uri (cran-uri "graphlayouts" version)) | |
15387 | (sha256 | |
15388 | (base32 | |
15389 | "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3")))) | |
15390 | (properties `((upstream-name . "graphlayouts"))) | |
15391 | (build-system r-build-system) | |
15392 | (propagated-inputs | |
15393 | `(("r-igraph" ,r-igraph) | |
15394 | ("r-rcpp" ,r-rcpp) | |
15395 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
15396 | (home-page "https://github.com/schochastics/graphlayouts") | |
15397 | (synopsis "Additional layout algorithms for network visualizations") | |
15398 | (description | |
15399 | "This package provides several layout algorithms to visualize networks | |
15400 | which are not part of the igraph library. Most are based on the concept of | |
15401 | stress majorization by Gansner et al. (2004) | |
15402 | <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to | |
15403 | emphasize hidden group structures in networks or focus on specific nodes.") | |
15404 | (license license:expat))) | |
9567bd8d RW |
15405 | |
15406 | (define-public r-tidygraph | |
15407 | (package | |
15408 | (name "r-tidygraph") | |
15409 | (version "1.1.2") | |
15410 | (source | |
15411 | (origin | |
15412 | (method url-fetch) | |
15413 | (uri (cran-uri "tidygraph" version)) | |
15414 | (sha256 | |
15415 | (base32 | |
15416 | "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn")))) | |
15417 | (properties `((upstream-name . "tidygraph"))) | |
15418 | (build-system r-build-system) | |
15419 | (propagated-inputs | |
15420 | `(("r-dplyr" ,r-dplyr) | |
15421 | ("r-igraph" ,r-igraph) | |
15422 | ("r-magrittr" ,r-magrittr) | |
15423 | ("r-pillar" ,r-pillar) | |
15424 | ("r-r6" ,r-r6) | |
15425 | ("r-rcpp" ,r-rcpp) | |
15426 | ("r-rlang" ,r-rlang) | |
15427 | ("r-tibble" ,r-tibble) | |
15428 | ("r-tidyr" ,r-tidyr))) | |
15429 | (home-page "https://github.com/thomasp85/tidygraph") | |
15430 | (synopsis "Tidy API for graph manipulation") | |
15431 | (description | |
15432 | "This package provides a graph implementation that can be thought of as | |
15433 | two tidy data frames describing node and edge data respectively. It provides | |
15434 | an approach to manipulate these two virtual data frames using the API defined | |
15435 | in the @code{dplyr} package, and it also provides tidy interfaces to a lot of | |
15436 | common graph algorithms.") | |
15437 | (license license:expat))) | |
3a341e82 RW |
15438 | |
15439 | (define-public r-soupx | |
15440 | (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8") | |
15441 | (revision "1")) | |
15442 | (package | |
15443 | (name "r-soupx") | |
15444 | (version (git-version "0.3.1" revision commit)) | |
15445 | (source | |
15446 | (origin | |
15447 | (method git-fetch) | |
15448 | (uri (git-reference | |
15449 | (url "https://github.com/constantAmateur/SoupX") | |
15450 | (commit commit))) | |
15451 | (file-name (git-file-name name version)) | |
15452 | (sha256 | |
15453 | (base32 | |
15454 | "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99")))) | |
15455 | (properties `((upstream-name . "SoupX"))) | |
15456 | (build-system r-build-system) | |
15457 | (propagated-inputs | |
15458 | `(("r-ggplot2" ,r-ggplot2) | |
15459 | ("r-matrix" ,r-matrix) | |
15460 | ("r-seurat" ,r-seurat))) | |
15461 | (home-page "https://github.com/constantAmateur/SoupX") | |
15462 | (synopsis "Single cell mRNA Soup eXterminator") | |
15463 | (description | |
15464 | "This package provides a package for quantifying, profiling and | |
15465 | removing cell free mRNA contamination (the \"soup\") from droplet based single | |
15466 | cell RNA-seq experiments.") | |
15467 | (license license:gpl2)))) | |
16fddf17 WŻ |
15468 | |
15469 | (define-public r-assertr | |
15470 | (package | |
15471 | (name "r-assertr") | |
15472 | (version "2.6") | |
15473 | (source | |
15474 | (origin | |
15475 | (method url-fetch) | |
15476 | (uri (cran-uri "assertr" version)) | |
15477 | (sha256 | |
15478 | (base32 | |
15479 | "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj")))) | |
15480 | (build-system r-build-system) | |
15481 | (propagated-inputs | |
15482 | `(("r-dplyr" ,r-dplyr) | |
15483 | ("r-mass" ,r-mass) | |
15484 | ("r-rlang" ,r-rlang))) | |
15485 | (native-inputs | |
15486 | `(("r-knitr" ,r-knitr))) ; needed for vignette | |
15487 | (home-page "https://github.com/ropensci/assertr") | |
15488 | (synopsis "Assertive programming for R analysis pipelines") | |
15489 | (description | |
15490 | "This package provides functionality to assert conditions that have to be | |
15491 | met so that errors in data used in analysis pipelines can fail quickly. It is | |
15492 | similar to @code{stopifnot()} but more powerful, friendly, and easier for use | |
15493 | in pipelines.") | |
15494 | (license license:expat))) | |
a5a79dd0 RW |
15495 | |
15496 | (define-public r-parameters | |
15497 | (package | |
15498 | (name "r-parameters") | |
446735de | 15499 | (version "0.2.0") |
a5a79dd0 RW |
15500 | (source |
15501 | (origin | |
15502 | (method url-fetch) | |
15503 | (uri (cran-uri "parameters" version)) | |
15504 | (sha256 | |
15505 | (base32 | |
446735de | 15506 | "1mgggb3l67wgjiccq4y84wbs2dw9qk01akd553yiwbwky9rpawgh")))) |
a5a79dd0 RW |
15507 | (properties `((upstream-name . "parameters"))) |
15508 | (build-system r-build-system) | |
15509 | (propagated-inputs | |
15510 | `(("r-bayestestr" ,r-bayestestr) | |
15511 | ("r-insight" ,r-insight))) | |
15512 | (home-page "https://cran.r-project.org/web/packages/parameters") | |
15513 | (synopsis "Processing of model parameters") | |
15514 | (description | |
15515 | "This package provides utilities for processing the parameters of various | |
15516 | statistical models. Beyond computing p values, CIs, and other indices for a | |
15517 | wide variety of models, this package implements features like standardization | |
15518 | or bootstrapping of parameters and models, feature reduction (feature | |
15519 | extraction and variable selection) as well as conversion between indices of | |
15520 | effect size.") | |
15521 | (license license:gpl3))) | |
a0244ef0 RW |
15522 | |
15523 | (define-public r-rgdal | |
15524 | (package | |
15525 | (name "r-rgdal") | |
908497b4 | 15526 | (version "1.4-6") |
a0244ef0 RW |
15527 | (source |
15528 | (origin | |
15529 | (method url-fetch) | |
15530 | (uri (cran-uri "rgdal" version)) | |
15531 | (sha256 | |
908497b4 | 15532 | (base32 "0lj1dax56dxxsj1hindxcvgz169p9dxd0y4wjypbyr01nja8rz4d")))) |
a0244ef0 RW |
15533 | (properties `((upstream-name . "rgdal"))) |
15534 | (build-system r-build-system) | |
15535 | (inputs | |
15536 | `(("gdal" ,gdal) | |
15537 | ("proj.4" ,proj.4) | |
15538 | ("zlib" ,zlib))) | |
15539 | (propagated-inputs | |
15540 | `(("r-sp" ,r-sp))) | |
15541 | (native-inputs | |
15542 | `(("pkg-config" ,pkg-config))) | |
15543 | (home-page "http://rgdal.r-forge.r-project.org") | |
15544 | (synopsis "Bindings for the Geospatial Data Abstraction Library") | |
15545 | (description | |
15546 | "This package provides bindings to the Geospatial Data Abstraction | |
15547 | Library (GDAL) and access to projection/transformation operations from the | |
15548 | PROJ.4 library.") | |
15549 | (license license:gpl2+))) | |
5ad9da9a RW |
15550 | |
15551 | (define-public r-insol | |
15552 | (package | |
15553 | (name "r-insol") | |
15554 | (version "1.2") | |
15555 | (source | |
15556 | (origin | |
15557 | (method url-fetch) | |
15558 | (uri (cran-uri "insol" version)) | |
15559 | (sha256 | |
15560 | (base32 | |
15561 | "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5")))) | |
15562 | (properties `((upstream-name . "insol"))) | |
15563 | (build-system r-build-system) | |
15564 | (propagated-inputs | |
15565 | `(("r-raster" ,r-raster) | |
15566 | ("r-rgdal" ,r-rgdal))) | |
15567 | (native-inputs | |
15568 | `(("gfortran" ,gfortran))) | |
15569 | (home-page "https://meteoexploration.com/R/insol/index.html") | |
15570 | (synopsis "Tools for calculating solar radiation") | |
15571 | (description | |
15572 | "This package provides functions to compute insolation on tilted | |
15573 | surfaces, computes atmospheric transmittance and related parameters such as: | |
15574 | Earth radius vector, declination, sunset and sunrise, daylength, equation of | |
15575 | time, vector in the direction of the sun, vector normal to surface, and some | |
15576 | atmospheric physics.") | |
15577 | (license license:gpl2+))) | |
f5b1354f RW |
15578 | |
15579 | (define-public r-lifecycle | |
15580 | (package | |
15581 | (name "r-lifecycle") | |
15582 | (version "0.1.0") | |
15583 | (source | |
15584 | (origin | |
15585 | (method url-fetch) | |
15586 | (uri (cran-uri "lifecycle" version)) | |
15587 | (sha256 | |
15588 | (base32 | |
15589 | "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n")))) | |
15590 | (properties `((upstream-name . "lifecycle"))) | |
15591 | (build-system r-build-system) | |
15592 | (propagated-inputs | |
15593 | `(("r-glue" ,r-glue) | |
15594 | ("r-rlang" ,r-rlang))) | |
15595 | (home-page "https://github.com/r-lib/lifecycle") | |
15596 | (synopsis "Manage the life cycle of your package functions") | |
15597 | (description | |
15598 | "Manage the life cycle of your exported functions with shared | |
15599 | conventions, documentation badges, and non-invasive deprecation warnings. The | |
15600 | lifecycle package defines four development stages (experimental, maturing, | |
15601 | stable, and questioning) and three deprecation stages (soft-deprecated, | |
15602 | deprecated, and defunct). It makes it easy to insert badges corresponding to | |
15603 | these stages in your documentation. Usage of deprecated functions are | |
15604 | signalled with increasing levels of non-invasive verbosity.") | |
15605 | (license license:gpl3))) | |
195854a5 WŻ |
15606 | |
15607 | (define-public r-assertable | |
15608 | (package | |
15609 | (name "r-assertable") | |
b1a112f4 | 15610 | (version "0.2.7") |
195854a5 WŻ |
15611 | (source |
15612 | (origin | |
15613 | (method url-fetch) | |
15614 | (uri (cran-uri "assertable" version)) | |
15615 | (sha256 | |
15616 | (base32 | |
b1a112f4 | 15617 | "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk")))) |
195854a5 WŻ |
15618 | (build-system r-build-system) |
15619 | (propagated-inputs | |
15620 | `(("r-data-table" ,r-data-table))) | |
15621 | (home-page "https://cran.r-project.org/web/packages/assertable/") | |
15622 | (synopsis "Verbose assertions for tabular data (data.frames and data.tables)") | |
15623 | (description "This package provides simple, flexible assertions on | |
15624 | data.frame or data.table objects with verbose output for vetting. While other | |
15625 | assertion packages apply towards more general use-cases, @code{assertable} is | |
15626 | tailored towards tabular data. It includes functions to check variable names | |
15627 | and values, whether the dataset contains all combinations of a given set of | |
15628 | unique identifiers, and whether it is a certain length. In addition, | |
15629 | @code{assertable} includes utility functions to check the existence of target | |
15630 | files and to efficiently import multiple tabular data files into one | |
15631 | data.table.") | |
15632 | (license license:gpl3))) |