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> |
14b78ca6 | 5 | ;;; Copyright © 2017, 2018 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> |
056468dc RW |
18 | ;;; |
19 | ;;; This file is part of GNU Guix. | |
20 | ;;; | |
21 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
22 | ;;; under the terms of the GNU General Public License as published by | |
23 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
24 | ;;; your option) any later version. | |
25 | ;;; | |
26 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
27 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
28 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
29 | ;;; GNU General Public License for more details. | |
30 | ;;; | |
31 | ;;; You should have received a copy of the GNU General Public License | |
32 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
33 | ||
34 | (define-module (gnu packages cran) | |
35 | #:use-module ((guix licenses) #:prefix license:) | |
36 | #:use-module (guix packages) | |
37 | #:use-module (guix download) | |
92ce1883 | 38 | #:use-module (guix git-download) |
056468dc | 39 | #:use-module (guix utils) |
c69d27db | 40 | #:use-module (guix build-system r) |
44b0c5b5 | 41 | #:use-module (gnu packages algebra) |
ff939ef4 | 42 | #:use-module (gnu packages base) |
f33cb7ab | 43 | #:use-module (gnu packages bioinformatics) |
7002c44f | 44 | #:use-module (gnu packages c) |
546fc4aa | 45 | #:use-module (gnu packages compression) |
92ce1883 | 46 | #:use-module (gnu packages curl) |
d9bec9a8 | 47 | #:use-module (gnu packages databases) |
f338e480 | 48 | #:use-module (gnu packages fontutils) |
062b6dbd | 49 | #:use-module (gnu packages gcc) |
d884e407 | 50 | #:use-module (gnu packages geo) |
d0eb09a1 | 51 | #:use-module (gnu packages ghostscript) |
f338e480 | 52 | #:use-module (gnu packages gl) |
01af264d | 53 | #:use-module (gnu packages gnome) |
3d62d98e | 54 | #:use-module (gnu packages graph) |
01af264d | 55 | #:use-module (gnu packages gtk) |
9b3ecb60 | 56 | #:use-module (gnu packages haskell) |
3f6e6e98 | 57 | #:use-module (gnu packages icu4c) |
f338e480 | 58 | #:use-module (gnu packages image) |
dab3e92c | 59 | #:use-module (gnu packages imagemagick) |
3f6e6e98 | 60 | #:use-module (gnu packages java) |
92ce1883 RW |
61 | #:use-module (gnu packages javascript) |
62 | #:use-module (gnu packages lisp) | |
f97ce815 | 63 | #:use-module (gnu packages machine-learning) |
521e0703 | 64 | #:use-module (gnu packages maths) |
94989d4b | 65 | #:use-module (gnu packages mpi) |
1ab51604 | 66 | #:use-module (gnu packages multiprecision) |
f313baf0 | 67 | #:use-module (gnu packages networking) |
3f6e6e98 | 68 | #:use-module (gnu packages pcre) |
e0268ff2 | 69 | #:use-module (gnu packages perl) |
e33498b8 | 70 | #:use-module (gnu packages pkg-config) |
9f56ceec | 71 | #:use-module (gnu packages python) |
984a8aa6 | 72 | #:use-module (gnu packages python-xyz) |
e0268ff2 | 73 | #:use-module (gnu packages statistics) |
9944399a | 74 | #:use-module (gnu packages tls) |
f338e480 RW |
75 | #:use-module (gnu packages web) |
76 | #:use-module (gnu packages xorg)) | |
056468dc | 77 | |
88e4ed55 RW |
78 | (define-public r-clipr |
79 | (package | |
80 | (name "r-clipr") | |
0c025a7f | 81 | (version "0.5.0") |
88e4ed55 RW |
82 | (source |
83 | (origin | |
84 | (method url-fetch) | |
85 | (uri (cran-uri "clipr" version)) | |
86 | (sha256 | |
87 | (base32 | |
0c025a7f | 88 | "1grx0lyww1cxmdvsr44wmbhz9i6zmiwxbchb97gxrfi9gy5kyc7x")))) |
88e4ed55 RW |
89 | (build-system r-build-system) |
90 | (home-page "https://github.com/mdlincoln/clipr") | |
91 | (synopsis "Read and write from the system clipboard") | |
92 | (description | |
93 | "This package provides simple utility functions to read from and write to | |
94 | the system clipboards.") | |
95 | (license license:gpl3))) | |
96 | ||
3f22a115 RW |
97 | (define-public r-ellipsis |
98 | (package | |
99 | (name "r-ellipsis") | |
100 | (version "0.1.0") | |
101 | (source | |
102 | (origin | |
103 | (method url-fetch) | |
104 | (uri (cran-uri "ellipsis" version)) | |
105 | (sha256 | |
106 | (base32 | |
107 | "0pw94qpg81xmsdsagpqxddv7m2cmdszmyyq99dk3caqqj01z7wg6")))) | |
108 | (build-system r-build-system) | |
109 | (home-page "https://github.com/hadley/ellipsis") | |
110 | (synopsis "Tools for working with additional arguments") | |
111 | (description | |
112 | "In S3 generics, it's useful to take @code{...} so that methods can have | |
113 | additional arguments. But this flexibility comes at a cost: misspelled | |
114 | arguments will be silently ignored. The @code{ellipsis} package is an | |
115 | experiment that allows a generic to warn if any arguments passed in @code{...} | |
116 | are not used.") | |
117 | (license license:gpl3))) | |
118 | ||
2b106a8d RW |
119 | (define-public r-sys |
120 | (package | |
121 | (name "r-sys") | |
ffd6e2fd | 122 | (version "3.1") |
2b106a8d RW |
123 | (source |
124 | (origin | |
125 | (method url-fetch) | |
126 | (uri (cran-uri "sys" version)) | |
127 | (sha256 | |
128 | (base32 | |
ffd6e2fd | 129 | "0aj3wcyah3r7c9s3rbs0c8nifd4vqmkzg9fqkrb7f838ww0qw24q")))) |
2b106a8d RW |
130 | (build-system r-build-system) |
131 | (home-page "https://github.com/jeroen/sys") | |
132 | (synopsis "Powerful and reliable tools for running system commands in R") | |
133 | (description | |
134 | "This package provides drop-in replacements for the base @code{system2()} | |
135 | function with fine control and consistent behavior across platforms. It | |
136 | supports clean interruption, timeout, background tasks, and streaming STDIN / | |
137 | STDOUT / STDERR over binary or text connections. The package also provides | |
138 | functions for evaluating expressions inside a temporary fork. Such | |
139 | evaluations have no side effects on the main R process, and support reliable | |
140 | interrupts and timeouts. This provides the basis for a sandboxing | |
141 | mechanism.") | |
142 | (license license:expat))) | |
143 | ||
9d3a4672 RW |
144 | (define-public r-askpass |
145 | (package | |
146 | (name "r-askpass") | |
147 | (version "1.1") | |
148 | (source | |
149 | (origin | |
150 | (method url-fetch) | |
151 | (uri (cran-uri "askpass" version)) | |
152 | (sha256 | |
153 | (base32 | |
154 | "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) | |
155 | (build-system r-build-system) | |
156 | (propagated-inputs `(("r-sys" ,r-sys))) | |
157 | (home-page "https://github.com/jeroen/askpass") | |
158 | (synopsis "Safe password entry for R") | |
159 | (description | |
160 | "This package provides cross-platform utilities for prompting the user | |
161 | for credentials or a passphrase, for example to authenticate with a server or | |
162 | read a protected key.") | |
163 | (license license:expat))) | |
164 | ||
c80fb90f RW |
165 | (define-public r-vegan |
166 | (package | |
167 | (name "r-vegan") | |
fadc49c6 | 168 | (version "2.5-4") |
c80fb90f RW |
169 | (source |
170 | (origin | |
171 | (method url-fetch) | |
172 | (uri (cran-uri "vegan" version)) | |
173 | (sha256 | |
174 | (base32 | |
fadc49c6 | 175 | "1q4khii0xbjwmkida0b35q8rmwhg325qizjwz6slkjhz250a85ji")))) |
c80fb90f RW |
176 | (build-system r-build-system) |
177 | (native-inputs | |
178 | `(("gfortran" ,gfortran))) | |
179 | (propagated-inputs | |
180 | `(("r-cluster" ,r-cluster) | |
181 | ("r-knitr" ,r-knitr) ; needed for vignettes | |
182 | ("r-lattice" ,r-lattice) | |
183 | ("r-mass" ,r-mass) | |
184 | ("r-mgcv" ,r-mgcv) | |
185 | ("r-permute" ,r-permute))) | |
186 | (home-page "https://cran.r-project.org/web/packages/vegan") | |
187 | (synopsis "Functions for community ecology") | |
188 | (description | |
189 | "The vegan package provides tools for descriptive community ecology. It | |
190 | has most basic functions of diversity analysis, community ordination and | |
191 | dissimilarity analysis. Most of its multivariate tools can be used for other | |
192 | data types as well.") | |
193 | (license license:gpl2+))) | |
194 | ||
786d3de2 CR |
195 | (define-public r-tidyverse |
196 | (package | |
197 | (name "r-tidyverse") | |
198 | (version "1.2.1") | |
199 | (source | |
200 | (origin | |
201 | (method url-fetch) | |
202 | (uri (cran-uri "tidyverse" version)) | |
203 | (sha256 | |
204 | (base32 | |
205 | "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd")))) | |
206 | (build-system r-build-system) | |
207 | (propagated-inputs | |
208 | `(("r-broom" ,r-broom) | |
209 | ("r-cli" ,r-cli) | |
210 | ("r-crayon" ,r-crayon) | |
211 | ("r-dbplyr" ,r-dbplyr) | |
212 | ("r-dplyr" ,r-dplyr) | |
213 | ("r-forcats" ,r-forcats) | |
214 | ("r-ggplot2" ,r-ggplot2) | |
215 | ("r-haven" ,r-haven) | |
216 | ("r-hms" ,r-hms) | |
217 | ("r-httr" ,r-httr) | |
218 | ("r-jsonlite" ,r-jsonlite) | |
219 | ("r-lubridate" ,r-lubridate) | |
220 | ("r-magrittr" ,r-magrittr) | |
221 | ("r-modelr" ,r-modelr) | |
222 | ("r-purrr" ,r-purrr) | |
223 | ("r-readr" ,r-readr) | |
224 | ("r-readxl" ,r-readxl) | |
225 | ("r-reprex" ,r-reprex) | |
226 | ("r-rlang" ,r-rlang) | |
227 | ("r-rstudioapi" ,r-rstudioapi) | |
228 | ("r-rvest" ,r-rvest) | |
229 | ("r-stringr" ,r-stringr) | |
230 | ("r-tibble" ,r-tibble) | |
231 | ("r-tidyr" ,r-tidyr) | |
232 | ("r-xml2" ,r-xml2))) | |
233 | (home-page "https://tidyverse.tidyverse.org") | |
234 | (synopsis "Install and load packages from the \"Tidyverse\"") | |
235 | (description | |
236 | "The @code{tidyverse} is a set of packages that work in harmony because | |
237 | they share common data representations and API design. This package is | |
238 | designed to make it easy to install and load multiple tidyverse packages in a | |
239 | single step.") | |
240 | (license license:gpl3))) | |
241 | ||
8a1ef6ac CR |
242 | (define-public r-rvest |
243 | (package | |
244 | (name "r-rvest") | |
245 | (version "0.3.2") | |
246 | (source | |
247 | (origin | |
248 | (method url-fetch) | |
249 | (uri (cran-uri "rvest" version)) | |
250 | (sha256 | |
251 | (base32 | |
252 | "04mv99z8dixywx96kfy4215g6ib23s7qvd77hcf9pxqxzcvqhvhd")))) | |
253 | (build-system r-build-system) | |
254 | (propagated-inputs | |
255 | `(("r-httr" ,r-httr) | |
256 | ("r-magrittr" ,r-magrittr) | |
257 | ("r-selectr" ,r-selectr) | |
258 | ("r-xml2" ,r-xml2))) | |
259 | (home-page "https://github.com/hadley/rvest") | |
260 | (synopsis "Simple web scraping for R") | |
261 | (description | |
262 | "@code{r-rvest} helps you scrape information from web pages. It is | |
263 | designed to work with @code{magrittr} to make it easy to express common web | |
264 | scraping tasks, inspired by libraries like @code{BeautifulSoup}.") | |
265 | (license license:gpl3))) | |
266 | ||
81a9d4a4 CR |
267 | (define-public r-selectr |
268 | (package | |
269 | (name "r-selectr") | |
41e8bd77 | 270 | (version "0.4-1") |
81a9d4a4 CR |
271 | (source |
272 | (origin | |
273 | (method url-fetch) | |
274 | (uri (cran-uri "selectr" version)) | |
275 | (sha256 | |
276 | (base32 | |
41e8bd77 | 277 | "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b")))) |
81a9d4a4 | 278 | (build-system r-build-system) |
41e8bd77 RW |
279 | (propagated-inputs |
280 | `(("r-stringr" ,r-stringr) | |
281 | ("r-r6" ,r-r6))) | |
81a9d4a4 CR |
282 | (home-page "https://sjp.co.nz/projects/selectr/") |
283 | (synopsis "Translate CSS selectors to XPath expressions") | |
284 | (description | |
285 | "@code{r-selectr} translates a CSS3 selector into an equivalent XPath | |
286 | expression. This allows you to use CSS selectors when working with the XML | |
287 | package as it can only evaluate XPath expressions. Also provided are | |
288 | convenience functions useful for using CSS selectors on XML nodes. This | |
289 | package is a port of the Python package @code{cssselect}.") | |
290 | (license license:bsd-3))) | |
291 | ||
948740b0 CR |
292 | (define-public r-reprex |
293 | (package | |
294 | (name "r-reprex") | |
1c9906c2 | 295 | (version "0.2.1") |
948740b0 CR |
296 | (source |
297 | (origin | |
298 | (method url-fetch) | |
299 | (uri (cran-uri "reprex" version)) | |
300 | (sha256 | |
301 | (base32 | |
1c9906c2 | 302 | "1ws5gds453xgfili87r35rz1wn2i7jbqissq98csbiddpkgls8sx")))) |
948740b0 CR |
303 | (build-system r-build-system) |
304 | (propagated-inputs | |
305 | `(("r-callr" ,r-callr) | |
e3c1e93e | 306 | ("r-clipr" ,r-clipr) |
1c9906c2 | 307 | ("r-fs" ,r-fs) |
e3c1e93e | 308 | ("r-rlang" ,r-rlang) |
948740b0 | 309 | ("r-rmarkdown" ,r-rmarkdown) |
e3c1e93e RW |
310 | ("r-whisker" ,r-whisker) |
311 | ("r-withr" ,r-withr))) | |
948740b0 CR |
312 | (home-page "https://github.com/tidyverse/reprex") |
313 | (synopsis "Prepare reproducible R code examples for sharing") | |
314 | (description | |
315 | "This package provides a convenience wrapper that uses the | |
316 | @code{rmarkdown} package to render small snippets of code to target formats | |
317 | that include both code and output. The goal is to encourage the sharing of | |
318 | small, reproducible, and runnable examples on code-oriented websites or email. | |
319 | @code{reprex} also extracts clean, runnable R code from various common formats, | |
320 | such as copy/paste from an R session.") | |
321 | (license license:expat))) | |
322 | ||
10487c30 CR |
323 | (define-public r-callr |
324 | (package | |
325 | (name "r-callr") | |
d1021421 | 326 | (version "3.2.0") |
10487c30 CR |
327 | (source |
328 | (origin | |
329 | (method url-fetch) | |
330 | (uri (cran-uri "callr" version)) | |
331 | (sha256 | |
332 | (base32 | |
d1021421 | 333 | "1s5h2k7c1vgbry90xczin66q89cbkc6mvh4679l5rsz83087pd2b")))) |
10487c30 CR |
334 | (build-system r-build-system) |
335 | (propagated-inputs | |
527c6055 | 336 | `(("r-r6" ,r-r6) |
6034a62a | 337 | ("r-processx" ,r-processx))) |
10487c30 CR |
338 | (home-page "https://github.com/r-lib/callr#readme") |
339 | (synopsis "Call R from R") | |
340 | (description | |
341 | "It is sometimes useful to perform a computation in a separate R process, | |
342 | without affecting the current R process at all. This packages does exactly | |
343 | that.") | |
344 | (license license:expat))) | |
345 | ||
d7637e5e CR |
346 | (define-public r-readxl |
347 | (package | |
348 | (name "r-readxl") | |
50d063b5 | 349 | (version "1.3.1") |
d7637e5e CR |
350 | (source |
351 | (origin | |
352 | (method url-fetch) | |
353 | (uri (cran-uri "readxl" version)) | |
354 | (sha256 | |
355 | (base32 | |
50d063b5 | 356 | "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14")))) |
d7637e5e CR |
357 | (build-system r-build-system) |
358 | (propagated-inputs | |
359 | `(("r-cellranger" ,r-cellranger) | |
b140569e | 360 | ("r-progress" ,r-progress) |
d7637e5e CR |
361 | ("r-rcpp" ,r-rcpp) |
362 | ("r-tibble" ,r-tibble))) | |
363 | (home-page "https://readxl.tidyverse.org") | |
364 | (synopsis "Read Excel files") | |
365 | (description | |
366 | "This package lets you import Excel files into R. It supports | |
367 | @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via | |
368 | the embedded @code{RapidXML} C++ library.") | |
369 | ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and | |
370 | ;; 'rapidxml' which is Boost. | |
371 | (license (list license:gpl3 license:bsd-2 license:boost1.0)))) | |
372 | ||
9a91c925 CR |
373 | (define-public r-modelr |
374 | (package | |
375 | (name "r-modelr") | |
34bac6c3 | 376 | (version "0.1.4") |
9a91c925 CR |
377 | (source |
378 | (origin | |
379 | (method url-fetch) | |
380 | (uri (cran-uri "modelr" version)) | |
381 | (sha256 | |
382 | (base32 | |
34bac6c3 | 383 | "1ngxphbjkv7yl1rg30sj36mfwhc76g452drjrq9abgab4k0pgnml")))) |
9a91c925 CR |
384 | (build-system r-build-system) |
385 | (propagated-inputs | |
386 | `(("r-broom" ,r-broom) | |
387 | ("r-dplyr" ,r-dplyr) | |
388 | ("r-lazyeval" ,r-lazyeval) | |
389 | ("r-magrittr" ,r-magrittr) | |
390 | ("r-purrr" ,r-purrr) | |
391 | ("r-tibble" ,r-tibble) | |
392 | ("r-tidyr" ,r-tidyr))) | |
393 | (home-page "https://github.com/tidyverse/modelr") | |
394 | (synopsis "Helper functions for modelling in pipelines") | |
395 | (description | |
396 | "Functions for modelling that help you seamlessly integrate modelling | |
397 | into a pipeline of data manipulation and visualisation.") | |
398 | (license license:gpl3))) | |
399 | ||
92ce1883 RW |
400 | (define-public r-httpuv |
401 | (package | |
402 | (name "r-httpuv") | |
0b8ef655 | 403 | (version "1.5.1") |
92ce1883 RW |
404 | (source (origin |
405 | (method url-fetch) | |
406 | (uri (cran-uri "httpuv" version)) | |
407 | (sha256 | |
408 | (base32 | |
0b8ef655 | 409 | "042piypg4c8sqrlcdl3dwajkafkbglsky3x7d0jpjv8s5wxnpfxm")))) |
92ce1883 | 410 | (build-system r-build-system) |
92ce1883 RW |
411 | (propagated-inputs |
412 | `(("r-bh" ,r-bh) | |
413 | ("r-later" ,r-later) | |
2391e97c RW |
414 | ("r-promises" ,r-promises) |
415 | ("r-r6" ,r-r6) | |
416 | ("r-rcpp" ,r-rcpp))) | |
92ce1883 RW |
417 | (home-page "https://github.com/rstudio/httpuv") |
418 | (synopsis "HTTP and WebSocket server library for R") | |
419 | (description | |
420 | "The httpuv package provides low-level socket and protocol support for | |
421 | handling HTTP and WebSocket requests directly from within R. It is primarily | |
422 | intended as a building block for other packages, rather than making it | |
423 | particularly easy to create complete web applications using httpuv alone.") | |
424 | ;; This package includes third-party code that was originally released | |
425 | ;; under various non-copyleft licenses. Full licensing information can be | |
426 | ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE | |
427 | (license license:gpl3+))) | |
428 | ||
429 | (define-public r-jsonlite | |
430 | (package | |
431 | (name "r-jsonlite") | |
a2315c67 | 432 | (version "1.6") |
92ce1883 RW |
433 | (source (origin |
434 | (method url-fetch) | |
435 | (uri (cran-uri "jsonlite" version)) | |
436 | (sha256 | |
437 | (base32 | |
a2315c67 | 438 | "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8")))) |
92ce1883 RW |
439 | (build-system r-build-system) |
440 | (home-page "http://arxiv.org/abs/1403.2805") | |
441 | (synopsis "Robust, high performance JSON parser and generator for R") | |
442 | (description | |
443 | "The jsonlite package provides a fast JSON parser and generator optimized | |
444 | for statistical data and the web. It offers flexible, robust, high | |
445 | performance tools for working with JSON in R and is particularly powerful for | |
446 | building pipelines and interacting with a web API. In addition to converting | |
447 | JSON data from/to R objects, jsonlite contains functions to stream, validate, | |
448 | and prettify JSON data. The unit tests included with the package verify that | |
449 | all edge cases are encoded and decoded consistently for use with dynamic data | |
450 | in systems and applications.") | |
451 | (license license:expat))) | |
452 | ||
453 | (define-public r-servr | |
454 | (package | |
455 | (name "r-servr") | |
790db519 | 456 | (version "0.13") |
92ce1883 RW |
457 | (source (origin |
458 | (method url-fetch) | |
459 | (uri (cran-uri "servr" version)) | |
460 | (sha256 | |
461 | (base32 | |
790db519 | 462 | "1n5haqkshrxcx557f1k7nrisvq3wak8v370s2r6yv691b8hvbscs")))) |
92ce1883 RW |
463 | (build-system r-build-system) |
464 | (propagated-inputs | |
465 | `(("r-httpuv" ,r-httpuv) | |
466 | ("r-jsonlite" ,r-jsonlite) | |
467 | ("r-mime" ,r-mime) | |
468 | ("r-xfun" ,r-xfun))) | |
469 | (home-page "https://github.com/yihui/servr") | |
470 | (synopsis "Simple HTTP server to serve static files or dynamic documents") | |
471 | (description | |
472 | "Servr provides an HTTP server in R to serve static files, or dynamic | |
473 | documents that can be converted to HTML files (e.g., R Markdown) under a given | |
474 | directory.") | |
475 | (license license:expat))) | |
476 | ||
477 | (define-public r-htmltools | |
478 | (package | |
479 | (name "r-htmltools") | |
480 | (version "0.3.6") | |
481 | (source (origin | |
482 | (method url-fetch) | |
483 | (uri (cran-uri "htmltools" version)) | |
484 | (sha256 | |
485 | (base32 | |
486 | "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4")))) | |
487 | (build-system r-build-system) | |
488 | (arguments | |
489 | `(#:phases | |
490 | (modify-phases %standard-phases | |
491 | ;; See https://github.com/rstudio/htmltools/pull/68 | |
492 | ;; The resource files are in the store and have mode 444. After | |
493 | ;; copying the files R fails to remove them again because it doesn't | |
494 | ;; have write access to them. | |
495 | (add-after 'unpack 'copy-files-without-mode | |
496 | (lambda _ | |
497 | (substitute* "R/html_dependency.R" | |
498 | (("file.copy\\(from, to, " prefix) | |
499 | (string-append prefix | |
500 | "copy.mode = FALSE, "))) | |
501 | #t))))) | |
502 | (propagated-inputs | |
503 | `(("r-digest" ,r-digest) | |
504 | ("r-rcpp" ,r-rcpp))) | |
505 | (home-page "https://cran.r-project.org/web/packages/htmltools") | |
506 | (synopsis "R tools for HTML") | |
507 | (description | |
508 | "This package provides tools for HTML generation and output in R.") | |
509 | (license license:expat))) | |
510 | ||
511 | (define-public r-htmlwidgets | |
512 | (package | |
513 | (name "r-htmlwidgets") | |
514 | (version "1.3") | |
515 | (source (origin | |
516 | (method url-fetch) | |
517 | (uri (cran-uri "htmlwidgets" version)) | |
518 | (sha256 | |
519 | (base32 | |
520 | "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i")))) | |
521 | (build-system r-build-system) | |
522 | (propagated-inputs | |
523 | `(("r-htmltools" ,r-htmltools) | |
524 | ("r-jsonlite" ,r-jsonlite) | |
525 | ("r-yaml" ,r-yaml))) | |
526 | (home-page "https://github.com/ramnathv/htmlwidgets") | |
527 | (synopsis "HTML Widgets for R") | |
528 | (description | |
529 | "HTML widgets is a framework for creating HTML widgets that render in | |
530 | various contexts including the R console, R Markdown documents, and Shiny web | |
531 | applications.") | |
532 | (license license:expat))) | |
533 | ||
534 | (define-public r-htmltable | |
535 | (package | |
536 | (name "r-htmltable") | |
1add168a | 537 | (version "1.13.1") |
92ce1883 RW |
538 | (source |
539 | (origin | |
540 | (method url-fetch) | |
541 | (uri (cran-uri "htmlTable" version)) | |
542 | (sha256 | |
543 | (base32 | |
1add168a | 544 | "1l44b33xgj2698k6nz17r8fl0ink14ryzng803apm9d6bnv357v8")))) |
92ce1883 RW |
545 | (properties `((upstream-name . "htmlTable"))) |
546 | (build-system r-build-system) | |
547 | (propagated-inputs | |
548 | `(("r-checkmate" ,r-checkmate) | |
549 | ("r-htmltools" ,r-htmltools) | |
550 | ("r-htmlwidgets" ,r-htmlwidgets) | |
551 | ("r-knitr" ,r-knitr) | |
552 | ("r-magrittr" ,r-magrittr) | |
553 | ("r-rstudioapi" ,r-rstudioapi) | |
554 | ("r-stringr" ,r-stringr))) | |
555 | (home-page "http://gforge.se/packages/") | |
556 | (synopsis "Advanced tables for Markdown/HTML") | |
557 | (description | |
558 | "This package provides functions to build tables with advanced layout | |
559 | elements such as row spanners, column spanners, table spanners, zebra | |
560 | striping, and more. While allowing advanced layout, the underlying | |
561 | CSS-structure is simple in order to maximize compatibility with word | |
562 | processors such as LibreOffice. The package also contains a few text | |
563 | formatting functions that help outputting text compatible with HTML or | |
564 | LaTeX.") | |
565 | (license license:gpl3+))) | |
566 | ||
567 | (define-public r-curl | |
568 | (package | |
569 | (name "r-curl") | |
646e1ef0 | 570 | (version "3.3") |
92ce1883 RW |
571 | (source (origin |
572 | (method url-fetch) | |
573 | (uri (cran-uri "curl" version)) | |
574 | (sha256 | |
575 | (base32 | |
646e1ef0 | 576 | "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c")))) |
92ce1883 RW |
577 | (build-system r-build-system) |
578 | (arguments | |
579 | `(#:phases | |
580 | (modify-phases %standard-phases | |
581 | ;; The environment variable CURL_CA_BUNDLE is only respected when | |
582 | ;; running Windows, so we disable the platform checks. | |
583 | ;; This can be removed once the libcurl has been patched. | |
584 | (add-after 'unpack 'allow-CURL_CA_BUNDLE | |
585 | (lambda _ | |
586 | (substitute* "R/onload.R" | |
587 | (("if \\(!grepl\\(\"mingw\".*") | |
588 | "if (FALSE)\n")) | |
589 | (substitute* "src/handle.c" | |
590 | (("#ifdef _WIN32") "#if 1")) | |
591 | #t))))) | |
592 | (inputs | |
646e1ef0 RW |
593 | `(("libcurl" ,curl) |
594 | ("zlib" ,zlib))) | |
595 | (native-inputs | |
596 | `(("pkg-config" ,pkg-config))) | |
92ce1883 RW |
597 | (home-page "https://github.com/jeroenooms/curl") |
598 | (synopsis "HTTP client for R") | |
599 | (description | |
600 | "The @code{curl()} and @code{curl_download()} functions provide highly | |
601 | configurable drop-in replacements for base @code{url()} and | |
602 | @code{download.file()} with better performance, support for encryption, gzip | |
603 | compression, authentication, and other @code{libcurl} goodies. The core of | |
604 | the package implements a framework for performing fully customized requests | |
605 | where data can be processed either in memory, on disk, or streaming via the | |
606 | callback or connection interfaces.") | |
607 | (license license:expat))) | |
608 | ||
609 | (define-public r-hwriter | |
610 | (package | |
611 | (name "r-hwriter") | |
612 | (version "1.3.2") | |
613 | (source | |
614 | (origin | |
615 | (method url-fetch) | |
616 | (uri (cran-uri "hwriter" version)) | |
617 | (sha256 | |
618 | (base32 | |
619 | "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb")))) | |
620 | (build-system r-build-system) | |
621 | (home-page "https://cran.r-project.org/web/packages/hwriter") | |
622 | (synopsis "Output R objects in HTML format") | |
623 | (description | |
624 | "This package provides easy-to-use and versatile functions to output R | |
625 | objects in HTML format.") | |
626 | (license license:lgpl2.1+))) | |
627 | ||
628 | (define-public r-rjson | |
629 | (package | |
630 | (name "r-rjson") | |
631 | (version "0.2.20") | |
632 | (source | |
633 | (origin | |
634 | (method url-fetch) | |
635 | (uri (cran-uri "rjson" version)) | |
636 | (sha256 | |
637 | (base32 | |
638 | "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) | |
639 | (build-system r-build-system) | |
640 | (home-page "https://cran.r-project.org/web/packages/rjson") | |
641 | (synopsis "JSON library for R") | |
642 | (description | |
643 | "This package provides functions to convert R objects into JSON objects | |
644 | and vice-versa.") | |
645 | (license license:gpl2+))) | |
646 | ||
647 | (define-public r-shiny | |
648 | (package | |
649 | (name "r-shiny") | |
d235cf72 | 650 | (version "1.2.0") |
92ce1883 RW |
651 | (source |
652 | (origin | |
653 | (method git-fetch) | |
654 | (uri (git-reference | |
655 | (url "https://github.com/rstudio/shiny.git") | |
656 | (commit (string-append "v" version)))) | |
657 | (file-name (git-file-name name version)) | |
658 | (sha256 | |
659 | (base32 | |
d235cf72 | 660 | "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4")))) |
92ce1883 RW |
661 | (build-system r-build-system) |
662 | (arguments | |
663 | `(#:modules ((guix build r-build-system) | |
664 | (guix build minify-build-system) | |
665 | (guix build utils) | |
666 | (ice-9 match)) | |
667 | #:imported-modules (,@%r-build-system-modules | |
668 | (guix build minify-build-system)) | |
669 | #:phases | |
670 | (modify-phases (@ (guix build r-build-system) %standard-phases) | |
671 | (add-after 'unpack 'replace-bundled-minified-JavaScript | |
672 | (lambda* (#:key inputs #:allow-other-keys) | |
673 | (let ((replace-file (lambda (old new) | |
674 | (format #t "replacing ~a with ~a\n" old new) | |
675 | (delete-file old) | |
676 | (symlink new old)))) | |
677 | ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ | |
678 | ;; contain just data. They are not minified code, so we don't | |
679 | ;; replace them. | |
680 | (with-directory-excursion "inst/www/shared" | |
681 | (replace-file "bootstrap/shim/respond.min.js" | |
682 | (string-append (assoc-ref inputs "js-respond") | |
683 | "/share/javascript/respond.min.js")) | |
684 | (replace-file "bootstrap/shim/html5shiv.min.js" | |
685 | (string-append (assoc-ref inputs "js-html5shiv") | |
686 | "/share/javascript/html5shiv.min.js")) | |
687 | (replace-file "json2-min.js" | |
688 | (string-append (assoc-ref inputs "js-json2") | |
689 | "/share/javascript/json2.min.js")) | |
690 | (replace-file "strftime/strftime-min.js" | |
691 | (string-append (assoc-ref inputs "js-strftime") | |
692 | "/share/javascript/strftime.min.js")) | |
693 | (replace-file "highlight/highlight.pack.js" | |
694 | (string-append (assoc-ref inputs "js-highlight") | |
695 | "/share/javascript/highlight.min.js")) | |
696 | (replace-file "datatables/js/jquery.dataTables.min.js" | |
697 | (string-append (assoc-ref inputs "js-datatables") | |
698 | "/share/javascript/jquery.dataTables.min.js")) | |
699 | (replace-file "selectize/js/selectize.min.js" | |
700 | (string-append (assoc-ref inputs "js-selectize") | |
701 | "/share/javascript/selectize.min.js")) | |
702 | (replace-file "selectize/js/es5-shim.min.js" | |
703 | (string-append (assoc-ref inputs "js-es5-shim") | |
704 | "/share/javascript/es5-shim.min.js")) | |
705 | (for-each (match-lambda | |
706 | ((source . target) | |
707 | (delete-file target) | |
708 | (minify source #:target target))) | |
709 | '(("jqueryui/jquery-ui.js" . | |
710 | "jqueryui/jquery-ui.min.js") | |
92ce1883 RW |
711 | ("datepicker/js/bootstrap-datepicker.js" . |
712 | "datepicker/js/bootstrap-datepicker.min.js") | |
713 | ("ionrangeslider/js/ion.rangeSlider.js" . | |
714 | "ionrangeslider/js/ion.rangeSlider.min.js") | |
715 | ("bootstrap/js/bootstrap.js" . | |
716 | "bootstrap/js/bootstrap.min.js") | |
717 | ("shiny.js" . | |
718 | "shiny.min.js") | |
719 | ("jquery.js" . | |
720 | "jquery.min.js"))))) | |
721 | #t))))) | |
722 | (propagated-inputs | |
723 | `(("r-crayon" ,r-crayon) | |
724 | ("r-httpuv" ,r-httpuv) | |
725 | ("r-mime" ,r-mime) | |
726 | ("r-jsonlite" ,r-jsonlite) | |
727 | ("r-xtable" ,r-xtable) | |
728 | ("r-digest" ,r-digest) | |
729 | ("r-htmltools" ,r-htmltools) | |
730 | ("r-r6" ,r-r6) | |
731 | ("r-sourcetools" ,r-sourcetools))) | |
732 | (inputs | |
733 | `(("js-datatables" ,js-datatables) | |
734 | ("js-html5shiv" ,js-html5shiv) | |
735 | ("js-json2" ,js-json2) | |
736 | ("js-respond" ,js-respond) | |
737 | ("js-selectize" ,js-selectize) | |
738 | ("js-strftime" ,js-strftime) | |
739 | ("js-highlight" ,js-highlight) | |
740 | ("js-es5-shim" ,js-es5-shim))) | |
741 | (home-page "http://shiny.rstudio.com") | |
742 | (synopsis "Easy interactive web applications with R") | |
743 | (description | |
744 | "Makes it incredibly easy to build interactive web applications | |
745 | with R. Automatic \"reactive\" binding between inputs and outputs and | |
746 | extensive prebuilt widgets make it possible to build beautiful, | |
747 | responsive, and powerful applications with minimal effort.") | |
748 | (license license:artistic2.0))) | |
749 | ||
750 | (define-public r-shinydashboard | |
751 | (package | |
752 | (name "r-shinydashboard") | |
753 | (version "0.7.1") | |
754 | (source (origin | |
755 | (method url-fetch) | |
756 | (uri (cran-uri "shinydashboard" version)) | |
757 | (sha256 | |
758 | (base32 | |
759 | "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) | |
760 | (build-system r-build-system) | |
761 | ;; The directory inst/AdminLTE/ contains a minified JavaScript file. | |
762 | ;; Regenerate it from the included sources. | |
763 | (arguments | |
764 | `(#:modules ((guix build utils) | |
765 | (guix build r-build-system) | |
766 | (ice-9 popen)) | |
767 | #:phases | |
768 | (modify-phases %standard-phases | |
769 | (add-after 'unpack 'generate-minified-javascript | |
770 | (lambda _ | |
771 | (with-directory-excursion "inst/AdminLTE" | |
772 | (delete-file "app.min.js") | |
773 | (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js"))) | |
774 | (call-with-output-file "app.min.js" | |
775 | (lambda (port) | |
776 | (dump-port minified port)))))))))) | |
777 | (propagated-inputs | |
778 | `(("r-htmltools" ,r-htmltools) | |
779 | ("r-promises" ,r-promises) | |
780 | ("r-shiny" ,r-shiny))) | |
781 | (native-inputs | |
782 | `(("uglify-js" ,uglify-js))) | |
783 | (home-page "http://rstudio.github.io/shinydashboard/") | |
784 | (synopsis "Create dashboards with shiny") | |
785 | (description "This package provides an extension to the Shiny web | |
786 | application framework for R, making it easy to create attractive dashboards.") | |
787 | ;; This package includes software that was released under the Expat | |
788 | ;; license, but the whole package is released under GPL version 2 or | |
789 | ;; later. | |
790 | (license license:gpl2+))) | |
791 | ||
792 | (define-public r-shinyfiles | |
793 | (package | |
794 | (name "r-shinyfiles") | |
795 | (version "0.7.2") | |
796 | (source | |
797 | (origin | |
798 | (method url-fetch) | |
799 | (uri (cran-uri "shinyFiles" version)) | |
800 | (sha256 | |
801 | (base32 | |
802 | "0dlcjrw96x72grg6j915070x8x98l7629pn86gf148iknflm7gd5")))) | |
803 | (properties `((upstream-name . "shinyFiles"))) | |
804 | (build-system r-build-system) | |
805 | (propagated-inputs | |
806 | `(("r-fs" ,r-fs) | |
807 | ("r-htmltools" ,r-htmltools) | |
808 | ("r-jsonlite" ,r-jsonlite) | |
809 | ("r-shiny" ,r-shiny) | |
810 | ("r-tibble" ,r-tibble))) | |
811 | (home-page "https://github.com/thomasp85/shinyFiles") | |
812 | (synopsis "Server-side file system viewer for Shiny") | |
813 | (description | |
814 | "This package provides functionality for client-side navigation of the | |
815 | server side file system in shiny apps. In case the app is running locally | |
816 | this gives the user direct access to the file system without the need to | |
817 | \"download\" files to a temporary location. Both file and folder selection as | |
818 | well as file saving is available.") | |
819 | (license license:gpl2+))) | |
820 | ||
821 | (define-public r-crosstalk | |
822 | (package | |
823 | (name "r-crosstalk") | |
824 | (version "1.0.0") | |
825 | (source | |
826 | (origin | |
827 | (method url-fetch) | |
828 | (uri (cran-uri "crosstalk" version)) | |
829 | (sha256 | |
830 | (base32 | |
831 | "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk")))) | |
832 | (build-system r-build-system) | |
833 | (propagated-inputs | |
834 | `(("r-ggplot2" ,r-ggplot2) | |
835 | ("r-htmltools" ,r-htmltools) | |
836 | ("r-jsonlite" ,r-jsonlite) | |
837 | ("r-lazyeval" ,r-lazyeval) | |
838 | ("r-r6" ,r-r6) | |
839 | ("r-shiny" ,r-shiny))) | |
840 | (home-page "https://rstudio.github.io/crosstalk/") | |
841 | (synopsis "Inter-widget interactivity for HTML widgets") | |
842 | (description | |
843 | "This package provides building blocks for allowing HTML widgets to | |
844 | communicate with each other, with Shiny or without (i.e. static @code{.html} | |
845 | files). It currently supports linked brushing and filtering.") | |
846 | (license license:expat))) | |
847 | ||
848 | (define-public r-rook | |
849 | (package | |
850 | (name "r-rook") | |
851 | (version "1.1-1") | |
852 | (source | |
853 | (origin | |
854 | (method url-fetch) | |
855 | (uri (cran-uri "Rook" version)) | |
856 | (sha256 | |
857 | (base32 | |
858 | "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) | |
859 | (properties `((upstream-name . "Rook"))) | |
860 | (build-system r-build-system) | |
861 | (propagated-inputs `(("r-brew" ,r-brew))) | |
862 | (home-page "https://cran.r-project.org/web/packages/Rook") | |
863 | (synopsis "Web server interface for R") | |
864 | (description | |
865 | "This package contains the Rook specification and convenience software | |
866 | for building and running Rook applications. A Rook application is an R | |
867 | reference class object that implements a @code{call} method or an R closure | |
868 | that takes exactly one argument, an environment, and returns a list with three | |
869 | named elements: the @code{status}, the @code{headers}, and the @code{body}.") | |
870 | (license license:gpl2))) | |
871 | ||
872 | (define-public r-miniui | |
873 | (package | |
874 | (name "r-miniui") | |
875 | (version "0.1.1.1") | |
876 | (source | |
877 | (origin | |
878 | (method url-fetch) | |
879 | (uri (cran-uri "miniUI" version)) | |
880 | (sha256 | |
881 | (base32 | |
882 | "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) | |
883 | (properties `((upstream-name . "miniUI"))) | |
884 | (build-system r-build-system) | |
885 | (propagated-inputs | |
886 | `(("r-htmltools" ,r-htmltools) | |
887 | ("r-shiny" ,r-shiny))) | |
888 | (home-page "https://cran.r-project.org/web/packages/miniUI/") | |
889 | (synopsis "Shiny UI widgets for small screens") | |
890 | (description | |
891 | "This package provides UI widget and layout functions for writing Shiny apps that | |
892 | work well on small screens.") | |
893 | (license license:gpl3))) | |
894 | ||
60a166c6 RW |
895 | (define-public r-feather |
896 | (package | |
897 | (name "r-feather") | |
1d7022f7 | 898 | (version "0.3.3") |
60a166c6 RW |
899 | (source |
900 | (origin | |
901 | (method url-fetch) | |
902 | (uri (cran-uri "feather" version)) | |
903 | (sha256 | |
904 | (base32 | |
1d7022f7 | 905 | "0ls8lmygyjq60467s88h66d7fczjp1d3a2106rfq4dx9lyfvdfsa")))) |
60a166c6 RW |
906 | (build-system r-build-system) |
907 | (propagated-inputs | |
908 | `(("r-hms" ,r-hms) | |
909 | ("r-rcpp" ,r-rcpp) | |
910 | ("r-tibble" ,r-tibble))) | |
911 | (home-page "https://github.com/wesm/feather") | |
912 | (synopsis "R Bindings to the Feather API") | |
913 | (description "Read and write feather files, a lightweight binary columnar | |
914 | data store designed for maximum speed.") | |
915 | (license license:asl2.0))) | |
916 | ||
2a2760a0 RW |
917 | (define-public r-maps |
918 | (package | |
919 | (name "r-maps") | |
920 | (version "3.3.0") | |
921 | (source | |
922 | (origin | |
923 | (method url-fetch) | |
924 | (uri (cran-uri "maps" version)) | |
925 | (sha256 | |
926 | (base32 | |
927 | "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr")))) | |
928 | (build-system r-build-system) | |
929 | (home-page "https://cran.r-project.org/web/packages/maps") | |
930 | (synopsis "Draw geographical maps") | |
931 | (description "This package provides an R module for display of maps. | |
36a4366d EF |
932 | Projection code and larger maps are in separate packages (@code{mapproj} and |
933 | @code{mapdata}).") | |
2a2760a0 RW |
934 | (license license:gpl2))) |
935 | ||
936 | (define-public r-mapproj | |
937 | (package | |
938 | (name "r-mapproj") | |
939 | (version "1.2.6") | |
940 | (source | |
941 | (origin | |
942 | (method url-fetch) | |
943 | (uri (cran-uri "mapproj" version)) | |
944 | (sha256 | |
945 | (base32 | |
946 | "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2")))) | |
947 | (build-system r-build-system) | |
948 | (propagated-inputs `(("r-maps" ,r-maps))) | |
949 | (home-page "https://cran.r-project.org/web/packages/mapproj") | |
950 | (synopsis "Map projection in R") | |
951 | (description "This package converts latitude/longitude into projected | |
952 | coordinates.") | |
953 | (license (list license:gpl2 ; The R interface | |
954 | (license:non-copyleft ; The C code | |
955 | "https://www.gnu.org/licenses/license-list.en.html#lucent102" | |
956 | "Lucent Public License Version 1.02"))))) | |
957 | ||
958 | (define-public r-rgooglemaps | |
959 | (package | |
960 | (name "r-rgooglemaps") | |
961 | (version "1.4.3") | |
962 | (source | |
963 | (origin | |
964 | (method url-fetch) | |
965 | (uri (cran-uri "RgoogleMaps" version)) | |
966 | (sha256 | |
967 | (base32 | |
968 | "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4")))) | |
969 | (properties `((upstream-name . "RgoogleMaps"))) | |
970 | (build-system r-build-system) | |
971 | (propagated-inputs `(("r-png" ,r-png))) | |
972 | (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") | |
973 | (synopsis "Use Google Maps in R") | |
974 | (description "This package serves two purposes: | |
975 | @enumerate | |
976 | @item Provide a comfortable R interface to query the Google server for static | |
977 | maps, and | |
978 | @item Use the map as a background image to overlay plots within R. This | |
979 | requires proper coordinate scaling. | |
980 | @end enumerate\n") | |
981 | (license license:gpl2+))) | |
982 | ||
983 | (define-public r-geosphere | |
984 | (package | |
985 | (name "r-geosphere") | |
986 | (version "1.5-7") | |
987 | (source | |
988 | (origin | |
989 | (method url-fetch) | |
990 | (uri (cran-uri "geosphere" version)) | |
991 | (sha256 | |
992 | (base32 | |
993 | "186qdm5niq7v3d4w4rngx71znsgi44hnam7698bsx9ar5mg5b6wx")))) | |
994 | (build-system r-build-system) | |
995 | (propagated-inputs `(("r-sp" ,r-sp))) | |
996 | (home-page "https://cran.r-project.org/web/packages/geosphere") | |
997 | (synopsis "Spherical trigonometry") | |
998 | (description "This package computes spherical trigonometry for geographic | |
999 | applications. That is, compute distances and related measures for angular | |
1000 | (longitude/latitude) locations.") | |
1001 | (license license:gpl3+))) | |
1002 | ||
1003 | (define-public r-ggmap | |
1004 | (package | |
1005 | (name "r-ggmap") | |
20662a30 | 1006 | (version "3.0.0") |
2a2760a0 RW |
1007 | (source |
1008 | (origin | |
1009 | (method url-fetch) | |
1010 | (uri (cran-uri "ggmap" version)) | |
1011 | (sha256 | |
1012 | (base32 | |
20662a30 | 1013 | "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) |
2a2760a0 RW |
1014 | (build-system r-build-system) |
1015 | (propagated-inputs | |
20662a30 RW |
1016 | `(("r-bitops" ,r-bitops) |
1017 | ("r-digest" ,r-digest) | |
1018 | ("r-dplyr" ,r-dplyr) | |
2a2760a0 | 1019 | ("r-ggplot2" ,r-ggplot2) |
20662a30 RW |
1020 | ("r-glue" ,r-glue) |
1021 | ("r-httr" ,r-httr) | |
2a2760a0 | 1022 | ("r-jpeg" ,r-jpeg) |
20662a30 | 1023 | ("r-magrittr" ,r-magrittr) |
2a2760a0 RW |
1024 | ("r-plyr" ,r-plyr) |
1025 | ("r-png" ,r-png) | |
20662a30 | 1026 | ("r-purrr" ,r-purrr) |
2a2760a0 RW |
1027 | ("r-rgooglemaps" ,r-rgooglemaps) |
1028 | ("r-rjson" ,r-rjson) | |
20662a30 RW |
1029 | ("r-scales" ,r-scales) |
1030 | ("r-stringr" ,r-stringr) | |
1031 | ("r-tibble" ,r-tibble) | |
1032 | ("r-tidyr" ,r-tidyr))) | |
2a2760a0 RW |
1033 | (home-page "https://github.com/dkahle/ggmap") |
1034 | (synopsis "Spatial visualization with ggplot2") | |
1035 | (description "This package provides a collection of functions to visualize | |
1036 | spatial data and models on top of static maps from various online sources (e.g | |
1037 | Google Maps and Stamen Maps). It includes tools common to those tasks, | |
1038 | including functions for geolocation and routing.") | |
1039 | (license license:gpl2))) | |
1040 | ||
d2a507ef CR |
1041 | (define-public r-haven |
1042 | (package | |
1043 | (name "r-haven") | |
bef78244 | 1044 | (version "2.1.0") |
d2a507ef CR |
1045 | (source |
1046 | (origin | |
1047 | (method url-fetch) | |
1048 | (uri (cran-uri "haven" version)) | |
1049 | (sha256 | |
1050 | (base32 | |
bef78244 | 1051 | "0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0")))) |
d2a507ef | 1052 | (build-system r-build-system) |
35b32367 TGR |
1053 | (inputs |
1054 | `(("zlib" ,zlib))) | |
d2a507ef CR |
1055 | (propagated-inputs |
1056 | `(("r-forcats" ,r-forcats) | |
1057 | ("r-hms" ,r-hms) | |
1058 | ("r-rcpp" ,r-rcpp) | |
1059 | ("r-readr" ,r-readr) | |
1060 | ("r-tibble" ,r-tibble))) | |
1061 | (home-page "https://haven.tidyverse.org") | |
1062 | (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files") | |
1063 | (description | |
1064 | "This package lets you mport foreign statistical formats into R via the | |
1065 | embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") | |
1066 | (license license:expat))) | |
1067 | ||
996bed06 RJ |
1068 | (define-public r-amap |
1069 | (package | |
1070 | (name "r-amap") | |
7c2a4646 | 1071 | (version "0.8-16") |
996bed06 RJ |
1072 | (source (origin |
1073 | (method url-fetch) | |
1074 | (uri (cran-uri "amap" version)) | |
1075 | (sha256 | |
1076 | (base32 | |
7c2a4646 | 1077 | "1qnl2x98x64iaipkx5126rsddq2sx5ml43h75xyiyn30yvbmlxyk")))) |
996bed06 RJ |
1078 | (build-system r-build-system) |
1079 | (inputs | |
1080 | `(("gfortran" ,gfortran))) | |
1081 | (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") | |
1082 | (synopsis "Another multidimensional analysis package") | |
1083 | (description "This package provides tools for clustering and principal | |
1084 | component analysis (with robust methods, and parallelized functions).") | |
1085 | (license license:gpl2+))) | |
1086 | ||
53cc59a1 RW |
1087 | (define-public r-ape |
1088 | (package | |
1089 | (name "r-ape") | |
8e91ad0b | 1090 | (version "5.3") |
53cc59a1 RW |
1091 | (source |
1092 | (origin | |
1093 | (method url-fetch) | |
1094 | (uri (cran-uri "ape" version)) | |
1095 | (sha256 | |
1096 | (base32 | |
8e91ad0b | 1097 | "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08")))) |
53cc59a1 RW |
1098 | (build-system r-build-system) |
1099 | (propagated-inputs | |
1100 | `(("r-lattice" ,r-lattice) | |
1101 | ("r-nlme" ,r-nlme) | |
1102 | ("r-rcpp" ,r-rcpp))) | |
1103 | (home-page "http://ape-package.ird.fr/") | |
1104 | (synopsis "Analyses of phylogenetics and evolution") | |
1105 | (description | |
1106 | "This package provides functions for reading, writing, plotting, and | |
1107 | manipulating phylogenetic trees, analyses of comparative data in a | |
1108 | phylogenetic framework, ancestral character analyses, analyses of | |
1109 | diversification and macroevolution, computing distances from DNA sequences, | |
1110 | and several other tools.") | |
1111 | (license license:gpl2+))) | |
1112 | ||
109b2f7c VV |
1113 | (define-public r-abbyyr |
1114 | (package | |
1115 | (name "r-abbyyr") | |
5479e3e6 | 1116 | (version "0.5.4") |
109b2f7c VV |
1117 | (source |
1118 | (origin | |
1119 | (method url-fetch) | |
1120 | (uri (cran-uri "abbyyR" version)) | |
1121 | (sha256 | |
1122 | (base32 | |
5479e3e6 | 1123 | "1jh1c1ad6mgw7brdh2isnza1qpjlfxnqr7jl76yd93axyfl76xjx")))) |
109b2f7c VV |
1124 | (properties `((upstream-name . "abbyyR"))) |
1125 | (build-system r-build-system) | |
1126 | (propagated-inputs | |
1127 | `(("r-curl" ,r-curl) | |
1128 | ("r-httr" ,r-httr) | |
1129 | ("r-plyr" ,r-plyr) | |
1130 | ("r-progress" ,r-progress) | |
1131 | ("r-readr" ,r-readr) | |
1132 | ("r-xml" ,r-xml))) | |
1133 | (home-page "https://github.com/soodoku/abbyyR") | |
1134 | (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") | |
1135 | (description | |
1136 | "This package provides tools to get text from images of text using Abbyy | |
1137 | Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily | |
1138 | OCR images, barcodes, forms, documents with machine readable zones, e.g. | |
1139 | passports and get the results in a variety of formats including plain text and | |
1140 | XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") | |
1141 | (license license:expat))) | |
1142 | ||
056468dc RW |
1143 | (define-public r-colorspace |
1144 | (package | |
1145 | (name "r-colorspace") | |
f9bc918b | 1146 | (version "1.4-1") |
056468dc RW |
1147 | (source |
1148 | (origin | |
1149 | (method url-fetch) | |
1150 | (uri (cran-uri "colorspace" version)) | |
1151 | (sha256 | |
f9bc918b | 1152 | (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9")))) |
056468dc | 1153 | (build-system r-build-system) |
e9960d8c | 1154 | (home-page "https://cran.r-project.org/web/packages/colorspace") |
056468dc RW |
1155 | (synopsis "Color space manipulation") |
1156 | (description | |
1157 | "This package carries out a mapping between assorted color spaces | |
1158 | including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar | |
1159 | CIELAB. Qualitative, sequential, and diverging color palettes based on HCL | |
1160 | colors are provided.") | |
1161 | (license license:bsd-3))) | |
5bee6bf4 RW |
1162 | |
1163 | (define-public r-glue | |
1164 | (package | |
1165 | (name "r-glue") | |
b21eb347 | 1166 | (version "1.3.1") |
5bee6bf4 RW |
1167 | (source |
1168 | (origin | |
1169 | (method url-fetch) | |
1170 | (uri (cran-uri "glue" version)) | |
1171 | (sha256 | |
1172 | (base32 | |
b21eb347 | 1173 | "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag")))) |
5bee6bf4 RW |
1174 | (build-system r-build-system) |
1175 | (home-page "https://github.com/tidyverse/glue") | |
1176 | (synopsis "Interpreted string literals") | |
1177 | (description | |
1178 | "This package provides an implementation of interpreted string literals, | |
1179 | inspired by Python's Literal String Interpolation (PEP-0498) and | |
1180 | Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") | |
1181 | (license license:expat))) | |
847b4572 | 1182 | |
ddbf2a98 RJ |
1183 | (define-public r-pastecs |
1184 | (package | |
1185 | (name "r-pastecs") | |
1186 | (version "1.3.21") | |
1187 | (source (origin | |
1188 | (method url-fetch) | |
1189 | (uri (cran-uri "pastecs" version)) | |
1190 | (sha256 | |
1191 | (base32 | |
1192 | "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) | |
1193 | (build-system r-build-system) | |
1194 | (propagated-inputs | |
1195 | `(("r-boot" ,r-boot))) | |
1196 | (home-page "http://www.sciviews.org/pastecs") | |
1197 | (synopsis "Analysis of space-time ecological series") | |
1198 | (description | |
1199 | "This package provides functions for regulation, decomposition and analysis | |
1200 | of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER | |
1201 | initiative to bring PASSTEC 2000 functionalities to R.") | |
1202 | (license license:gpl2+))) | |
1203 | ||
847b4572 RW |
1204 | (define-public r-plogr |
1205 | (package | |
1206 | (name "r-plogr") | |
0e947804 | 1207 | (version "0.2.0") |
847b4572 RW |
1208 | (source |
1209 | (origin | |
1210 | (method url-fetch) | |
1211 | (uri (cran-uri "plogr" version)) | |
1212 | (sha256 | |
1213 | (base32 | |
0e947804 | 1214 | "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf")))) |
847b4572 RW |
1215 | (build-system r-build-system) |
1216 | (home-page "https://github.com/krlmlr/plogr") | |
1217 | (synopsis "R bindings for the plog C++ logging library") | |
1218 | (description | |
1219 | "This package provides the header files for a stripped-down version of | |
1220 | the plog header-only C++ logging library, and a method to log to R's standard | |
1221 | error stream.") | |
1222 | (license license:expat))) | |
a8cba9dd | 1223 | |
a86049d9 TGR |
1224 | (define-public r-pls |
1225 | (package | |
1226 | (name "r-pls") | |
6f2fa038 | 1227 | (version "2.7-1") |
a86049d9 TGR |
1228 | (source |
1229 | (origin | |
1230 | (method url-fetch) | |
1231 | (uri (cran-uri "pls" version)) | |
1232 | (sha256 | |
1233 | (base32 | |
6f2fa038 | 1234 | "0jw3zl5z06023zxr74phnvwax8m3i4a4i6lsqiq6j15aq9zq3zgq")))) |
a86049d9 TGR |
1235 | (build-system r-build-system) |
1236 | (home-page "http://mevik.net/work/software/pls.html") | |
1237 | (synopsis "Partial Least Squares and Principal Component Regression") | |
1238 | (description | |
1239 | "The pls package implements multivariate regression methods: Partial Least | |
1240 | Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and | |
1241 | Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports: | |
1242 | ||
1243 | @itemize | |
1244 | @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS | |
1245 | algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd} | |
1246 | @item multi-response models (or @dfn{PLS2}) | |
1247 | @item flexible cross-validation | |
1248 | @item Jackknife variance estimates of regression coefficients | |
1249 | @item extensive and flexible plots: scores, loadings, predictions, coefficients, | |
1250 | (R)MSEP, R², and correlation loadings | |
1251 | @item formula interface, modelled after @code{lm()}, with methods for predict, | |
1252 | print, summary, plot, update, etc. | |
1253 | @item extraction functions for coefficients, scores, and loadings | |
1254 | @item MSEP, RMSEP, and R² estimates | |
1255 | @item multiplicative scatter correction (@dfn{MSC}) | |
1256 | @end itemize\n") | |
1257 | (license license:gpl2))) | |
1258 | ||
b55e64d4 TGR |
1259 | (define-public r-ps |
1260 | (package | |
1261 | (name "r-ps") | |
422dea17 | 1262 | (version "1.3.0") |
b55e64d4 TGR |
1263 | (source |
1264 | (origin | |
1265 | (method url-fetch) | |
1266 | (uri (cran-uri "ps" version)) | |
1267 | (sha256 | |
422dea17 | 1268 | (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498")))) |
b55e64d4 TGR |
1269 | (build-system r-build-system) |
1270 | (home-page "http://ps.r-lib.org") | |
1271 | (synopsis "List, query, and manipulate system processes") | |
1272 | (description | |
1273 | "The ps package implements an API to list, query, and manipulate system | |
1274 | processes. Most of its code is based on the @code{psutil} Python package.") | |
1275 | (license license:bsd-3))) | |
1276 | ||
4f8247b5 RW |
1277 | (define-public r-pkgbuild |
1278 | (package | |
1279 | (name "r-pkgbuild") | |
4c871a55 | 1280 | (version "1.0.3") |
4f8247b5 RW |
1281 | (source |
1282 | (origin | |
1283 | (method url-fetch) | |
1284 | (uri (cran-uri "pkgbuild" version)) | |
1285 | (sha256 | |
1286 | (base32 | |
4c871a55 | 1287 | "0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9")))) |
4f8247b5 RW |
1288 | (build-system r-build-system) |
1289 | (propagated-inputs | |
1290 | `(("r-callr" ,r-callr) | |
2657e666 | 1291 | ("r-cli" ,r-cli) |
4f8247b5 RW |
1292 | ("r-crayon" ,r-crayon) |
1293 | ("r-desc" ,r-desc) | |
2657e666 | 1294 | ("r-prettyunits" ,r-prettyunits) |
4f8247b5 RW |
1295 | ("r-r6" ,r-r6) |
1296 | ("r-rprojroot" ,r-rprojroot) | |
1297 | ("r-withr" ,r-withr))) | |
1298 | (home-page "https://github.com/r-pkgs/pkgbuild") | |
1299 | (synopsis "Find tools needed to build R packages") | |
1300 | (description | |
1301 | "This package provides functions used to build R packages. It locates | |
1302 | compilers needed to build R packages on various platforms and ensures the PATH | |
1303 | is configured appropriately so R can use them.") | |
1304 | (license license:gpl3))) | |
1305 | ||
e362be8e RW |
1306 | (define-public r-pkgload |
1307 | (package | |
1308 | (name "r-pkgload") | |
65dd0e67 | 1309 | (version "1.0.2") |
e362be8e RW |
1310 | (source |
1311 | (origin | |
1312 | (method url-fetch) | |
1313 | (uri (cran-uri "pkgload" version)) | |
1314 | (sha256 | |
1315 | (base32 | |
65dd0e67 | 1316 | "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii")))) |
e362be8e RW |
1317 | (build-system r-build-system) |
1318 | (propagated-inputs | |
1319 | `(("r-desc" ,r-desc) | |
1320 | ("r-pkgbuild" ,r-pkgbuild) | |
1321 | ("r-rlang" ,r-rlang) | |
1322 | ("r-rprojroot" ,r-rprojroot) | |
1323 | ("r-rstudioapi" ,r-rstudioapi) | |
1324 | ("r-withr" ,r-withr))) | |
1325 | (home-page "https://github.com/r-lib/pkgload") | |
1326 | (synopsis "Simulate package installation and attach") | |
1327 | (description | |
1328 | "This package simulates the process of installing a package and then | |
1329 | attaching it. This is a key part of the @code{devtools} package as it allows | |
1330 | you to rapidly iterate while developing a package.") | |
1331 | (license license:gpl3))) | |
1332 | ||
a8cba9dd RW |
1333 | (define-public r-rcpp |
1334 | (package | |
1335 | (name "r-rcpp") | |
06070c03 | 1336 | (version "1.0.1") |
a8cba9dd RW |
1337 | (source |
1338 | (origin | |
1339 | (method url-fetch) | |
1340 | (uri (cran-uri "Rcpp" version)) | |
1341 | (sha256 | |
06070c03 | 1342 | (base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7")))) |
a8cba9dd | 1343 | (build-system r-build-system) |
f87a18e6 RW |
1344 | (native-inputs |
1345 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
a8cba9dd RW |
1346 | (home-page "http://www.rcpp.org") |
1347 | (synopsis "Seamless R and C++ integration") | |
1348 | (description | |
1349 | "The Rcpp package provides R functions as well as C++ classes which offer | |
1350 | a seamless integration of R and C++. Many R data types and objects can be | |
1351 | mapped back and forth to C++ equivalents which facilitates both writing of new | |
1352 | code as well as easier integration of third-party libraries. Documentation | |
1353 | about Rcpp is provided by several vignettes included in this package, via the | |
36a4366d | 1354 | @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel |
a8cba9dd | 1355 | and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see |
36a4366d | 1356 | @code{citation(\"Rcpp\")} for details on these last two.") |
a8cba9dd | 1357 | (license license:gpl2+))) |
eed58a08 RW |
1358 | |
1359 | (define-public r-bindr | |
1360 | (package | |
1361 | (name "r-bindr") | |
eb575e95 | 1362 | (version "0.1.1") |
eed58a08 RW |
1363 | (source |
1364 | (origin | |
1365 | (method url-fetch) | |
1366 | (uri (cran-uri "bindr" version)) | |
1367 | (sha256 | |
1368 | (base32 | |
eb575e95 | 1369 | "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) |
eed58a08 RW |
1370 | (build-system r-build-system) |
1371 | (home-page "https://github.com/krlmlr/bindr") | |
1372 | (synopsis "Parametrized active bindings") | |
1373 | (description | |
1374 | "This package provides a simple interface for creating active bindings | |
1375 | where the bound function accepts additional arguments.") | |
1376 | (license license:expat))) | |
4bb0b4cc RW |
1377 | |
1378 | (define-public r-bindrcpp | |
1379 | (package | |
1380 | (name "r-bindrcpp") | |
9f17c056 | 1381 | (version "0.2.2") |
4bb0b4cc RW |
1382 | (source |
1383 | (origin | |
1384 | (method url-fetch) | |
1385 | (uri (cran-uri "bindrcpp" version)) | |
1386 | (sha256 | |
1387 | (base32 | |
9f17c056 | 1388 | "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) |
4bb0b4cc RW |
1389 | (build-system r-build-system) |
1390 | (propagated-inputs | |
1391 | `(("r-bindr" ,r-bindr) | |
1392 | ("r-plogr" ,r-plogr) | |
1393 | ("r-rcpp" ,r-rcpp))) | |
1394 | (home-page "https://github.com/krlmlr/bindrcpp") | |
1395 | (synopsis "Rcpp interface to active bindings") | |
1396 | (description | |
1397 | "This package provides an easy way to fill an environment with active | |
1398 | bindings that call a C++ function.") | |
1399 | (license license:expat))) | |
33ce12e2 RW |
1400 | |
1401 | (define-public r-auc | |
1402 | (package | |
1403 | (name "r-auc") | |
1404 | (version "0.3.0") | |
1405 | (source | |
1406 | (origin | |
1407 | (method url-fetch) | |
1408 | (uri (cran-uri "AUC" version)) | |
1409 | (sha256 | |
1410 | (base32 | |
1411 | "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7")))) | |
1412 | (properties `((upstream-name . "AUC"))) | |
1413 | (build-system r-build-system) | |
e9960d8c | 1414 | (home-page "https://cran.r-project.org/web/packages/AUC") |
33ce12e2 RW |
1415 | (synopsis "Compute the area under the curve of selected measures") |
1416 | (description | |
1417 | "This package includes functions to compute the area under the curve of | |
1418 | selected measures: the area under the sensitivity curve (AUSEC), the area | |
1419 | under the specificity curve (AUSPC), the area under the accuracy | |
1420 | curve (AUACC), and the area under the receiver operating characteristic | |
1421 | curve (AUROC). The curves can also be visualized. Support for partial areas | |
1422 | is provided.") | |
1423 | (license license:gpl2+))) | |
c69d27db RW |
1424 | |
1425 | (define-public r-calibrate | |
1426 | (package | |
1427 | (name "r-calibrate") | |
1428 | (version "1.7.2") | |
1429 | (source | |
1430 | (origin | |
1431 | (method url-fetch) | |
1432 | (uri (cran-uri "calibrate" version)) | |
1433 | (sha256 | |
1434 | (base32 | |
1435 | "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq")))) | |
1436 | (build-system r-build-system) | |
1437 | (propagated-inputs | |
1438 | `(("r-mass" ,r-mass))) | |
e9960d8c | 1439 | (home-page "https://cran.r-project.org/web/packages/calibrate") |
c69d27db RW |
1440 | (synopsis "Calibration of scatterplot and biplot axes") |
1441 | (description | |
1442 | "This is a package for drawing calibrated scales with tick marks | |
1443 | on (non-orthogonal) variable vectors in scatterplots and biplots.") | |
1444 | (license license:gpl2))) | |
2bdb5c3f RW |
1445 | |
1446 | (define-public r-shape | |
1447 | (package | |
1448 | (name "r-shape") | |
fe5b8893 | 1449 | (version "1.4.4") |
2bdb5c3f RW |
1450 | (source |
1451 | (origin | |
1452 | (method url-fetch) | |
1453 | (uri (cran-uri "shape" version)) | |
1454 | (sha256 | |
1455 | (base32 | |
fe5b8893 | 1456 | "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl")))) |
2bdb5c3f | 1457 | (build-system r-build-system) |
e9960d8c | 1458 | (home-page "https://cran.r-project.org/web/packages/shape") |
2bdb5c3f RW |
1459 | (synopsis "Functions for plotting graphical shapes") |
1460 | (description | |
1461 | "This package provides functions for plotting graphical shapes such as | |
1462 | ellipses, circles, cylinders, arrows, ...") | |
1463 | (license license:gpl3+))) | |
4847a62e RW |
1464 | |
1465 | (define-public r-globaloptions | |
1466 | (package | |
1467 | (name "r-globaloptions") | |
693b4d0b | 1468 | (version "0.1.0") |
4847a62e RW |
1469 | (source |
1470 | (origin | |
1471 | (method url-fetch) | |
1472 | (uri (cran-uri "GlobalOptions" version)) | |
1473 | (sha256 | |
1474 | (base32 | |
693b4d0b | 1475 | "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn")))) |
4847a62e RW |
1476 | (properties `((upstream-name . "GlobalOptions"))) |
1477 | (build-system r-build-system) | |
1478 | (home-page "https://github.com/jokergoo/GlobalOptions") | |
1479 | (synopsis "Generate functions to get or set global options") | |
1480 | (description | |
1481 | "This package provides more controls on the option values such as | |
1482 | validation and filtering on the values, making options invisible or private.") | |
1483 | (license license:gpl2+))) | |
2856369f RW |
1484 | |
1485 | (define-public r-circlize | |
1486 | (package | |
1487 | (name "r-circlize") | |
b15c5c0e | 1488 | (version "0.4.6") |
2856369f RW |
1489 | (source |
1490 | (origin | |
1491 | (method url-fetch) | |
1492 | (uri (cran-uri "circlize" version)) | |
1493 | (sha256 | |
1494 | (base32 | |
b15c5c0e | 1495 | "1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f")))) |
2856369f RW |
1496 | (build-system r-build-system) |
1497 | (propagated-inputs | |
1498 | `(("r-colorspace" ,r-colorspace) | |
1499 | ("r-globaloptions" ,r-globaloptions) | |
1500 | ("r-shape" ,r-shape))) | |
1501 | (home-page "https://github.com/jokergoo/circlize") | |
1502 | (synopsis "Circular visualization") | |
1503 | (description | |
031462ba TGR |
1504 | "Circular layout is an efficient way to visualise huge amounts of |
1505 | information. This package provides an implementation of circular layout | |
1506 | generation in R as well as an enhancement of available software. Its | |
1507 | flexibility is based on the usage of low-level graphics functions such that | |
1508 | self-defined high-level graphics can be easily implemented by users for | |
1509 | specific purposes. Together with the seamless connection between the powerful | |
1510 | computational and visual environment in R, it gives users more convenience and | |
1511 | freedom to design figures for better understanding complex patterns behind | |
1512 | multi-dimensional data.") | |
2856369f | 1513 | (license license:gpl2+))) |
5cc79c9c RW |
1514 | |
1515 | (define-public r-powerlaw | |
1516 | (package | |
1517 | (name "r-powerlaw") | |
397dba01 | 1518 | (version "0.70.2") |
5cc79c9c RW |
1519 | (source |
1520 | (origin | |
1521 | (method url-fetch) | |
1522 | (uri (cran-uri "poweRlaw" version)) | |
1523 | (sha256 | |
1524 | (base32 | |
397dba01 | 1525 | "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4")))) |
5cc79c9c RW |
1526 | (properties `((upstream-name . "poweRlaw"))) |
1527 | (build-system r-build-system) | |
1528 | (propagated-inputs | |
1529 | `(("r-vgam" ,r-vgam))) | |
1530 | (home-page "https://github.com/csgillespie/poweRlaw") | |
1531 | (synopsis "Tools for the analysis of heavy tailed distributions") | |
1532 | (description | |
1533 | "This package provides an implementation of maximum likelihood estimators | |
1534 | for a variety of heavy tailed distributions, including both the discrete and | |
1535 | continuous power law distributions. Additionally, a goodness-of-fit based | |
1536 | approach is used to estimate the lower cut-off for the scaling region.") | |
1537 | ;; Any of these GPL versions. | |
1538 | (license (list license:gpl2 license:gpl3)))) | |
05486604 RW |
1539 | |
1540 | (define-public r-compare | |
1541 | (package | |
1542 | (name "r-compare") | |
1543 | (version "0.2-6") | |
1544 | (source | |
1545 | (origin | |
1546 | (method url-fetch) | |
1547 | (uri (cran-uri "compare" version)) | |
1548 | (sha256 | |
1549 | (base32 | |
1550 | "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw")))) | |
1551 | (build-system r-build-system) | |
e9960d8c | 1552 | (home-page "https://cran.r-project.org/web/packages/compare") |
05486604 RW |
1553 | (synopsis "Comparing objects for differences") |
1554 | (description | |
1555 | "This package provides functions to compare a model object to a | |
1556 | comparison object. If the objects are not identical, the functions can be | |
1557 | instructed to explore various modifications of the objects (e.g., sorting | |
1558 | rows, dropping names) to see if the modified versions are identical.") | |
1559 | (license license:gpl2+))) | |
d3c67e1b RW |
1560 | |
1561 | (define-public r-dendextend | |
1562 | (package | |
1563 | (name "r-dendextend") | |
df045099 | 1564 | (version "1.10.0") |
d3c67e1b RW |
1565 | (source |
1566 | (origin | |
1567 | (method url-fetch) | |
1568 | (uri (cran-uri "dendextend" version)) | |
1569 | (sha256 | |
1570 | (base32 | |
df045099 | 1571 | "091jznl549d44w1h8kk1vwddzhijkyh0wpgkykd494fnc8rzpw48")))) |
d3c67e1b RW |
1572 | (build-system r-build-system) |
1573 | (propagated-inputs | |
1574 | `(("r-fpc" ,r-fpc) | |
1575 | ("r-ggplot2" ,r-ggplot2) | |
1576 | ("r-magrittr" ,r-magrittr) | |
1577 | ("r-viridis" ,r-viridis) | |
1578 | ("r-whisker" ,r-whisker))) | |
1579 | (home-page "https://cran.r-project.org/web/packages/dendextend") | |
1580 | (synopsis "Extending 'dendrogram' functionality in R") | |
1581 | (description | |
1582 | "This package offers a set of functions for extending @code{dendrogram} | |
1583 | objects in R, letting you visualize and compare trees of hierarchical | |
1584 | clusterings. You can adjust a tree's graphical parameters (the color, size, | |
1585 | type, etc of its branches, nodes and labels) and visually and statistically | |
1586 | compare different dendrograms to one another.") | |
1587 | ;; Any of these versions | |
1588 | (license (list license:gpl2 license:gpl3)))) | |
e0268ff2 RW |
1589 | |
1590 | (define-public r-getoptlong | |
1591 | (package | |
1592 | (name "r-getoptlong") | |
5fa9be11 | 1593 | (version "0.1.7") |
e0268ff2 RW |
1594 | (source |
1595 | (origin | |
1596 | (method url-fetch) | |
1597 | (uri (cran-uri "GetoptLong" version)) | |
1598 | (sha256 | |
1599 | (base32 | |
5fa9be11 | 1600 | "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr")))) |
e0268ff2 RW |
1601 | (properties `((upstream-name . "GetoptLong"))) |
1602 | (build-system r-build-system) | |
1603 | (inputs | |
1604 | `(("perl" ,perl))) | |
1605 | (propagated-inputs | |
1606 | `(("r-globaloptions" ,r-globaloptions) | |
1607 | ("r-rjson" ,r-rjson))) | |
1608 | (home-page "https://github.com/jokergoo/GetoptLong") | |
1609 | (synopsis "Parsing command-line arguments and variable interpolation") | |
1610 | (description | |
1611 | "This is yet another command-line argument parser which wraps the | |
1612 | powerful Perl module @code{Getopt::Long} and with some adaptation for easier | |
1613 | use in R. It also provides a simple way for variable interpolation in R.") | |
1614 | (license license:gpl2+))) | |
f2e974e1 RW |
1615 | |
1616 | (define-public r-fastmatch | |
1617 | (package | |
1618 | (name "r-fastmatch") | |
1619 | (version "1.1-0") | |
1620 | (source | |
1621 | (origin | |
1622 | (method url-fetch) | |
1623 | (uri (cran-uri "fastmatch" version)) | |
1624 | (sha256 | |
1625 | (base32 | |
1626 | "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) | |
1627 | (build-system r-build-system) | |
1628 | (home-page "http://www.rforge.net/fastmatch") | |
1629 | (synopsis "Fast match function") | |
1630 | (description | |
1631 | "This package provides a fast @code{match} replacement for cases that | |
1632 | require repeated look-ups. It is slightly faster that R's built-in | |
1633 | @code{match} function on first match against a table, but extremely fast on | |
1634 | any subsequent lookup as it keeps the hash table in memory.") | |
1635 | (license license:gpl2))) | |
a7f0faa2 RW |
1636 | |
1637 | (define-public r-ff | |
1638 | (package | |
1639 | (name "r-ff") | |
207c497e | 1640 | (version "2.2-14") |
a7f0faa2 RW |
1641 | (source |
1642 | (origin | |
1643 | (method url-fetch) | |
1644 | (uri (cran-uri "ff" version)) | |
1645 | (sha256 | |
1646 | (base32 | |
207c497e | 1647 | "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw")))) |
a7f0faa2 RW |
1648 | (build-system r-build-system) |
1649 | (propagated-inputs `(("r-bit" ,r-bit))) | |
1650 | (home-page "http://ff.r-forge.r-project.org/") | |
1651 | (synopsis "Memory-efficient storage of large data on disk and access functions") | |
1652 | (description | |
1653 | "This package provides data structures that are stored on disk but | |
1654 | behave (almost) as if they were in RAM by transparently mapping only a section | |
1655 | in main memory.") | |
a6e67d86 EF |
1656 | ;; error Architecture not supported. |
1657 | (supported-systems (delete "aarch64-linux" %supported-systems)) | |
a7f0faa2 | 1658 | (license license:gpl2))) |
49c9c297 RW |
1659 | |
1660 | (define-public r-ffbase | |
1661 | (package | |
1662 | (name "r-ffbase") | |
ec0ee085 | 1663 | (version "0.12.7") |
49c9c297 RW |
1664 | (source |
1665 | (origin | |
1666 | (method url-fetch) | |
1667 | (uri (cran-uri "ffbase" version)) | |
1668 | (sha256 | |
1669 | (base32 | |
ec0ee085 | 1670 | "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw")))) |
49c9c297 RW |
1671 | (build-system r-build-system) |
1672 | (propagated-inputs | |
1673 | `(("r-bit" ,r-bit) | |
1674 | ("r-fastmatch" ,r-fastmatch) | |
1675 | ("r-ff" ,r-ff))) | |
1676 | (home-page "http://github.com/edwindj/ffbase") | |
1677 | (synopsis "Basic statistical functions for package 'ff'") | |
1678 | (description | |
1679 | "This package extends the out of memory vectors of @code{ff} with | |
1680 | statistical functions and other utilities to ease their usage.") | |
1681 | (license license:gpl3))) | |
18a16ceb RW |
1682 | |
1683 | (define-public r-prettyunits | |
1684 | (package | |
1685 | (name "r-prettyunits") | |
1686 | (version "1.0.2") | |
1687 | (source | |
1688 | (origin | |
1689 | (method url-fetch) | |
1690 | (uri (cran-uri "prettyunits" version)) | |
1691 | (sha256 | |
1692 | (base32 | |
1693 | "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m")))) | |
1694 | (build-system r-build-system) | |
1695 | (propagated-inputs | |
1696 | `(("r-assertthat" ,r-assertthat) | |
1697 | ("r-magrittr" ,r-magrittr))) | |
1698 | (home-page "https://github.com/gaborcsardi/prettyunits") | |
1699 | (synopsis "Pretty, human readable formatting of quantities") | |
1700 | (description | |
1701 | "This package provides tools for pretty, human readable formatting of | |
1702 | quantities.") | |
1703 | (license license:expat))) | |
71be51d5 RW |
1704 | |
1705 | (define-public r-reshape | |
1706 | (package | |
1707 | (name "r-reshape") | |
2b8126a4 | 1708 | (version "0.8.8") |
71be51d5 RW |
1709 | (source |
1710 | (origin | |
1711 | (method url-fetch) | |
1712 | (uri (cran-uri "reshape" version)) | |
1713 | (sha256 | |
1714 | (base32 | |
2b8126a4 | 1715 | "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) |
71be51d5 RW |
1716 | (build-system r-build-system) |
1717 | (propagated-inputs | |
1718 | `(("r-plyr" ,r-plyr) | |
1719 | ("r-rcpp" ,r-rcpp))) | |
1720 | (home-page "http://had.co.nz/reshape") | |
1721 | (synopsis "Flexibly reshape data") | |
1722 | (description | |
1723 | "Flexibly restructure and aggregate data using just two functions: | |
1724 | @code{melt} and @code{cast}. This package provides them.") | |
1725 | (license license:expat))) | |
c9c6f4b5 RW |
1726 | |
1727 | (define-public r-progress | |
1728 | (package | |
1729 | (name "r-progress") | |
9de9dcd9 | 1730 | (version "1.2.0") |
c9c6f4b5 RW |
1731 | (source |
1732 | (origin | |
1733 | (method url-fetch) | |
1734 | (uri (cran-uri "progress" version)) | |
1735 | (sha256 | |
1736 | (base32 | |
9de9dcd9 | 1737 | "1rhwm0bdw30z3rvl0bn56xprjl3zrdy7150w4gl4bkvn2d6h9fav")))) |
c9c6f4b5 RW |
1738 | (build-system r-build-system) |
1739 | (propagated-inputs | |
9de9dcd9 RW |
1740 | `(("r-crayon" ,r-crayon) |
1741 | ("r-hms" ,r-hms) | |
1742 | ("r-prettyunits" ,r-prettyunits) | |
c9c6f4b5 RW |
1743 | ("r-r6" ,r-r6))) |
1744 | (home-page "https://github.com/gaborcsardi/progress") | |
1745 | (synopsis "Terminal progress bars") | |
1746 | (description | |
1747 | "This package provides configurable progress bars. They may include | |
1748 | percentage, elapsed time, and/or the estimated completion time. They work in | |
1749 | terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The | |
1750 | package also provides a C++ API, that works with or without Rcpp.") | |
1751 | (license license:expat))) | |
ac840207 RW |
1752 | |
1753 | (define-public r-ggally | |
1754 | (package | |
1755 | (name "r-ggally") | |
9944399a | 1756 | (version "1.4.0") |
ac840207 RW |
1757 | (source |
1758 | (origin | |
1759 | (method url-fetch) | |
1760 | (uri (cran-uri "GGally" version)) | |
1761 | (sha256 | |
1762 | (base32 | |
9944399a | 1763 | "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws")))) |
ac840207 RW |
1764 | (properties `((upstream-name . "GGally"))) |
1765 | (build-system r-build-system) | |
9944399a RW |
1766 | (inputs |
1767 | `(("libressl" ,libressl))) | |
ac840207 RW |
1768 | (propagated-inputs |
1769 | `(("r-ggplot2" ,r-ggplot2) | |
1770 | ("r-gtable" ,r-gtable) | |
1771 | ("r-plyr" ,r-plyr) | |
1772 | ("r-progress" ,r-progress) | |
1773 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9944399a RW |
1774 | ("r-reshape" ,r-reshape) |
1775 | ("r-rlang" ,r-rlang))) | |
ac840207 RW |
1776 | (home-page "https://ggobi.github.io/ggally") |
1777 | (synopsis "Extension to ggplot2") | |
1778 | (description | |
1779 | "The R package ggplot2 is a plotting system based on the grammar of | |
1780 | graphics. GGally extends ggplot2 by adding several functions to reduce the | |
1781 | complexity of combining geometric objects with transformed data. Some of | |
1782 | these functions include a pairwise plot matrix, a two group pairwise plot | |
1783 | matrix, a parallel coordinates plot, a survival plot, and several functions to | |
1784 | plot networks.") | |
1785 | (license license:gpl2+))) | |
3349faec RW |
1786 | |
1787 | (define-public r-proxy | |
1788 | (package | |
1789 | (name "r-proxy") | |
e190d9af | 1790 | (version "0.4-23") |
3349faec RW |
1791 | (source |
1792 | (origin | |
1793 | (method url-fetch) | |
1794 | (uri (cran-uri "proxy" version)) | |
1795 | (sha256 | |
1796 | (base32 | |
e190d9af | 1797 | "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x")))) |
3349faec | 1798 | (build-system r-build-system) |
e9960d8c | 1799 | (home-page "https://cran.r-project.org/web/packages/proxy") |
3349faec RW |
1800 | (synopsis "Distance and similarity measures") |
1801 | (description | |
1802 | "This package provides an extensible framework for the efficient | |
1803 | calculation of auto- and cross-proximities, along with implementations of the | |
1804 | most popular ones.") | |
1805 | (license license:gpl2))) | |
bc0081e7 RW |
1806 | |
1807 | (define-public r-sp | |
1808 | (package | |
1809 | (name "r-sp") | |
d87130cb | 1810 | (version "1.3-1") |
bc0081e7 RW |
1811 | (source |
1812 | (origin | |
1813 | (method url-fetch) | |
1814 | (uri (cran-uri "sp" version)) | |
1815 | (sha256 | |
1816 | (base32 | |
d87130cb | 1817 | "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p")))) |
bc0081e7 RW |
1818 | (build-system r-build-system) |
1819 | (propagated-inputs | |
1820 | `(("r-lattice" ,r-lattice))) | |
e9960d8c | 1821 | (home-page "https://cran.r-project.org/web/packages/sp") |
bc0081e7 RW |
1822 | (synopsis "Classes and methods for spatial data") |
1823 | (description | |
1824 | "This package provides classes and methods for spatial data; the classes | |
1825 | document where the spatial location information resides, for 2D or 3D data. | |
1826 | Utility functions are provided, e.g. for plotting data as maps, spatial | |
1827 | selection, as well as methods for retrieving coordinates, for subsetting, | |
1828 | print, summary, etc.") | |
1829 | (license license:gpl2+))) | |
e389d10f RW |
1830 | |
1831 | (define-public r-rmtstat | |
1832 | (package | |
1833 | (name "r-rmtstat") | |
1834 | (version "0.3") | |
1835 | (source | |
1836 | (origin | |
1837 | (method url-fetch) | |
1838 | (uri (cran-uri "RMTstat" version)) | |
1839 | (sha256 | |
1840 | (base32 | |
1841 | "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1")))) | |
1842 | (properties `((upstream-name . "RMTstat"))) | |
1843 | (build-system r-build-system) | |
e9960d8c | 1844 | (home-page "https://cran.r-project.org/web/packages/RMTstat") |
e389d10f RW |
1845 | (synopsis "Distributions, statistics and tests derived from random matrix theory") |
1846 | (description | |
1847 | "This package provides functions for working with the Tracy-Widom laws | |
1848 | and other distributions related to the eigenvalues of large Wishart | |
1849 | matrices.") | |
1850 | (license license:bsd-3))) | |
6427e620 | 1851 | |
94989d4b RJ |
1852 | (define-public r-rmpi |
1853 | (package | |
1854 | (name "r-rmpi") | |
5e8282a4 | 1855 | (version "0.6-9") |
94989d4b RJ |
1856 | (source (origin |
1857 | (method url-fetch) | |
1858 | (uri (cran-uri "Rmpi" version)) | |
1859 | (sha256 | |
1860 | (base32 | |
5e8282a4 | 1861 | "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) |
94989d4b RJ |
1862 | (properties `((upstream-name . "Rmpi"))) |
1863 | (build-system r-build-system) | |
1864 | (arguments | |
56d447ba EB |
1865 | `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"") |
1866 | #:phases (modify-phases %standard-phases | |
1867 | (add-before 'install 'mpi-setup | |
1868 | ,%openmpi-setup)))) | |
94989d4b RJ |
1869 | (inputs |
1870 | `(("openmpi" ,openmpi))) | |
9ebfdcd3 RW |
1871 | (native-inputs |
1872 | `(("pkg-config" ,pkg-config))) | |
94989d4b RJ |
1873 | (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") |
1874 | (synopsis "R interface to message-passing interface (MPI)") | |
1875 | (description | |
1876 | "This package provides an interface (wrapper) to MPI APIs. It also | |
1877 | provides an interactive R manager and worker environment.") | |
1878 | (license license:gpl2+))) | |
1879 | ||
6427e620 RW |
1880 | (define-public r-lmoments |
1881 | (package | |
1882 | (name "r-lmoments") | |
739135b2 | 1883 | (version "1.3-1") |
6427e620 RW |
1884 | (source |
1885 | (origin | |
1886 | (method url-fetch) | |
1887 | (uri (cran-uri "Lmoments" version)) | |
1888 | (sha256 | |
1889 | (base32 | |
739135b2 | 1890 | "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw")))) |
6427e620 RW |
1891 | (properties `((upstream-name . "Lmoments"))) |
1892 | (build-system r-build-system) | |
739135b2 RW |
1893 | (propagated-inputs |
1894 | `(("r-rcpp" ,r-rcpp) | |
1895 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
6427e620 RW |
1896 | (home-page "http://www.tilastotiede.fi/juha_karvanen.html") |
1897 | (synopsis "L-moments and quantile mixtures") | |
1898 | (description | |
1899 | "This package contains functions to estimate L-moments and trimmed | |
1900 | L-moments from the data. It also contains functions to estimate the | |
1901 | parameters of the normal polynomial quantile mixture and the Cauchy polynomial | |
1902 | quantile mixture from L-moments and trimmed L-moments.") | |
1903 | (license license:gpl2))) | |
28476b4b RW |
1904 | |
1905 | (define-public r-distillery | |
1906 | (package | |
1907 | (name "r-distillery") | |
28f2f893 | 1908 | (version "1.0-4") |
28476b4b RW |
1909 | (source |
1910 | (origin | |
1911 | (method url-fetch) | |
1912 | (uri (cran-uri "distillery" version)) | |
1913 | (sha256 | |
1914 | (base32 | |
28f2f893 | 1915 | "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix")))) |
28476b4b RW |
1916 | (build-system r-build-system) |
1917 | (home-page "http://www.ral.ucar.edu/staff/ericg") | |
1918 | (synopsis "Functions for confidence intervals and object information") | |
1919 | (description | |
1920 | "This package provides some very simple method functions for confidence | |
1921 | interval calculation and to distill pertinent information from a potentially | |
1922 | complex object; primarily used in common with the packages extRemes and | |
1923 | SpatialVx.") | |
1924 | (license license:gpl2+))) | |
58db98c9 RW |
1925 | |
1926 | (define-public r-extremes | |
1927 | (package | |
1928 | (name "r-extremes") | |
a151f1e6 | 1929 | (version "2.0-9") |
58db98c9 RW |
1930 | (source |
1931 | (origin | |
1932 | (method url-fetch) | |
1933 | (uri (cran-uri "extRemes" version)) | |
1934 | (sha256 | |
1935 | (base32 | |
a151f1e6 | 1936 | "0cpvcajk9xyy7662nqkyx333vrxpwsc5nmv0bfnhsbgijz5y0hvm")))) |
58db98c9 RW |
1937 | (properties `((upstream-name . "extRemes"))) |
1938 | (build-system r-build-system) | |
1939 | (propagated-inputs | |
1940 | `(("r-car" ,r-car) | |
1941 | ("r-distillery" ,r-distillery) | |
1942 | ("r-lmoments" ,r-lmoments))) | |
1943 | (home-page "http://www.assessment.ucar.edu/toolkit/") | |
1944 | (synopsis "Extreme value analysis") | |
1945 | (description | |
1946 | "ExtRemes is a suite of functions for carrying out analyses on the | |
1947 | extreme values of a process of interest; be they block maxima over long blocks | |
1948 | or excesses over a high threshold.") | |
1949 | (license license:gpl2+))) | |
062b6dbd RW |
1950 | |
1951 | (define-public r-lmtest | |
1952 | (package | |
1953 | (name "r-lmtest") | |
ba578d93 | 1954 | (version "0.9-36") |
062b6dbd RW |
1955 | (source |
1956 | (origin | |
1957 | (method url-fetch) | |
1958 | (uri (cran-uri "lmtest" version)) | |
1959 | (sha256 | |
1960 | (base32 | |
ba578d93 | 1961 | "0sym9sm1vl6bbgq01jhz1plxqmgh8hrgrn7rw0mwvsalcn6id7xy")))) |
062b6dbd RW |
1962 | (build-system r-build-system) |
1963 | (propagated-inputs | |
1964 | `(("r-zoo" ,r-zoo))) | |
1965 | (native-inputs | |
1966 | `(("gfortran" ,gfortran))) | |
e9960d8c | 1967 | (home-page "https://cran.r-project.org/web/packages/lmtest") |
062b6dbd RW |
1968 | (synopsis "Testing linear regression models") |
1969 | (description | |
1970 | "This package provides a collection of tests, data sets, and examples for | |
1971 | diagnostic checking in linear regression models. Furthermore, some generic | |
1972 | tools for inference in parametric models are provided.") | |
1973 | ;; Either version is okay | |
1974 | (license (list license:gpl2 license:gpl3)))) | |
d6b156dc | 1975 | |
c974008d RJ |
1976 | (define-public r-idr |
1977 | (package | |
1978 | (name "r-idr") | |
1979 | (version "1.2") | |
1980 | (source (origin | |
1981 | (method url-fetch) | |
1982 | (uri (cran-uri "idr" version)) | |
1983 | (sha256 | |
1984 | (base32 | |
1985 | "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb")))) | |
1986 | (build-system r-build-system) | |
1987 | (home-page "https://cran.r-project.org/web/packages/idr/") | |
1988 | (synopsis "Irreproducible discovery rate") | |
1989 | (description | |
1990 | "This is a package for estimating the copula mixture model and plotting | |
1991 | correspondence curves in \"Measuring reproducibility of high-throughput | |
1992 | experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, | |
1993 | by Li, Brown, Huang, and Bickel") | |
1994 | (license license:gpl2+))) | |
1995 | ||
d6b156dc RW |
1996 | (define-public r-inline |
1997 | (package | |
1998 | (name "r-inline") | |
0acbf8bb | 1999 | (version "0.3.15") |
d6b156dc RW |
2000 | (source (origin |
2001 | (method url-fetch) | |
2002 | (uri (cran-uri "inline" version)) | |
2003 | (sha256 | |
2004 | (base32 | |
0acbf8bb | 2005 | "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z")))) |
d6b156dc | 2006 | (build-system r-build-system) |
e9960d8c | 2007 | (home-page "https://cran.r-project.org/web/packages/inline") |
d6b156dc RW |
2008 | (synopsis "Functions to inline C, C++, Fortran function calls from R") |
2009 | (description | |
2010 | "This package provides functionality to dynamically define R functions | |
2011 | and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and | |
2012 | @code{.Call} calling conventions.") | |
2013 | ;; Any version of the LGPL. | |
2014 | (license license:lgpl3+))) | |
8c72b830 RW |
2015 | |
2016 | (define-public r-bbmle | |
2017 | (package | |
2018 | (name "r-bbmle") | |
84078220 | 2019 | (version "1.0.20") |
8c72b830 RW |
2020 | (source |
2021 | (origin | |
2022 | (method url-fetch) | |
2023 | (uri (cran-uri "bbmle" version)) | |
2024 | (sha256 | |
2025 | (base32 | |
84078220 | 2026 | "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc")))) |
8c72b830 RW |
2027 | (build-system r-build-system) |
2028 | (propagated-inputs | |
2029 | `(("r-lattice" ,r-lattice) | |
2030 | ("r-mass" ,r-mass) | |
2031 | ("r-numderiv" ,r-numderiv))) | |
e9960d8c | 2032 | (home-page "https://cran.r-project.org/web/packages/bbmle") |
8c72b830 RW |
2033 | (synopsis "Tools for General Maximum Likelihood Estimation") |
2034 | (description | |
c151b0b6 RW |
2035 | "This package provides methods and functions for fitting maximum |
2036 | likelihood models in R. This package modifies and extends the @code{mle} | |
2037 | classes in the @code{stats4} package.") | |
8c72b830 | 2038 | ;; Any version of the GPL |
c151b0b6 | 2039 | (license license:gpl2+))) |
b31e4a96 RW |
2040 | |
2041 | (define-public r-emdbook | |
2042 | (package | |
2043 | (name "r-emdbook") | |
59c51342 | 2044 | (version "1.3.11") |
b31e4a96 RW |
2045 | (source |
2046 | (origin | |
2047 | (method url-fetch) | |
2048 | (uri (cran-uri "emdbook" version)) | |
2049 | (sha256 | |
2050 | (base32 | |
59c51342 | 2051 | "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q")))) |
b31e4a96 RW |
2052 | (build-system r-build-system) |
2053 | (propagated-inputs | |
2054 | `(("r-bbmle" ,r-bbmle) | |
2055 | ("r-coda" ,r-coda) | |
2056 | ("r-lattice" ,r-lattice) | |
2057 | ("r-mass" ,r-mass) | |
2058 | ("r-plyr" ,r-plyr) | |
2059 | ("r-rcpp" ,r-rcpp))) | |
2060 | (home-page "http://www.math.mcmaster.ca/bolker/emdbook") | |
2061 | (synopsis "Support functions and data for \"Ecological Models and Data\"") | |
2062 | (description | |
2063 | "This package provides auxiliary functions and data sets for \"Ecological | |
2064 | Models and Data\", a book presenting maximum likelihood estimation and related | |
2065 | topics for ecologists (ISBN 978-0-691-12522-0).") | |
2066 | ;; Any GPL version | |
2067 | (license (list license:gpl2 license:gpl3)))) | |
a3e36d37 RW |
2068 | |
2069 | (define-public r-lpsolve | |
2070 | (package | |
2071 | (name "r-lpsolve") | |
2072 | (version "5.6.13") | |
2073 | (source | |
2074 | (origin | |
2075 | (method url-fetch) | |
2076 | (uri (cran-uri "lpSolve" version)) | |
2077 | (sha256 | |
2078 | (base32 | |
2079 | "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m")))) | |
2080 | (properties `((upstream-name . "lpSolve"))) | |
2081 | (build-system r-build-system) | |
e9960d8c | 2082 | (home-page "https://cran.r-project.org/web/packages/lpSolve") |
a3e36d37 RW |
2083 | (synopsis "R interface to Lp_solve to solve linear/integer programs") |
2084 | (description | |
2085 | "Lp_solve is software for solving linear, integer and mixed integer | |
2086 | programs. This implementation supplies a \"wrapper\" function in C and some R | |
2087 | functions that solve general linear/integer problems, assignment problems, and | |
2088 | transportation problems.") | |
2089 | (license license:lgpl2.0))) | |
521e0703 RW |
2090 | |
2091 | (define-public r-limsolve | |
2092 | (package | |
2093 | (name "r-limsolve") | |
2094 | (version "1.5.5.3") | |
2095 | (source | |
2096 | (origin | |
2097 | (method url-fetch) | |
2098 | (uri (cran-uri "limSolve" version)) | |
2099 | (sha256 | |
2100 | (base32 | |
2101 | "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg")))) | |
2102 | (properties `((upstream-name . "limSolve"))) | |
2103 | (build-system r-build-system) | |
2104 | (propagated-inputs | |
2105 | `(("r-lpsolve" ,r-lpsolve) | |
2106 | ("r-mass" ,r-mass) | |
2107 | ("r-quadprog" ,r-quadprog))) | |
2108 | (native-inputs `(("gfortran" ,gfortran))) | |
e9960d8c | 2109 | (home-page "https://cran.r-project.org/web/packages/limSolve") |
521e0703 RW |
2110 | (synopsis "Solving linear inverse models") |
2111 | (description | |
2112 | "This package provides functions that: | |
2113 | ||
2114 | @enumerate | |
2115 | @item find the minimum/maximum of a linear or quadratic function, | |
2116 | @item sample an underdetermined or overdetermined system, | |
2117 | @item solve a linear system Ax=B for the unknown x. | |
2118 | @end enumerate | |
2119 | ||
2120 | It includes banded and tridiagonal linear systems. The package calls Fortran | |
2121 | functions from LINPACK.") | |
2122 | ;; Any GPL version. | |
2123 | (license (list license:gpl2+ license:gpl3+)))) | |
6b4a9aec RW |
2124 | |
2125 | (define-public r-fitdistrplus | |
2126 | (package | |
2127 | (name "r-fitdistrplus") | |
9e0162df | 2128 | (version "1.0-14") |
6b4a9aec RW |
2129 | (source |
2130 | (origin | |
2131 | (method url-fetch) | |
2132 | (uri (cran-uri "fitdistrplus" version)) | |
2133 | (sha256 | |
2134 | (base32 | |
9e0162df | 2135 | "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245")))) |
6b4a9aec RW |
2136 | (build-system r-build-system) |
2137 | (propagated-inputs | |
2138 | `(("r-mass" ,r-mass) | |
8c456dff | 2139 | ("r-npsurv" ,r-npsurv) |
6b4a9aec RW |
2140 | ("r-survival" ,r-survival))) |
2141 | (home-page "http://riskassessment.r-forge.r-project.org") | |
2142 | (synopsis "Fitting a parametric distribution from data") | |
2143 | (description | |
2144 | "This package extends the @code{fitdistr} function of the MASS package | |
2145 | with several functions to help the fit of a parametric distribution to | |
2146 | non-censored or censored data. Censored data may contain left-censored, | |
2147 | right-censored and interval-censored values, with several lower and upper | |
2148 | bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package | |
2149 | provides moment matching (MME), quantile matching (QME) and maximum | |
2150 | goodness-of-fit estimation (MGE) methods (available only for non-censored | |
2151 | data). Weighted versions of MLE, MME and QME are available.") | |
2152 | (license license:gpl2+))) | |
8d220073 RW |
2153 | |
2154 | (define-public r-energy | |
2155 | (package | |
2156 | (name "r-energy") | |
9c112bee | 2157 | (version "1.7-5") |
8d220073 RW |
2158 | (source |
2159 | (origin | |
2160 | (method url-fetch) | |
2161 | (uri (cran-uri "energy" version)) | |
2162 | (sha256 | |
2163 | (base32 | |
9c112bee | 2164 | "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4")))) |
8d220073 RW |
2165 | (build-system r-build-system) |
2166 | (propagated-inputs | |
2167 | `(("r-boot" ,r-boot) | |
2168 | ("r-rcpp" ,r-rcpp))) | |
e9960d8c | 2169 | (home-page "https://cran.r-project.org/web/packages/energy") |
8d220073 RW |
2170 | (synopsis "Multivariate inference via the energy of data") |
2171 | (description | |
2172 | "This package provides e-statistics (energy) tests and statistics for | |
2173 | multivariate and univariate inference, including distance correlation, | |
2174 | one-sample, two-sample, and multi-sample tests for comparing multivariate | |
2175 | distributions, are implemented. Measuring and testing multivariate | |
2176 | independence based on distance correlation, partial distance correlation, | |
2177 | multivariate goodness-of-fit tests, clustering based on energy distance, | |
2178 | testing for multivariate normality, distance components (disco) for | |
2179 | non-parametric analysis of structured data, and other energy | |
2180 | statistics/methods are implemented.") | |
2181 | (license license:gpl2+))) | |
abcb8494 RW |
2182 | |
2183 | (define-public r-suppdists | |
2184 | (package | |
2185 | (name "r-suppdists") | |
2186 | (version "1.1-9.4") | |
2187 | (source | |
2188 | (origin | |
2189 | (method url-fetch) | |
2190 | (uri (cran-uri "SuppDists" version)) | |
2191 | (sha256 | |
2192 | (base32 | |
2193 | "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw")))) | |
2194 | (properties `((upstream-name . "SuppDists"))) | |
2195 | (build-system r-build-system) | |
e9960d8c | 2196 | (home-page "https://cran.r-project.org/web/packages/SuppDists") |
abcb8494 RW |
2197 | (synopsis "Supplementary distributions") |
2198 | (description | |
2199 | "This package provides ten distributions supplementing those built into | |
2200 | R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, | |
2201 | Spearman's rho, maximum F ratio, the Pearson product moment correlation | |
2202 | coefficient, Johnson distributions, normal scores and generalized | |
2203 | hypergeometric distributions. In addition two random number generators of | |
2204 | George Marsaglia are included.") | |
2205 | (license license:gpl2+))) | |
05e8a3ef RW |
2206 | |
2207 | (define-public r-ksamples | |
2208 | (package | |
2209 | (name "r-ksamples") | |
c152c6b3 | 2210 | (version "1.2-8") |
05e8a3ef RW |
2211 | (source |
2212 | (origin | |
2213 | (method url-fetch) | |
2214 | (uri (cran-uri "kSamples" version)) | |
2215 | (sha256 | |
2216 | (base32 | |
c152c6b3 | 2217 | "15d5q5vpp4wx5rk5kjxjdxpwc8mkq5sbdz8gi07iscrvhzb5rzfr")))) |
05e8a3ef RW |
2218 | (properties `((upstream-name . "kSamples"))) |
2219 | (build-system r-build-system) | |
2220 | (propagated-inputs | |
2221 | `(("r-suppdists" ,r-suppdists))) | |
e9960d8c | 2222 | (home-page "https://cran.r-project.org/web/packages/kSamples") |
05e8a3ef RW |
2223 | (synopsis "K-Sample rank tests and their combinations") |
2224 | (description | |
2225 | "This package provides tools to compares k samples using the | |
2226 | Anderson-Darling test, Kruskal-Wallis type tests with different rank score | |
2227 | criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) | |
2228 | test. It computes asymptotic, simulated or (limited) exact P-values, all | |
2229 | valid under randomization, with or without ties, or conditionally under random | |
2230 | sampling from populations, given the observed tie pattern. Except for Steel's | |
2231 | test and the JT test it also combines these tests across several blocks of | |
2232 | samples.") | |
2233 | (license license:gpl2+))) | |
f97ce815 RW |
2234 | |
2235 | (define-public r-cvst | |
2236 | (package | |
2237 | (name "r-cvst") | |
b13b5674 | 2238 | (version "0.2-2") |
f97ce815 RW |
2239 | (source |
2240 | (origin | |
2241 | (method url-fetch) | |
2242 | (uri (cran-uri "CVST" version)) | |
2243 | (sha256 | |
2244 | (base32 | |
b13b5674 | 2245 | "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5")))) |
f97ce815 RW |
2246 | (properties `((upstream-name . "CVST"))) |
2247 | (build-system r-build-system) | |
2248 | (propagated-inputs | |
2249 | `(("r-kernlab" ,r-kernlab) | |
2250 | ("r-matrix" ,r-matrix))) | |
e9960d8c | 2251 | (home-page "https://cran.r-project.org/web/packages/CVST") |
f97ce815 RW |
2252 | (synopsis "Fast cross-validation via sequential testing") |
2253 | (description | |
2254 | "This package implements the fast cross-validation via sequential | |
2255 | testing (CVST) procedure. CVST is an improved cross-validation procedure | |
2256 | which uses non-parametric testing coupled with sequential analysis to | |
2257 | determine the best parameter set on linearly increasing subsets of the data. | |
2258 | Additionally to the CVST the package contains an implementation of the | |
2259 | ordinary k-fold cross-validation with a flexible and powerful set of helper | |
2260 | objects and methods to handle the overall model selection process. The | |
2261 | implementations of the Cochran's Q test with permutations and the sequential | |
2262 | testing framework of Wald are generic and can therefore also be used in other | |
2263 | contexts.") | |
2264 | (license license:gpl2+))) | |
797e1dfb | 2265 | |
c5f033e0 RW |
2266 | (define-public r-squarem |
2267 | (package | |
2268 | (name "r-squarem") | |
2269 | (version "2017.10-1") | |
2270 | (source | |
2271 | (origin | |
2272 | (method url-fetch) | |
2273 | (uri (cran-uri "SQUAREM" version)) | |
2274 | (sha256 | |
2275 | (base32 | |
2276 | "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv")))) | |
2277 | (properties `((upstream-name . "SQUAREM"))) | |
2278 | (build-system r-build-system) | |
2279 | (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html") | |
2280 | (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms") | |
2281 | (description | |
2282 | "This package provides algorithms for accelerating the convergence of | |
2283 | slow, monotone sequences from smooth, contraction mapping such as the EM | |
2284 | algorithm. It can be used to accelerate any smooth, linearly convergent | |
2285 | acceleration scheme. A tutorial style introduction to this package is | |
2286 | available in a vignette.") | |
2287 | (license license:gpl2+))) | |
2288 | ||
797e1dfb RW |
2289 | (define-public r-lava |
2290 | (package | |
2291 | (name "r-lava") | |
bf6c8960 | 2292 | (version "1.6.5") |
797e1dfb RW |
2293 | (source |
2294 | (origin | |
2295 | (method url-fetch) | |
2296 | (uri (cran-uri "lava" version)) | |
2297 | (sha256 | |
2298 | (base32 | |
bf6c8960 | 2299 | "13rlqdg42ylnz4hc932bl50xismrcr4d9ykcd9zs19cw5mckjx0f")))) |
797e1dfb RW |
2300 | (build-system r-build-system) |
2301 | (propagated-inputs | |
2302 | `(("r-numderiv" ,r-numderiv) | |
92e4534c | 2303 | ("r-squarem" ,r-squarem) |
797e1dfb RW |
2304 | ("r-survival" ,r-survival))) |
2305 | (home-page "https://github.com/kkholst/lava") | |
2306 | (synopsis "Latent variable models") | |
2307 | (description | |
2308 | "This package provides tools for the estimation and simulation of latent | |
2309 | variable models.") | |
2310 | (license license:gpl3))) | |
d26b7c1b RW |
2311 | |
2312 | (define-public r-drr | |
2313 | (package | |
2314 | (name "r-drr") | |
0f001b3c | 2315 | (version "0.0.3") |
d26b7c1b RW |
2316 | (source |
2317 | (origin | |
2318 | (method url-fetch) | |
2319 | (uri (cran-uri "DRR" version)) | |
2320 | (sha256 | |
2321 | (base32 | |
0f001b3c | 2322 | "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl")))) |
d26b7c1b RW |
2323 | (properties `((upstream-name . "DRR"))) |
2324 | (build-system r-build-system) | |
2325 | (propagated-inputs | |
2326 | `(("r-cvst" ,r-cvst) | |
2327 | ("r-kernlab" ,r-kernlab) | |
2328 | ("r-matrix" ,r-matrix))) | |
e9960d8c | 2329 | (home-page "https://cran.r-project.org/web/packages/DRR") |
d26b7c1b RW |
2330 | (synopsis "Dimensionality reduction via regression") |
2331 | (description | |
2332 | "This package provides an implementation of dimensionality reduction via | |
2333 | regression using Kernel Ridge Regression.") | |
2334 | (license license:gpl3))) | |
9dd707f0 RW |
2335 | |
2336 | (define-public r-prodlim | |
2337 | (package | |
2338 | (name "r-prodlim") | |
9ee81a36 | 2339 | (version "2018.04.18") |
9dd707f0 RW |
2340 | (source |
2341 | (origin | |
2342 | (method url-fetch) | |
2343 | (uri (cran-uri "prodlim" version)) | |
2344 | (sha256 | |
2345 | (base32 | |
9ee81a36 | 2346 | "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb")))) |
9dd707f0 RW |
2347 | (build-system r-build-system) |
2348 | (propagated-inputs | |
2349 | `(("r-kernsmooth" ,r-kernsmooth) | |
2350 | ("r-lava" ,r-lava) | |
2351 | ("r-rcpp" ,r-rcpp) | |
2352 | ("r-survival" ,r-survival))) | |
e9960d8c | 2353 | (home-page "https://cran.r-project.org/web/packages/prodlim") |
9dd707f0 RW |
2354 | (synopsis "Product-limit estimation for censored event history analysis") |
2355 | (description | |
2356 | "This package provides a fast and user-friendly implementation of | |
2357 | nonparametric estimators for censored event history (survival) analysis with | |
2358 | the Kaplan-Meier and Aalen-Johansen methods.") | |
2359 | (license license:gpl2+))) | |
b561f563 RW |
2360 | |
2361 | (define-public r-dimred | |
2362 | (package | |
2363 | (name "r-dimred") | |
e21659c7 | 2364 | (version "0.2.2") |
b561f563 RW |
2365 | (source |
2366 | (origin | |
2367 | (method url-fetch) | |
2368 | (uri (cran-uri "dimRed" version)) | |
2369 | (sha256 | |
2370 | (base32 | |
e21659c7 | 2371 | "0ssy2qriiy6zdawriqcbl67qiq68ipml3frq7aqlq70r2fqyyw48")))) |
b561f563 RW |
2372 | (properties `((upstream-name . "dimRed"))) |
2373 | (build-system r-build-system) | |
77f97229 RW |
2374 | (propagated-inputs |
2375 | `(("r-drr" ,r-drr) | |
2376 | ("r-magrittr" ,r-magrittr))) | |
b561f563 RW |
2377 | (home-page "https://github.com/gdkrmr/dimRed") |
2378 | (synopsis "Framework for dimensionality reduction") | |
2379 | (description | |
2380 | "This package provides a collection of dimensionality reduction | |
2381 | techniques from R packages and provides a common interface for calling the | |
2382 | methods.") | |
2383 | (license license:gpl3))) | |
1b663184 RW |
2384 | |
2385 | (define-public r-timedate | |
2386 | (package | |
2387 | (name "r-timedate") | |
51b7b0e3 | 2388 | (version "3043.102") |
1b663184 RW |
2389 | (source |
2390 | (origin | |
2391 | (method url-fetch) | |
2392 | (uri (cran-uri "timeDate" version)) | |
2393 | (sha256 | |
2394 | (base32 | |
51b7b0e3 | 2395 | "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p")))) |
1b663184 RW |
2396 | (properties `((upstream-name . "timeDate"))) |
2397 | (build-system r-build-system) | |
2398 | (home-page "https://www.rmetrics.org") | |
2399 | (synopsis "Chronological and calendar objects") | |
2400 | (description | |
2401 | "This package provides an environment for teaching \"Financial | |
2402 | Engineering and Computational Finance\" and for managing chronological and | |
2403 | calendar objects.") | |
2404 | (license license:gpl2+))) | |
f57b883e | 2405 | |
ce4e81cb RW |
2406 | (define-public r-magic |
2407 | (package | |
2408 | (name "r-magic") | |
bba80fad | 2409 | (version "1.5-9") |
ce4e81cb RW |
2410 | (source |
2411 | (origin | |
2412 | (method url-fetch) | |
2413 | (uri (cran-uri "magic" version)) | |
2414 | (sha256 | |
2415 | (base32 | |
bba80fad | 2416 | "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) |
ce4e81cb RW |
2417 | (build-system r-build-system) |
2418 | (propagated-inputs | |
2419 | `(("r-abind" ,r-abind))) | |
2420 | (home-page "https://github.com/RobinHankin/magic.git") | |
2421 | (synopsis "Create and investigate magic squares") | |
2422 | (description | |
2423 | "This package provides a collection of efficient, vectorized algorithms | |
2424 | for the creation and investigation of magic squares and hypercubes, including | |
2425 | a variety of functions for the manipulation and analysis of arbitrarily | |
2426 | dimensioned arrays.") | |
2427 | (license license:gpl2))) | |
2428 | ||
d9bec9a8 RW |
2429 | (define-public r-rmysql |
2430 | (package | |
2431 | (name "r-rmysql") | |
937e1557 | 2432 | (version "0.10.17") |
d9bec9a8 RW |
2433 | (source |
2434 | (origin | |
2435 | (method url-fetch) | |
2436 | (uri (cran-uri "RMySQL" version)) | |
2437 | (sha256 | |
2438 | (base32 | |
937e1557 | 2439 | "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm")))) |
d9bec9a8 RW |
2440 | (properties `((upstream-name . "RMySQL"))) |
2441 | (build-system r-build-system) | |
d9bec9a8 RW |
2442 | (inputs |
2443 | `(("mariadb" ,mariadb) | |
2444 | ("zlib" ,zlib))) | |
2445 | (propagated-inputs | |
2446 | `(("r-dbi" ,r-dbi))) | |
2447 | (home-page "https://github.com/r-dbi/RMySQL") | |
2448 | (synopsis "Database interface and MySQL driver for R") | |
2449 | (description | |
2450 | "This package provides a DBI interface to MySQL / MariaDB. The RMySQL | |
2451 | package contains an old implementation based on legacy code from S-PLUS which | |
2452 | is being phased out. A modern MySQL client based on Rcpp is available from | |
2453 | the RMariaDB package.") | |
2454 | (license license:gpl2))) | |
2455 | ||
5574cb81 RW |
2456 | (define-public r-rpostgresql |
2457 | (package | |
2458 | (name "r-rpostgresql") | |
2459 | (version "0.6-2") | |
2460 | (source | |
2461 | (origin | |
2462 | (method url-fetch) | |
2463 | (uri (cran-uri "RPostgreSQL" version)) | |
2464 | (sha256 | |
2465 | (base32 | |
2466 | "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) | |
2467 | (properties `((upstream-name . "RPostgreSQL"))) | |
2468 | (build-system r-build-system) | |
2469 | (inputs | |
2470 | `(("postgresql" ,postgresql))) | |
2471 | (propagated-inputs | |
2472 | `(("r-dbi" ,r-dbi))) | |
2473 | (home-page "https://github.com/tomoakin/RPostgreSQL") | |
2474 | (synopsis "R interface to the PostgreSQL database system") | |
2475 | (description | |
2476 | "This package provides a Database Interface (DBI) compliant driver for R | |
2477 | to access PostgreSQL database systems.") | |
2478 | ;; The whole package is released under GPL version 2. It includes code | |
2479 | ;; under the PostgreSQL license. | |
2480 | (license license:gpl2))) | |
2481 | ||
9604429d RW |
2482 | (define-public r-geometry |
2483 | (package | |
2484 | (name "r-geometry") | |
3d17dc5d | 2485 | (version "0.4.1") |
9604429d RW |
2486 | (source |
2487 | (origin | |
2488 | (method url-fetch) | |
2489 | (uri (cran-uri "geometry" version)) | |
2490 | (sha256 | |
2491 | (base32 | |
3d17dc5d | 2492 | "0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm")))) |
9604429d | 2493 | (build-system r-build-system) |
a023d43d BG |
2494 | (propagated-inputs |
2495 | `(("r-magic" ,r-magic) | |
2496 | ("r-lpsolve" ,r-lpsolve) | |
2497 | ("r-rcpp" ,r-rcpp) | |
3d17dc5d | 2498 | ("r-rcppprogress" ,r-rcppprogress))) |
9604429d RW |
2499 | (home-page "http://geometry.r-forge.r-project.org/") |
2500 | (synopsis "Mesh generation and surface tesselation") | |
2501 | (description | |
2502 | "This package makes the qhull library available in R, in a similar manner | |
2503 | as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace | |
2504 | intersections about a point, Voronoi diagrams, furthest-site Delaunay | |
2505 | triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, | |
2506 | and higher dimensions. It implements the Quickhull algorithm for computing | |
2507 | the convex hull. Qhull does not support constrained Delaunay triangulations, | |
2508 | or mesh generation of non-convex objects, but the package does include some R | |
2509 | functions that allow for this. Currently the package only gives access to | |
2510 | Delaunay triangulation and convex hull computation.") | |
2511 | ;; The Qhull sources are included and are distributed under a custom | |
2512 | ;; non-copyleft license. The R sources are released under GPL version 2. | |
2513 | (license (list license:gpl2 | |
2514 | (license:non-copyleft "http://www.qhull.org/COPYING.txt"))))) | |
2515 | ||
f57b883e RW |
2516 | (define-public r-ddalpha |
2517 | (package | |
2518 | (name "r-ddalpha") | |
fc74de42 | 2519 | (version "1.3.8") |
f57b883e RW |
2520 | (source |
2521 | (origin | |
2522 | (method url-fetch) | |
2523 | (uri (cran-uri "ddalpha" version)) | |
2524 | (sha256 | |
2525 | (base32 | |
fc74de42 | 2526 | "0gi0hl14ghgf65zxsvgzh9z6xx1nyi49cpx192lmwrwqn3dy7ba0")))) |
f57b883e RW |
2527 | (build-system r-build-system) |
2528 | (propagated-inputs | |
2529 | `(("r-bh" ,r-bh) | |
2530 | ("r-class" ,r-class) | |
4f184233 | 2531 | ("r-geometry" ,r-geometry) |
f57b883e RW |
2532 | ("r-mass" ,r-mass) |
2533 | ("r-rcpp" ,r-rcpp) | |
e90456b9 RW |
2534 | ("r-robustbase" ,r-robustbase) |
2535 | ("r-sfsmisc" ,r-sfsmisc))) | |
2536 | (native-inputs | |
2537 | `(("gfortran" ,gfortran))) | |
e9960d8c | 2538 | (home-page "https://cran.r-project.org/web/packages/ddalpha") |
f57b883e RW |
2539 | (synopsis "Depth-Based classification and calculation of data depth") |
2540 | (description | |
2541 | "This package contains procedures for depth-based supervised learning, | |
2542 | which are entirely non-parametric, in particular the DDalpha-procedure (Lange, | |
2543 | Mosler and Mozharovskyi, 2014). The training data sample is transformed by a | |
2544 | statistical depth function to a compact low-dimensional space, where the final | |
2545 | classification is done. It also offers an extension to functional data and | |
2546 | routines for calculating certain notions of statistical depth functions. 50 | |
2547 | multivariate and 5 functional classification problems are included.") | |
2548 | (license license:gpl2))) | |
5a87093f RW |
2549 | |
2550 | (define-public r-gower | |
2551 | (package | |
2552 | (name "r-gower") | |
2170a36c | 2553 | (version "0.2.0") |
5a87093f RW |
2554 | (source |
2555 | (origin | |
2556 | (method url-fetch) | |
2557 | (uri (cran-uri "gower" version)) | |
2558 | (sha256 | |
2559 | (base32 | |
2170a36c | 2560 | "0x16k0nixgbayh3g4didacn0gmnl5fdfxa0l323phphmimyj49zl")))) |
5a87093f | 2561 | (build-system r-build-system) |
5a87093f RW |
2562 | (home-page "https://github.com/markvanderloo/gower") |
2563 | (synopsis "Gower's distance") | |
2564 | (description | |
2565 | "This package provides tools to compute Gower's distance (or similarity) | |
2566 | coefficient between records, and to compute the top-n matches between records. | |
2567 | Core algorithms are executed in parallel on systems supporting OpenMP.") | |
2568 | (license license:gpl3))) | |
649cf27c RW |
2569 | |
2570 | (define-public r-rcpproll | |
2571 | (package | |
2572 | (name "r-rcpproll") | |
d0396c8e | 2573 | (version "0.3.0") |
649cf27c RW |
2574 | (source |
2575 | (origin | |
2576 | (method url-fetch) | |
2577 | (uri (cran-uri "RcppRoll" version)) | |
2578 | (sha256 | |
2579 | (base32 | |
d0396c8e | 2580 | "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) |
649cf27c RW |
2581 | (properties `((upstream-name . "RcppRoll"))) |
2582 | (build-system r-build-system) | |
2583 | (propagated-inputs | |
2584 | `(("r-rcpp" ,r-rcpp))) | |
e9960d8c | 2585 | (home-page "https://cran.r-project.org/web/packages/RcppRoll") |
649cf27c RW |
2586 | (synopsis "Efficient rolling and windowed operations") |
2587 | (description | |
2588 | "This package provides fast and efficient routines for common rolling / | |
2589 | windowed operations. Routines for the efficient computation of windowed mean, | |
2590 | median, sum, product, minimum, maximum, standard deviation and variance are | |
2591 | provided.") | |
2592 | (license license:gpl2+))) | |
6c3d42d6 RW |
2593 | |
2594 | (define-public r-ipred | |
2595 | (package | |
2596 | (name "r-ipred") | |
56af171f | 2597 | (version "0.9-8") |
6c3d42d6 RW |
2598 | (source |
2599 | (origin | |
2600 | (method url-fetch) | |
2601 | (uri (cran-uri "ipred" version)) | |
2602 | (sha256 | |
2603 | (base32 | |
56af171f | 2604 | "01xcg3c121ndfpz9dirqxszknh4yb1p222p7f1wbwwhdrg1i27cw")))) |
6c3d42d6 RW |
2605 | (build-system r-build-system) |
2606 | (propagated-inputs | |
2607 | `(("r-class" ,r-class) | |
2608 | ("r-mass" ,r-mass) | |
2609 | ("r-nnet" ,r-nnet) | |
2610 | ("r-prodlim" ,r-prodlim) | |
2611 | ("r-rpart" ,r-rpart) | |
2612 | ("r-survival" ,r-survival))) | |
e9960d8c | 2613 | (home-page "https://cran.r-project.org/web/packages/ipred") |
6c3d42d6 RW |
2614 | (synopsis "Improved predictors") |
2615 | (description | |
2616 | "This package provides improved predictive models by indirect | |
2617 | classification and bagging for classification, regression and survival | |
2618 | problems as well as resampling based estimators of prediction error.") | |
2619 | (license license:gpl2+))) | |
ba4527ab | 2620 | |
cdc129dc RW |
2621 | (define-public r-psych |
2622 | (package | |
2623 | (name "r-psych") | |
523762e3 | 2624 | (version "1.8.12") |
cdc129dc RW |
2625 | (source |
2626 | (origin | |
2627 | (method url-fetch) | |
2628 | (uri (cran-uri "psych" version)) | |
2629 | (sha256 | |
2630 | (base32 | |
523762e3 | 2631 | "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf")))) |
cdc129dc RW |
2632 | (build-system r-build-system) |
2633 | (propagated-inputs | |
2634 | `(("r-foreign" ,r-foreign) | |
2635 | ("r-lattice" ,r-lattice) | |
2636 | ("r-mnormt" ,r-mnormt) | |
2637 | ("r-nlme" ,r-nlme))) | |
e9960d8c | 2638 | (home-page "https://cran.r-project.org/web/packages/psych/") |
cdc129dc RW |
2639 | (synopsis "Procedures for psychological, psychometric, and personality research") |
2640 | (description | |
2641 | "This package provides a general purpose toolbox for personality, | |
2642 | psychometric theory and experimental psychology. Functions are primarily for | |
2643 | multivariate analysis and scale construction using factor analysis, principal | |
2644 | component analysis, cluster analysis and reliability analysis, although others | |
2645 | provide basic descriptive statistics. Item Response Theory is done using | |
2646 | factor analysis of tetrachoric and polychoric correlations. Functions for | |
2647 | analyzing data at multiple levels include within and between group statistics, | |
2648 | including correlations and factor analysis. Functions for simulating and | |
2649 | testing particular item and test structures are included. Several functions | |
2650 | serve as a useful front end for structural equation modeling. Graphical | |
2651 | displays of path diagrams, factor analysis and structural equation models are | |
2652 | created using basic graphics.") | |
2653 | (license license:gpl2+))) | |
2654 | ||
25c67ecf RW |
2655 | (define-public r-generics |
2656 | (package | |
2657 | (name "r-generics") | |
2658 | (version "0.0.2") | |
2659 | (source | |
2660 | (origin | |
2661 | (method url-fetch) | |
2662 | (uri (cran-uri "generics" version)) | |
2663 | (sha256 | |
2664 | (base32 | |
2665 | "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) | |
2666 | (build-system r-build-system) | |
2667 | (home-page "https://github.com/r-lib/generics") | |
2668 | (synopsis "Common S3 generics not provided by base R methods") | |
2669 | (description | |
2670 | "In order to reduce potential package dependencies and conflicts, | |
2671 | generics provides a number of commonly used S3 generics that are not provided | |
2672 | by base R methods related to model fitting.") | |
2673 | (license license:gpl2))) | |
2674 | ||
6c8c8c6b RW |
2675 | (define-public r-broom |
2676 | (package | |
2677 | (name "r-broom") | |
813d9c51 | 2678 | (version "0.5.1") |
6c8c8c6b RW |
2679 | (source |
2680 | (origin | |
2681 | (method url-fetch) | |
2682 | (uri (cran-uri "broom" version)) | |
2683 | (sha256 | |
2684 | (base32 | |
813d9c51 | 2685 | "0bmf38yvwalqf5j5yrr48nsk5k3n75s0gwcw621hp5lgrgvnp7ns")))) |
6c8c8c6b RW |
2686 | (build-system r-build-system) |
2687 | (propagated-inputs | |
45c156bf RW |
2688 | `(("r-backports" ,r-backports) |
2689 | ("r-dplyr" ,r-dplyr) | |
813d9c51 | 2690 | ("r-generics" ,r-generics) |
6c8c8c6b | 2691 | ("r-nlme" ,r-nlme) |
45c156bf | 2692 | ("r-purrr" ,r-purrr) |
6c8c8c6b RW |
2693 | ("r-reshape2" ,r-reshape2) |
2694 | ("r-stringr" ,r-stringr) | |
45c156bf | 2695 | ("r-tibble" ,r-tibble) |
6c8c8c6b | 2696 | ("r-tidyr" ,r-tidyr))) |
6e19d50e | 2697 | (home-page "https://github.com/tidyverse/broom") |
6c8c8c6b RW |
2698 | (synopsis "Convert statistical analysis objects into tidy data frames") |
2699 | (description | |
2700 | "This package provides tools to convert statistical analysis objects from | |
2701 | R into tidy data frames, so that they can more easily be combined, reshaped | |
2702 | and otherwise processed with tools like @code{dplyr}, @code{tidyr} and | |
2703 | @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which | |
2704 | summarizes a model's statistical findings such as coefficients of a | |
2705 | regression; @code{augment}, which adds columns to the original data such as | |
2706 | predictions, residuals and cluster assignments; and @code{glance}, which | |
2707 | provides a one-row summary of model-level statistics.") | |
2708 | (license license:expat))) | |
2709 | ||
ba4527ab RW |
2710 | (define-public r-recipes |
2711 | (package | |
2712 | (name "r-recipes") | |
decea6ee | 2713 | (version "0.1.5") |
ba4527ab RW |
2714 | (source |
2715 | (origin | |
2716 | (method url-fetch) | |
2717 | (uri (cran-uri "recipes" version)) | |
2718 | (sha256 | |
2719 | (base32 | |
decea6ee | 2720 | "056zv4vhayyy8q9izcdknbb9hff2gxivg21g5mkssia78vw8g3mg")))) |
ba4527ab RW |
2721 | (build-system r-build-system) |
2722 | (propagated-inputs | |
decea6ee RW |
2723 | `(("r-dplyr" ,r-dplyr) |
2724 | ("r-generics" ,r-generics) | |
2725 | ("r-glue" ,r-glue) | |
ba4527ab RW |
2726 | ("r-gower" ,r-gower) |
2727 | ("r-ipred" ,r-ipred) | |
2728 | ("r-lubridate" ,r-lubridate) | |
2729 | ("r-magrittr" ,r-magrittr) | |
18a11c6d | 2730 | ("r-matrix" ,r-matrix) |
ba4527ab RW |
2731 | ("r-purrr" ,r-purrr) |
2732 | ("r-rcpproll" ,r-rcpproll) | |
2733 | ("r-rlang" ,r-rlang) | |
2734 | ("r-tibble" ,r-tibble) | |
decea6ee | 2735 | ("r-tidyr" ,r-tidyr) |
ba4527ab | 2736 | ("r-tidyselect" ,r-tidyselect) |
57039918 RW |
2737 | ("r-timedate" ,r-timedate) |
2738 | ("r-withr" ,r-withr))) | |
ba4527ab RW |
2739 | (home-page "https://github.com/topepo/recipes") |
2740 | (synopsis "Preprocessing tools to create design matrices") | |
2741 | (description | |
2742 | "Recipes is an extensible framework to create and preprocess design | |
2743 | matrices. Recipes consist of one or more data manipulation and analysis | |
2744 | \"steps\". Statistical parameters for the steps can be estimated from an | |
2745 | initial data set and then applied to other data sets. The resulting design | |
2746 | matrices can then be used as inputs into statistical or machine learning | |
2747 | models.") | |
2748 | (license license:gpl2))) | |
1ab867be RW |
2749 | |
2750 | (define-public r-pdist | |
2751 | (package | |
2752 | (name "r-pdist") | |
2753 | (version "1.2") | |
2754 | (source | |
2755 | (origin | |
2756 | (method url-fetch) | |
2757 | (uri (cran-uri "pdist" version)) | |
2758 | (sha256 | |
2759 | (base32 | |
2760 | "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd")))) | |
2761 | (build-system r-build-system) | |
2762 | (home-page "https://github.com/jeffwong/pdist") | |
2763 | (synopsis "Partitioned distance function") | |
2764 | (description | |
2765 | "Pdist computes the euclidean distance between rows of a matrix X and | |
2766 | rows of another matrix Y. Previously, this could be done by binding the two | |
2767 | matrices together and calling @code{dist}, but this creates unnecessary | |
2768 | computation by computing the distances between a row of X and another row of | |
2769 | X, and likewise for Y. Pdist strictly computes distances across the two | |
2770 | matrices, not within the same matrix, making computations significantly faster | |
2771 | for certain use cases.") | |
2772 | (license license:gpl3+))) | |
81e0b625 RW |
2773 | |
2774 | (define-public r-ggrepel | |
2775 | (package | |
2776 | (name "r-ggrepel") | |
0759d87d | 2777 | (version "0.8.0") |
81e0b625 RW |
2778 | (source |
2779 | (origin | |
2780 | (method url-fetch) | |
2781 | (uri (cran-uri "ggrepel" version)) | |
2782 | (sha256 | |
2783 | (base32 | |
0759d87d | 2784 | "1m3p84d6nh9mzzvxb82vgig3ngcvkz86rjwzl9a66ckdf5p611k3")))) |
81e0b625 RW |
2785 | (build-system r-build-system) |
2786 | (propagated-inputs | |
2787 | `(("r-ggplot2" ,r-ggplot2) | |
2788 | ("r-rcpp" ,r-rcpp) | |
2789 | ("r-scales" ,r-scales))) | |
2790 | (home-page "http://github.com/slowkow/ggrepel") | |
2791 | (synopsis "Repulsive text and label geometries for ggplot2") | |
2792 | (description | |
2793 | "This package provides text and label geometries for ggplot2 that help to | |
2794 | avoid overlapping text labels. Labels repel away from each other and away | |
2795 | from the data points.") | |
2796 | (license license:gpl3))) | |
6b968c4c RW |
2797 | |
2798 | (define-public r-corrplot | |
2799 | (package | |
2800 | (name "r-corrplot") | |
2801 | (version "0.84") | |
2802 | (source | |
2803 | (origin | |
2804 | (method url-fetch) | |
2805 | (uri (cran-uri "corrplot" version)) | |
2806 | (sha256 | |
2807 | (base32 | |
2808 | "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd")))) | |
2809 | (build-system r-build-system) | |
2810 | (home-page "https://github.com/taiyun/corrplot") | |
2811 | (synopsis "Visualization of a correlation matrix") | |
2812 | (description | |
2813 | "This package provides a graphical display of a correlation matrix or | |
2814 | general matrix. It also contains some algorithms to do matrix reordering. In | |
2815 | addition, corrplot is good at details, including choosing color, text labels, | |
2816 | color labels, layout, etc.") | |
2817 | ;; Any version of the GPL | |
2818 | (license license:gpl2+))) | |
a40a04fd RW |
2819 | |
2820 | (define-public r-stringdist | |
2821 | (package | |
2822 | (name "r-stringdist") | |
2bce7795 | 2823 | (version "0.9.5.1") |
a40a04fd RW |
2824 | (source |
2825 | (origin | |
2826 | (method url-fetch) | |
2827 | (uri (cran-uri "stringdist" version)) | |
2828 | (sha256 | |
2829 | (base32 | |
2bce7795 | 2830 | "0gap1g9xwhp0zxqsznkc2carpvi80z03prr4q8m528684lznx2xa")))) |
a40a04fd RW |
2831 | (build-system r-build-system) |
2832 | (home-page "https://github.com/markvanderloo/stringdist") | |
2833 | (synopsis "Approximate string matching and string distance functions") | |
2834 | (description | |
2835 | "This package implements an approximate string matching version of R's | |
2836 | native @code{match} function. It can calculate various string distances based | |
2837 | on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), | |
2838 | qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, | |
2839 | Jaro-Winkler). An implementation of soundex is provided as well. Distances | |
2840 | can be computed between character vectors while taking proper care of encoding | |
2841 | or between integer vectors representing generic sequences.") | |
2842 | (license license:gpl3+))) | |
10e16fa9 | 2843 | |
dc668352 RW |
2844 | (define-public r-ucminf |
2845 | (package | |
2846 | (name "r-ucminf") | |
2847 | (version "1.1-4") | |
2848 | (source | |
2849 | (origin | |
2850 | (method url-fetch) | |
2851 | (uri (cran-uri "ucminf" version)) | |
2852 | (sha256 | |
2853 | (base32 | |
2854 | "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) | |
2855 | (build-system r-build-system) | |
2856 | (native-inputs `(("gfortran" ,gfortran))) | |
2857 | (home-page "https://cran.r-project.org/web/packages/ucminf/") | |
2858 | (synopsis "General-purpose unconstrained non-linear optimization") | |
2859 | (description | |
2860 | "This package provides an implementation of an algorithm for | |
2861 | general-purpose unconstrained non-linear optimization. The algorithm is of | |
2862 | quasi-Newton type with BFGS updating of the inverse Hessian and soft line | |
2863 | search with a trust region type monitoring of the input to the line search | |
2864 | algorithm. The interface of @code{ucminf} is designed for easy interchange | |
2865 | with the package @code{optim}.") | |
2866 | (license license:gpl2+))) | |
2867 | ||
b8f6e2f8 RW |
2868 | (define-public r-ordinal |
2869 | (package | |
2870 | (name "r-ordinal") | |
5275f9d7 | 2871 | (version "2019.3-9") |
b8f6e2f8 RW |
2872 | (source |
2873 | (origin | |
2874 | (method url-fetch) | |
2875 | (uri (cran-uri "ordinal" version)) | |
2876 | (sha256 | |
2877 | (base32 | |
5275f9d7 | 2878 | "0xsr2715ghh1q5hjnx7d8lyavzfvpi370blm1xdljn3p4kar8ldi")))) |
b8f6e2f8 RW |
2879 | (build-system r-build-system) |
2880 | (propagated-inputs | |
2881 | `(("r-mass" ,r-mass) | |
2882 | ("r-matrix" ,r-matrix) | |
2883 | ("r-numderiv" ,r-numderiv) | |
2884 | ("r-ucminf" ,r-ucminf))) | |
2885 | (home-page "https://github.com/runehaubo/ordinal") | |
2886 | (synopsis "Regression models for ordinal data") | |
2887 | (description | |
2888 | "This package provides an implementation of cumulative link (mixed) | |
2889 | models also known as ordered regression models, proportional odds models, | |
2890 | proportional hazards models for grouped survival times and ordered models. | |
2891 | Estimation is via maximum likelihood and mixed models are fitted with the | |
2892 | Laplace approximation and adaptive Gauss-Hermite quadrature.") | |
2893 | (license license:gpl2+))) | |
2894 | ||
fe1495e3 RW |
2895 | (define-public r-jomo |
2896 | (package | |
2897 | (name "r-jomo") | |
532b3598 | 2898 | (version "2.6-7") |
fe1495e3 RW |
2899 | (source |
2900 | (origin | |
2901 | (method url-fetch) | |
2902 | (uri (cran-uri "jomo" version)) | |
2903 | (sha256 | |
2904 | (base32 | |
532b3598 | 2905 | "0lyvi32aikkvwdj0y2hc13kmmi0cw1icg8z9lcw10l8326sxm0vf")))) |
fe1495e3 RW |
2906 | (build-system r-build-system) |
2907 | (propagated-inputs | |
2908 | `(("r-lme4" ,r-lme4) | |
fccb2450 | 2909 | ("r-mass" ,r-mass) |
e7630cc9 | 2910 | ("r-ordinal" ,r-ordinal) |
fe1495e3 RW |
2911 | ("r-survival" ,r-survival))) |
2912 | (home-page "https://cran.r-project.org/web/packages/jomo/") | |
2913 | (synopsis "Multilevel Joint Modelling Multiple Imputation") | |
2914 | (description | |
2915 | "Similarly to Schafer's package pan, jomo is a package for multilevel | |
2916 | joint modelling multiple imputation @url{Carpenter and Kenward (2013), | |
2917 | http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the | |
2918 | possibility of handling binary and categorical data through latent normal | |
2919 | variables, the option to use cluster-specific covariance matrices and to | |
2920 | impute compatibly with the substantive model.") | |
2921 | (license license:gpl2))) | |
2922 | ||
03e718fb RW |
2923 | (define-public r-pan |
2924 | (package | |
2925 | (name "r-pan") | |
a7265593 | 2926 | (version "1.6") |
03e718fb RW |
2927 | (source |
2928 | (origin | |
2929 | (method url-fetch) | |
2930 | (uri (cran-uri "pan" version)) | |
2931 | (sha256 | |
2932 | (base32 | |
a7265593 | 2933 | "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) |
03e718fb RW |
2934 | (build-system r-build-system) |
2935 | (native-inputs `(("gfortran" ,gfortran))) | |
2936 | (home-page "https://cran.r-project.org/web/packages/pan/") | |
2937 | (synopsis "Multiple imputation for multivariate panel or clustered data") | |
2938 | (description | |
2939 | "This package implements multiple imputation for multivariate panel or | |
2940 | clustered data.") | |
2941 | (license license:gpl3))) | |
2942 | ||
84e7147a RW |
2943 | (define-public r-mitml |
2944 | (package | |
2945 | (name "r-mitml") | |
1c6d199e | 2946 | (version "0.3-7") |
84e7147a RW |
2947 | (source |
2948 | (origin | |
2949 | (method url-fetch) | |
2950 | (uri (cran-uri "mitml" version)) | |
2951 | (sha256 | |
2952 | (base32 | |
1c6d199e | 2953 | "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) |
84e7147a RW |
2954 | (build-system r-build-system) |
2955 | (propagated-inputs | |
2956 | `(("r-haven" ,r-haven) | |
2957 | ("r-jomo" ,r-jomo) | |
2958 | ("r-pan" ,r-pan))) | |
2959 | (home-page "https://cran.r-project.org/web/packages/mitml/") | |
2960 | (synopsis "Tools for multiple imputation in multilevel modeling") | |
2961 | (description | |
2962 | "This package provides tools for multiple imputation of missing data in | |
2963 | multilevel modeling. It includes a user-friendly interface to the packages | |
2964 | pan and jomo, and several functions for visualization, data management and the | |
2965 | analysis of multiply imputed data sets.") | |
2966 | (license license:gpl2+))) | |
2967 | ||
10e16fa9 RW |
2968 | (define-public r-mice |
2969 | (package | |
2970 | (name "r-mice") | |
d2cd541c | 2971 | (version "3.4.0") |
10e16fa9 RW |
2972 | (source |
2973 | (origin | |
2974 | (method url-fetch) | |
2975 | (uri (cran-uri "mice" version)) | |
2976 | (sha256 | |
2977 | (base32 | |
d2cd541c | 2978 | "0rdamj1j9z3kxmi27pc79v6mhh8rgxaxz4xz70ybf8kqh2x66cgm")))) |
10e16fa9 RW |
2979 | (build-system r-build-system) |
2980 | (propagated-inputs | |
aea3be25 RW |
2981 | `(("r-broom" ,r-broom) |
2982 | ("r-dplyr" ,r-dplyr) | |
2983 | ("r-lattice" ,r-lattice) | |
10e16fa9 | 2984 | ("r-mass" ,r-mass) |
aea3be25 | 2985 | ("r-mitml" ,r-mitml) |
10e16fa9 RW |
2986 | ("r-nnet" ,r-nnet) |
2987 | ("r-rcpp" ,r-rcpp) | |
aea3be25 | 2988 | ("r-rlang" ,r-rlang) |
10e16fa9 RW |
2989 | ("r-rpart" ,r-rpart) |
2990 | ("r-survival" ,r-survival))) | |
2991 | (home-page "https://cran.r-project.org/web/packages/mice/") | |
2992 | (synopsis "Multivariate imputation by chained equations") | |
2993 | (description | |
2994 | "Multiple imputation using @dfn{Fully Conditional Specification} (FCS) | |
2995 | implemented by the MICE algorithm as described in @url{Van Buuren and | |
2996 | Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each | |
2997 | variable has its own imputation model. Built-in imputation models are | |
2998 | provided for continuous data (predictive mean matching, normal), binary | |
2999 | data (logistic regression), unordered categorical data (polytomous logistic | |
3000 | regression) and ordered categorical data (proportional odds). MICE can also | |
3001 | impute continuous two-level data (normal model, pan, second-level variables). | |
3002 | Passive imputation can be used to maintain consistency between variables. | |
3003 | Various diagnostic plots are available to inspect the quality of the | |
3004 | imputations.") | |
3005 | ;; Any of these two versions. | |
3006 | (license (list license:gpl2 license:gpl3)))) | |
7fd5f60b | 3007 | |
02cdb45f RW |
3008 | (define-public r-truncnorm |
3009 | (package | |
3010 | (name "r-truncnorm") | |
9d6f3925 | 3011 | (version "1.0-8") |
02cdb45f RW |
3012 | (source |
3013 | (origin | |
3014 | (method url-fetch) | |
3015 | (uri (cran-uri "truncnorm" version)) | |
3016 | (sha256 | |
3017 | (base32 | |
9d6f3925 | 3018 | "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9")))) |
02cdb45f | 3019 | (build-system r-build-system) |
e9960d8c | 3020 | (home-page "https://cran.r-project.org/web/packages/truncnorm/") |
02cdb45f RW |
3021 | (synopsis "Truncated normal distribution") |
3022 | (description "This package provides functions for the truncated normal | |
3023 | distribution with mean equal to @code{mean} and standard deviation equal to | |
3024 | @code{sd}. It includes density, distribution, quantile, and expected value | |
3025 | functions, as well as a random generation function.") | |
3026 | (license license:gpl2))) | |
3027 | ||
cb8b4c11 RW |
3028 | (define-public r-rsolnp |
3029 | (package | |
3030 | (name "r-rsolnp") | |
3031 | (version "1.16") | |
3032 | (source | |
3033 | (origin | |
3034 | (method url-fetch) | |
3035 | (uri (cran-uri "Rsolnp" version)) | |
3036 | (sha256 | |
3037 | (base32 | |
3038 | "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii")))) | |
3039 | (properties `((upstream-name . "Rsolnp"))) | |
3040 | (build-system r-build-system) | |
3041 | (propagated-inputs | |
3042 | `(("r-truncnorm" ,r-truncnorm))) | |
e9960d8c | 3043 | (home-page "https://cran.r-project.org/web/packages/Rsolnp/") |
cb8b4c11 RW |
3044 | (synopsis "General non-linear optimization") |
3045 | (description "The Rsolnp package implements a general non-linear augmented | |
3046 | Lagrange multiplier method solver, a @dfn{sequential quadratic | |
3047 | programming} (SQP) based solver).") | |
3048 | ;; Any version of the GPL. | |
3049 | (license license:gpl2+))) | |
3050 | ||
7fd5f60b RW |
3051 | (define-public r-hardyweinberg |
3052 | (package | |
3053 | (name "r-hardyweinberg") | |
da5cca36 | 3054 | (version "1.6.1") |
7fd5f60b RW |
3055 | (source |
3056 | (origin | |
3057 | (method url-fetch) | |
3058 | (uri (cran-uri "HardyWeinberg" version)) | |
3059 | (sha256 | |
3060 | (base32 | |
da5cca36 | 3061 | "16n8qanxx0p5ny5zqxafn8hwb1xv94y1wig1iql8as5a5qh8lwcz")))) |
7fd5f60b RW |
3062 | (properties `((upstream-name . "HardyWeinberg"))) |
3063 | (build-system r-build-system) | |
3064 | (propagated-inputs | |
3065 | `(("r-mice" ,r-mice) | |
d0394944 RW |
3066 | ("r-rcpp" ,r-rcpp) |
3067 | ("r-rsolnp" ,r-rsolnp))) | |
7fd5f60b RW |
3068 | (home-page "https://cran.r-project.org/package=HardyWeinberg") |
3069 | (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") | |
3070 | (description | |
3071 | "This package contains tools for exploring Hardy-Weinberg equilibrium for | |
3072 | diallelic genetic marker data. All classical tests (chi-square, exact, | |
3073 | likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are | |
3074 | included in the package, as well as functions for power computation and for | |
3075 | the simulation of marker data under equilibrium and disequilibrium. Routines | |
3076 | for dealing with markers on the X-chromosome are included. Functions for | |
3077 | testing equilibrium in the presence of missing data by using multiple | |
3078 | imputation are also provided. Implements several graphics for exploring the | |
3079 | equilibrium status of a large set of diallelic markers: ternary plots with | |
3080 | acceptance regions, log-ratio plots and Q-Q plots.") | |
3081 | (license license:gpl2+))) | |
3a22732c RW |
3082 | |
3083 | (define-public r-sm | |
3084 | (package | |
3085 | (name "r-sm") | |
5621b840 | 3086 | (version "2.2-5.6") |
3a22732c RW |
3087 | (source |
3088 | (origin | |
3089 | (method url-fetch) | |
3090 | (uri (cran-uri "sm" version)) | |
3091 | (sha256 | |
3092 | (base32 | |
5621b840 | 3093 | "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q")))) |
3a22732c RW |
3094 | (build-system r-build-system) |
3095 | (native-inputs `(("gfortran" ,gfortran))) | |
3096 | (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") | |
3097 | (synopsis "Smoothing methods for nonparametric regression and density estimation") | |
3098 | (description | |
3099 | "This is software accompanying the book 'Applied Smoothing Techniques for | |
3100 | Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford | |
3101 | University Press. It provides smoothing methods for nonparametric regression | |
3102 | and density estimation") | |
3103 | (license license:gpl2+))) | |
9232cac4 | 3104 | |
6174db2b RJ |
3105 | (define-public r-venndiagram |
3106 | (package | |
3107 | (name "r-venndiagram") | |
3108 | (version "1.6.20") | |
3109 | (source (origin | |
3110 | (method url-fetch) | |
3111 | (uri (cran-uri "VennDiagram" version)) | |
3112 | (sha256 | |
3113 | (base32 | |
3114 | "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775")))) | |
3115 | (properties `((upstream-name . "VennDiagram"))) | |
3116 | (build-system r-build-system) | |
3117 | (propagated-inputs | |
3118 | `(("r-futile-logger" ,r-futile-logger))) | |
3119 | (home-page "https://cran.r-project.org/web/packages/VennDiagram/") | |
3120 | (synopsis "Generate High-Resolution Venn and Euler Plots") | |
3121 | (description | |
3122 | "This package provides a set of functions to generate high-resolution | |
3123 | Venn and Euler plots. It includes handling for several special cases, | |
3124 | including two-case scaling, and extensive customization of plot shape and | |
3125 | structure.") | |
3126 | (license license:gpl2+))) | |
3127 | ||
9232cac4 RW |
3128 | (define-public r-vioplot |
3129 | (package | |
3130 | (name "r-vioplot") | |
7d4b9818 | 3131 | (version "0.3.0") |
9232cac4 RW |
3132 | (source |
3133 | (origin | |
3134 | (method url-fetch) | |
3135 | (uri (cran-uri "vioplot" version)) | |
3136 | (sha256 | |
3137 | (base32 | |
7d4b9818 | 3138 | "1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn")))) |
9232cac4 | 3139 | (build-system r-build-system) |
7d4b9818 RW |
3140 | (propagated-inputs |
3141 | `(("r-sm" ,r-sm) | |
3142 | ("r-zoo" ,r-zoo))) | |
9232cac4 RW |
3143 | (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") |
3144 | (synopsis "Violin plot") | |
3145 | (description | |
3146 | "This package provides a violin plot, which is a combination of a box | |
3147 | plot and a kernel density plot.") | |
3148 | (license license:bsd-3))) | |
7b0569c0 RW |
3149 | |
3150 | (define-public r-rsofia | |
3151 | (package | |
3152 | (name "r-rsofia") | |
3153 | (version "1.1") | |
3154 | (source (origin | |
3155 | (method url-fetch) | |
3156 | ;; This package has been removed from CRAN, so we can | |
3157 | ;; only fetch it from the archives. | |
3158 | (uri (string-append "https://cran.r-project.org/src/" | |
3159 | "contrib/Archive/RSofia/RSofia_" | |
3160 | version ".tar.gz")) | |
3161 | (sha256 | |
3162 | (base32 | |
3163 | "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn")))) | |
3164 | (properties `((upstream-name . "RSofia"))) | |
3165 | (build-system r-build-system) | |
3166 | (propagated-inputs | |
3167 | `(("r-rcpp" ,r-rcpp))) | |
3168 | (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") | |
3169 | (synopsis "Port of sofia-ml to R") | |
3170 | (description "This package is a port of sofia-ml to R. Sofia-ml is a | |
3171 | suite of fast incremental algorithms for machine learning that can be used for | |
3172 | training models for classification or ranking.") | |
3173 | (license license:asl2.0))) | |
738dda83 | 3174 | |
3699383e RW |
3175 | (define-public r-xts |
3176 | (package | |
3177 | (name "r-xts") | |
cea8a607 | 3178 | (version "0.11-2") |
3699383e RW |
3179 | (source |
3180 | (origin | |
3181 | (method url-fetch) | |
3182 | (uri (cran-uri "xts" version)) | |
3183 | (sha256 | |
3184 | (base32 | |
cea8a607 | 3185 | "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj")))) |
3699383e RW |
3186 | (build-system r-build-system) |
3187 | (propagated-inputs `(("r-zoo" ,r-zoo))) | |
3699383e RW |
3188 | (home-page "https://github.com/joshuaulrich/xts") |
3189 | (synopsis "Extensible time series") | |
3190 | (description | |
3191 | "This package provides for uniform handling of R's different time-based | |
3192 | data classes by extending @code{zoo}, maximizing native format information | |
3193 | preservation and allowing for user-level customization and extension, while | |
3194 | simplifying cross-class interoperability.") | |
3195 | (license license:gpl2+))) | |
b72b42cf RW |
3196 | |
3197 | (define-public r-performanceanalytics | |
3198 | (package | |
3199 | (name "r-performanceanalytics") | |
081d143d | 3200 | (version "1.5.2") |
b72b42cf RW |
3201 | (source |
3202 | (origin | |
3203 | (method url-fetch) | |
3204 | (uri (cran-uri "PerformanceAnalytics" version)) | |
3205 | (sha256 | |
3206 | (base32 | |
081d143d | 3207 | "01bgm57z079g6r505w3bj293zkbd49fwa8sg55z87vizwavipml6")))) |
b72b42cf RW |
3208 | (properties |
3209 | `((upstream-name . "PerformanceAnalytics"))) | |
3210 | (build-system r-build-system) | |
3211 | (propagated-inputs | |
081d143d RW |
3212 | `(("r-quadprog" ,r-quadprog) |
3213 | ("r-xts" ,r-xts) | |
b72b42cf | 3214 | ("r-zoo" ,r-zoo))) |
d062957a | 3215 | (home-page "https://r-forge.r-project.org/projects/returnanalytics/") |
b72b42cf RW |
3216 | (synopsis "Econometric tools for performance and risk analysis") |
3217 | (description "This is a collection of econometric functions for | |
3218 | performance and risk analysis. This package aims to aid practitioners and | |
3219 | researchers in utilizing the latest research in analysis of non-normal return | |
3220 | streams. In general, it is most tested on return (rather than price) data on | |
3221 | a regular scale, but most functions will work with irregular return data as | |
3222 | well, and increasing numbers of functions will work with P&L or price data | |
3223 | where possible.") | |
3224 | ;; Either version may be picked. | |
3225 | (license (list license:gpl2 license:gpl3)))) | |
018cf270 RW |
3226 | |
3227 | (define-public r-laeken | |
3228 | (package | |
3229 | (name "r-laeken") | |
ed46a05c | 3230 | (version "0.5.0") |
018cf270 RW |
3231 | (source |
3232 | (origin | |
3233 | (method url-fetch) | |
3234 | (uri (cran-uri "laeken" version)) | |
3235 | (sha256 | |
3236 | (base32 | |
ed46a05c | 3237 | "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa")))) |
018cf270 RW |
3238 | (build-system r-build-system) |
3239 | (propagated-inputs | |
3240 | `(("r-boot" ,r-boot) | |
3241 | ("r-mass" ,r-mass))) | |
e9960d8c | 3242 | (home-page "https://cran.r-project.org/web/packages/laeken/") |
018cf270 RW |
3243 | (synopsis "Estimation of indicators on social exclusion and poverty") |
3244 | (description "This package provides tools for the estimation of indicators | |
3245 | on social exclusion and poverty, as well as an implementation of Pareto tail | |
3246 | modeling for empirical income distributions.") | |
3247 | (license license:gpl2+))) | |
e5c17b8d RW |
3248 | |
3249 | (define-public r-vcd | |
3250 | (package | |
3251 | (name "r-vcd") | |
2960f965 | 3252 | (version "1.4-4") |
e5c17b8d RW |
3253 | (source |
3254 | (origin | |
3255 | (method url-fetch) | |
3256 | (uri (cran-uri "vcd" version)) | |
3257 | (sha256 | |
3258 | (base32 | |
2960f965 | 3259 | "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5")))) |
e5c17b8d RW |
3260 | (build-system r-build-system) |
3261 | (propagated-inputs | |
3262 | `(("r-colorspace" ,r-colorspace) | |
3263 | ("r-lmtest" ,r-lmtest) | |
3264 | ("r-mass" ,r-mass))) | |
e9960d8c | 3265 | (home-page "https://cran.r-project.org/web/packages/vcd/") |
e5c17b8d RW |
3266 | (synopsis "Visualizing categorical data") |
3267 | (description "This package provides visualization techniques, data sets, | |
3268 | summary and inference procedures aimed particularly at categorical data. | |
3269 | Special emphasis is given to highly extensible grid graphics. The package was | |
3270 | originally inspired by the book \"Visualizing Categorical Data\" by Michael | |
3271 | Friendly and is now the main support package for a new book, \"Discrete Data | |
3272 | Analysis with R\" by Michael Friendly and David Meyer (2015).") | |
3273 | (license license:gpl2))) | |
ae164260 RW |
3274 | |
3275 | (define-public r-ica | |
3276 | (package | |
3277 | (name "r-ica") | |
fabf0993 | 3278 | (version "1.0-2") |
ae164260 RW |
3279 | (source |
3280 | (origin | |
3281 | (method url-fetch) | |
3282 | (uri (cran-uri "ica" version)) | |
3283 | (sha256 | |
3284 | (base32 | |
fabf0993 | 3285 | "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7")))) |
ae164260 | 3286 | (build-system r-build-system) |
e9960d8c | 3287 | (home-page "https://cran.r-project.org/web/packages/ica/") |
ae164260 RW |
3288 | (synopsis "Independent component analysis") |
3289 | (description "This package provides tools for @dfn{Independent Component | |
3290 | Analysis} (ICA) using various algorithms: FastICA, | |
3291 | Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization | |
3292 | of Eigenmatrices} (JADE).") | |
3293 | (license license:gpl2+))) | |
bf025ff6 RW |
3294 | |
3295 | (define-public r-dtw | |
3296 | (package | |
3297 | (name "r-dtw") | |
cda93e83 | 3298 | (version "1.20-1") |
bf025ff6 RW |
3299 | (source |
3300 | (origin | |
3301 | (method url-fetch) | |
3302 | (uri (cran-uri "dtw" version)) | |
3303 | (sha256 | |
3304 | (base32 | |
cda93e83 | 3305 | "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3")))) |
bf025ff6 RW |
3306 | (build-system r-build-system) |
3307 | (propagated-inputs `(("r-proxy" ,r-proxy))) | |
3308 | (home-page "http://dtw.r-forge.r-project.org/") | |
3309 | (synopsis "Dynamic Time Warping Algorithms") | |
3310 | (description "This package provides a comprehensive implementation of | |
3311 | @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the | |
3312 | optimal (least cumulative distance) alignment between points of two time | |
3313 | series. Common DTW variants covered include local (slope) and global (window) | |
3314 | constraints, subsequence matches, arbitrary distance definitions, | |
3315 | normalizations, minimum variance matching, and so on.") | |
3316 | (license license:gpl2+))) | |
15ef07f0 RW |
3317 | |
3318 | (define-public r-sdmtools | |
3319 | (package | |
3320 | (name "r-sdmtools") | |
3321 | (version "1.1-221") | |
3322 | (source | |
3323 | (origin | |
3324 | (method url-fetch) | |
3325 | (uri (cran-uri "SDMTools" version)) | |
3326 | (sha256 | |
3327 | (base32 | |
3328 | "1kacrpamshv7wz83yn45sfbw4m9c44xrrngzcklnwx8gcxx2knm6")))) | |
3329 | (properties `((upstream-name . "SDMTools"))) | |
3330 | (build-system r-build-system) | |
3331 | (propagated-inputs `(("r-r-utils" ,r-r-utils))) | |
3332 | (home-page "http://www.rforge.net/SDMTools/") | |
3333 | (synopsis "Species distribution modelling tools") | |
3334 | (description "This packages provides a set of tools for post processing | |
3335 | the outcomes of species distribution modeling exercises. It includes novel | |
3336 | methods for comparing models and tracking changes in distributions through | |
3337 | time. It further includes methods for visualizing outcomes, selecting | |
3338 | thresholds, calculating measures of accuracy and landscape fragmentation | |
3339 | statistics, etc.") | |
3340 | (license license:gpl3+))) | |
ae3f2079 RW |
3341 | |
3342 | (define-public r-scatterplot3d | |
3343 | (package | |
3344 | (name "r-scatterplot3d") | |
5ade82bb | 3345 | (version "0.3-41") |
ae3f2079 RW |
3346 | (source |
3347 | (origin | |
3348 | (method url-fetch) | |
3349 | (uri (cran-uri "scatterplot3d" version)) | |
3350 | (sha256 | |
3351 | (base32 | |
5ade82bb | 3352 | "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc")))) |
ae3f2079 | 3353 | (build-system r-build-system) |
e9960d8c | 3354 | (home-page "https://cran.r-project.org/web/packages/scatterplot3d/") |
ae3f2079 RW |
3355 | (synopsis "3D scatter plot") |
3356 | (description "This package provides an implementation of scatter plots for | |
3357 | plotting. a three dimensional point cloud.") | |
3358 | (license license:gpl2))) | |
f90018e5 RW |
3359 | |
3360 | (define-public r-ggridges | |
3361 | (package | |
3362 | (name "r-ggridges") | |
16a39c2d | 3363 | (version "0.5.1") |
f90018e5 RW |
3364 | (source |
3365 | (origin | |
3366 | (method url-fetch) | |
3367 | (uri (cran-uri "ggridges" version)) | |
3368 | (sha256 | |
3369 | (base32 | |
16a39c2d | 3370 | "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01")))) |
f90018e5 RW |
3371 | (build-system r-build-system) |
3372 | (propagated-inputs | |
3373 | `(("r-ggplot2" ,r-ggplot2) | |
3374 | ("r-plyr" ,r-plyr) | |
0edd2fd1 RW |
3375 | ("r-scales" ,r-scales) |
3376 | ("r-withr" ,r-withr))) | |
f90018e5 RW |
3377 | (home-page "https://github.com/clauswilke/ggridges") |
3378 | (synopsis "Ridgeline plots in ggplot2") | |
3379 | (description | |
3380 | "Ridgeline plots provide a convenient way of visualizing changes in | |
3381 | distributions over time or space. This package enables the creation of such | |
3382 | plots in @code{ggplot2}.") | |
3383 | (license license:gpl2))) | |
007f6d98 RW |
3384 | |
3385 | (define-public r-ggjoy | |
3386 | (package | |
3387 | (name "r-ggjoy") | |
c36745cf | 3388 | (version "0.4.1") |
007f6d98 RW |
3389 | (source |
3390 | (origin | |
3391 | (method url-fetch) | |
3392 | (uri (cran-uri "ggjoy" version)) | |
3393 | (sha256 | |
3394 | (base32 | |
c36745cf | 3395 | "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) |
007f6d98 RW |
3396 | (build-system r-build-system) |
3397 | (propagated-inputs | |
3398 | `(("r-ggplot2" ,r-ggplot2) | |
3399 | ("r-ggridges" ,r-ggridges))) | |
3400 | (home-page "https://github.com/clauswilke/ggjoy") | |
3401 | (synopsis "Joyplots in ggplot2") | |
3402 | (description "Joyplots provide a convenient way of visualizing changes in | |
3403 | distributions over time or space. This package enables the creation of such | |
3404 | plots in @code{ggplot2}.") | |
3405 | (license license:gpl2))) | |
2976f304 RW |
3406 | |
3407 | (define-public r-cli | |
3408 | (package | |
3409 | (name "r-cli") | |
78e29738 | 3410 | (version "1.1.0") |
2976f304 RW |
3411 | (source |
3412 | (origin | |
3413 | (method url-fetch) | |
3414 | (uri (cran-uri "cli" version)) | |
3415 | (sha256 | |
3416 | (base32 | |
78e29738 | 3417 | "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g")))) |
2976f304 RW |
3418 | (build-system r-build-system) |
3419 | (propagated-inputs | |
3420 | `(("r-assertthat" ,r-assertthat) | |
3421 | ("r-crayon" ,r-crayon))) | |
3422 | (home-page "https://github.com/r-lib/cli#readme") | |
3423 | (synopsis "Helpers for developing command line interfaces") | |
3424 | (description "This package provides a suite of tools designed to build | |
3425 | attractive command line interfaces (CLIs). It includes tools for drawing | |
3426 | rules, boxes, trees, and Unicode symbols with ASCII alternatives.") | |
3427 | (license license:expat))) | |
55577393 RW |
3428 | |
3429 | (define-public r-argparser | |
3430 | (package | |
3431 | (name "r-argparser") | |
3432 | (version "0.4") | |
3433 | (source | |
3434 | (origin | |
3435 | (method url-fetch) | |
3436 | (uri (cran-uri "argparser" version)) | |
3437 | (sha256 | |
3438 | (base32 | |
3439 | "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9")))) | |
3440 | (build-system r-build-system) | |
3441 | (home-page "https://bitbucket.org/djhshih/argparser") | |
3442 | (synopsis "Command-line argument parser") | |
3443 | (description | |
3444 | "This package provides a cross-platform command-line argument parser | |
3445 | written purely in R with no external dependencies. It is useful with the | |
3446 | Rscript front-end and facilitates turning an R script into an executable | |
3447 | script.") | |
3448 | (license license:gpl3+))) | |
a3257d42 RW |
3449 | |
3450 | (define-public r-debugme | |
3451 | (package | |
3452 | (name "r-debugme") | |
3453 | (version "1.1.0") | |
3454 | (source | |
3455 | (origin | |
3456 | (method url-fetch) | |
3457 | (uri (cran-uri "debugme" version)) | |
3458 | (sha256 | |
3459 | (base32 | |
3460 | "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) | |
3461 | (build-system r-build-system) | |
3462 | (propagated-inputs `(("r-crayon" ,r-crayon))) | |
3463 | (home-page "https://github.com/r-lib/debugme#readme") | |
3464 | (synopsis "Debug R packages") | |
3465 | (description | |
3466 | "This package allows the user to specify debug messages as special string | |
3467 | constants, and control debugging of packages via environment variables.") | |
3468 | (license license:expat))) | |
2058e37d RW |
3469 | |
3470 | (define-public r-processx | |
3471 | (package | |
3472 | (name "r-processx") | |
76cbfb5a | 3473 | (version "3.3.0") |
2058e37d RW |
3474 | (source |
3475 | (origin | |
3476 | (method url-fetch) | |
3477 | (uri (cran-uri "processx" version)) | |
3478 | (sha256 | |
3479 | (base32 | |
76cbfb5a | 3480 | "0ipdcl4080z92jdnd1w4hm4w484spxcrp6j5x9p76ksb401qdca1")))) |
2058e37d RW |
3481 | (build-system r-build-system) |
3482 | (propagated-inputs | |
0e87bf01 RW |
3483 | `(("r-ps" ,r-ps) |
3484 | ("r-r6" ,r-r6))) | |
2058e37d RW |
3485 | (home-page "https://github.com/r-lib/processx3") |
3486 | (synopsis "Execute and control system processes") | |
3487 | (description | |
3488 | "This package provides portable tools to run system processes in the | |
3489 | background. It can check if a background process is running; wait on a | |
3490 | background process to finish; get the exit status of finished processes; kill | |
3491 | background processes and their children; restart processes. It can read the | |
3492 | standard output and error of the processes, using non-blocking connections. | |
3493 | @code{processx} can poll a process for standard output or error, with a | |
3494 | timeout. It can also poll several processes at once.") | |
3495 | (license license:expat))) | |
f285346a RW |
3496 | |
3497 | (define-public r-tsp | |
3498 | (package | |
3499 | (name "r-tsp") | |
127522c4 | 3500 | (version "1.1-6") |
f285346a RW |
3501 | (source |
3502 | (origin | |
3503 | (method url-fetch) | |
3504 | (uri (cran-uri "TSP" version)) | |
3505 | (sha256 | |
3506 | (base32 | |
127522c4 | 3507 | "1ym97xl2icjpfkrici0wig29w06bb704hp51v7h5liygjlwpkhlc")))) |
f285346a RW |
3508 | (properties `((upstream-name . "TSP"))) |
3509 | (build-system r-build-system) | |
3510 | (propagated-inputs `(("r-foreach" ,r-foreach))) | |
3511 | (home-page "https://cran.r-project.org/web/packages/TSP/") | |
3512 | (synopsis "Traveling salesperson problem (TSP)") | |
3513 | (description "This package provides basic infrastructure and some | |
3514 | algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the | |
3515 | traveling salesman problem).") | |
3516 | (license license:gpl3))) | |
ffb59bce RW |
3517 | |
3518 | (define-public r-qap | |
3519 | (package | |
3520 | (name "r-qap") | |
3521 | (version "0.1-1") | |
3522 | (source | |
3523 | (origin | |
3524 | (method url-fetch) | |
3525 | (uri (cran-uri "qap" version)) | |
3526 | (sha256 | |
3527 | (base32 | |
3528 | "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) | |
3529 | (build-system r-build-system) | |
3530 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 3531 | (home-page "https://cran.r-project.org/web/packages/qap/") |
ffb59bce RW |
3532 | (synopsis "Heuristics for the quadratic assignment problem (QAP)") |
3533 | (description "This package implements heuristics for the @dfn{quadratic | |
3534 | assignment problem} (QAP). Currently only a simulated annealing heuristic is | |
3535 | available.") | |
3536 | (license license:gpl3))) | |
7fe49f2a RW |
3537 | |
3538 | (define-public r-gclus | |
3539 | (package | |
3540 | (name "r-gclus") | |
111516f9 | 3541 | (version "1.3.2") |
7fe49f2a RW |
3542 | (source |
3543 | (origin | |
3544 | (method url-fetch) | |
3545 | (uri (cran-uri "gclus" version)) | |
3546 | (sha256 | |
3547 | (base32 | |
111516f9 | 3548 | "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) |
7fe49f2a RW |
3549 | (build-system r-build-system) |
3550 | (propagated-inputs `(("r-cluster" ,r-cluster))) | |
d062957a | 3551 | (home-page "https://cran.r-project.org/web/packages/gclus/") |
7fe49f2a RW |
3552 | (synopsis "Clustering graphics") |
3553 | (description "This package orders panels in scatterplot matrices and | |
3554 | parallel coordinate displays by some merit index. It contains various indices | |
3555 | of merit, ordering functions, and enhanced versions of @code{pairs} and | |
3556 | @code{parcoord} which color panels according to their merit level.") | |
3557 | (license license:gpl2+))) | |
8e5e26d2 RW |
3558 | |
3559 | (define-public r-webshot | |
3560 | (package | |
3561 | (name "r-webshot") | |
8871a513 | 3562 | (version "0.5.1") |
8e5e26d2 RW |
3563 | (source |
3564 | (origin | |
3565 | (method url-fetch) | |
3566 | (uri (cran-uri "webshot" version)) | |
3567 | (sha256 | |
3568 | (base32 | |
8871a513 | 3569 | "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr")))) |
8e5e26d2 RW |
3570 | (build-system r-build-system) |
3571 | (propagated-inputs | |
8871a513 RW |
3572 | `(("r-callr" ,r-callr) |
3573 | ("r-jsonlite" ,r-jsonlite) | |
3574 | ("r-magrittr" ,r-magrittr))) | |
8e5e26d2 RW |
3575 | (home-page "https://github.com/wch/webshot/") |
3576 | (synopsis "Take screenshots of web pages") | |
3577 | (description | |
3578 | "Webshot makes it easy to take screenshots of web pages from within R. | |
3579 | It can also run Shiny applications locally and take screenshots of the | |
3580 | application; and it can render and screenshot static as well as interactive R | |
3581 | Markdown documents.") | |
3582 | (license license:gpl2))) | |
2e9d187b RW |
3583 | |
3584 | (define-public r-seriation | |
3585 | (package | |
3586 | (name "r-seriation") | |
3587 | (version "1.2-3") | |
3588 | (source | |
3589 | (origin | |
3590 | (method url-fetch) | |
3591 | (uri (cran-uri "seriation" version)) | |
3592 | (sha256 | |
3593 | (base32 | |
3594 | "1q6hw4hjw224b4y0dc0j630v2pgj6sn455nwkilb70w8k31hpk92")))) | |
3595 | (build-system r-build-system) | |
3596 | (propagated-inputs | |
3597 | `(("r-cluster" ,r-cluster) | |
3598 | ("r-colorspace" ,r-colorspace) | |
3599 | ("r-dendextend" ,r-dendextend) | |
3600 | ("r-gclus" ,r-gclus) | |
3601 | ("r-gplots" ,r-gplots) | |
3602 | ("r-mass" ,r-mass) | |
3603 | ("r-qap" ,r-qap) | |
3604 | ("r-registry" ,r-registry) | |
3605 | ("r-tsp" ,r-tsp))) | |
3606 | (native-inputs `(("gfortran" ,gfortran))) | |
3607 | (home-page "http://s2.smu.edu/IDA/seriation/") | |
3608 | (synopsis "Infrastructure for ordering objects using seriation") | |
3609 | (description | |
3610 | "This package provides infrastructure for seriation with an | |
3611 | implementation of several seriation/sequencing techniques to reorder matrices, | |
3612 | dissimilarity matrices, and dendrograms. It also provides (optimally) | |
3613 | reordered heatmaps, color images and clustering visualizations like | |
3614 | dissimilarity plots, and visual assessment of cluster tendency plots (VAT and | |
3615 | iVAT).") | |
3616 | (license license:gpl3))) | |
e9e78d2c | 3617 | |
f6d2b45c RW |
3618 | (define-public r-xfun |
3619 | (package | |
3620 | (name "r-xfun") | |
22777c86 | 3621 | (version "0.5") |
f6d2b45c RW |
3622 | (source |
3623 | (origin | |
3624 | (method url-fetch) | |
3625 | (uri (cran-uri "xfun" version)) | |
3626 | (sha256 | |
3627 | (base32 | |
22777c86 | 3628 | "1wkrapc490r9l9z6mz623zn9ijq64mckc17xg2s7n3s9yaxj98lb")))) |
f6d2b45c RW |
3629 | (build-system r-build-system) |
3630 | (home-page "https://github.com/yihui/xfun") | |
3631 | (synopsis "Miscellaneous functions") | |
3632 | (description | |
3633 | "This package provides miscellaneous functions commonly used in other | |
3634 | packages maintained by Yihui Xie.") | |
3635 | (license license:expat))) | |
f2442968 RW |
3636 | |
3637 | (define-public r-utf8 | |
3638 | (package | |
3639 | (name "r-utf8") | |
65ea783f | 3640 | (version "1.1.4") |
f2442968 RW |
3641 | (source |
3642 | (origin | |
3643 | (method url-fetch) | |
3644 | (uri (cran-uri "utf8" version)) | |
3645 | (sha256 | |
3646 | (base32 | |
65ea783f | 3647 | "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) |
f2442968 RW |
3648 | (build-system r-build-system) |
3649 | (home-page "https://github.com/patperry/r-utf8") | |
3650 | (synopsis "Unicode text processing") | |
3651 | (description | |
3652 | "This package provides tools to process and print UTF-8 encoded | |
3653 | international text (Unicode). Input, validate, normalize, encode, format, and | |
3654 | display.") | |
3655 | (license license:asl2.0))) | |
c555ccab RW |
3656 | |
3657 | (define-public r-pillar | |
3658 | (package | |
3659 | (name "r-pillar") | |
fc00a1f0 | 3660 | (version "1.3.1") |
c555ccab RW |
3661 | (source |
3662 | (origin | |
3663 | (method url-fetch) | |
3664 | (uri (cran-uri "pillar" version)) | |
3665 | (sha256 | |
3666 | (base32 | |
fc00a1f0 | 3667 | "1xnbb9sr5wn9dmp6m7cr4z7i6pmjvyabnfcx6x7i7mvdjmgvaf5k")))) |
c555ccab RW |
3668 | (build-system r-build-system) |
3669 | (propagated-inputs | |
3670 | `(("r-cli" ,r-cli) | |
3671 | ("r-crayon" ,r-crayon) | |
6f5b157e | 3672 | ("r-fansi" ,r-fansi) |
c555ccab RW |
3673 | ("r-rlang" ,r-rlang) |
3674 | ("r-utf8" ,r-utf8))) | |
3675 | (home-page "https://github.com/r-lib/pillar") | |
3676 | (synopsis "Coloured formatting for columns") | |
3677 | (description | |
3678 | "This package provides a @code{pillar} generic designed for formatting | |
3679 | columns of data using the full range of colours provided by modern | |
3680 | terminals.") | |
3681 | (license license:gpl3))) | |
1c791925 RW |
3682 | |
3683 | (define-public r-uuid | |
3684 | (package | |
3685 | (name "r-uuid") | |
3686 | (version "0.1-2") | |
3687 | (source | |
3688 | (origin | |
3689 | (method url-fetch) | |
3690 | (uri (cran-uri "uuid" version)) | |
3691 | (sha256 | |
3692 | (base32 | |
3693 | "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx")))) | |
3694 | (build-system r-build-system) | |
3695 | (home-page "http://www.rforge.net/uuid") | |
3696 | (synopsis "Tools for generating and handling of UUIDs") | |
3697 | (description | |
3698 | "This package provides tools for generating and handling of | |
3699 | @dfn{Universally Unique Identifiers} (UUIDs).") | |
3700 | (license license:expat))) | |
846f4c23 RW |
3701 | |
3702 | (define-public r-tinytex | |
3703 | (package | |
3704 | (name "r-tinytex") | |
35fe7882 | 3705 | (version "0.11") |
846f4c23 RW |
3706 | (source |
3707 | (origin | |
3708 | (method url-fetch) | |
3709 | (uri (cran-uri "tinytex" version)) | |
3710 | (sha256 | |
3711 | (base32 | |
35fe7882 | 3712 | "017g0niwmx8qafsn9b01gp60j5fgwxch0dnkmjgpxxr1k4h1r64x")))) |
846f4c23 | 3713 | (build-system r-build-system) |
8b0701d9 TGR |
3714 | (propagated-inputs |
3715 | `(("r-xfun" ,r-xfun))) | |
846f4c23 RW |
3716 | (home-page "https://github.com/yihui/tinytex") |
3717 | (synopsis "Helper functions for TeX Live and compiling LaTeX documents") | |
3718 | (description | |
3719 | "This package provides helper functions to install and maintain the LaTeX | |
3720 | distribution named TinyTeX, a lightweight, cross-platform, portable, and | |
3721 | easy-to-maintain version of TeX Live. This package also contains helper | |
3722 | functions to compile LaTeX documents, and install missing LaTeX packages | |
3723 | automatically.") | |
3724 | (license license:expat))) | |
4376166b RW |
3725 | |
3726 | (define-public r-metap | |
3727 | (package | |
3728 | (name "r-metap") | |
87bb1b8c | 3729 | (version "1.1") |
4376166b RW |
3730 | (source |
3731 | (origin | |
3732 | (method url-fetch) | |
3733 | (uri (cran-uri "metap" version)) | |
3734 | (sha256 | |
3735 | (base32 | |
87bb1b8c | 3736 | "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0")))) |
4376166b RW |
3737 | (build-system r-build-system) |
3738 | (propagated-inputs | |
e32368c1 RW |
3739 | `(("r-lattice" ,r-lattice) |
3740 | ("r-rdpack" ,r-rdpack))) | |
4376166b RW |
3741 | (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") |
3742 | (synopsis "Meta-analysis of significance values") | |
3743 | (description | |
3744 | "The canonical way to perform meta-analysis involves using effect sizes. | |
3745 | When they are not available this package provides a number of methods for | |
3746 | meta-analysis of significance values including the methods of Edgington, | |
3747 | Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate | |
3748 | published results; and a routine for graphical display.") | |
3749 | (license license:gpl2))) | |
5f4565b1 RW |
3750 | |
3751 | (define-public r-network | |
3752 | (package | |
3753 | (name "r-network") | |
75cbc800 | 3754 | (version "1.14-377") |
5f4565b1 RW |
3755 | (source |
3756 | (origin | |
3757 | (method url-fetch) | |
3758 | (uri (cran-uri "network" version)) | |
3759 | (sha256 | |
3760 | (base32 | |
75cbc800 | 3761 | "0iiy5n17kysrdfs20zr7qald4lwkvws0axi1qkr8f7vzv7w04g01")))) |
5f4565b1 | 3762 | (build-system r-build-system) |
75cbc800 RW |
3763 | (propagated-inputs |
3764 | `(("r-magrittr" ,r-magrittr) | |
3765 | ("r-tibble" ,r-tibble))) | |
40862677 | 3766 | (home-page "https://statnet.org/") |
5f4565b1 RW |
3767 | (synopsis "Classes for relational data") |
3768 | (description | |
3769 | "This package provides tools to create and modify network objects. The | |
3770 | @code{network} class can represent a range of relational data types, and | |
3771 | supports arbitrary vertex/edge/graph attributes.") | |
3772 | (license license:gpl2+))) | |
07a2f34d RW |
3773 | |
3774 | (define-public r-statnet-common | |
3775 | (package | |
3776 | (name "r-statnet-common") | |
9d831327 | 3777 | (version "4.2.0") |
07a2f34d RW |
3778 | (source |
3779 | (origin | |
3780 | (method url-fetch) | |
3781 | (uri (cran-uri "statnet.common" version)) | |
3782 | (sha256 | |
3783 | (base32 | |
9d831327 | 3784 | "0q942g6kqmqxfss1cxb3yg8y5r1k1h5cyy99s1cfisrn6hqc6xhi")))) |
07a2f34d RW |
3785 | (properties |
3786 | `((upstream-name . "statnet.common"))) | |
3787 | (build-system r-build-system) | |
1268a995 RW |
3788 | (propagated-inputs |
3789 | `(("r-coda" ,r-coda))) | |
40862677 | 3790 | (home-page "https://statnet.org") |
07a2f34d RW |
3791 | (synopsis "R scripts and utilities used by the Statnet software") |
3792 | (description "This package provides non-statistical utilities used by the | |
3793 | software developed by the Statnet Project.") | |
3794 | (license license:gpl3))) | |
1088744d RW |
3795 | |
3796 | (define-public r-sna | |
3797 | (package | |
3798 | (name "r-sna") | |
3799 | (version "2.4") | |
3800 | (source | |
3801 | (origin | |
3802 | (method url-fetch) | |
3803 | (uri (cran-uri "sna" version)) | |
3804 | (sha256 | |
3805 | (base32 | |
3806 | "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2")))) | |
3807 | (build-system r-build-system) | |
3808 | (propagated-inputs | |
3809 | `(("r-network" ,r-network) | |
3810 | ("r-statnet-common" ,r-statnet-common))) | |
40862677 | 3811 | (home-page "https://statnet.org") |
1088744d RW |
3812 | (synopsis "Tools for social network analysis") |
3813 | (description | |
3814 | "This package provides a range of tools for social network analysis, | |
3815 | including node and graph-level indices, structural distance and covariance | |
3816 | methods, structural equivalence detection, network regression, random graph | |
3817 | generation, and 2D/3D network visualization.") | |
3818 | (license license:gpl2+))) | |
93c21ddc RW |
3819 | |
3820 | (define-public r-ttr | |
3821 | (package | |
3822 | (name "r-ttr") | |
534bf85b | 3823 | (version "0.23-4") |
93c21ddc RW |
3824 | (source |
3825 | (origin | |
3826 | (method url-fetch) | |
3827 | (uri (cran-uri "TTR" version)) | |
3828 | (sha256 | |
3829 | (base32 | |
534bf85b | 3830 | "18mzyv6cmxmqyqsfwlx2b2k055887mfgc2jgj8xkn8c6m56n05zb")))) |
93c21ddc RW |
3831 | (properties `((upstream-name . "TTR"))) |
3832 | (build-system r-build-system) | |
3833 | (propagated-inputs | |
3834 | `(("r-curl" ,r-curl) | |
3835 | ("r-xts" ,r-xts) | |
3836 | ("r-zoo" ,r-zoo))) | |
3837 | (native-inputs `(("gfortran" ,gfortran))) | |
3838 | (home-page "https://github.com/joshuaulrich/TTR") | |
3839 | (synopsis "Technical trading rules") | |
3840 | (description | |
3841 | "This package provides functions and data to construct technical trading | |
3842 | rules with R.") | |
3843 | (license license:gpl2))) | |
0b64332c RW |
3844 | |
3845 | (define-public r-leaps | |
3846 | (package | |
3847 | (name "r-leaps") | |
3848 | (version "3.0") | |
3849 | (source | |
3850 | (origin | |
3851 | (method url-fetch) | |
3852 | (uri (cran-uri "leaps" version)) | |
3853 | (sha256 | |
3854 | (base32 | |
3855 | "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m")))) | |
3856 | (build-system r-build-system) | |
3857 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 3858 | (home-page "https://cran.r-project.org/web/packages/leaps/") |
0b64332c RW |
3859 | (synopsis "Regression subset selection") |
3860 | (description | |
3861 | "This package provides tools for regression subset selection, including | |
3862 | exhaustive search.") | |
3863 | (license license:gpl2+))) | |
d3cb62e5 RW |
3864 | |
3865 | (define-public r-splus2r | |
3866 | (package | |
3867 | (name "r-splus2r") | |
3868 | (version "1.2-2") | |
3869 | (source | |
3870 | (origin | |
3871 | (method url-fetch) | |
3872 | (uri (cran-uri "splus2R" version)) | |
3873 | (sha256 | |
3874 | (base32 | |
3875 | "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz")))) | |
3876 | (properties `((upstream-name . "splus2R"))) | |
3877 | (build-system r-build-system) | |
3878 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 3879 | (home-page "https://cran.r-project.org/web/packages/splus2R/") |
d3cb62e5 RW |
3880 | (synopsis "Supplemental S-PLUS functionality in R") |
3881 | (description | |
3882 | "Currently there are many functions in S-PLUS that are missing in R. To | |
3883 | facilitate the conversion of S-PLUS packages to R packages, this package | |
3884 | provides some missing S-PLUS functionality in R.") | |
3885 | (license license:gpl2))) | |
034ac9d6 RW |
3886 | |
3887 | (define-public r-ifultools | |
3888 | (package | |
3889 | (name "r-ifultools") | |
d8787b33 | 3890 | (version "2.0-5") |
034ac9d6 RW |
3891 | (source |
3892 | (origin | |
3893 | (method url-fetch) | |
3894 | (uri (cran-uri "ifultools" version)) | |
3895 | (sha256 | |
3896 | (base32 | |
d8787b33 | 3897 | "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j")))) |
034ac9d6 RW |
3898 | (build-system r-build-system) |
3899 | (propagated-inputs | |
3900 | `(("r-mass" ,r-mass) | |
3901 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 3902 | (home-page "https://cran.r-project.org/web/packages/ifultools/") |
034ac9d6 RW |
3903 | (synopsis "Insightful research tools") |
3904 | (description "This package provides C code used by the wmtsa, fractal, and | |
3905 | sapa R packages.") | |
3906 | (license license:gpl2))) | |
0be7effe RW |
3907 | |
3908 | (define-public r-sapa | |
3909 | (package | |
3910 | (name "r-sapa") | |
3911 | (version "2.0-2") | |
3912 | (source | |
3913 | (origin | |
3914 | (method url-fetch) | |
3915 | (uri (cran-uri "sapa" version)) | |
3916 | (sha256 | |
3917 | (base32 | |
3918 | "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds")))) | |
3919 | (build-system r-build-system) | |
3920 | (propagated-inputs | |
3921 | `(("r-ifultools" ,r-ifultools) | |
3922 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 3923 | (home-page "https://cran.r-project.org/web/packages/sapa/") |
0be7effe RW |
3924 | (synopsis "Spectral analysis for physical applications") |
3925 | (description "This package provides software for the book Spectral | |
3926 | Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, | |
3927 | Cambridge University Press, 1993.") | |
3928 | (license license:gpl2))) | |
dceb1592 | 3929 | |
3a4c6288 RW |
3930 | (define-public r-aggregation |
3931 | (package | |
3932 | (name "r-aggregation") | |
3933 | (version "1.0.1") | |
3934 | (source | |
3935 | (origin | |
3936 | (method url-fetch) | |
3937 | (uri (cran-uri "aggregation" version)) | |
3938 | (sha256 | |
3939 | (base32 | |
3940 | "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46")))) | |
3941 | (build-system r-build-system) | |
3942 | (home-page "https://cran.r-project.org/web/packages/aggregation/") | |
3943 | (synopsis "Methods for p-value aggregation") | |
3944 | (description | |
3945 | "This package contains functionality for performing the following methods | |
3946 | of p-value aggregation: Fisher's method, the Lancaster method (weighted | |
3947 | Fisher's method), and Sidak correction.") | |
3948 | (license license:gpl3))) | |
3949 | ||
dceb1592 RW |
3950 | (define-public r-quantmod |
3951 | (package | |
3952 | (name "r-quantmod") | |
42e7552d | 3953 | (version "0.4-14") |
dceb1592 RW |
3954 | (source |
3955 | (origin | |
3956 | (method url-fetch) | |
3957 | (uri (cran-uri "quantmod" version)) | |
3958 | (sha256 | |
3959 | (base32 | |
42e7552d | 3960 | "1csljagnpkr1mmc18h70b64zbyj07kx972nip9dng39jfg7ilnyr")))) |
dceb1592 RW |
3961 | (build-system r-build-system) |
3962 | (propagated-inputs | |
3963 | `(("r-curl" ,r-curl) | |
3964 | ("r-ttr" ,r-ttr) | |
3965 | ("r-xts" ,r-xts) | |
3966 | ("r-zoo" ,r-zoo))) | |
d062957a | 3967 | (home-page "https://cran.r-project.org/web/packages/quantmod/") |
dceb1592 RW |
3968 | (synopsis "Quantitative financial modelling framework") |
3969 | (description "This package provides a quantitative financial modelling | |
3970 | framework to allow users to specify, build, trade, and analyse quantitative | |
3971 | financial trading strategies.") | |
3972 | (license license:gpl3))) | |
b6dc3255 RW |
3973 | |
3974 | (define-public r-tseries | |
3975 | (package | |
3976 | (name "r-tseries") | |
7abb15f2 | 3977 | (version "0.10-46") |
b6dc3255 RW |
3978 | (source |
3979 | (origin | |
3980 | (method url-fetch) | |
3981 | (uri (cran-uri "tseries" version)) | |
3982 | (sha256 | |
3983 | (base32 | |
7abb15f2 | 3984 | "08kjw0bfj5gfcrxpblwqxwna8a5g9gnr7ya61qb02r263pyhm50j")))) |
b6dc3255 RW |
3985 | (build-system r-build-system) |
3986 | (propagated-inputs | |
3987 | `(("r-quadprog" ,r-quadprog) | |
3988 | ("r-quantmod" ,r-quantmod) | |
3989 | ("r-zoo" ,r-zoo))) | |
3990 | (native-inputs | |
3991 | `(("gfortran" ,gfortran))) | |
d062957a | 3992 | (home-page "https://cran.r-project.org/web/packages/tseries/") |
b6dc3255 RW |
3993 | (synopsis "Time series analysis and computational finance") |
3994 | (description | |
3995 | "This package provides functions relating to time series analysis and | |
3996 | computational finance.") | |
3997 | (license license:gpl2))) | |
a2c079a7 RW |
3998 | |
3999 | (define-public r-wmtsa | |
4000 | (package | |
4001 | (name "r-wmtsa") | |
4002 | (version "2.0-3") | |
4003 | (source | |
4004 | (origin | |
4005 | (method url-fetch) | |
4006 | (uri (cran-uri "wmtsa" version)) | |
4007 | (sha256 | |
4008 | (base32 | |
4009 | "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) | |
4010 | (build-system r-build-system) | |
4011 | (propagated-inputs | |
4012 | `(("r-ifultools" ,r-ifultools) | |
4013 | ("r-mass" ,r-mass) | |
4014 | ("r-splus2r" ,r-splus2r))) | |
d062957a | 4015 | (home-page "https://cran.r-project.org/web/packages/wmtsa/") |
a2c079a7 RW |
4016 | (synopsis "Wavelet methods for time series analysis") |
4017 | (description | |
4018 | "This package provides software to accompany the book \"Wavelet Methods | |
4019 | for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge | |
4020 | University Press, 2000.") | |
4021 | (license license:gpl2))) | |
4993a02a RW |
4022 | |
4023 | (define-public r-tsa | |
4024 | (package | |
4025 | (name "r-tsa") | |
1fe9919a | 4026 | (version "1.2") |
4993a02a RW |
4027 | (source |
4028 | (origin | |
4029 | (method url-fetch) | |
4030 | (uri (cran-uri "TSA" version)) | |
4031 | (sha256 | |
4032 | (base32 | |
1fe9919a | 4033 | "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q")))) |
4993a02a RW |
4034 | (properties `((upstream-name . "TSA"))) |
4035 | (build-system r-build-system) | |
4036 | (propagated-inputs | |
4037 | `(("r-leaps" ,r-leaps) | |
4038 | ("r-locfit" ,r-locfit) | |
1fe9919a | 4039 | ("r-mgcv" ,r-mgcv))) |
4993a02a RW |
4040 | (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm") |
4041 | (synopsis "Time series analysis") | |
4042 | (description | |
4043 | "This package contains R functions and datasets detailed in the book | |
4044 | \"Time Series Analysis with Applications in R (second edition)\" by Jonathan | |
4045 | Cryer and Kung-Sik Chan.") | |
4046 | (license license:gpl2+))) | |
19da7fe3 RW |
4047 | |
4048 | (define-public r-extradistr | |
4049 | (package | |
4050 | (name "r-extradistr") | |
905734fd | 4051 | (version "1.8.10") |
19da7fe3 RW |
4052 | (source |
4053 | (origin | |
4054 | (method url-fetch) | |
4055 | (uri (cran-uri "extraDistr" version)) | |
4056 | (sha256 | |
4057 | (base32 | |
905734fd | 4058 | "00lvqp5bb3iak5myiz4rqm887bkq9sdh7aybmz84mmfni6q01m28")))) |
19da7fe3 RW |
4059 | (properties `((upstream-name . "extraDistr"))) |
4060 | (build-system r-build-system) | |
4061 | (propagated-inputs | |
4062 | `(("r-rcpp" ,r-rcpp))) | |
4063 | (home-page "https://github.com/twolodzko/extraDistr") | |
4064 | (synopsis "Additional univariate and multivariate distributions") | |
4065 | (description | |
4066 | "This package implements density, distribution functions, quantile | |
4067 | functions and random generation functions for a large number of univariate and | |
4068 | multivariate distributions.") | |
4069 | (license license:gpl2))) | |
5b25bc55 RW |
4070 | |
4071 | (define-public r-fractal | |
4072 | (package | |
4073 | (name "r-fractal") | |
4074 | (version "2.0-4") | |
4075 | (source | |
4076 | (origin | |
4077 | (method url-fetch) | |
4078 | (uri (cran-uri "fractal" version)) | |
4079 | (sha256 | |
4080 | (base32 | |
4081 | "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) | |
4082 | (build-system r-build-system) | |
4083 | (propagated-inputs | |
4084 | `(("r-ifultools" ,r-ifultools) | |
4085 | ("r-mass" ,r-mass) | |
4086 | ("r-sapa" ,r-sapa) | |
4087 | ("r-scatterplot3d" ,r-scatterplot3d) | |
4088 | ("r-splus2r" ,r-splus2r) | |
4089 | ("r-wmtsa" ,r-wmtsa))) | |
d062957a | 4090 | (home-page "https://cran.r-project.org/web/packages/fractal/") |
5b25bc55 RW |
4091 | (synopsis "Fractal time series modeling and analysis") |
4092 | (description | |
4093 | "This package provides tools for stochastic fractal and deterministic | |
4094 | chaotic time series analysis.") | |
4095 | (license license:gpl2))) | |
6615a364 RW |
4096 | |
4097 | (define-public r-urca | |
4098 | (package | |
4099 | (name "r-urca") | |
4100 | (version "1.3-0") | |
4101 | (source | |
4102 | (origin | |
4103 | (method url-fetch) | |
4104 | (uri (cran-uri "urca" version)) | |
4105 | (sha256 | |
4106 | (base32 | |
4107 | "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732")))) | |
4108 | (build-system r-build-system) | |
4109 | (propagated-inputs `(("r-nlme" ,r-nlme))) | |
4110 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4111 | (home-page "https://cran.r-project.org/web/packages/urca/") |
6615a364 RW |
4112 | (synopsis "Unit root and cointegration tests for time series data") |
4113 | (description | |
4114 | "This package provides unit root and cointegration tests encountered in | |
4115 | applied econometric analysis.") | |
4116 | (license license:gpl2+))) | |
d32e5724 RW |
4117 | |
4118 | (define-public r-cubature | |
4119 | (package | |
4120 | (name "r-cubature") | |
5f1f1104 | 4121 | (version "2.0.3") |
d32e5724 RW |
4122 | (source |
4123 | (origin | |
4124 | (method url-fetch) | |
4125 | (uri (cran-uri "cubature" version)) | |
4126 | (sha256 | |
4127 | (base32 | |
5f1f1104 | 4128 | "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr")))) |
d32e5724 RW |
4129 | (build-system r-build-system) |
4130 | (propagated-inputs | |
4131 | `(("r-rcpp" ,r-rcpp))) | |
4132 | (home-page "https://github.com/bnaras/cubature") | |
4133 | (synopsis "Adaptive multivariate integration over hypercubes") | |
4134 | (description | |
4135 | "This package is an R wrapper around the cubature C library for adaptive | |
4136 | multivariate integration over hypercubes. This version provides both | |
4137 | @code{hcubature} and @code{pcubature} routines in addition to a vector | |
4138 | interface.") | |
4139 | ;; The included cubature C library is released under GPLv2+, but the | |
4140 | ;; wrapper declares the license to be GPLv3+. | |
4141 | (license (list license:gpl2+ license:gpl3+)))) | |
7531ee84 RW |
4142 | |
4143 | (define-public r-trend | |
4144 | (package | |
4145 | (name "r-trend") | |
cd4abb6d | 4146 | (version "1.1.1") |
7531ee84 RW |
4147 | (source |
4148 | (origin | |
4149 | (method url-fetch) | |
4150 | (uri (cran-uri "trend" version)) | |
4151 | (sha256 | |
4152 | (base32 | |
cd4abb6d | 4153 | "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q")))) |
7531ee84 RW |
4154 | (build-system r-build-system) |
4155 | (propagated-inputs | |
4156 | `(("r-extradistr" ,r-extradistr))) | |
4157 | (native-inputs | |
4158 | `(("gfortran" ,gfortran))) | |
d062957a | 4159 | (home-page "https://cran.r-project.org/web/packages/trend/") |
7531ee84 RW |
4160 | (synopsis "Non-parametric trend tests and change-point detection") |
4161 | (description | |
4162 | "The analysis of environmental data often requires the detection of | |
4163 | trends and change-points. This package includes tests for trend | |
4164 | detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) | |
4165 | Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) | |
4166 | Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman | |
4167 | correlation trend test), change-point detection (Lanzante's test procedures, | |
4168 | Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal | |
4169 | Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency | |
4170 | Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two | |
4171 | sample Robust Rank-Order Distributional Test.") | |
4172 | (license license:gpl3))) | |
f96eda90 RW |
4173 | |
4174 | (define-public r-expm | |
4175 | (package | |
4176 | (name "r-expm") | |
a11d29b4 | 4177 | (version "0.999-4") |
f96eda90 RW |
4178 | (source |
4179 | (origin | |
4180 | (method url-fetch) | |
4181 | (uri (cran-uri "expm" version)) | |
4182 | (sha256 | |
4183 | (base32 | |
a11d29b4 | 4184 | "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q")))) |
f96eda90 RW |
4185 | (build-system r-build-system) |
4186 | (propagated-inputs `(("r-matrix" ,r-matrix))) | |
4187 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4188 | (home-page "https://r-forge.r-project.org/projects/expm/") |
f96eda90 RW |
4189 | (synopsis "Tools for matrix exponentials and related quantities") |
4190 | (description | |
4191 | "This package provides tools for the computation of the matrix | |
4192 | exponential, logarithm, square root, and related quantities.") | |
4193 | (license license:gpl2+))) | |
68b6a67e RW |
4194 | |
4195 | (define-public r-complexplus | |
4196 | (package | |
4197 | (name "r-complexplus") | |
4198 | (version "2.1") | |
4199 | (source | |
4200 | (origin | |
4201 | (method url-fetch) | |
4202 | (uri (cran-uri "complexplus" version)) | |
4203 | (sha256 | |
4204 | (base32 | |
4205 | "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) | |
4206 | (build-system r-build-system) | |
4207 | (propagated-inputs | |
4208 | `(("r-expm" ,r-expm) | |
4209 | ("r-matrix" ,r-matrix))) | |
d062957a | 4210 | (home-page "https://cran.r-project.org/web/packages/complexplus/") |
68b6a67e RW |
4211 | (synopsis "Functions of complex or real variables") |
4212 | (description | |
4213 | "This package extends several functions to the complex domain, including | |
4214 | the matrix exponential and logarithm, and the determinant.") | |
4215 | (license license:gpl2))) | |
7b81a7ea RW |
4216 | |
4217 | (define-public r-phontools | |
4218 | (package | |
4219 | (name "r-phontools") | |
4220 | (version "0.2-2.1") | |
4221 | (source | |
4222 | (origin | |
4223 | (method url-fetch) | |
4224 | (uri (cran-uri "phonTools" version)) | |
4225 | (sha256 | |
4226 | (base32 | |
4227 | "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7")))) | |
4228 | (properties `((upstream-name . "phonTools"))) | |
4229 | (build-system r-build-system) | |
4230 | (home-page "http://www.santiagobarreda.com/rscripts.html") | |
4231 | (synopsis "Tools for phonetic and acoustic analyses") | |
4232 | (description | |
4233 | "This package contains tools for the organization, display, and analysis | |
4234 | of the sorts of data frequently encountered in phonetics research and | |
4235 | experimentation, including the easy creation of IPA vowel plots, and the | |
4236 | creation and manipulation of WAVE audio files.") | |
4237 | (license license:bsd-2))) | |
d976454c RW |
4238 | |
4239 | (define-public r-np | |
4240 | (package | |
4241 | (name "r-np") | |
02c57c01 | 4242 | (version "0.60-9") |
d976454c RW |
4243 | (source |
4244 | (origin | |
4245 | (method url-fetch) | |
4246 | (uri (cran-uri "np" version)) | |
4247 | (sha256 | |
4248 | (base32 | |
02c57c01 | 4249 | "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy")))) |
d976454c RW |
4250 | (build-system r-build-system) |
4251 | (propagated-inputs | |
4252 | `(("r-boot" ,r-boot) | |
4253 | ("r-cubature" ,r-cubature) | |
65d66b3e | 4254 | ("r-quadprog" ,r-quadprog) |
d976454c RW |
4255 | ("r-quantreg" ,r-quantreg))) |
4256 | (home-page "https://github.com/JeffreyRacine/R-Package-np") | |
4257 | (synopsis "Non-parametric kernel smoothing methods for mixed data types") | |
4258 | (description "This package provides non-parametric (and semi-parametric) | |
4259 | kernel methods that seamlessly handle a mix of continuous, unordered, and | |
4260 | ordered factor data types.") | |
4261 | ;; Any version of the GPL. | |
4262 | (license license:gpl3+))) | |
2a112be0 RW |
4263 | |
4264 | (define-public r-powerplus | |
4265 | (package | |
4266 | (name "r-powerplus") | |
4267 | (version "3.1") | |
4268 | (source | |
4269 | (origin | |
4270 | (method url-fetch) | |
4271 | (uri (cran-uri "powerplus" version)) | |
4272 | (sha256 | |
4273 | (base32 | |
4274 | "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) | |
4275 | (build-system r-build-system) | |
4276 | (propagated-inputs | |
4277 | `(("r-complexplus" ,r-complexplus) | |
4278 | ("r-expm" ,r-expm) | |
4279 | ("r-mass" ,r-mass) | |
4280 | ("r-matrix" ,r-matrix) | |
4281 | ("r-phontools" ,r-phontools))) | |
d062957a | 4282 | (home-page "https://cran.r-project.org/web/packages/powerplus/") |
2a112be0 RW |
4283 | (synopsis "Exponentiation operations") |
4284 | (description | |
4285 | "This package provides tools for the computation of matrix and scalar | |
4286 | exponentiation.") | |
4287 | (license license:gpl2))) | |
021caafa RW |
4288 | |
4289 | (define-public r-heatmaply | |
4290 | (package | |
4291 | (name "r-heatmaply") | |
19950821 | 4292 | (version "0.15.2") |
021caafa RW |
4293 | (source |
4294 | (origin | |
4295 | (method url-fetch) | |
4296 | (uri (cran-uri "heatmaply" version)) | |
4297 | (sha256 | |
4298 | (base32 | |
19950821 | 4299 | "0h8s5djzj4mrmaswlcaap6jbwxrkbzc43bbqik3qf8vrqz335w04")))) |
021caafa RW |
4300 | (build-system r-build-system) |
4301 | (propagated-inputs | |
4302 | `(("r-assertthat" ,r-assertthat) | |
4303 | ("r-colorspace" ,r-colorspace) | |
4304 | ("r-dendextend" ,r-dendextend) | |
4305 | ("r-ggplot2" ,r-ggplot2) | |
4306 | ("r-gplots" ,r-gplots) | |
4307 | ("r-htmlwidgets" ,r-htmlwidgets) | |
d0f34274 | 4308 | ("r-knitr" ,r-knitr) ; needed for vignettes |
021caafa RW |
4309 | ("r-magrittr" ,r-magrittr) |
4310 | ("r-plotly" ,r-plotly) | |
4311 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
4312 | ("r-reshape2" ,r-reshape2) | |
4313 | ("r-scales" ,r-scales) | |
4314 | ("r-seriation" ,r-seriation) | |
4315 | ("r-viridis" ,r-viridis) | |
4316 | ("r-webshot" ,r-webshot))) | |
4317 | (home-page "https://cran.r-project.org/package=heatmaply") | |
4318 | (synopsis "Interactive cluster heat maps using plotly") | |
4319 | (description | |
4320 | "This package enables you to create interactive cluster heatmaps that can | |
4321 | be saved as a stand-alone HTML file, embedded in R Markdown documents or in a | |
4322 | Shiny app, and made available in the RStudio viewer pane. Hover the mouse | |
4323 | pointer over a cell to show details or drag a rectangle to zoom. A heatmap is | |
4324 | a popular graphical method for visualizing high-dimensional data, in which a | |
4325 | table of numbers is encoded as a grid of colored cells. The rows and columns | |
4326 | of the matrix are ordered to highlight patterns and are often accompanied by | |
4327 | dendrograms.") | |
4328 | ;; Either version of the license. | |
4329 | (license (list license:gpl2 license:gpl3)))) | |
b2dc4cb4 | 4330 | |
ff939ef4 RW |
4331 | (define-public r-h5 |
4332 | (package | |
4333 | (name "r-h5") | |
4334 | (version "0.9.9") | |
4335 | (source | |
4336 | (origin | |
4337 | (method url-fetch) | |
4338 | (uri (cran-uri "h5" version)) | |
4339 | (sha256 | |
4340 | (base32 | |
4341 | "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) | |
4342 | (build-system r-build-system) | |
4343 | (inputs | |
4344 | `(("zlib" ,zlib) | |
4345 | ("hdf5" ,hdf5))) | |
4346 | (native-inputs | |
4347 | `(("which" ,which))) | |
4348 | (propagated-inputs | |
4349 | `(("r-rcpp" ,r-rcpp))) | |
4350 | (home-page "https://github.com/mannau/h5") | |
4351 | (synopsis "Interface to the HDF5 Library") | |
4352 | (description | |
4353 | "This package provides an S4 interface to the HDF5 library supporting | |
4354 | fast storage and retrieval of R-objects like vectors, matrices and arrays to | |
4355 | binary files in a language independent format. The HDF5 format can therefore | |
4356 | be used as an alternative to R's save/load mechanism. Since h5 is able to | |
4357 | access only subsets of stored data it can also handle data sets which do not | |
4358 | fit into memory.") | |
4359 | (license license:bsd-2))) | |
4360 | ||
b2dc4cb4 RW |
4361 | (define-public r-cgdsr |
4362 | (package | |
4363 | (name "r-cgdsr") | |
4364 | (version "1.2.10") | |
4365 | (source | |
4366 | (origin | |
4367 | (method url-fetch) | |
4368 | (uri (cran-uri "cgdsr" version)) | |
4369 | (sha256 | |
4370 | (base32 | |
4371 | "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23")))) | |
4372 | (build-system r-build-system) | |
4373 | (propagated-inputs | |
4374 | `(("r-r-methodss3" ,r-r-methodss3) | |
4375 | ("r-r-oo" ,r-r-oo))) | |
4376 | (home-page "https://github.com/cBioPortal/cgdsr") | |
4377 | (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") | |
4378 | (description | |
4379 | "This package provides a basic set of R functions for querying the Cancer | |
4380 | Genomics Data Server (CGDS), hosted by the Computational Biology Center at | |
4381 | Memorial-Sloan-Kettering Cancer Center (MSKCC).") | |
4382 | (license license:lgpl3))) | |
a00968b7 RW |
4383 | |
4384 | (define-public r-import | |
4385 | (package | |
4386 | (name "r-import") | |
4387 | (version "1.1.0") | |
4388 | (source | |
4389 | (origin | |
4390 | (method url-fetch) | |
4391 | (uri (cran-uri "import" version)) | |
4392 | (sha256 | |
4393 | (base32 | |
4394 | "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji")))) | |
4395 | (build-system r-build-system) | |
4396 | (home-page "https://github.com/smbache/import") | |
4397 | (synopsis "Import mechanism for R") | |
4398 | (description | |
4399 | "This is an alternative mechanism for importing objects from packages. | |
4400 | The syntax allows for importing multiple objects from a package with a single | |
4401 | command in an expressive way. The import package bridges some of the gap | |
4402 | between using @code{library} (or @code{require}) and direct (single-object) | |
4403 | imports. Furthermore the imported objects are not placed in the current | |
4404 | environment. It is also possible to import objects from stand-alone @code{.R} | |
4405 | files.") | |
4406 | (license license:expat))) | |
5d9b82ac RW |
4407 | |
4408 | (define-public r-shinyace | |
4409 | (package | |
4410 | (name "r-shinyace") | |
f0fe1a5a | 4411 | (version "0.3.3") |
5d9b82ac RW |
4412 | (source |
4413 | (origin | |
4414 | (method url-fetch) | |
4415 | (uri (cran-uri "shinyAce" version)) | |
4416 | (sha256 | |
4417 | (base32 | |
f0fe1a5a | 4418 | "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j")))) |
5d9b82ac RW |
4419 | (properties `((upstream-name . "shinyAce"))) |
4420 | (build-system r-build-system) | |
4421 | (propagated-inputs | |
e86d3cc5 RW |
4422 | `(("r-shiny" ,r-shiny) |
4423 | ("r-jsonlite" ,r-jsonlite))) | |
5d9b82ac RW |
4424 | (home-page "http://cran.r-project.org/web/packages/shinyAce") |
4425 | (synopsis "Ace editor bindings for Shiny") | |
4426 | (description | |
4427 | "This package provides Ace editor bindings to enable a rich text editing | |
4428 | environment within Shiny.") | |
4429 | (license license:expat))) | |
f64fea1d RW |
4430 | |
4431 | (define-public r-radiant-data | |
4432 | (package | |
4433 | (name "r-radiant-data") | |
cb40b6eb | 4434 | (version "0.9.9") |
f64fea1d RW |
4435 | (source |
4436 | (origin | |
4437 | (method url-fetch) | |
4438 | (uri (cran-uri "radiant.data" version)) | |
4439 | (sha256 | |
4440 | (base32 | |
cb40b6eb | 4441 | "17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn")) |
f64fea1d RW |
4442 | (modules '((guix build utils))) |
4443 | (snippet | |
4444 | '(begin | |
4445 | ;; Delete files that are under CC-NC-SA. | |
4446 | (delete-file-recursively "inst/app/tools/help") | |
4447 | #t)))) | |
4448 | (properties `((upstream-name . "radiant.data"))) | |
4449 | (build-system r-build-system) | |
4450 | (propagated-inputs | |
4451 | `(("r-base64enc" ,r-base64enc) | |
4452 | ("r-broom" ,r-broom) | |
4453 | ("r-car" ,r-car) | |
4454 | ("r-curl" ,r-curl) | |
4455 | ("r-dplyr" ,r-dplyr) | |
4456 | ("r-dt" ,r-dt) | |
36dc3591 | 4457 | ("r-glue" ,r-glue) |
f64fea1d RW |
4458 | ("r-ggplot2" ,r-ggplot2) |
4459 | ("r-gridextra" ,r-gridextra) | |
4460 | ("r-import" ,r-import) | |
4461 | ("r-jsonlite" ,r-jsonlite) | |
4462 | ("r-knitr" ,r-knitr) | |
4463 | ("r-lubridate" ,r-lubridate) | |
4464 | ("r-magrittr" ,r-magrittr) | |
4465 | ("r-markdown" ,r-markdown) | |
36dc3591 | 4466 | ("r-plotly" ,r-plotly) |
f64fea1d RW |
4467 | ("r-psych" ,r-psych) |
4468 | ("r-readr" ,r-readr) | |
36dc3591 RW |
4469 | ("r-readxl" ,r-readxl) |
4470 | ("r-rlang" ,r-rlang) | |
f64fea1d RW |
4471 | ("r-rmarkdown" ,r-rmarkdown) |
4472 | ("r-rstudioapi" ,r-rstudioapi) | |
4473 | ("r-scales" ,r-scales) | |
4474 | ("r-shiny" ,r-shiny) | |
e5f9e9fa | 4475 | ("r-shinyfiles" ,r-shinyfiles) |
f64fea1d | 4476 | ("r-shinyace" ,r-shinyace) |
cb40b6eb | 4477 | ("r-stringi" ,r-stringi) |
f64fea1d | 4478 | ("r-tibble" ,r-tibble) |
36dc3591 RW |
4479 | ("r-tidyr" ,r-tidyr) |
4480 | ("r-writexl" ,r-writexl))) | |
f64fea1d RW |
4481 | (home-page "https://github.com/radiant-rstats/radiant.data") |
4482 | (synopsis "Data menu for Radiant: business analytics using R and Shiny") | |
4483 | (description | |
4484 | "The Radiant Data menu includes interfaces for loading, saving, viewing, | |
4485 | visualizing, summarizing, transforming, and combining data. It also contains | |
4486 | functionality to generate reproducible reports of the analyses conducted in | |
4487 | the application.") | |
4488 | (license license:agpl3))) | |
e2cafc24 RW |
4489 | |
4490 | (define-public r-algdesign | |
4491 | (package | |
4492 | (name "r-algdesign") | |
4493 | (version "1.1-7.3") | |
4494 | (source | |
4495 | (origin | |
4496 | (method url-fetch) | |
4497 | (uri (cran-uri "AlgDesign" version)) | |
4498 | (sha256 | |
4499 | (base32 | |
4500 | "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz")))) | |
4501 | (properties `((upstream-name . "AlgDesign"))) | |
4502 | (build-system r-build-system) | |
4503 | (home-page "https://github.com/jvbraun/AlgDesign") | |
4504 | (synopsis "Algorithmic experimental design") | |
4505 | (description | |
4506 | "This package provides tools to calculate exact and approximate theory | |
4507 | experimental designs for D, A, and I criteria. Very large designs may be | |
4508 | created. Experimental designs may be blocked or blocked designs created from | |
4509 | a candidate list, using several criteria. The blocking can be done when whole | |
4510 | and within plot factors interact.") | |
4511 | (license license:gpl2+))) | |
35b0c051 RW |
4512 | |
4513 | (define-public r-signal | |
4514 | (package | |
4515 | (name "r-signal") | |
4516 | (version "0.7-6") | |
4517 | (source | |
4518 | (origin | |
4519 | (method url-fetch) | |
4520 | (uri (cran-uri "signal" version)) | |
4521 | (sha256 | |
4522 | (base32 | |
4523 | "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b")))) | |
4524 | (build-system r-build-system) | |
4525 | (propagated-inputs `(("r-mass" ,r-mass))) | |
4526 | (native-inputs `(("gfortran" ,gfortran))) | |
d062957a | 4527 | (home-page "https://cran.r-project.org/web/packages/signal/") |
35b0c051 RW |
4528 | (synopsis "Signal processing") |
4529 | (description | |
4530 | "This package provides a set of signal processing functions originally | |
4531 | written for Matlab and GNU Octave. It includes filter generation utilities, | |
4532 | filtering functions, resampling routines, and visualization of filter models. | |
4533 | It also includes interpolation functions.") | |
4534 | (license license:gpl2))) | |
db80dd4a | 4535 | |
3dab50d9 RW |
4536 | (define-public r-gsubfn |
4537 | (package | |
4538 | (name "r-gsubfn") | |
2acc0e5f | 4539 | (version "0.7") |
3dab50d9 RW |
4540 | (source |
4541 | (origin | |
4542 | (method url-fetch) | |
4543 | (uri (cran-uri "gsubfn" version)) | |
4544 | (sha256 | |
4545 | (base32 | |
2acc0e5f | 4546 | "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) |
3dab50d9 RW |
4547 | (build-system r-build-system) |
4548 | (propagated-inputs `(("r-proto" ,r-proto))) | |
4549 | (home-page "http://gsubfn.googlecode.com") | |
4550 | (synopsis "Utilities for strings and function arguments.") | |
4551 | (description | |
4552 | "This package provides @code{gsubfn} which is like @code{gsub} but can | |
4553 | take a replacement function or certain other objects instead of the | |
4554 | replacement string. Matches and back references are input to the replacement | |
4555 | function and replaced by the function output. @code{gsubfn} can be used to | |
4556 | split strings based on content rather than delimiters and for quasi-perl-style | |
4557 | string interpolation. The package also has facilities for translating | |
4558 | formulas to functions and allowing such formulas in function calls instead of | |
4559 | functions.") | |
4560 | (license license:gpl2+))) | |
3a563a41 RW |
4561 | |
4562 | (define-public r-sqldf | |
4563 | (package | |
4564 | (name "r-sqldf") | |
4565 | (version "0.4-11") | |
4566 | (source | |
4567 | (origin | |
4568 | (method url-fetch) | |
4569 | (uri (cran-uri "sqldf" version)) | |
4570 | (sha256 | |
4571 | (base32 | |
4572 | "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff")))) | |
4573 | (build-system r-build-system) | |
4574 | (propagated-inputs | |
4575 | `(("r-chron" ,r-chron) | |
4576 | ("r-dbi" ,r-dbi) | |
4577 | ("r-gsubfn" ,r-gsubfn) | |
4578 | ("r-proto" ,r-proto) | |
4579 | ("r-rsqlite" ,r-rsqlite))) | |
4580 | (home-page "https://github.com/ggrothendieck/sqldf") | |
4581 | (synopsis "Manipulate R data frames using SQL") | |
4582 | (description | |
4583 | "The @code{sqldf} function is typically passed a single argument which is | |
4584 | an SQL select statement where the table names are ordinary R data frame names. | |
4585 | @code{sqldf} transparently sets up a database, imports the data frames into | |
4586 | that database, performs the SQL statement and returns the result using a | |
4587 | heuristic to determine which class to assign to each column of the returned | |
4588 | data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be | |
4589 | used to read filtered files into R even if the original files are larger than | |
4590 | R itself can handle.") | |
4591 | (license license:gpl2))) | |
94e46cab RW |
4592 | |
4593 | (define-public r-abind | |
4594 | (package | |
4595 | (name "r-abind") | |
4596 | (version "1.4-5") | |
4597 | (source | |
4598 | (origin | |
4599 | (method url-fetch) | |
4600 | (uri (cran-uri "abind" version)) | |
4601 | (sha256 | |
4602 | (base32 | |
4603 | "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) | |
4604 | (build-system r-build-system) | |
d062957a | 4605 | (home-page "https://cran.r-project.org/web/packages/abind/") |
94e46cab RW |
4606 | (synopsis "Combine multidimensional arrays") |
4607 | (description | |
4608 | "This package provides tools to combine multidimensional arrays into a | |
4609 | single array. This is a generalization of @code{cbind} and @code{rbind}. It | |
4610 | works with vectors, matrices, and higher-dimensional arrays. It also provides | |
4611 | the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating, | |
4612 | extracting and replacing data in arrays.") | |
4613 | (license license:lgpl2.0+))) | |
fc784b66 RW |
4614 | |
4615 | (define-public r-prroc | |
4616 | (package | |
4617 | (name "r-prroc") | |
0430eb66 | 4618 | (version "1.3.1") |
fc784b66 RW |
4619 | (source |
4620 | (origin | |
4621 | (method url-fetch) | |
4622 | (uri (cran-uri "PRROC" version)) | |
4623 | (sha256 | |
4624 | (base32 | |
0430eb66 | 4625 | "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7")))) |
fc784b66 RW |
4626 | (properties `((upstream-name . "PRROC"))) |
4627 | (build-system r-build-system) | |
d062957a | 4628 | (home-page "https://cran.r-project.org/web/packages/PRROC/") |
fc784b66 RW |
4629 | (synopsis "Precision-Recall and ROC curves for weighted and unweighted data") |
4630 | (description | |
4631 | "This package computes the areas under the @dfn{precision-recall} (PR) | |
4632 | and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In | |
4633 | contrast to other implementations, the interpolation between points of the PR | |
4634 | curve is done by a non-linear piecewise function. In addition to the areas | |
4635 | under the curves, the curves themselves can also be computed and plotted by a | |
4636 | specific S3-method.") | |
4637 | (license license:gpl3))) | |
661bb51e RW |
4638 | |
4639 | (define-public r-vim | |
4640 | (package | |
4641 | (name "r-vim") | |
8b2c80b8 | 4642 | (version "4.8.0") |
661bb51e RW |
4643 | (source |
4644 | (origin | |
4645 | (method url-fetch) | |
4646 | (uri (cran-uri "VIM" version)) | |
4647 | (sha256 | |
4648 | (base32 | |
8b2c80b8 | 4649 | "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw")))) |
661bb51e RW |
4650 | (properties `((upstream-name . "VIM"))) |
4651 | (build-system r-build-system) | |
4652 | (propagated-inputs | |
4653 | `(("r-car" ,r-car) | |
4654 | ("r-colorspace" ,r-colorspace) | |
4655 | ("r-data-table" ,r-data-table) | |
4656 | ("r-e1071" ,r-e1071) | |
4657 | ("r-laeken" ,r-laeken) | |
4658 | ("r-mass" ,r-mass) | |
4659 | ("r-nnet" ,r-nnet) | |
8b2c80b8 | 4660 | ("r-ranger" ,r-ranger) |
661bb51e RW |
4661 | ("r-rcpp" ,r-rcpp) |
4662 | ("r-robustbase" ,r-robustbase) | |
4663 | ("r-sp" ,r-sp) | |
4664 | ("r-vcd" ,r-vcd))) | |
4665 | (home-page "https://github.com/alexkowa/VIM") | |
4666 | (synopsis "Visualization and imputation of missing values") | |
4667 | (description | |
4668 | "This package provides tools for the visualization of missing and/or | |
4669 | imputed values are introduced, which can be used for exploring the data and | |
4670 | the structure of the missing and/or imputed values. Depending on this | |
4671 | structure of the missing values, the corresponding methods may help to | |
4672 | identify the mechanism generating the missing values and allows to explore the | |
4673 | data including missing values. In addition, the quality of imputation can be | |
4674 | visually explored using various univariate, bivariate, multiple and | |
4675 | multivariate plot methods.") | |
4676 | (license license:gpl2+))) | |
d10b0952 RW |
4677 | |
4678 | (define-public r-fnn | |
4679 | (package | |
4680 | (name "r-fnn") | |
b9b10413 | 4681 | (version "1.1.3") |
d10b0952 RW |
4682 | (source |
4683 | (origin | |
4684 | (method url-fetch) | |
4685 | (uri (cran-uri "FNN" version)) | |
4686 | (sha256 | |
4687 | (base32 | |
b9b10413 | 4688 | "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny")))) |
d10b0952 RW |
4689 | (properties `((upstream-name . "FNN"))) |
4690 | (build-system r-build-system) | |
1b5905fe | 4691 | (home-page "https://cran.r-project.org/web/packages/FNN") |
d10b0952 RW |
4692 | (synopsis "Fast nearest neighbor search algorithms and applications") |
4693 | (description | |
4694 | "This package provides cover-tree and kd-tree fast k-nearest neighbor | |
4695 | search algorithms. Related applications including KNN classification, | |
4696 | regression and information measures are implemented.") | |
4697 | ;; The DESCRIPTION file erroneously states that GPL version 2.1 or | |
4698 | ;; later can be used. | |
4699 | (license license:gpl2+))) | |
be815dbd RW |
4700 | |
4701 | (define-public r-smoother | |
4702 | (package | |
4703 | (name "r-smoother") | |
4704 | (version "1.1") | |
4705 | (source | |
4706 | (origin | |
4707 | (method url-fetch) | |
4708 | (uri (cran-uri "smoother" version)) | |
4709 | (sha256 | |
4710 | (base32 | |
4711 | "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci")))) | |
4712 | (build-system r-build-system) | |
4713 | (propagated-inputs | |
4714 | `(("r-ttr" ,r-ttr))) | |
4715 | (home-page "http://cran.r-project.org/web/packages/smoother") | |
4716 | (synopsis "Functions relating to the smoothing of numerical data") | |
4717 | (description | |
4718 | "This package provides a collection of methods for smoothing numerical | |
4719 | data, commencing with a port of the Matlab gaussian window smoothing function. | |
4720 | In addition, several functions typically used in smoothing of financial data | |
4721 | are included.") | |
4722 | (license license:gpl2))) | |
0efd09ac RW |
4723 | |
4724 | (define-public r-riverplot | |
4725 | (package | |
4726 | (name "r-riverplot") | |
4727 | (version "0.6") | |
4728 | (source | |
4729 | (origin | |
4730 | (method url-fetch) | |
4731 | (uri (cran-uri "riverplot" version)) | |
4732 | (sha256 | |
4733 | (base32 | |
4734 | "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z")))) | |
4735 | (build-system r-build-system) | |
4736 | (home-page "https://logfc.wordpress.com") | |
4737 | (synopsis "Sankey or ribbon plots") | |
4738 | (description | |
4739 | "Sankey plots are a type of diagram that is convenient to illustrate how | |
4740 | flow of information, resources etc. separates and joins, much like observing | |
4741 | how rivers split and merge. For example, they can be used to compare | |
4742 | different clusterings. This package provides an implementation of Sankey | |
4743 | plots for R.") | |
4744 | (license license:gpl2+))) | |
c56739df SY |
4745 | |
4746 | (define-public r-dyn | |
4747 | (package | |
4748 | (name "r-dyn") | |
4749 | (version "0.2-9.6") | |
4750 | (source | |
4751 | (origin | |
4752 | (method url-fetch) | |
4753 | (uri (cran-uri "dyn" version)) | |
4754 | (sha256 | |
4755 | (base32 | |
4756 | "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb")))) | |
4757 | (build-system r-build-system) | |
4758 | (propagated-inputs | |
4759 | `(("r-zoo" ,r-zoo))) | |
4760 | (home-page "https://cran.r-project.org/web/packages/dyn") | |
4761 | (synopsis "Time series regression") | |
4762 | (description | |
4763 | "This package provides the dyn class interfaces @code{ts}, @code{irts}, | |
4764 | @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm}, | |
4765 | @code{loess}, @code{quantreg::rq}, @code{MASS::rlm}, | |
4766 | @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()}, | |
4767 | @code{randomForest::randomForest()} and other regression functions, allowing | |
4768 | those functions to be used with time series including specifications that may | |
4769 | contain lags, diffs and missing values.") | |
4770 | ;; Any GPL version. | |
4771 | (license license:gpl2+))) | |
24fa6bca SY |
4772 | |
4773 | (define-public r-catdap | |
4774 | (package | |
4775 | (name "r-catdap") | |
4776 | (version "1.3.4") | |
4777 | (source | |
4778 | (origin | |
4779 | (method url-fetch) | |
4780 | (uri (cran-uri "catdap" version)) | |
4781 | (sha256 | |
4782 | (base32 | |
4783 | "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2")))) | |
4784 | (build-system r-build-system) | |
4785 | (native-inputs | |
4786 | `(("gfortran" ,gfortran))) | |
4787 | (home-page "https://cran.r-project.org/web/packages/catdap/") | |
4788 | (synopsis "Tools for categorical data analysis") | |
4789 | (description | |
4790 | "This package provides functions for analyzing multivariate data. | |
4791 | Dependencies of the distribution of the specified variable (response | |
4792 | variable) to other variables (explanatory variables) are derived and | |
4793 | evaluated by the @dfn{Akaike Information Criterion} (AIC).") | |
4794 | (license license:gpl2+))) | |
96e22362 SS |
4795 | |
4796 | (define-public r-arules | |
4797 | (package | |
4798 | (name "r-arules") | |
ea010aa3 | 4799 | (version "1.6-3") |
96e22362 SS |
4800 | (source |
4801 | (origin | |
4802 | (method url-fetch) | |
4803 | (uri (cran-uri "arules" version)) | |
4804 | (sha256 | |
4805 | (base32 | |
ea010aa3 | 4806 | "0dimrq1pz449z0mz9m87nhm5bpc0v789bcc3lghhh97wwi5zah9y")))) |
96e22362 SS |
4807 | (build-system r-build-system) |
4808 | (propagated-inputs | |
4809 | `(("r-matrix" ,r-matrix))) | |
4810 | (home-page "https://github.com/mhahsler/arules") | |
4811 | (synopsis "Mining association rules and frequent itemsets") | |
4812 | (description | |
4813 | "This package provides an infrastructure for representing, manipulating | |
4814 | and analyzing transaction data and patterns (frequent itemsets and association rules). | |
4815 | It also provides C implementations of the association mining algorithms Apriori | |
4816 | and Eclat.") | |
4817 | (license license:gpl3))) | |
1cde7467 KH |
4818 | |
4819 | (define-public r-parsedate | |
4820 | (package | |
4821 | (name "r-parsedate") | |
4822 | (version "1.1.3") | |
4823 | (source | |
4824 | (origin | |
4825 | (method url-fetch) | |
4826 | (uri (cran-uri "parsedate" version)) | |
4827 | (sha256 | |
4828 | (base32 | |
4829 | "0mg7hbm3903iwvmpn51gjpaaq03rsp72hjb1g8h5g84r81iha002")))) | |
4830 | (build-system r-build-system) | |
4831 | (home-page "https://github.com/gaborcsardi/parsedate") | |
4832 | (synopsis | |
4833 | "Recognize and parse dates in various formats") | |
4834 | (description | |
4835 | "This package provides three functions for dealing with dates: | |
4836 | @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and | |
4837 | time formats, @code{parse_date} parses dates in unspecified formats, | |
4838 | and @code{format_iso_8601} formats a date in ISO 8601 format.") | |
4839 | (license license:gpl2))) | |
2a27c0bb SY |
4840 | |
4841 | (define-public r-abc-data | |
4842 | (package | |
4843 | (name "r-abc-data") | |
4844 | (version "1.0") | |
4845 | (source | |
4846 | (origin | |
4847 | (method url-fetch) | |
4848 | (uri (cran-uri "abc.data" version)) | |
4849 | (sha256 | |
4850 | (base32 | |
4851 | "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj")))) | |
4852 | (properties `((upstream-name . "abc.data"))) | |
4853 | (build-system r-build-system) | |
4854 | (home-page "https://cran.r-project.org/web/packages/abc.data/") | |
4855 | (synopsis "Data for Approximate Bayesian Computation (ABC) package") | |
4856 | (description | |
4857 | "This package contains data which are used by functions of the abc | |
4858 | package which implements several @dfn{Approximate Bayesian Computation} (ABC) | |
4859 | algorithms for performing parameter estimation, model selection, and | |
4860 | goodness-of-fit.") | |
4861 | (license license:gpl3+))) | |
82c8e0ae SY |
4862 | |
4863 | (define-public r-abc | |
4864 | (package | |
4865 | (name "r-abc") | |
4866 | (version "2.1") | |
4867 | (source | |
4868 | (origin | |
4869 | (method url-fetch) | |
4870 | (uri (cran-uri "abc" version)) | |
4871 | (sha256 | |
4872 | (base32 | |
4873 | "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) | |
4874 | (build-system r-build-system) | |
4875 | (propagated-inputs | |
4876 | `(("r-abc-data" ,r-abc-data) | |
4877 | ("r-locfit" ,r-locfit) | |
4878 | ("r-mass" ,r-mass) | |
4879 | ("r-nnet" ,r-nnet) | |
4880 | ("r-quantreg" ,r-quantreg))) | |
4881 | (home-page "https://cran.r-project.org/web/packages/abc/") | |
4882 | (synopsis "Tools for Approximate Bayesian Computation (ABC)") | |
4883 | (description | |
4884 | "This package implements several @dfn{Approximate Bayesian | |
4885 | Computation} (ABC) algorithms for performing parameter estimation, model | |
4886 | selection, and goodness-of-fit. Cross-validation tools are also available for | |
4887 | measuring the accuracy of ABC estimates, and to calculate the | |
4888 | misclassification probabilities of different models.") | |
4889 | (license license:gpl3+))) | |
4b1f7a3e | 4890 | |
d182828f RW |
4891 | (define-public r-zip |
4892 | (package | |
4893 | (name "r-zip") | |
e469e10e | 4894 | (version "2.0.1") |
d182828f RW |
4895 | (source |
4896 | (origin | |
4897 | (method url-fetch) | |
4898 | (uri (cran-uri "zip" version)) | |
4899 | (sha256 | |
4900 | (base32 | |
e469e10e | 4901 | "0cchbzp2s2qz7r4n9qdwgfgik5xzr0dzxmj25r8435i85k86ysi1")))) |
d182828f RW |
4902 | (build-system r-build-system) |
4903 | (home-page "https://github.com/gaborcsardi/zip") | |
4904 | (synopsis "Cross-platform Zip compression") | |
4905 | (description | |
4906 | "This package provides a cross-platform Zip compression library for R. | |
4907 | It is a replacement for the @code{zip} function, that does not require any | |
4908 | additional external tools on any platform.") | |
4909 | (license license:cc0))) | |
4910 | ||
4b1f7a3e RW |
4911 | (define-public r-openxlsx |
4912 | (package | |
4913 | (name "r-openxlsx") | |
a8b4677b | 4914 | (version "4.1.0") |
4b1f7a3e RW |
4915 | (source |
4916 | (origin | |
4917 | (method url-fetch) | |
4918 | (uri (cran-uri "openxlsx" version)) | |
4919 | (sha256 | |
4920 | (base32 | |
a8b4677b | 4921 | "1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb")))) |
4b1f7a3e | 4922 | (build-system r-build-system) |
a8b4677b RW |
4923 | (propagated-inputs |
4924 | `(("r-rcpp" ,r-rcpp) | |
4925 | ("r-zip" ,r-zip))) | |
4b1f7a3e RW |
4926 | (home-page "https://github.com/awalker89/openxlsx") |
4927 | (synopsis "Read, write and edit XLSX files") | |
4928 | (description | |
4929 | "This package simplifies the creation of Excel @code{.xlsx} files by | |
4930 | providing a high level interface to writing, styling and editing worksheets. | |
4931 | Through the use of Rcpp, read/write times are comparable to the @code{xlsx} | |
4932 | and @code{XLConnect} packages with the added benefit of removing the | |
4933 | dependency on Java.") | |
4934 | (license license:gpl3))) | |
c9920f25 RW |
4935 | |
4936 | (define-public r-rio | |
4937 | (package | |
4938 | (name "r-rio") | |
1417d5f1 | 4939 | (version "0.5.16") |
c9920f25 RW |
4940 | (source |
4941 | (origin | |
4942 | (method url-fetch) | |
4943 | (uri (cran-uri "rio" version)) | |
4944 | (sha256 | |
4945 | (base32 | |
1417d5f1 | 4946 | "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) |
c9920f25 RW |
4947 | (build-system r-build-system) |
4948 | (propagated-inputs | |
4949 | `(("r-curl" ,r-curl) | |
4950 | ("r-data-table" ,r-data-table) | |
4951 | ("r-foreign" ,r-foreign) | |
4952 | ("r-haven" ,r-haven) | |
4953 | ("r-openxlsx" ,r-openxlsx) | |
4954 | ("r-readxl" ,r-readxl) | |
4955 | ("r-tibble" ,r-tibble))) | |
4956 | (home-page "https://github.com/leeper/rio") | |
4957 | (synopsis "Swiss-army knife for data I/O") | |
4958 | (description | |
4959 | "This package provides streamlined data import and export infrastructure | |
4960 | by making assumptions that the user is probably willing to make: @code{import} | |
4961 | and @code{export} determine the data structure from the file extension, | |
4962 | reasonable defaults are used for data import and export (e.g., | |
4963 | @code{stringsAsFactors=FALSE}), web-based import is natively | |
4964 | supported (including from SSL/HTTPS), compressed files can be read directly | |
4965 | without explicit decompression, and fast import packages are used where | |
4966 | appropriate. An additional convenience function, @code{convert}, provides a | |
4967 | simple method for converting between file types.") | |
4968 | (license license:gpl2))) | |
08dac3d9 RW |
4969 | |
4970 | (define-public r-maptools | |
4971 | (package | |
4972 | (name "r-maptools") | |
bbe94211 | 4973 | (version "0.9-5") |
08dac3d9 RW |
4974 | (source |
4975 | (origin | |
4976 | (method url-fetch) | |
4977 | (uri (cran-uri "maptools" version)) | |
4978 | (sha256 | |
4979 | (base32 | |
bbe94211 | 4980 | "1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax")))) |
08dac3d9 RW |
4981 | (build-system r-build-system) |
4982 | (propagated-inputs | |
4983 | `(("r-foreign" ,r-foreign) | |
4984 | ("r-lattice" ,r-lattice) | |
4985 | ("r-sp" ,r-sp))) | |
4986 | (home-page "http://r-forge.r-project.org/projects/maptools/") | |
4987 | (synopsis "Tools for reading and handling spatial objects") | |
4988 | (description | |
4989 | "This package provides a set of tools for manipulating and reading | |
4990 | geographic data, in particular ESRI Shapefiles. It includes binary access to | |
4991 | GSHHG shoreline files. The package also provides interface wrappers for | |
4992 | exchanging spatial objects with other R packages.") | |
4993 | ;; The C source files from shapelib are released under the Expat license. | |
4994 | ;; The R code is released under GPL version 2 or later. | |
4995 | (license (list license:gpl2+ | |
4996 | license:expat)))) | |
284179bb RW |
4997 | |
4998 | (define-public r-later | |
4999 | (package | |
5000 | (name "r-later") | |
00fb3203 | 5001 | (version "0.8.0") |
284179bb RW |
5002 | (source |
5003 | (origin | |
5004 | (method url-fetch) | |
5005 | (uri (cran-uri "later" version)) | |
5006 | (sha256 | |
5007 | (base32 | |
00fb3203 | 5008 | "08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb")))) |
284179bb RW |
5009 | (build-system r-build-system) |
5010 | (propagated-inputs | |
5011 | `(("r-bh" ,r-bh) | |
5012 | ("r-rcpp" ,r-rcpp) | |
5013 | ("r-rlang" ,r-rlang))) | |
5014 | (home-page "https://github.com/r-lib/later") | |
5015 | (synopsis "Utilities for delaying function execution") | |
5016 | (description | |
5017 | "This package provides tools to execute arbitrary R or C functions some | |
5018 | time after the current time, after the R execution stack has emptied.") | |
5019 | (license license:gpl2+))) | |
d9d66ba9 RW |
5020 | |
5021 | (define-public r-promises | |
5022 | (package | |
5023 | (name "r-promises") | |
5024 | (version "1.0.1") | |
5025 | (source | |
5026 | (origin | |
5027 | (method url-fetch) | |
5028 | (uri (cran-uri "promises" version)) | |
5029 | (sha256 | |
5030 | (base32 | |
5031 | "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2")))) | |
5032 | (build-system r-build-system) | |
5033 | (propagated-inputs | |
5034 | `(("r-later" ,r-later) | |
5035 | ("r-magrittr" ,r-magrittr) | |
5036 | ("r-r6" ,r-r6) | |
5037 | ("r-rcpp" ,r-rcpp) | |
5038 | ("r-rlang" ,r-rlang))) | |
5039 | (home-page "https://rstudio.github.io/promises") | |
5040 | (synopsis "Abstractions for promise-based asynchronous programming") | |
5041 | (description | |
5042 | "This package provides fundamental abstractions for doing asynchronous | |
5043 | programming in R using promises. Asynchronous programming is useful for | |
5044 | allowing a single R process to orchestrate multiple tasks in the background | |
5045 | while also attending to something else. Semantics are similar to JavaScript | |
5046 | promises, but with a syntax that is idiomatic R.") | |
5047 | (license license:expat))) | |
3cf9ae2f RW |
5048 | |
5049 | (define-public r-dosnow | |
5050 | (package | |
5051 | (name "r-dosnow") | |
5052 | (version "1.0.16") | |
5053 | (source | |
5054 | (origin | |
5055 | (method url-fetch) | |
5056 | (uri (cran-uri "doSNOW" version)) | |
5057 | (sha256 | |
5058 | (base32 | |
5059 | "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n")))) | |
5060 | (properties `((upstream-name . "doSNOW"))) | |
5061 | (build-system r-build-system) | |
5062 | (propagated-inputs | |
5063 | `(("r-foreach" ,r-foreach) | |
5064 | ("r-iterators" ,r-iterators) | |
5065 | ("r-snow" ,r-snow))) | |
5066 | (home-page "https://cran.r-project.org/web/packages/doSNOW") | |
5067 | (synopsis "Foreach parallel adaptor for the snow package") | |
5068 | (description | |
5069 | "This package provides a parallel backend for the @code{%dopar%} function | |
5070 | using the @code{snow} package.") | |
5071 | (license license:gpl2))) | |
fdc3a05d RJ |
5072 | |
5073 | (define-public r-snowfall | |
5074 | (package | |
5075 | (name "r-snowfall") | |
5076 | (version "1.84-6.1") | |
5077 | (source (origin | |
5078 | (method url-fetch) | |
5079 | (uri (cran-uri "snowfall" version)) | |
5080 | (sha256 | |
5081 | (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) | |
5082 | (build-system r-build-system) | |
5083 | (propagated-inputs | |
5084 | `(("r-snow" ,r-snow))) | |
5085 | (home-page "http://cran.r-project.org/web/packages/snowfall/") | |
5086 | (synopsis "Easier cluster computing") | |
5087 | (description "This package is a usability wrapper around snow for easier | |
5088 | development of parallel R programs. This package offers e.g. extended error | |
5089 | checks, and additional functions. All functions work in sequential mode, too, | |
5090 | if no cluster is present or wished. The package is also designed as connector | |
5091 | to the cluster management tool @code{sfCluster}, but can also used without | |
5092 | it.") | |
5093 | (license license:gpl2+))) | |
e09d74ec | 5094 | |
94a8990f RW |
5095 | (define-public r-rappdirs |
5096 | (package | |
5097 | (name "r-rappdirs") | |
5098 | (version "0.3.1") | |
5099 | (source | |
5100 | (origin | |
5101 | (method url-fetch) | |
5102 | (uri (cran-uri "rappdirs" version)) | |
5103 | (sha256 | |
5104 | (base32 | |
5105 | "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g")))) | |
5106 | (build-system r-build-system) | |
5107 | (home-page "https://cran.r-project.org/web/packages/rappdirs/") | |
5108 | (synopsis "Determine where to save data, caches, and logs") | |
5109 | (description | |
5110 | "This package provides an easy way to determine which directories on the | |
5111 | user's computer should be used to save data, caches and logs. It is a port of | |
5112 | Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") | |
5113 | (license license:expat))) | |
2b47ebe1 RW |
5114 | |
5115 | (define-public r-learnr | |
5116 | (package | |
5117 | (name "r-learnr") | |
7d0370ed | 5118 | (version "0.9.2.1") |
2b47ebe1 RW |
5119 | (source |
5120 | (origin | |
5121 | (method url-fetch) | |
5122 | (uri (cran-uri "learnr" version)) | |
5123 | (sha256 | |
5124 | (base32 | |
7d0370ed | 5125 | "0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5")))) |
2b47ebe1 RW |
5126 | (build-system r-build-system) |
5127 | (propagated-inputs | |
5128 | `(("r-evaluate" ,r-evaluate) | |
5129 | ("r-htmltools" ,r-htmltools) | |
5130 | ("r-htmlwidgets" ,r-htmlwidgets) | |
5131 | ("r-jsonlite" ,r-jsonlite) | |
5132 | ("r-knitr" ,r-knitr) | |
5133 | ("r-markdown" ,r-markdown) | |
5134 | ("r-rappdirs" ,r-rappdirs) | |
5135 | ("r-rmarkdown" ,r-rmarkdown) | |
5136 | ("r-rprojroot" ,r-rprojroot) | |
5137 | ("r-shiny" ,r-shiny) | |
5138 | ("r-withr" ,r-withr))) | |
5139 | (home-page "https://rstudio.github.io/learnr/") | |
5140 | (synopsis "Interactive tutorials for R") | |
5141 | (description | |
5142 | "This package provides tools to create interactive tutorials using R | |
5143 | Markdown. Use a combination of narrative, figures, videos, exercises, and | |
5144 | quizzes to create self-paced tutorials for learning about R and R packages.") | |
5145 | (license license:asl2.0))) | |
12591673 RW |
5146 | |
5147 | (define-public r-analytics | |
5148 | (package | |
5149 | (name "r-analytics") | |
7a06cdfa | 5150 | (version "3.0") |
12591673 RW |
5151 | (source |
5152 | (origin | |
5153 | (method url-fetch) | |
5154 | (uri (cran-uri "analytics" version)) | |
5155 | (sha256 | |
5156 | (base32 | |
7a06cdfa | 5157 | "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) |
12591673 RW |
5158 | (build-system r-build-system) |
5159 | (propagated-inputs | |
5160 | `(("r-car" ,r-car) | |
5161 | ("r-cluster" ,r-cluster) | |
5162 | ("r-fractal" ,r-fractal) | |
5163 | ("r-lmtest" ,r-lmtest) | |
5164 | ("r-mass" ,r-mass) | |
5165 | ("r-np" ,r-np) | |
5166 | ("r-powerplus" ,r-powerplus) | |
5167 | ("r-robust" ,r-robust) | |
5168 | ("r-trend" ,r-trend) | |
5169 | ("r-tsa" ,r-tsa) | |
7a06cdfa RW |
5170 | ("r-urca" ,r-urca) |
5171 | ("r-vim" ,r-vim))) | |
12591673 RW |
5172 | (home-page "https://cran.r-project.org/web/packages/analytics/") |
5173 | (synopsis "Collection of data analysis tools") | |
5174 | (description | |
5175 | "This package is a collection of data analysis tools. It includes tools | |
5176 | for regression outlier detection in a fitted linear model, stationary | |
5177 | bootstrap using a truncated geometric distribution, a comprehensive test for | |
5178 | weak stationarity, column means by group, weighted biplots, and a heuristic to | |
5179 | obtain a better initial configuration in non-metric MDS.") | |
5180 | (license license:gpl2))) | |
9f56ceec RW |
5181 | |
5182 | (define-public r-reticulate | |
5183 | (package | |
5184 | (name "r-reticulate") | |
d3f22f0a | 5185 | (version "1.11.1") |
9f56ceec RW |
5186 | (source |
5187 | (origin | |
5188 | (method url-fetch) | |
5189 | (uri (cran-uri "reticulate" version)) | |
5190 | (sha256 | |
5191 | (base32 | |
d3f22f0a | 5192 | "1cyb92dvv9iibsk28i0gm5hm2xqbsn0y6d67id74c8rhai9y8i9v")))) |
9f56ceec RW |
5193 | (build-system r-build-system) |
5194 | (inputs `(("python" ,python))) | |
5195 | (propagated-inputs | |
5196 | `(("r-jsonlite" ,r-jsonlite) | |
5197 | ("r-matrix" ,r-matrix) | |
5198 | ("r-rcpp" ,r-rcpp))) | |
5199 | (home-page "https://github.com/rstudio/reticulate") | |
5200 | (synopsis "R interface to Python") | |
5201 | (description | |
5202 | "This package provides an interface from R to Python modules, classes, | |
5203 | and functions. When calling into Python, R data types are automatically | |
5204 | converted to their equivalent Python types. When values are returned from | |
5205 | Python to R they are converted back to R types.") | |
5206 | (license license:asl2.0))) | |
11de8673 RW |
5207 | |
5208 | (define-public r-bibtex | |
5209 | (package | |
5210 | (name "r-bibtex") | |
5211 | (version "0.4.2") | |
5212 | (source | |
5213 | (origin | |
5214 | (method url-fetch) | |
5215 | (uri (cran-uri "bibtex" version)) | |
5216 | (sha256 | |
5217 | (base32 | |
5218 | "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz")))) | |
5219 | (build-system r-build-system) | |
5220 | (propagated-inputs `(("r-stringr" ,r-stringr))) | |
5221 | (home-page "https://github.com/romainfrancois/bibtex") | |
5222 | (synopsis "Bibtex parser") | |
5223 | (description "This package provides a utility for R to parse a bibtex | |
5224 | file.") | |
5225 | (license license:gpl2+))) | |
e67acae7 RW |
5226 | |
5227 | (define-public r-ggseqlogo | |
5228 | (package | |
5229 | (name "r-ggseqlogo") | |
5230 | (version "0.1") | |
5231 | (source | |
5232 | (origin | |
5233 | (method url-fetch) | |
5234 | (uri (cran-uri "ggseqlogo" version)) | |
5235 | (sha256 | |
5236 | (base32 | |
5237 | "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1")))) | |
5238 | (build-system r-build-system) | |
5239 | (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) | |
5240 | (home-page "https://github.com/omarwagih/ggseqlogo") | |
5241 | (synopsis "ggplot2 extension for drawing genetic sequence logos") | |
5242 | (description | |
5243 | "The range of functions provided by this package makes it possible to | |
5244 | draw highly versatile genomic sequence logos. Features include, but are not | |
5245 | limited to, modifying colour schemes and fonts used to draw the logo, | |
5246 | generating multiple logo plots, and aiding the visualisation with annotations. | |
5247 | Sequence logos can easily be combined with other ggplot2 plots.") | |
5248 | ;; Unspecified version of the LGPL. | |
5249 | (license license:lgpl3+))) | |
85df1a86 RW |
5250 | |
5251 | (define-public r-ggsci | |
5252 | (package | |
5253 | (name "r-ggsci") | |
5254 | (version "2.9") | |
5255 | (source | |
5256 | (origin | |
5257 | (method url-fetch) | |
5258 | (uri (cran-uri "ggsci" version)) | |
5259 | (sha256 | |
5260 | (base32 | |
5261 | "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) | |
5262 | (build-system r-build-system) | |
5263 | (propagated-inputs | |
5264 | `(("r-ggplot2" ,r-ggplot2) | |
5265 | ("r-scales" ,r-scales))) | |
5266 | (home-page "https://nanx.me/ggsci/") | |
5267 | (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") | |
5268 | (description | |
5269 | "This package provides a collection of ggplot2 color palettes inspired by | |
5270 | plots in scientific journals, data visualization libraries, science fiction | |
5271 | movies, and TV shows.") | |
5272 | (license license:gpl3))) | |
5219c5c5 RW |
5273 | |
5274 | (define-public r-ggsignif | |
5275 | (package | |
5276 | (name "r-ggsignif") | |
6e4a9b83 | 5277 | (version "0.5.0") |
5219c5c5 RW |
5278 | (source |
5279 | (origin | |
5280 | (method url-fetch) | |
5281 | (uri (cran-uri "ggsignif" version)) | |
5282 | (sha256 | |
5283 | (base32 | |
6e4a9b83 | 5284 | "0z04g5kqdj66fyfxb5d2m7njkqd7idbiy4xgsnxdh5pbh3cr643x")))) |
5219c5c5 RW |
5285 | (build-system r-build-system) |
5286 | (propagated-inputs | |
5287 | `(("r-ggplot2" ,r-ggplot2))) | |
5288 | (home-page "https://github.com/const-ae/ggsignif") | |
5289 | (synopsis "Significance brackets for ggplot2") | |
5290 | (description | |
5291 | "Enrich your ggplots with group-wise comparisons. This package provides | |
5292 | an easy way to indicate if two groups are significantly different. Commonly | |
5293 | this is shown by a bracket on top connecting the groups of interest which | |
5294 | itself is annotated with the level of significance. The package provides a | |
5295 | single layer that takes the groups for comparison and the test as arguments | |
5296 | and adds the annotation to the plot.") | |
5297 | (license license:gpl3))) | |
5cbaaee8 RW |
5298 | |
5299 | (define-public r-ggpubr | |
5300 | (package | |
5301 | (name "r-ggpubr") | |
1659c5dd | 5302 | (version "0.2") |
5cbaaee8 RW |
5303 | (source |
5304 | (origin | |
5305 | (method url-fetch) | |
5306 | (uri (cran-uri "ggpubr" version)) | |
5307 | (sha256 | |
5308 | (base32 | |
1659c5dd | 5309 | "0rkpcjb1x7lvhj68aam5airbi534jqyiq12x5xk40a25iifhghq6")))) |
5cbaaee8 RW |
5310 | (build-system r-build-system) |
5311 | (propagated-inputs | |
5312 | `(("r-cowplot" ,r-cowplot) | |
5313 | ("r-dplyr" ,r-dplyr) | |
5314 | ("r-ggplot2" ,r-ggplot2) | |
5315 | ("r-ggrepel" ,r-ggrepel) | |
5316 | ("r-ggsci" ,r-ggsci) | |
5317 | ("r-ggsignif" ,r-ggsignif) | |
caaec886 | 5318 | ("r-glue" ,r-glue) |
5cbaaee8 RW |
5319 | ("r-gridextra" ,r-gridextra) |
5320 | ("r-magrittr" ,r-magrittr) | |
caaec886 | 5321 | ("r-polynom" ,r-polynom) |
5cbaaee8 RW |
5322 | ("r-purrr" ,r-purrr) |
5323 | ("r-scales" ,r-scales) | |
5324 | ("r-tidyr" ,r-tidyr))) | |
5325 | (home-page "http://www.sthda.com/english/rpkgs/ggpubr") | |
5326 | (synopsis "ggplot2-based publication-ready plots") | |
5327 | (description | |
5328 | "The ggplot2 package is an excellent and flexible package for elegant | |
5329 | data visualization in R. However the default generated plots require some | |
5330 | formatting before we can send them for publication. The ggpubr package | |
5331 | provides some easy-to-use functions for creating and customizing ggplot2-based | |
5332 | publication-ready plots.") | |
5333 | (license license:gpl2))) | |
141e43bd RW |
5334 | |
5335 | (define-public r-ellipse | |
5336 | (package | |
5337 | (name "r-ellipse") | |
5338 | (version "0.4.1") | |
5339 | (source | |
5340 | (origin | |
5341 | (method url-fetch) | |
5342 | (uri (cran-uri "ellipse" version)) | |
5343 | (sha256 | |
5344 | (base32 | |
5345 | "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs")))) | |
5346 | (build-system r-build-system) | |
5347 | (home-page "https://cran.r-project.org/web/packages/ellipse/") | |
5348 | (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") | |
5349 | (description | |
5350 | "This package contains various routines for drawing ellipses and | |
5351 | ellipse-like confidence regions, implementing the plots described in Murdoch | |
5352 | and Chow (1996), A graphical display of large correlation matrices, The | |
5353 | American Statistician 50, 178-180. There are also routines implementing the | |
5354 | profile plots described in Bates and Watts (1988), Nonlinear Regression | |
5355 | Analysis and its Applications.") | |
5356 | (license license:gpl2+))) | |
cbf6017d RW |
5357 | |
5358 | (define-public r-flashclust | |
5359 | (package | |
5360 | (name "r-flashclust") | |
5361 | (version "1.01-2") | |
5362 | (source | |
5363 | (origin | |
5364 | (method url-fetch) | |
5365 | (uri (cran-uri "flashClust" version)) | |
5366 | (sha256 | |
5367 | (base32 | |
5368 | "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) | |
5369 | (properties `((upstream-name . "flashClust"))) | |
5370 | (build-system r-build-system) | |
5371 | (native-inputs `(("gfortran" ,gfortran))) | |
5372 | (home-page "https://cran.r-project.org/web/packages/flashClust/") | |
5373 | (synopsis "Implementation of optimal hierarchical clustering") | |
5374 | (description | |
5375 | "This package provides a fast implementation of hierarchical | |
5376 | clustering.") | |
5377 | (license license:gpl2+))) | |
e83841a2 RW |
5378 | |
5379 | (define-public r-factominer | |
5380 | (package | |
5381 | (name "r-factominer") | |
5382 | (version "1.41") | |
5383 | (source | |
5384 | (origin | |
5385 | (method url-fetch) | |
5386 | (uri (cran-uri "FactoMineR" version)) | |
5387 | (sha256 | |
5388 | (base32 | |
5389 | "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259")))) | |
5390 | (properties `((upstream-name . "FactoMineR"))) | |
5391 | (build-system r-build-system) | |
5392 | (propagated-inputs | |
5393 | `(("r-car" ,r-car) | |
5394 | ("r-cluster" ,r-cluster) | |
5395 | ("r-ellipse" ,r-ellipse) | |
5396 | ("r-flashclust" ,r-flashclust) | |
5397 | ("r-lattice" ,r-lattice) | |
5398 | ("r-leaps" ,r-leaps) | |
5399 | ("r-mass" ,r-mass) | |
5400 | ("r-scatterplot3d" ,r-scatterplot3d))) | |
5401 | (home-page "http://factominer.free.fr") | |
5402 | (synopsis "Multivariate exploratory data analysis and data mining") | |
5403 | (description | |
5404 | "This package provides exploratory data analysis methods to summarize, | |
5405 | visualize and describe datasets. The main principal component methods are | |
5406 | available, those with the largest potential in terms of applications: | |
5407 | principal component analysis (PCA) when variables are quantitative, | |
5408 | correspondence analysis (CA) and multiple correspondence analysis (MCA) when | |
5409 | variables are categorical, Multiple Factor Analysis when variables are | |
5410 | structured in groups, etc. and hierarchical cluster analysis.") | |
5411 | (license license:gpl2+))) | |
f22bfee9 RW |
5412 | |
5413 | (define-public r-factoextra | |
5414 | (package | |
5415 | (name "r-factoextra") | |
5416 | (version "1.0.5") | |
5417 | (source | |
5418 | (origin | |
5419 | (method url-fetch) | |
5420 | (uri (cran-uri "factoextra" version)) | |
5421 | (sha256 | |
5422 | (base32 | |
5423 | "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1")))) | |
5424 | (build-system r-build-system) | |
5425 | (propagated-inputs | |
5426 | `(("r-abind" ,r-abind) | |
5427 | ("r-cluster" ,r-cluster) | |
5428 | ("r-dendextend" ,r-dendextend) | |
5429 | ("r-factominer" ,r-factominer) | |
5430 | ("r-ggplot2" ,r-ggplot2) | |
5431 | ("r-ggpubr" ,r-ggpubr) | |
5432 | ("r-ggrepel" ,r-ggrepel) | |
5433 | ("r-reshape2" ,r-reshape2) | |
5434 | ("r-tidyr" ,r-tidyr))) | |
5435 | (home-page "http://www.sthda.com/english/rpkgs/factoextra") | |
5436 | (synopsis "Extract and visualize the results of multivariate data analyses") | |
5437 | (description | |
5438 | "This package provides some easy-to-use functions to extract and | |
5439 | visualize the output of multivariate data analyses, including | |
6ccd88e8 RW |
5440 | @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence |
5441 | Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor | |
5442 | Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and | |
f22bfee9 RW |
5443 | @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R |
5444 | packages. It contains also functions for simplifying some clustering analysis | |
5445 | steps and provides ggplot2-based elegant data visualization.") | |
5446 | (license license:gpl2))) | |
0c9868aa | 5447 | |
356230da RW |
5448 | (define-public r-fansi |
5449 | (package | |
5450 | (name "r-fansi") | |
08645fcf | 5451 | (version "0.4.0") |
356230da RW |
5452 | (source |
5453 | (origin | |
5454 | (method url-fetch) | |
5455 | (uri (cran-uri "fansi" version)) | |
5456 | (sha256 | |
5457 | (base32 | |
08645fcf | 5458 | "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171")))) |
356230da RW |
5459 | (build-system r-build-system) |
5460 | (native-inputs | |
5461 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
5462 | (home-page "https://github.com/brodieG/fansi") | |
5463 | (synopsis "ANSI control sequence aware string functions") | |
5464 | (description | |
5465 | "This package provides counterparts to R string manipulation functions | |
5466 | that account for the effects of ANSI text formatting control sequences.") | |
5467 | (license license:gpl2+))) | |
5468 | ||
0c9868aa RW |
5469 | (define-public r-nbclust |
5470 | (package | |
5471 | (name "r-nbclust") | |
5472 | (version "3.0") | |
5473 | (source | |
5474 | (origin | |
5475 | (method url-fetch) | |
5476 | (uri (cran-uri "NbClust" version)) | |
5477 | (sha256 | |
5478 | (base32 | |
5479 | "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c")))) | |
5480 | (properties `((upstream-name . "NbClust"))) | |
5481 | (build-system r-build-system) | |
5482 | (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package") | |
5483 | (synopsis "Determine the best number of clusters in a data set") | |
5484 | (description | |
5485 | "NbClust provides 30 indexes for determining the optimal number of | |
5486 | clusters in a data set and offers the best clustering scheme from different | |
5487 | results to the user.") | |
5488 | (license license:gpl2))) | |
546fc4aa RW |
5489 | |
5490 | (define-public r-hdf5r | |
5491 | (package | |
5492 | (name "r-hdf5r") | |
a12c527d | 5493 | (version "1.1.1") |
546fc4aa RW |
5494 | (source |
5495 | (origin | |
5496 | (method url-fetch) | |
5497 | (uri (cran-uri "hdf5r" version)) | |
5498 | (sha256 | |
5499 | (base32 | |
a12c527d | 5500 | "1cq4rdfd0rqvy29ml3x1iid142ljnscs8f4d2y1na13hlvkl3k05")))) |
546fc4aa RW |
5501 | (build-system r-build-system) |
5502 | (inputs | |
5503 | `(("hdf5" ,hdf5) | |
5504 | ("zlib" ,zlib))) | |
5505 | (propagated-inputs | |
5506 | `(("r-bit64" ,r-bit64) | |
5507 | ("r-r6" ,r-r6))) | |
5508 | (home-page "https://hhoeflin.github.io/hdf5r") | |
5509 | (synopsis "Interface to the HDF5 binary data format") | |
5510 | (description | |
5511 | "HDF5 is a data model, library and file format for storing and managing | |
5512 | large amounts of data. This package provides a nearly feature complete, | |
5513 | object oriented wrapper for the HDF5 API using R6 classes. Additionally, | |
5514 | functionality is added so that HDF5 objects behave very similar to their | |
5515 | corresponding R counterparts.") | |
5516 | (license license:asl2.0))) | |
846325a8 | 5517 | |
3568b823 RW |
5518 | (define-public r-itertools |
5519 | (package | |
5520 | (name "r-itertools") | |
5521 | (version "0.1-3") | |
5522 | (source | |
5523 | (origin | |
5524 | (method url-fetch) | |
5525 | (uri (cran-uri "itertools" version)) | |
5526 | (sha256 | |
5527 | (base32 | |
5528 | "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn")))) | |
5529 | (build-system r-build-system) | |
5530 | (propagated-inputs | |
5531 | `(("r-iterators" ,r-iterators))) | |
5532 | (home-page "https://cran.r-project.org/web/packages/itertools/") | |
5533 | (synopsis "Iterator tools") | |
5534 | (description | |
5535 | "This package provides various tools for creating iterators, many | |
5536 | patterned after functions in the Python @code{itertools} module, and others | |
5537 | patterned after functions in the snow package.") | |
5538 | (license license:gpl2))) | |
5539 | ||
53718658 RW |
5540 | (define-public r-polynom |
5541 | (package | |
5542 | (name "r-polynom") | |
3be585cf | 5543 | (version "1.4-0") |
53718658 RW |
5544 | (source |
5545 | (origin | |
5546 | (method url-fetch) | |
5547 | (uri (cran-uri "polynom" version)) | |
5548 | (sha256 | |
5549 | (base32 | |
3be585cf | 5550 | "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5")))) |
53718658 RW |
5551 | (build-system r-build-system) |
5552 | (home-page "https://cran.r-project.org/web/packages/polynom/") | |
5553 | (synopsis "Functions for univariate polynomial manipulations") | |
5554 | (description | |
5555 | "This package provides a collection of functions to implement a class for | |
5556 | univariate polynomial manipulations.") | |
5557 | (license license:gpl2))) | |
5558 | ||
dd954dd7 RW |
5559 | (define-public r-gbrd |
5560 | (package | |
5561 | (name "r-gbrd") | |
5562 | (version "0.4-11") | |
5563 | (source | |
5564 | (origin | |
5565 | (method url-fetch) | |
5566 | (uri (cran-uri "gbRd" version)) | |
5567 | (sha256 | |
5568 | (base32 | |
5569 | "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82")))) | |
5570 | (properties `((upstream-name . "gbRd"))) | |
5571 | (build-system r-build-system) | |
5572 | (home-page "https://cran.r-project.org/web/packages/gbRd/") | |
5573 | (synopsis "Utilities for processing Rd objects and files") | |
5574 | (description | |
5575 | "This package provides utilities for processing Rd objects and files. | |
5576 | Extract argument descriptions and other parts of the help pages of | |
5577 | functions.") | |
5578 | (license license:gpl2+))) | |
5579 | ||
0c92f373 RW |
5580 | (define-public r-rjags |
5581 | (package | |
5582 | (name "r-rjags") | |
5583 | (version "4-8") | |
5584 | (source | |
5585 | (origin | |
5586 | (method url-fetch) | |
5587 | (uri (cran-uri "rjags" version)) | |
5588 | (sha256 | |
5589 | (base32 | |
5590 | "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m")))) | |
5591 | (build-system r-build-system) | |
5592 | (propagated-inputs | |
5593 | `(("r-coda" ,r-coda))) | |
5594 | (inputs | |
5595 | `(("jags" ,jags))) | |
5596 | (native-inputs | |
5597 | `(("pkg-config" ,pkg-config))) | |
5598 | (home-page "http://mcmc-jags.sourceforge.net") | |
5599 | (synopsis "Bayesian graphical models using MCMC") | |
5600 | (description | |
5601 | "This package provides an R interface to the JAGS MCMC library. JAGS is | |
5602 | Just Another Gibbs Sampler. It is a program for analysis of Bayesian | |
5603 | hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") | |
5604 | (license license:gpl2))) | |
5605 | ||
6a846975 RW |
5606 | (define-public r-rdpack |
5607 | (package | |
5608 | (name "r-rdpack") | |
71d99539 | 5609 | (version "0.10-1") |
6a846975 RW |
5610 | (source |
5611 | (origin | |
5612 | (method url-fetch) | |
5613 | (uri (cran-uri "Rdpack" version)) | |
5614 | (sha256 | |
5615 | (base32 | |
71d99539 | 5616 | "0bbjnw88h54v40hzim00i8yd3p4rk9i84zfdmgcbnylscwvsf0av")))) |
6a846975 RW |
5617 | (properties `((upstream-name . "Rdpack"))) |
5618 | (build-system r-build-system) | |
5619 | (propagated-inputs | |
5620 | `(("r-bibtex" ,r-bibtex) | |
5621 | ("r-gbrd" ,r-gbrd))) | |
5622 | (home-page "https://github.com/GeoBosh/Rdpack") | |
5623 | (synopsis "Update and manipulate Rd documentation objects") | |
5624 | (description | |
5625 | "This package provides functions for manipulation of R documentation | |
5626 | objects, including functions @code{reprompt()} and @code{ereprompt()} for | |
5627 | updating Rd documentation for functions, methods and classes; it also includes | |
5628 | Rd macros for citations and import of references from bibtex files for use in | |
5629 | Rd files and roxygen2 comments, as well as many functions for manipulation of | |
5630 | references and Rd files.") | |
5631 | (license license:gpl2+))) | |
5632 | ||
c183fa26 RW |
5633 | (define-public r-officer |
5634 | (package | |
5635 | (name "r-officer") | |
fd1a17a5 | 5636 | (version "0.3.3") |
c183fa26 RW |
5637 | (source |
5638 | (origin | |
5639 | (method url-fetch) | |
5640 | (uri (cran-uri "officer" version)) | |
5641 | (sha256 | |
5642 | (base32 | |
fd1a17a5 | 5643 | "1ggdp8pbspn24sjshx1h48klivrx401vwk2df49j4wpwxh6dx26y")))) |
c183fa26 RW |
5644 | (build-system r-build-system) |
5645 | (propagated-inputs | |
5646 | `(("r-base64enc" ,r-base64enc) | |
5647 | ("r-digest" ,r-digest) | |
5648 | ("r-htmltools" ,r-htmltools) | |
5649 | ("r-magrittr" ,r-magrittr) | |
5650 | ("r-r6" ,r-r6) | |
5651 | ("r-rcpp" ,r-rcpp) | |
fd1a17a5 | 5652 | ("r-rlang" ,r-rlang) |
c183fa26 RW |
5653 | ("r-uuid" ,r-uuid) |
5654 | ("r-xml2" ,r-xml2) | |
5655 | ("r-zip" ,r-zip))) | |
5656 | (home-page "https://davidgohel.github.io/officer") | |
5657 | (synopsis "Manipulation of Word and PowerPoint documents") | |
5658 | (description | |
5659 | "This package provides tools to access and manipulate Word and PowerPoint | |
5660 | documents from R. The package focuses on tabular and graphical reporting from | |
5661 | R; it also provides two functions that let users get document content into | |
5662 | data objects. A set of functions lets add and remove images, tables and | |
5663 | paragraphs of text in new or existing documents. When working with PowerPoint | |
5664 | presentations, slides can be added or removed; shapes inside slides can also | |
5665 | be added or removed. When working with Word documents, a cursor can be used | |
5666 | to help insert or delete content at a specific location in the document.") | |
5667 | (license license:gpl3))) | |
5668 | ||
488dc4e1 RW |
5669 | (define-public r-abn |
5670 | (package | |
5671 | (name "r-abn") | |
fbd263cd | 5672 | (version "1.3") |
488dc4e1 RW |
5673 | (source |
5674 | (origin | |
5675 | (method url-fetch) | |
5676 | (uri (cran-uri "abn" version)) | |
5677 | (sha256 | |
5678 | (base32 | |
fbd263cd | 5679 | "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm")))) |
488dc4e1 RW |
5680 | (build-system r-build-system) |
5681 | (inputs | |
5682 | `(("gsl" ,gsl))) | |
5683 | (propagated-inputs | |
5684 | `(("r-cairo" ,r-cairo) | |
5685 | ("r-lme4" ,r-lme4) | |
5686 | ("r-mass" ,r-mass) | |
5687 | ("r-nnet" ,r-nnet) | |
5688 | ("r-rcpp" ,r-rcpp) | |
5689 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
5690 | ("r-rjags" ,r-rjags))) | |
5691 | (home-page "http://www.r-bayesian-networks.org") | |
5692 | (synopsis "Modelling multivariate data with additive bayesian networks") | |
5693 | (description | |
5694 | "Bayesian network analysis is a form of probabilistic graphical models | |
5695 | which derives from empirical data a directed acyclic graph, DAG, describing | |
5696 | the dependency structure between random variables. An additive Bayesian | |
5697 | network model consists of a form of a DAG where each node comprises a | |
5698 | @dfn{generalized linear model} (GLM). Additive Bayesian network models are | |
5699 | equivalent to Bayesian multivariate regression using graphical modelling, they | |
5700 | generalises the usual multivariable regression, GLM, to multiple dependent | |
5701 | variables. This package provides routines to help determine optimal Bayesian | |
5702 | network models for a given data set, where these models are used to identify | |
5703 | statistical dependencies in messy, complex data.") | |
5704 | (license license:gpl2+))) | |
5705 | ||
ffdeda3c RW |
5706 | (define-public r-acd |
5707 | (package | |
5708 | (name "r-acd") | |
5709 | (version "1.5.3") | |
5710 | (source | |
5711 | (origin | |
5712 | (method url-fetch) | |
5713 | (uri (cran-uri "ACD" version)) | |
5714 | (sha256 | |
5715 | (base32 | |
5716 | "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6")))) | |
5717 | (properties `((upstream-name . "ACD"))) | |
5718 | (build-system r-build-system) | |
5719 | (home-page "https://cran.r-project.org/web/packages/ACD/") | |
5720 | (synopsis "Categorical data analysis with complete or missing responses") | |
5721 | (description | |
5722 | "This package provides tools for categorical data analysis with complete | |
5723 | or missing responses.") | |
5724 | (license license:gpl2+))) | |
5725 | ||
acbf23da RW |
5726 | (define-public r-acdm |
5727 | (package | |
5728 | (name "r-acdm") | |
5729 | (version "1.0.4") | |
5730 | (source | |
5731 | (origin | |
5732 | (method url-fetch) | |
5733 | (uri (cran-uri "ACDm" version)) | |
5734 | (sha256 | |
5735 | (base32 | |
5736 | "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil")))) | |
5737 | (properties `((upstream-name . "ACDm"))) | |
5738 | (build-system r-build-system) | |
5739 | (propagated-inputs | |
5740 | `(("r-dplyr" ,r-dplyr) | |
5741 | ("r-ggplot2" ,r-ggplot2) | |
5742 | ("r-plyr" ,r-plyr) | |
5743 | ("r-rsolnp" ,r-rsolnp) | |
5744 | ("r-zoo" ,r-zoo))) | |
5745 | (home-page "https://cran.r-project.org/web/packages/ACDm/") | |
5746 | (synopsis "Tools for Autoregressive Conditional Duration Models") | |
5747 | (description | |
5748 | "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle | |
5749 | and Russell, 1998) models. It creates trade, price or volume durations from | |
5750 | transactions (tic) data, performs diurnal adjustments, fits various ACD models | |
5751 | and tests them.") | |
5752 | (license license:gpl2+))) | |
5753 | ||
08bf097a RW |
5754 | (define-public r-overlap |
5755 | (package | |
5756 | (name "r-overlap") | |
5757 | (version "0.3.2") | |
5758 | (source | |
5759 | (origin | |
5760 | (method url-fetch) | |
5761 | (uri (cran-uri "overlap" version)) | |
5762 | (sha256 | |
5763 | (base32 | |
5764 | "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy")))) | |
5765 | (build-system r-build-system) | |
5766 | (home-page "https://cran.r-project.org/web/packages/overlap/") | |
5767 | (synopsis "Estimates of coefficient of overlapping for animal activity patterns") | |
5768 | (description | |
5769 | "This package provides functions to fit kernel density functions to data | |
5770 | on temporal activity patterns of animals; estimate coefficients of overlapping | |
5771 | of densities for two species; and calculate bootstrap estimates of confidence | |
5772 | intervals.") | |
5773 | (license license:gpl3+))) | |
5774 | ||
bfee9ce8 RW |
5775 | (define-public r-snakecase |
5776 | (package | |
5777 | (name "r-snakecase") | |
5778 | (version "0.9.2") | |
5779 | (source | |
5780 | (origin | |
5781 | (method url-fetch) | |
5782 | (uri (cran-uri "snakecase" version)) | |
5783 | (sha256 | |
5784 | (base32 | |
5785 | "1g6xai53dl24ws0mwhqrkcv583ziaq505cv3z8v5dhjgy98kilyj")))) | |
5786 | (build-system r-build-system) | |
5787 | (propagated-inputs | |
5788 | `(("r-stringi" ,r-stringi) | |
5789 | ("r-stringr" ,r-stringr))) | |
5790 | (home-page "https://github.com/Tazinho/snakecase") | |
5791 | (synopsis "Convert strings into any case") | |
5792 | (description | |
5793 | "This package provides a consistent, flexible and easy to use tool to | |
5794 | parse and convert strings into cases like snake or camel among others.") | |
5795 | (license license:gpl3))) | |
5796 | ||
de059e4b RW |
5797 | (define-public r-prediction |
5798 | (package | |
5799 | (name "r-prediction") | |
77545570 | 5800 | (version "0.3.6.2") |
de059e4b RW |
5801 | (source |
5802 | (origin | |
5803 | (method url-fetch) | |
5804 | (uri (cran-uri "prediction" version)) | |
5805 | (sha256 | |
5806 | (base32 | |
77545570 | 5807 | "0kx7xbm2j6c8h6gk1iig4vfpg877psg16j74hl7zc2mv40sc6dy5")))) |
de059e4b RW |
5808 | (build-system r-build-system) |
5809 | (propagated-inputs | |
5810 | `(("r-data-table" ,r-data-table))) | |
5811 | (home-page "https://github.com/leeper/prediction") | |
5812 | (synopsis "Tidy, type-safe prediction methods") | |
5813 | (description | |
5814 | "This package provides the @code{prediction()} function, a type-safe | |
5815 | alternative to @code{predict()} that always returns a data frame. The package | |
5816 | currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"}) | |
5817 | from the @code{stats} package, as well as numerous other model classes from | |
5818 | other add-on packages.") | |
5819 | (license license:expat))) | |
5820 | ||
d14c770d RW |
5821 | (define-public r-insight |
5822 | (package | |
5823 | (name "r-insight") | |
5824 | (version "0.1.2") | |
5825 | (source | |
5826 | (origin | |
5827 | (method url-fetch) | |
5828 | (uri (cran-uri "insight" version)) | |
5829 | (sha256 | |
5830 | (base32 | |
5831 | "0cy00j4m9r690hrjdmv8wzwn8mbnkjd3g527nvsmid64h9jgks5f")))) | |
5832 | (build-system r-build-system) | |
5833 | (home-page "https://easystats.github.io/insight/") | |
5834 | (synopsis "Easy access to model information for various model objects") | |
5835 | (description | |
5836 | "This package provides a tool to provide an easy, intuitive and | |
5837 | consistent access to information contained in various R models, like model | |
5838 | formulas, model terms, information about random effects, data that was used to | |
5839 | fit the model or data from response variables. The package mainly revolves | |
5840 | around two types of functions: Functions that find (the names of) information, | |
5841 | starting with @code{find_}, and functions that get the underlying data, | |
5842 | starting with @code{get_}. The package has a consistent syntax and works with | |
5843 | many different model objects, where otherwise functions to access these | |
5844 | information are missing.") | |
5845 | (license license:gpl3))) | |
5846 | ||
cfc06314 RW |
5847 | (define-public r-sjlabelled |
5848 | (package | |
5849 | (name "r-sjlabelled") | |
5e16dff9 | 5850 | (version "1.0.17") |
cfc06314 RW |
5851 | (source |
5852 | (origin | |
5853 | (method url-fetch) | |
5854 | (uri (cran-uri "sjlabelled" version)) | |
5855 | (sha256 | |
5856 | (base32 | |
5e16dff9 | 5857 | "00c0c22ynpihgf2bvmcfnkvqwqvxax2zzb7wldsmg2f7z5a32aa6")))) |
cfc06314 RW |
5858 | (build-system r-build-system) |
5859 | (propagated-inputs | |
5e16dff9 | 5860 | `(("r-dplyr" ,r-dplyr) |
cfc06314 | 5861 | ("r-haven" ,r-haven) |
5e16dff9 | 5862 | ("r-insight" ,r-insight) |
cfc06314 | 5863 | ("r-magrittr" ,r-magrittr) |
cfc06314 | 5864 | ("r-purrr" ,r-purrr) |
5e16dff9 | 5865 | ("r-rlang" ,r-rlang))) |
cfc06314 RW |
5866 | (home-page "https://github.com/strengejacke/sjlabelled") |
5867 | (synopsis "Labelled data utility functions") | |
5868 | (description | |
5869 | "This package provides a collection of functions dealing with labelled | |
5870 | data, like reading and writing data between R and other statistical software | |
5871 | packages. This includes easy ways to get, set or change value and variable | |
5872 | label attributes, to convert labelled vectors into factors or numeric (and | |
5873 | vice versa), or to deal with multiple declared missing values.") | |
5874 | (license license:gpl3))) | |
5875 | ||
1f560b9c RW |
5876 | (define-public r-sjmisc |
5877 | (package | |
5878 | (name "r-sjmisc") | |
31af2e7f | 5879 | (version "2.7.9") |
1f560b9c RW |
5880 | (source |
5881 | (origin | |
5882 | (method url-fetch) | |
5883 | (uri (cran-uri "sjmisc" version)) | |
5884 | (sha256 | |
5885 | (base32 | |
31af2e7f | 5886 | "11iiap0w5v0dszgwx4pi3j1zf9vnlw1ml1wjvq1hg9iz1plgbfnc")))) |
1f560b9c RW |
5887 | (build-system r-build-system) |
5888 | (propagated-inputs | |
31af2e7f | 5889 | `(("r-dplyr" ,r-dplyr) |
1f560b9c RW |
5890 | ("r-haven" ,r-haven) |
5891 | ("r-magrittr" ,r-magrittr) | |
1f560b9c RW |
5892 | ("r-purrr" ,r-purrr) |
5893 | ("r-rlang" ,r-rlang) | |
31af2e7f | 5894 | ("r-sjlabelled" ,r-sjlabelled))) |
1f560b9c RW |
5895 | (home-page "https://github.com/strengejacke/sjmisc") |
5896 | (synopsis "Data and variable transformation functions") | |
5897 | (description | |
5898 | "This package is a collection of miscellaneous utility functions, | |
5899 | supporting data transformation tasks like recoding, dichotomizing or grouping | |
5900 | variables, setting and replacing missing values. The data transformation | |
5901 | functions also support labelled data, and all integrate seamlessly into a | |
5902 | tidyverse workflow.") | |
5903 | (license license:gpl3))) | |
5904 | ||
aaed237d RW |
5905 | (define-public r-nortest |
5906 | (package | |
5907 | (name "r-nortest") | |
5908 | (version "1.0-4") | |
5909 | (source | |
5910 | (origin | |
5911 | (method url-fetch) | |
5912 | (uri (cran-uri "nortest" version)) | |
5913 | (sha256 | |
5914 | (base32 | |
5915 | "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3")))) | |
5916 | (build-system r-build-system) | |
5917 | (home-page "https://cran.r-project.org/web/packages/nortest/") | |
5918 | (synopsis "Tests for normality") | |
5919 | (description | |
5920 | "This package provides five omnibus tests for testing the composite | |
5921 | hypothesis of normality.") | |
5922 | (license license:gpl2+))) | |
5923 | ||
0fd7d59d RW |
5924 | (define-public r-moonbook |
5925 | (package | |
5926 | (name "r-moonbook") | |
5927 | (version "0.2.3") | |
5928 | (source | |
5929 | (origin | |
5930 | (method url-fetch) | |
5931 | (uri (cran-uri "moonBook" version)) | |
5932 | (sha256 | |
5933 | (base32 | |
5934 | "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6")))) | |
5935 | (properties `((upstream-name . "moonBook"))) | |
5936 | (build-system r-build-system) | |
5937 | (propagated-inputs | |
5938 | `(("r-magrittr" ,r-magrittr) | |
5939 | ("r-nortest" ,r-nortest) | |
5940 | ("r-purrr" ,r-purrr) | |
5941 | ("r-sjmisc" ,r-sjmisc) | |
5942 | ("r-stringr" ,r-stringr) | |
5943 | ("r-survival" ,r-survival))) | |
5944 | (home-page "https://github.com/cardiomoon/moonBook") | |
5945 | (synopsis "Functions and datasets for the book by Keon-Woong Moon") | |
5946 | (description | |
5947 | "This package provides several analysis-related functions for the book | |
5948 | entitled \"R statistics and graph for medical articles\" (written in Korean), | |
5949 | version 1, by Keon-Woong Moon with Korean demographic data with several plot | |
5950 | functions.") | |
5951 | (license license:gpl2))) | |
5952 | ||
589bd1c4 RW |
5953 | (define-public r-flextable |
5954 | (package | |
5955 | (name "r-flextable") | |
e89d5427 | 5956 | (version "0.5.1") |
589bd1c4 RW |
5957 | (source |
5958 | (origin | |
5959 | (method url-fetch) | |
5960 | (uri (cran-uri "flextable" version)) | |
5961 | (sha256 | |
5962 | (base32 | |
e89d5427 | 5963 | "0arxgal67ahsq8v0zbvc767qadn7lg3f7mmqa9gjjz6sri0y6gsx")))) |
589bd1c4 RW |
5964 | (build-system r-build-system) |
5965 | (propagated-inputs | |
e89d5427 RW |
5966 | `(("r-data-table" ,r-data-table) |
5967 | ("r-gdtools" ,r-gdtools) | |
589bd1c4 RW |
5968 | ("r-htmltools" ,r-htmltools) |
5969 | ("r-knitr" ,r-knitr) | |
e89d5427 | 5970 | ("r-magick" ,r-magick) |
589bd1c4 | 5971 | ("r-officer" ,r-officer) |
e89d5427 | 5972 | ("r-rlang" ,r-rlang) |
589bd1c4 | 5973 | ("r-rmarkdown" ,r-rmarkdown) |
589bd1c4 RW |
5974 | ("r-xml2" ,r-xml2))) |
5975 | (home-page "https://davidgohel.github.io/flextable") | |
5976 | (synopsis "Functions for tabular reporting") | |
5977 | (description | |
5978 | "This package provides tools to create pretty tables for HTML documents | |
5979 | and other formats. Functions are provided to let users create tables, modify | |
5980 | and format their content. It extends the @code{officer} package and can be | |
5981 | used within R markdown documents when rendering to HTML and to Word | |
5982 | documents.") | |
5983 | (license license:gpl3))) | |
5984 | ||
846325a8 RW |
5985 | (define-public r-writexl |
5986 | (package | |
5987 | (name "r-writexl") | |
04a18a81 | 5988 | (version "1.1") |
846325a8 RW |
5989 | (source |
5990 | (origin | |
5991 | (method url-fetch) | |
5992 | (uri (cran-uri "writexl" version)) | |
5993 | (sha256 | |
5994 | (base32 | |
04a18a81 | 5995 | "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46")))) |
846325a8 RW |
5996 | (build-system r-build-system) |
5997 | (inputs `(("zlib" ,zlib))) | |
5998 | (home-page "https://github.com/ropensci/writexl") | |
5999 | (synopsis "Export data frames to xlsx format") | |
6000 | (description | |
6001 | "This package provides a data frame to xlsx exporter based on | |
6002 | libxlsxwriter.") | |
6003 | (license license:bsd-2))) | |
64abd245 RW |
6004 | |
6005 | (define-public r-biasedurn | |
6006 | (package | |
6007 | (name "r-biasedurn") | |
6008 | (version "1.07") | |
6009 | (source | |
6010 | (origin | |
6011 | (method url-fetch) | |
6012 | (uri (cran-uri "BiasedUrn" version)) | |
6013 | (sha256 | |
6014 | (base32 | |
6015 | "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) | |
6016 | (properties `((upstream-name . "BiasedUrn"))) | |
6017 | (build-system r-build-system) | |
6018 | (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") | |
6019 | (synopsis "Biased Urn model distributions") | |
6020 | (description | |
6021 | "This package provides statistical models of biased sampling in the form | |
6022 | of univariate and multivariate noncentral hypergeometric distributions, | |
6023 | including Wallenius' noncentral hypergeometric distribution and Fisher's | |
6024 | noncentral hypergeometric distribution (also called extended hypergeometric | |
6025 | distribution).") | |
6026 | (license license:gpl3))) | |
87ba9508 RW |
6027 | |
6028 | (define-public r-goplot | |
6029 | (package | |
6030 | (name "r-goplot") | |
6031 | (version "1.0.2") | |
6032 | (source | |
6033 | (origin | |
6034 | (method url-fetch) | |
6035 | (uri (cran-uri "GOplot" version)) | |
6036 | (sha256 | |
6037 | (base32 | |
6038 | "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix")))) | |
6039 | (properties `((upstream-name . "GOplot"))) | |
6040 | (build-system r-build-system) | |
6041 | (propagated-inputs | |
6042 | `(("r-ggdendro" ,r-ggdendro) | |
6043 | ("r-ggplot2" ,r-ggplot2) | |
6044 | ("r-gridextra" ,r-gridextra) | |
6045 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
6046 | (home-page "https://github.com/wencke/wencke.github.io") | |
6047 | (synopsis "Visualization of functional analysis data") | |
6048 | (description | |
6049 | "This package provides an implementation of multilayered visualizations | |
6050 | for enhanced graphical representation of functional analysis data. It | |
6051 | combines and integrates omics data derived from expression and functional | |
6052 | annotation enrichment analyses. Its plotting functions have been developed | |
6053 | with an hierarchical structure in mind: starting from a general overview to | |
6054 | identify the most enriched categories (modified bar plot, bubble plot) to a | |
6055 | more detailed one displaying different types of relevant information for the | |
6056 | molecules in a given set of categories (circle plot, chord plot, cluster plot, | |
6057 | Venn diagram, heatmap).") | |
6058 | (license license:gpl2))) | |
aec7d6be RW |
6059 | |
6060 | (define-public r-getopt | |
6061 | (package | |
6062 | (name "r-getopt") | |
104ec4c9 | 6063 | (version "1.20.3") |
aec7d6be RW |
6064 | (source |
6065 | (origin | |
6066 | (method url-fetch) | |
6067 | (uri (cran-uri "getopt" version)) | |
6068 | (sha256 | |
6069 | (base32 | |
104ec4c9 | 6070 | "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk")))) |
aec7d6be RW |
6071 | (build-system r-build-system) |
6072 | (home-page "https://github.com/trevorld/getopt") | |
6073 | (synopsis "Command-line option processor for R") | |
6074 | (description | |
6075 | "This package is designed to be used with Rscript to write shebang | |
6076 | scripts that accept short and long options. Many users will prefer to | |
6077 | use the packages @code{optparse} or @code{argparse} which add extra | |
6078 | features like automatically generated help options and usage texts, | |
6079 | support for default values, positional argument support, etc.") | |
6080 | (license license:gpl2+))) | |
3629622b RW |
6081 | |
6082 | (define-public r-findpython | |
6083 | (package | |
6084 | (name "r-findpython") | |
fcb84565 | 6085 | (version "1.0.5") |
3629622b RW |
6086 | (source |
6087 | (origin | |
6088 | (method url-fetch) | |
6089 | (uri (cran-uri "findpython" version)) | |
6090 | (sha256 | |
6091 | (base32 | |
fcb84565 | 6092 | "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy")))) |
3629622b RW |
6093 | (build-system r-build-system) |
6094 | (home-page "https://github.com/trevorld/findpython") | |
6095 | (synopsis "Functions to find an acceptable Python binary") | |
6096 | (description | |
6097 | "This package was designed to find an acceptable Python binary that | |
6098 | matches version and feature constraints.") | |
6099 | (license license:expat))) | |
fa697599 RW |
6100 | |
6101 | ;; This in not the same as "r-argparser" | |
6102 | (define-public r-argparse | |
6103 | (package | |
6104 | (name "r-argparse") | |
37317189 | 6105 | (version "2.0.1") |
fa697599 RW |
6106 | (source |
6107 | (origin | |
6108 | (method url-fetch) | |
6109 | (uri (cran-uri "argparse" version)) | |
6110 | (sha256 | |
6111 | (base32 | |
37317189 | 6112 | "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l")))) |
fa697599 RW |
6113 | (build-system r-build-system) |
6114 | (inputs `(("python" ,python))) | |
6115 | (propagated-inputs | |
6116 | `(("r-findpython" ,r-findpython) | |
fa697599 | 6117 | ("r-jsonlite" ,r-jsonlite) |
11a36548 | 6118 | ("r-r6" ,r-r6))) |
fa697599 RW |
6119 | (home-page "https://github.com/trevorld/argparse") |
6120 | (synopsis "Command line optional and positional argument parser") | |
6121 | (description | |
6122 | "This package provides a command line parser to be used with Rscript to | |
6123 | write shebang scripts that gracefully accept positional and optional arguments | |
6124 | and automatically generate usage notices.") | |
6125 | (license license:gpl2+))) | |
4646d18e RW |
6126 | |
6127 | (define-public r-hash | |
6128 | (package | |
6129 | (name "r-hash") | |
a431c381 | 6130 | (version "2.2.6.1") |
4646d18e RW |
6131 | (source |
6132 | (origin | |
6133 | (method url-fetch) | |
6134 | (uri (cran-uri "hash" version)) | |
6135 | (sha256 | |
6136 | (base32 | |
a431c381 | 6137 | "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056")))) |
4646d18e RW |
6138 | (build-system r-build-system) |
6139 | (home-page "https://cran.r-project.org/web/packages/hash/") | |
6140 | (synopsis "Implementation of hash/associated arrays/dictionaries") | |
6141 | (description | |
6142 | "This package implements a data structure similar to hashes in Perl and | |
6143 | dictionaries in Python but with a purposefully R flavor. For objects of | |
6144 | appreciable size, access using hashes outperforms native named lists and | |
6145 | vectors.") | |
6146 | (license license:gpl2+))) | |
06a45ad6 RW |
6147 | |
6148 | (define-public r-orddom | |
6149 | (package | |
6150 | (name "r-orddom") | |
6151 | (version "3.1") | |
6152 | (source | |
6153 | (origin | |
6154 | (method url-fetch) | |
6155 | (uri (cran-uri "orddom" version)) | |
6156 | (sha256 | |
6157 | (base32 | |
6158 | "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) | |
6159 | (build-system r-build-system) | |
6160 | (propagated-inputs `(("r-psych" ,r-psych))) | |
6161 | (home-page "https://cran.r-project.org/web/packages/orddom/") | |
6162 | (synopsis "Ordinal dominance statistics") | |
6163 | (description | |
6164 | "This package provides tools to compute ordinal, statistics and effect | |
6165 | sizes as an alternative to mean comparison: Cliff's delta or success rate | |
6166 | difference (SRD), Vargha and Delaney's A or the Area Under a Receiver | |
6167 | Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's | |
6168 | Common Language Effect Size (CLES) or Grissom & Kim's Probability of | |
6169 | Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover, | |
6170 | comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of | |
6171 | Group (Non-)Overlap considerations.") | |
6172 | (license license:gpl2))) | |
0fccd15f RW |
6173 | |
6174 | (define-public r-doby | |
6175 | (package | |
6176 | (name "r-doby") | |
cb96d81b | 6177 | (version "4.6-2") |
0fccd15f RW |
6178 | (source |
6179 | (origin | |
6180 | (method url-fetch) | |
6181 | (uri (cran-uri "doBy" version)) | |
6182 | (sha256 | |
6183 | (base32 | |
cb96d81b | 6184 | "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb")))) |
0fccd15f RW |
6185 | (properties `((upstream-name . "doBy"))) |
6186 | (build-system r-build-system) | |
6187 | (propagated-inputs | |
6188 | `(("r-dplyr" ,r-dplyr) | |
6189 | ("r-magrittr" ,r-magrittr) | |
6190 | ("r-mass" ,r-mass) | |
6191 | ("r-matrix" ,r-matrix) | |
6192 | ("r-plyr" ,r-plyr))) | |
6193 | (home-page "http://people.math.aau.dk/~sorenh/software/doBy/") | |
6194 | (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") | |
6195 | (description | |
6196 | "This package contains: | |
6197 | ||
6198 | @itemize | |
6199 | @item facilities for working with grouped data: @code{do} | |
6200 | something to data stratified @code{by} some variables. | |
6201 | @item implementations of least-squares means, general linear contrasts, and | |
6202 | @item miscellaneous other utilities. | |
6203 | @end itemize\n") | |
6204 | (license license:gpl2+))) | |
5850c5b3 RW |
6205 | |
6206 | (define-public r-refgenome | |
6207 | (package | |
6208 | (name "r-refgenome") | |
2652e253 | 6209 | (version "1.7.3.1") |
5850c5b3 RW |
6210 | (source |
6211 | (origin | |
6212 | (method url-fetch) | |
6213 | (uri (cran-uri "refGenome" version)) | |
6214 | (sha256 | |
6215 | (base32 | |
2652e253 | 6216 | "1s4lxv5pqk6d0f0a9iclgv88yl346fwvzgraxh0gwpbym1yhh787")))) |
5850c5b3 RW |
6217 | (properties `((upstream-name . "refGenome"))) |
6218 | (build-system r-build-system) | |
6219 | (propagated-inputs | |
6220 | `(("r-dbi" ,r-dbi) | |
6221 | ("r-doby" ,r-doby) | |
6222 | ("r-rsqlite" ,r-rsqlite))) | |
6223 | (home-page "https://cran.r-project.org/web/packages/refGenome/") | |
6224 | (synopsis | |
6225 | "Gene and splice site annotation using annotation data from Ensembl and UCSC") | |
6226 | (description | |
6227 | "This package contains functionality for importing and managing of | |
6228 | downloaded genome annotation data from the Ensembl genome browser (European | |
6229 | Bioinformatics Institute) and from the UCSC genome browser (University of | |
6230 | California, Santa Cruz) and annotation routines for genomic positions and | |
6231 | splice site positions.") | |
6232 | (license license:gpl2))) | |
ff7d53a7 RW |
6233 | |
6234 | (define-public r-basix | |
6235 | (package | |
6236 | (name "r-basix") | |
6237 | (version "1.1") | |
6238 | (source | |
6239 | (origin | |
6240 | (method url-fetch) | |
6241 | (uri (cran-uri "BASIX" version)) | |
6242 | (sha256 | |
6243 | (base32 | |
6244 | "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id")))) | |
6245 | (properties `((upstream-name . "BASIX"))) | |
6246 | (build-system r-build-system) | |
6247 | (home-page "https://cran.r-project.org/web/packages/BASIX/") | |
6248 | (synopsis "Efficient C/C++ toolset for R") | |
6249 | (description | |
6250 | "BASIX provides some efficient C/C++ implementations of native R | |
6251 | procedures to speed up calculations in R.") | |
6252 | (license license:gpl2))) | |
65e74814 RW |
6253 | |
6254 | (define-public r-blockfest | |
6255 | (package | |
6256 | (name "r-blockfest") | |
6257 | (version "1.6") | |
6258 | (source | |
6259 | (origin | |
6260 | (method url-fetch) | |
6261 | (uri (cran-uri "BlockFeST" version)) | |
6262 | (sha256 | |
6263 | (base32 | |
6264 | "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) | |
6265 | (properties `((upstream-name . "BlockFeST"))) | |
6266 | (build-system r-build-system) | |
6267 | (propagated-inputs `(("r-basix" ,r-basix))) | |
6268 | (home-page "https://cran.r-project.org/web/packages/BlockFeST/") | |
6269 | (synopsis "Bayesian calculation of region-specific fixation index") | |
6270 | (description | |
6271 | "This package provides an R implementation of an extension of the | |
6272 | BayeScan software for codominant markers, adding the option to group | |
6273 | individual SNPs into pre-defined blocks. A typical application of this new | |
6274 | approach is the identification of genomic regions, genes, or gene sets | |
6275 | containing one or more SNPs that evolved under directional selection.") | |
6276 | (license license:gpl2))) | |
b9ff2599 | 6277 | |
fbdf05b1 RW |
6278 | (define-public r-proc |
6279 | (package | |
6280 | (name "r-proc") | |
a3daf011 | 6281 | (version "1.14.0") |
fbdf05b1 RW |
6282 | (source |
6283 | (origin | |
6284 | (method url-fetch) | |
6285 | (uri (cran-uri "pROC" version)) | |
6286 | (sha256 | |
6287 | (base32 | |
a3daf011 | 6288 | "0ki1pvj5iaki81crapvwqllg5avn5qlvv62axnsdkdcmv9xc3wg0")))) |
fbdf05b1 RW |
6289 | (properties `((upstream-name . "pROC"))) |
6290 | (build-system r-build-system) | |
6291 | (propagated-inputs | |
a3daf011 | 6292 | `(("r-plyr" ,r-plyr) |
fbdf05b1 RW |
6293 | ("r-rcpp" ,r-rcpp))) |
6294 | (home-page "http://expasy.org/tools/pROC/") | |
6295 | (synopsis "Display and analyze ROC curves") | |
6296 | (description | |
6297 | "This package provides tools for visualizing, smoothing and comparing | |
6298 | receiver operating characteristic (ROC curves). The area under the | |
6299 | curve (AUC) can be compared with statistical tests based on U-statistics or | |
6300 | bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") | |
6301 | (license license:gpl3+))) | |
cea4d360 RW |
6302 | |
6303 | (define-public r-rootsolve | |
6304 | (package | |
6305 | (name "r-rootsolve") | |
6306 | (version "1.7") | |
6307 | (source | |
6308 | (origin | |
6309 | (method url-fetch) | |
6310 | (uri (cran-uri "rootSolve" version)) | |
6311 | (sha256 | |
6312 | (base32 | |
6313 | "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8")))) | |
6314 | (properties `((upstream-name . "rootSolve"))) | |
6315 | (build-system r-build-system) | |
6316 | (native-inputs `(("gfortran" ,gfortran))) | |
6317 | (home-page "https://cran.r-project.org/web/packages/rootSolve/") | |
6318 | (synopsis "Tools for the analysis of ordinary differential equations") | |
6319 | (description | |
6320 | "This package provides routines to find the root of nonlinear functions, | |
6321 | and to perform steady-state and equilibrium analysis of @dfn{ordinary | |
6322 | differential equations} (ODE). It includes routines that: | |
6323 | ||
6324 | @enumerate | |
6325 | @item generate gradient and jacobian matrices (full and banded), | |
6326 | @item find roots of non-linear equations by the Newton-Raphson method, | |
6327 | @item estimate steady-state conditions of a system of (differential) equations | |
6328 | in full, banded or sparse form, using the Newton-Raphson method, or by | |
6329 | dynamically running, | |
6330 | @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, | |
6331 | and 3-D partial differential equations, that have been converted to ordinary | |
6332 | differential equations by numerical differencing (using the method-of-lines | |
6333 | approach). | |
6334 | @end enumerate\n") | |
6335 | (license license:gpl2+))) | |
c994418b | 6336 | |
6337 | (define-public r-abcanalysis | |
6338 | (package | |
6339 | (name "r-abcanalysis") | |
6340 | (version "1.2.1") | |
6341 | (source | |
6342 | (origin | |
6343 | (method url-fetch) | |
6344 | (uri (cran-uri "ABCanalysis" version)) | |
6345 | (sha256 | |
6346 | (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) | |
6347 | (properties `((upstream-name . "ABCanalysis"))) | |
6348 | (build-system r-build-system) | |
6349 | (propagated-inputs `(("r-plotrix" ,r-plotrix))) | |
6350 | (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") | |
6351 | (synopsis "Computed ABC Analysis") | |
6352 | (description | |
6353 | "Multivariate data sets often differ in several factors or derived statistical | |
6354 | parameters, which have to be selected for a valid interpretation. Basing this | |
6355 | selection on traditional statistical limits leads occasionally to the perception | |
6356 | of losing information from a data set. This package provides tools to calculate | |
6357 | these limits on the basis of the mathematical properties of the distribution of | |
6358 | the analyzed items.") | |
6359 | (license license:gpl3))) | |
87b576aa | 6360 | |
6361 | (define-public r-slam | |
6362 | (package | |
6363 | (name "r-slam") | |
1007b1b6 | 6364 | (version "0.1-45") |
87b576aa | 6365 | (source |
6366 | (origin | |
6367 | (method url-fetch) | |
6368 | (uri (cran-uri "slam" version)) | |
6369 | (sha256 | |
1007b1b6 | 6370 | (base32 "0xvj8va6xd7zkn3l4a5ad7v62s7xmkz8frq7gpcl3b6vqwckkaw4")))) |
87b576aa | 6371 | (build-system r-build-system) |
6372 | (home-page "https://cran.r-project.org/web/packages/slam/") | |
6373 | (synopsis "Sparse lightweight arrays and matrices") | |
6374 | (description | |
6375 | "This package contains data structures and algorithms for sparse arrays and matrices, | |
6376 | based on index arrays and simple triplet representations, respectively.") | |
6377 | (license license:gpl2))) | |
881cc61c | 6378 | |
6379 | (define-public r-manipulatewidget | |
6380 | (package | |
6381 | (name "r-manipulatewidget") | |
6382 | (version "0.10.0") | |
6383 | (source | |
6384 | (origin | |
6385 | (method url-fetch) | |
6386 | (uri (cran-uri "manipulateWidget" version)) | |
6387 | (sha256 | |
6388 | (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x")))) | |
6389 | (properties | |
6390 | `((upstream-name . "manipulateWidget"))) | |
6391 | (build-system r-build-system) | |
6392 | (propagated-inputs | |
6393 | `(("r-base64enc" ,r-base64enc) | |
6394 | ("r-codetools" ,r-codetools) | |
6395 | ("r-htmltools" ,r-htmltools) | |
6396 | ("r-htmlwidgets" ,r-htmlwidgets) | |
6397 | ("r-knitr" ,r-knitr) | |
6398 | ("r-miniui" ,r-miniui) | |
6399 | ("r-shiny" ,r-shiny) | |
6400 | ("r-webshot" ,r-webshot))) | |
6401 | (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") | |
6402 | (synopsis "Add even more interactivity to interactive charts") | |
6403 | (description | |
6404 | "This package lets you create in just a few lines of R code a nice user interface to | |
6405 | modify the data or the graphical parameters of one or multiple interactive | |
6406 | charts. It is useful to quickly explore visually some data or for package | |
6407 | developers to generate user interfaces easy to maintain.") | |
6408 | (license license:gpl2+))) | |
16b0e8da | 6409 | |
6410 | (define-public r-a3 | |
6411 | (package | |
6412 | (name "r-a3") | |
6413 | (version "1.0.0") | |
6414 | (source | |
6415 | (origin | |
6416 | (method url-fetch) | |
6417 | (uri (cran-uri "A3" version)) | |
6418 | (sha256 | |
6419 | (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) | |
6420 | (properties `((upstream-name . "A3"))) | |
6421 | (build-system r-build-system) | |
6422 | (propagated-inputs | |
6423 | `(("r-pbapply" ,r-pbapply) | |
6424 | ("r-xtable" ,r-xtable))) | |
6425 | (home-page "https://cran.r-project.org/web/packages/A3/") | |
6426 | (synopsis "Error metrics for predictive models") | |
6427 | (description | |
6428 | "This package supplies tools for tabulating and analyzing the results of predictive | |
6429 | models. The methods employed are applicable to virtually any predictive model | |
6430 | and make comparisons between different methodologies straightforward.") | |
6431 | (license license:gpl2+))) | |
59b55def RW |
6432 | |
6433 | (define-public r-infotheo | |
6434 | (package | |
6435 | (name "r-infotheo") | |
6436 | (version "1.2.0") | |
6437 | (source | |
6438 | (origin | |
6439 | (method url-fetch) | |
6440 | (uri (cran-uri "infotheo" version)) | |
6441 | (sha256 | |
6442 | (base32 | |
6443 | "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv")))) | |
6444 | (build-system r-build-system) | |
6445 | (home-page "http://homepage.meyerp.com/software") | |
6446 | (synopsis "Information-theoretic measures") | |
6447 | (description | |
6448 | "This package implements various measures of information theory based on | |
6449 | several entropy estimators.") | |
6450 | (license license:gpl3+))) | |
9e21f217 | 6451 | |
6452 | (define-public r-abcoptim | |
6453 | (package | |
6454 | (name "r-abcoptim") | |
6455 | (version "0.15.0") | |
6456 | (source | |
6457 | (origin | |
6458 | (method url-fetch) | |
6459 | (uri (cran-uri "ABCoptim" version)) | |
6460 | (sha256 | |
6461 | (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) | |
6462 | (properties `((upstream-name . "ABCoptim"))) | |
6463 | (build-system r-build-system) | |
6464 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
6465 | (home-page "https://github.com/gvegayon/ABCoptim/") | |
6466 | (synopsis "Optimization of Artificial Bee Colony algorithm") | |
6467 | (description | |
6468 | "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis | |
6469 | Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as | |
6470 | simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) | |
6471 | algorithms, and uses only common control parameters such as colony size and | |
6472 | maximum cycle number. The @code{r-abcoptim} implements the Artificial bee | |
6473 | colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. | |
6474 | This version is a work-in-progress and is written in R code.") | |
6475 | (license license:expat))) | |
40c10917 | 6476 | |
6477 | (define-public r-abcp2 | |
6478 | (package | |
6479 | (name "r-abcp2") | |
6480 | (version "1.2") | |
6481 | (source | |
6482 | (origin | |
6483 | (method url-fetch) | |
6484 | (uri (cran-uri "ABCp2" version)) | |
6485 | (sha256 | |
6486 | (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) | |
6487 | (properties `((upstream-name . "ABCp2"))) | |
6488 | (build-system r-build-system) | |
6489 | (propagated-inputs `(("r-mass" ,r-mass))) | |
6490 | (home-page "https://cran.r-project.org/web/packages/ABCp2/") | |
6491 | (synopsis "Approximate Bayesian Computational Model for Estimating P2") | |
6492 | (description | |
6493 | "This package tests the goodness of fit of a distribution of offspring to the Normal, | |
6494 | Poisson, and Gamma distribution and estimates the proportional paternity of the | |
6495 | second male (P2) based on the best fit distribution.") | |
6496 | (license license:gpl2))) | |
cadc10a5 | 6497 | |
6498 | (define-public r-abcrf | |
6499 | (package | |
6500 | (name "r-abcrf") | |
6501 | (version "1.7.1") | |
6502 | (source | |
6503 | (origin | |
6504 | (method url-fetch) | |
6505 | (uri (cran-uri "abcrf" version)) | |
6506 | (sha256 | |
6507 | (base32 "06vy3inikrr9hv36q4djhrgzi9zizdfnhz17wpra8kadmr7qj441")))) | |
6508 | (build-system r-build-system) | |
6509 | (propagated-inputs | |
6510 | `(("r-mass" ,r-mass) | |
6511 | ("r-matrixstats" ,r-matrixstats) | |
6512 | ("r-ranger" ,r-ranger) | |
6513 | ("r-rcpp" ,r-rcpp) | |
6514 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6515 | ("r-readr" ,r-readr) | |
6516 | ("r-stringr" ,r-stringr))) | |
6517 | (home-page "https://cran.r-project.org/web/packages/abcrf/") | |
6518 | (synopsis "Approximate bayesian computation via random forests") | |
6519 | (description | |
6520 | "This package performs approximate bayesian computation (ABC) model choice and | |
6521 | parameter inference via random forests. This machine learning tool named random | |
6522 | forests (RF) can conduct selection among the highly complex models covered by | |
6523 | ABC algorithms.") | |
6524 | (license license:gpl2+))) | |
12da2a5e | 6525 | |
6526 | (define-public r-abctools | |
6527 | (package | |
6528 | (name "r-abctools") | |
6529 | (version "1.1.3") | |
6530 | (source | |
6531 | (origin | |
6532 | (method url-fetch) | |
6533 | (uri (cran-uri "abctools" version)) | |
6534 | (sha256 | |
6535 | (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) | |
6536 | (build-system r-build-system) | |
6537 | (propagated-inputs | |
6538 | `(("r-abc" ,r-abc) | |
6539 | ("r-abind" ,r-abind) | |
6540 | ("r-hmisc" ,r-hmisc) | |
6541 | ("r-plyr" ,r-plyr))) | |
6542 | (home-page "https://github.com/dennisprangle/abctools/") | |
6543 | (synopsis "Tools for ABC analyses") | |
6544 | (description | |
6545 | "This @code{r-abctools} package provides tools for approximate Bayesian computation | |
6546 | including summary statistic selection and assessing coverage. This includes | |
6547 | recent dimension reduction algorithms to tune the choice of summary statistics, | |
6548 | and coverage methods to tune the choice of threshold.") | |
6549 | (license license:gpl2+))) | |
77b33e0e | 6550 | |
6551 | (define-public r-ggstance | |
6552 | (package | |
6553 | (name "r-ggstance") | |
6554 | (version "0.3.1") | |
6555 | (source | |
6556 | (origin | |
6557 | (method url-fetch) | |
6558 | (uri (cran-uri "ggstance" version)) | |
6559 | (sha256 | |
6560 | (base32 "0v7f3xdaaridw6d4jvnsfwxmpjrasvx5vl555wsrn50aah17fkvh")))) | |
6561 | (build-system r-build-system) | |
6562 | (propagated-inputs | |
6563 | `(("r-ggplot2" ,r-ggplot2) | |
6564 | ("r-plyr" ,r-plyr) | |
6565 | ("r-rlang" ,r-rlang) | |
6566 | ("r-withr" ,r-withr))) | |
6567 | (home-page "https://cran.r-project.org/web/packages/ggstance/") | |
6568 | (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") | |
6569 | (description | |
6570 | "This package is a @code{r-ggplot2} extension that provides flipped components: | |
6571 | @enumerate | |
6572 | @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms; | |
6573 | @item vertical versions of @code{r-ggplot2} positions. | |
6574 | @end enumerate") | |
6575 | (license license:gpl3))) | |
c61f7bc5 | 6576 | |
6577 | (define-public r-mosaiccore | |
6578 | (package | |
6579 | (name "r-mosaiccore") | |
6580 | (version "0.6.0") | |
6581 | (source | |
6582 | (origin | |
6583 | (method url-fetch) | |
6584 | (uri (cran-uri "mosaicCore" version)) | |
6585 | (sha256 | |
6586 | (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z")))) | |
6587 | (properties `((upstream-name . "mosaicCore"))) | |
6588 | (build-system r-build-system) | |
6589 | (propagated-inputs | |
6590 | `(("r-dplyr" ,r-dplyr) | |
6591 | ("r-lazyeval" ,r-lazyeval) | |
6592 | ("r-mass" ,r-mass) | |
6593 | ("r-rlang" ,r-rlang) | |
6594 | ("r-tidyr" ,r-tidyr))) | |
6595 | (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") | |
6596 | (synopsis "Common utilities for mosaic family packages") | |
6597 | (description | |
6598 | "Common utilities used in other Mosaic family packages are collected here.") | |
6599 | (license license:gpl2+))) | |
214452ff | 6600 | |
6601 | (define-public r-ggformula | |
6602 | (package | |
6603 | (name "r-ggformula") | |
104e7c3c | 6604 | (version "0.9.1") |
214452ff | 6605 | (source |
6606 | (origin | |
6607 | (method url-fetch) | |
6608 | (uri (cran-uri "ggformula" version)) | |
6609 | (sha256 | |
104e7c3c | 6610 | (base32 "01ngx8qh9lhmagng6abx2ky54zi3iyj5bpxlnw59slagwv7l6icx")))) |
214452ff | 6611 | (build-system r-build-system) |
6612 | (propagated-inputs | |
6613 | `(("r-ggplot2" ,r-ggplot2) | |
6614 | ("r-ggstance" ,r-ggstance) | |
6615 | ("r-magrittr" ,r-magrittr) | |
6616 | ("r-mosaiccore" ,r-mosaiccore) | |
6617 | ("r-rlang" ,r-rlang) | |
6618 | ("r-stringr" ,r-stringr) | |
6619 | ("r-tibble" ,r-tibble) | |
6620 | ("r-tidyr" ,r-tidyr))) | |
6621 | (home-page "https://github.com/ProjectMOSAIC/ggformula/") | |
6622 | (synopsis "Formula interface for the @code{r-ggplot2}") | |
6623 | (description | |
6624 | "The @code{r-ggformula} introduces a family of graphics functions, gf_point(), | |
6625 | gf_density(), and so on, bring the formula interface to ggplot(). This captures | |
6626 | and extends the excellent simplicity of the lattice-graphics formula interface, | |
6627 | while providing the intuitive capabilities of @code{r-ggplot2}.") | |
6628 | (license license:expat))) | |
2f195b6f | 6629 | |
6630 | (define-public r-mosaicdata | |
6631 | (package | |
6632 | (name "r-mosaicdata") | |
6633 | (version "0.17.0") | |
6634 | (source | |
6635 | (origin | |
6636 | (method url-fetch) | |
6637 | (uri (cran-uri "mosaicData" version)) | |
6638 | (sha256 | |
6639 | (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9")))) | |
6640 | (properties `((upstream-name . "mosaicData"))) | |
6641 | (build-system r-build-system) | |
6642 | (home-page "https://cran.r-project.org/web/packages/mosaicData/") | |
6643 | (synopsis "Data sets for project Mosaic") | |
6644 | (description | |
6645 | "This package provides data sets from project Mosaic @url{http://mosaic-web.org} | |
6646 | used to teach mathematics, statistics, computation and modeling.") | |
6647 | (license license:gpl2+))) | |
6c6ce2d0 | 6648 | |
82acd43c RW |
6649 | (define-public r-raster |
6650 | (package | |
6651 | (name "r-raster") | |
aff13de3 | 6652 | (version "2.8-19") |
82acd43c RW |
6653 | (source |
6654 | (origin | |
6655 | (method url-fetch) | |
6656 | (uri (cran-uri "raster" version)) | |
6657 | (sha256 | |
6658 | (base32 | |
aff13de3 | 6659 | "1lmhf7p7is8ai7lv7zsj2rdzf83j7ccl4x7a9vwxxa824zy4bkf4")))) |
82acd43c RW |
6660 | (build-system r-build-system) |
6661 | (propagated-inputs | |
6662 | `(("r-rcpp" ,r-rcpp) | |
6663 | ("r-sp" ,r-sp))) | |
aff13de3 | 6664 | (home-page "https://www.rspatial.org/") |
82acd43c RW |
6665 | (synopsis "Geographic data analysis and modeling") |
6666 | (description | |
6667 | "The package implements basic and high-level functions for reading, | |
6668 | writing, manipulating, analyzing and modeling of gridded spatial data. | |
6669 | Processing of very large files is supported.") | |
6670 | (license license:gpl3+))) | |
6671 | ||
6c6ce2d0 | 6672 | (define-public r-mosaic |
6673 | (package | |
6674 | (name "r-mosaic") | |
6675 | (version "1.4.0") | |
6676 | (source | |
6677 | (origin | |
6678 | (method url-fetch) | |
6679 | (uri (cran-uri "mosaic" version)) | |
6680 | (sha256 | |
6681 | (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2")))) | |
6682 | (build-system r-build-system) | |
6683 | (propagated-inputs | |
6684 | `(("r-broom" ,r-broom) | |
6685 | ("r-dplyr" ,r-dplyr) | |
6686 | ("r-ggdendro" ,r-ggdendro) | |
6687 | ("r-ggformula" ,r-ggformula) | |
6688 | ("r-ggplot2" ,r-ggplot2) | |
6689 | ("r-ggrepel" ,r-ggrepel) | |
6690 | ("r-glue" ,r-glue) | |
6691 | ("r-gridextra" ,r-gridextra) | |
6692 | ("r-lattice" ,r-lattice) | |
6693 | ("r-latticeextra" ,r-latticeextra) | |
6694 | ("r-lazyeval" ,r-lazyeval) | |
6695 | ("r-mass" ,r-mass) | |
6696 | ("r-matrix" ,r-matrix) | |
6697 | ("r-mosaiccore" ,r-mosaiccore) | |
6698 | ("r-mosaicdata" ,r-mosaicdata) | |
6699 | ("r-readr" ,r-readr) | |
6700 | ("r-tidyr" ,r-tidyr))) | |
6701 | (home-page "https://github.com/ProjectMOSAIC/mosaic/") | |
6702 | (synopsis "Mathematics, statistics, and computation teaching utilities") | |
6703 | (description | |
6704 | "This package contain data sets and utilities from | |
6705 | @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics, | |
6706 | statistics, computation and modeling. Project MOSAIC is a community of | |
6707 | educators working to tie together aspects of quantitative work that students | |
6708 | in science, technology, engineering and mathematics will need in their | |
6709 | professional lives, but which are usually taught in isolation, if at all.") | |
6710 | (license license:gpl2+))) | |
cbb0edd1 | 6711 | |
6712 | (define-public r-abd | |
6713 | (package | |
6714 | (name "r-abd") | |
6715 | (version "0.2-8") | |
6716 | (source | |
6717 | (origin | |
6718 | (method url-fetch) | |
6719 | (uri (cran-uri "abd" version)) | |
6720 | (sha256 | |
6721 | (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7")))) | |
6722 | (build-system r-build-system) | |
6723 | (propagated-inputs | |
6724 | `(("r-lattice" ,r-lattice) | |
6725 | ("r-mosaic" ,r-mosaic) | |
6726 | ("r-nlme" ,r-nlme))) | |
6727 | (home-page "https://cran.r-project.org/web/packages/abd/") | |
6728 | (synopsis "Analysis of biological data") | |
6729 | (description | |
6730 | "The @code{r-abd} package contains data sets and sample code for the Analysis of | |
6731 | biological data by Michael Whitlock and Dolph Schluter.") | |
6732 | (license license:gpl2))) | |
01af264d MIP |
6733 | |
6734 | (define-public r-svgui | |
6735 | (package | |
6736 | (name "r-svgui") | |
6737 | (version "1.0.0") | |
6738 | (source | |
6739 | (origin | |
6740 | (method url-fetch) | |
6741 | (uri (cran-uri "svGUI" version)) | |
6742 | (sha256 | |
6743 | (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc")))) | |
6744 | (properties `((upstream-name . "svGUI"))) | |
6745 | (build-system r-build-system) | |
6746 | (home-page "https://github.com/SciViews/svGUI/") | |
6747 | (synopsis "Functions for managing GUI clients in R") | |
6748 | (description | |
6749 | "The SciViews @code{svGUI} package eases the management of Graphical User | |
6750 | Interfaces (GUI) in R. It is independent from any particular GUI widgets. It | |
6751 | centralizes info about GUI elements currently used, and it dispatches GUI | |
6752 | calls to the particular toolkits in use in function of the context.") | |
6753 | (license license:gpl2))) | |
d1ca3d72 | 6754 | |
6755 | (define-public r-svdialogs | |
6756 | (package | |
6757 | (name "r-svdialogs") | |
6758 | (version "1.0.0") | |
6759 | (source | |
6760 | (origin | |
6761 | (method url-fetch) | |
6762 | (uri (cran-uri "svDialogs" version)) | |
6763 | (sha256 | |
6764 | (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97")))) | |
6765 | (properties `((upstream-name . "svDialogs"))) | |
6766 | (build-system r-build-system) | |
6767 | (inputs | |
6768 | `(("yad" ,yad) | |
6769 | ("zenity" ,zenity))) | |
6770 | (propagated-inputs | |
6771 | `(("r-rstudioapi" ,r-rstudioapi) | |
6772 | ("r-svgui" ,r-svgui))) | |
6773 | (home-page "https://github.com/SciViews/svDialogs/") | |
6774 | (synopsis "Portable dialog boxes") | |
6775 | (description | |
6776 | "This package helps to construct standard dialog boxes for your GUI, including | |
6777 | message boxes, input boxes, list, file or directory selection, and others. In | |
6778 | case R cannot display GUI dialog boxes, a simpler command line version of these | |
6779 | interactive elements is also provided as a fallback solution.") | |
6780 | (license license:gpl2))) | |
3cadd3ce | 6781 | |
6782 | (define-public r-abe | |
6783 | (package | |
6784 | (name "r-abe") | |
6785 | (version "3.0.1") | |
6786 | (source | |
6787 | (origin | |
6788 | (method url-fetch) | |
6789 | (uri (cran-uri "abe" version)) | |
6790 | (sha256 | |
6791 | (base32 | |
6792 | "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6")))) | |
6793 | (build-system r-build-system) | |
6794 | (home-page "https://cran.r-project.org/web/packages/abe/") | |
6795 | (synopsis "Augmented backward elimination") | |
6796 | (description | |
6797 | "This package performs augmented backward elimination and checks the | |
6798 | stability of the obtained model. Augmented backward elimination combines | |
6799 | significance or information based criteria with the change in estimate to | |
6800 | either select the optimal model for prediction purposes or to serve as a tool | |
6801 | to obtain a practically sound, highly interpretable model.") | |
6802 | (license license:gpl2+))) | |
ef26400b | 6803 | |
6804 | (define-public r-abf2 | |
6805 | (package | |
6806 | (name "r-abf2") | |
6807 | (version "0.7-1") | |
6808 | (source | |
6809 | (origin | |
6810 | (method url-fetch) | |
6811 | (uri (cran-uri "abf2" version)) | |
6812 | (sha256 | |
6813 | (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx")))) | |
6814 | (build-system r-build-system) | |
6815 | (home-page "https://cran.r-project.org/web/packages/abf2/") | |
6816 | (synopsis "Load gap-free axon @code{r-abf2} files") | |
6817 | (description | |
6818 | "This package loads electrophysiology data from ABF2 files, as created by | |
6819 | Axon Instruments/Molecular Devices software. Only files recorded in gap-free | |
6820 | mode are currently supported.") | |
6821 | (license license:artistic2.0))) | |
1efcd0f1 | 6822 | |
6823 | (define-public r-abhgenotyper | |
6824 | (package | |
6825 | (name "r-abhgenotyper") | |
6826 | (version "1.0.1") | |
6827 | (source | |
6828 | (origin | |
6829 | (method url-fetch) | |
6830 | (uri (cran-uri "ABHgenotypeR" version)) | |
6831 | (sha256 | |
6832 | (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l")))) | |
6833 | (properties `((upstream-name . "ABHgenotypeR"))) | |
6834 | (build-system r-build-system) | |
6835 | (propagated-inputs | |
6836 | `(("r-ggplot2" ,r-ggplot2) | |
6837 | ("r-reshape2" ,r-reshape2))) | |
6838 | (home-page "https://github.com/StefanReuscher/ABHgenotypeR/") | |
6839 | (synopsis "Visualize and manipulate ABH genotypes") | |
6840 | (description | |
6841 | "The @code{r-abhgenotyper} package provides simple imputation, | |
6842 | error-correction and plotting capacities for genotype data. The package is | |
6843 | supposed to serve as an intermediate but independent analysis tool between the | |
6844 | TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities | |
6845 | not found in either TASSEL or @code{r-qtl} in addition to visualization of | |
6846 | genotypes as \"graphical genotypes\".") | |
6847 | (license license:gpl3))) | |
ebb3cdb1 | 6848 | |
6e8b38d3 RW |
6849 | (define-public r-furrr |
6850 | (package | |
6851 | (name "r-furrr") | |
6852 | (version "0.1.0") | |
6853 | (source | |
6854 | (origin | |
6855 | (method url-fetch) | |
6856 | (uri (cran-uri "furrr" version)) | |
6857 | (sha256 | |
6858 | (base32 | |
6859 | "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx")))) | |
6860 | (build-system r-build-system) | |
6861 | (propagated-inputs | |
6862 | `(("r-future" ,r-future) | |
6863 | ("r-globals" ,r-globals) | |
6864 | ("r-purrr" ,r-purrr) | |
6865 | ("r-rlang" ,r-rlang))) | |
6866 | (home-page "https://github.com/DavisVaughan/furrr") | |
6867 | (synopsis "Apply mapping functions in parallel using futures") | |
6868 | (description | |
6869 | "This package provides implementations of the family of @code{map()} | |
6870 | functions from the @code{purrr} package that can be resolved using any | |
6871 | @code{future}-supported backend, e.g. parallel on the local machine or | |
6872 | distributed on a compute cluster.") | |
6873 | (license license:lgpl2.1+))) | |
6874 | ||
ebb3cdb1 | 6875 | (define-public r-abjutils |
6876 | (package | |
6877 | (name "r-abjutils") | |
3d5bcae0 | 6878 | (version "0.2.3") |
ebb3cdb1 | 6879 | (source |
6880 | (origin | |
6881 | (method url-fetch) | |
6882 | (uri (cran-uri "abjutils" version)) | |
6883 | (sha256 | |
3d5bcae0 | 6884 | (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv")))) |
ebb3cdb1 | 6885 | (build-system r-build-system) |
6886 | (propagated-inputs | |
6887 | `(("r-devtools" ,r-devtools) | |
6888 | ("r-dplyr" ,r-dplyr) | |
3d5bcae0 RW |
6889 | ("r-furrr" ,r-furrr) |
6890 | ("r-future" ,r-future) | |
ebb3cdb1 | 6891 | ("r-glue" ,r-glue) |
6892 | ("r-httr" ,r-httr) | |
6893 | ("r-magrittr" ,r-magrittr) | |
ebb3cdb1 | 6894 | ("r-progress" ,r-progress) |
6895 | ("r-purrr" ,r-purrr) | |
3d5bcae0 RW |
6896 | ("r-readr" ,r-readr) |
6897 | ("r-rlang" ,r-rlang) | |
ebb3cdb1 | 6898 | ("r-rstudioapi" ,r-rstudioapi) |
6899 | ("r-scales" ,r-scales) | |
6900 | ("r-stringi" ,r-stringi) | |
6901 | ("r-stringr" ,r-stringr) | |
6902 | ("r-tibble" ,r-tibble) | |
6903 | ("r-tidyr" ,r-tidyr))) | |
6904 | (home-page "https://github.com/abjur/abjutils/") | |
6905 | (synopsis "Collection of tools for jurimetrical analysis") | |
6906 | (description | |
6907 | "This package implements general purpose tools, such as functions for | |
6908 | sampling and basic manipulation of Brazilian lawsuits identification number. | |
6909 | It also implements functions for text cleaning, such as accentuation | |
6910 | removal.") | |
6911 | (license license:expat))) | |
b6afe7b7 | 6912 | |
6913 | (define-public r-abnormality | |
6914 | (package | |
6915 | (name "r-abnormality") | |
6916 | (version "0.1.0") | |
6917 | (source | |
6918 | (origin | |
6919 | (method url-fetch) | |
6920 | (uri (cran-uri "abnormality" version)) | |
6921 | (sha256 | |
6922 | (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) | |
6923 | (build-system r-build-system) | |
6924 | (propagated-inputs | |
6925 | `(("r-mass" ,r-mass) | |
6926 | ("r-matrix" ,r-matrix))) | |
6927 | (home-page "https://cran.r-project.org/web/packages/abnormality/") | |
6928 | (synopsis "Measure a subject's abnormality with respect to a reference population") | |
6929 | (description | |
6930 | "This package contains functions to implement the methodology and | |
6931 | considerations laid out by Marks et al. in the article \"Measuring abnormality | |
6932 | in high dimensional spaces: applications in biomechanical gait analysis\". | |
6933 | Using high-dimensional datasets to measure a subject's overall level of | |
6934 | abnormality as compared to a reference population is often needed in outcomes | |
6935 | research.") | |
6936 | (license license:expat))) | |
016cabf7 | 6937 | |
6938 | (define-public r-abodoutlier | |
6939 | (package | |
6940 | (name "r-abodoutlier") | |
6941 | (version "0.1") | |
6942 | (source | |
6943 | (origin | |
6944 | (method url-fetch) | |
6945 | (uri (cran-uri "abodOutlier" version)) | |
6946 | (sha256 | |
6947 | (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj")))) | |
6948 | (properties `((upstream-name . "abodOutlier"))) | |
6949 | (build-system r-build-system) | |
6950 | (propagated-inputs | |
6951 | `(("r-cluster" ,r-cluster))) | |
6952 | (home-page "https://cran.r-project.org/web/packages/abodOutlier/") | |
6953 | (synopsis "Angle-based outlier detection") | |
6954 | (description | |
6955 | "This package performs angle-based outlier detection on a given data | |
6956 | frame. It offers three methods to process data: | |
6957 | @enumerate | |
6958 | @item full but slow implementation using all the data that has cubic | |
6959 | complexity; | |
6960 | @item a fully randomized method; | |
6961 | @item a method using k-nearest neighbours. | |
6962 | @end enumerate | |
6963 | These algorithms are well suited for high dimensional data outlier | |
6964 | detection.") | |
6965 | (license license:expat))) | |
03c95f04 | 6966 | |
6967 | (define-public r-abps | |
6968 | (package | |
6969 | (name "r-abps") | |
bec74196 | 6970 | (version "0.3") |
03c95f04 | 6971 | (source |
6972 | (origin | |
6973 | (method url-fetch) | |
6974 | (uri (cran-uri "ABPS" version)) | |
6975 | (sha256 | |
bec74196 | 6976 | (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) |
03c95f04 | 6977 | (properties `((upstream-name . "ABPS"))) |
6978 | (build-system r-build-system) | |
6979 | (propagated-inputs `(("r-kernlab" ,r-kernlab))) | |
6980 | (home-page "https://cran.r-project.org/web/packages/ABPS/") | |
6981 | (synopsis "Abnormal blood profile score to detect blood doping") | |
6982 | (description | |
6983 | "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS). | |
6984 | The ABPS is a part of the Athlete biological passport program of the World | |
6985 | anti-doping agency, which combines several blood parameters into a single | |
6986 | score in order to detect blood doping. The package also contains functions to | |
6987 | calculate other scores used in anti-doping programs, such as the ratio of | |
6988 | hemoglobin to reticulocytes (OFF-score), as well as example data.") | |
6989 | (license license:gpl2+))) | |
26358ac5 RW |
6990 | |
6991 | (define-public r-parmigene | |
6992 | (package | |
6993 | (name "r-parmigene") | |
6994 | (version "1.0.2") | |
6995 | (source | |
6996 | (origin | |
6997 | (method url-fetch) | |
6998 | (uri (cran-uri "parmigene" version)) | |
6999 | (sha256 | |
7000 | (base32 | |
7001 | "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d")))) | |
7002 | (build-system r-build-system) | |
7003 | (home-page "https://cran.r-project.org/web/packages/parmigene/") | |
7004 | (synopsis "Mutual information estimation for gene network reconstruction") | |
7005 | (description | |
7006 | "This package provides a parallel estimation of the mutual information | |
7007 | based on entropy estimates from k-nearest neighbors distances and algorithms | |
7008 | for the reconstruction of gene regulatory networks.") | |
7009 | (license license:agpl3+))) | |
b2bf43b2 | 7010 | |
7011 | (define-public r-pscl | |
7012 | (package | |
7013 | (name "r-pscl") | |
7014 | (version "1.5.2") | |
7015 | (source | |
7016 | (origin | |
7017 | (method url-fetch) | |
7018 | (uri (cran-uri "pscl" version)) | |
7019 | (sha256 | |
7020 | (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc")))) | |
7021 | (build-system r-build-system) | |
7022 | (propagated-inputs | |
7023 | `(("r-mass" ,r-mass))) | |
7024 | (home-page "https://github.com/atahk/pscl/") | |
7025 | (synopsis "Political science computational laboratory") | |
7026 | (description | |
7027 | "The @code{pscl} is an R package providing classes and methods for: | |
7028 | @enumerate | |
7029 | @item Bayesian analysis of roll call data (item-response models); | |
7030 | @item elementary Bayesian statistics; | |
7031 | @item maximum likelihood estimation of zero-inflated and hurdle models for count | |
7032 | data; | |
7033 | @item utility functions. | |
7034 | @end enumerate") | |
7035 | (license license:gpl2))) | |
e710d1a4 | 7036 | |
7037 | (define-public r-accelmissing | |
7038 | (package | |
7039 | (name "r-accelmissing") | |
7040 | (version "1.4") | |
7041 | (source | |
7042 | (origin | |
7043 | (method url-fetch) | |
7044 | (uri (cran-uri "accelmissing" version)) | |
7045 | (sha256 | |
7046 | (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) | |
7047 | (build-system r-build-system) | |
7048 | (propagated-inputs | |
7049 | `(("r-mice" ,r-mice) | |
7050 | ("r-pscl" ,r-pscl))) | |
7051 | (home-page "https://cran.r-project.org/web/packages/accelmissing/") | |
7052 | (synopsis "Missing value imputation for accelerometer data") | |
7053 | (description | |
7054 | "This package provides a statistical method to impute the missing values in | |
7055 | accelerometer data. The methodology includes both parametric and | |
7056 | semi-parametric multiple imputations under the zero-inflated Poisson lognormal | |
7057 | model. It also provides multiple functions to preprocess the accelerometer data | |
7058 | previous to the missing data imputation. These include detecting the wearing | |
7059 | and the non-wearing time, selecting valid days and subjects, and creating plots.") | |
7060 | (license license:gpl2+))) | |
f359b115 | 7061 | |
7062 | (define-public r-mhsmm | |
7063 | (package | |
7064 | (name "r-mhsmm") | |
7065 | (version "0.4.16") | |
7066 | (source | |
7067 | (origin | |
7068 | (method url-fetch) | |
7069 | (uri (cran-uri "mhsmm" version)) | |
7070 | (sha256 | |
7071 | (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) | |
7072 | (build-system r-build-system) | |
7073 | (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) | |
7074 | (home-page "https://github.com/jaredo/mhsmm/") | |
7075 | (synopsis "Inference for hidden Markov and semi-Markov models") | |
7076 | (description | |
7077 | "The @code{r-mhsmm} package implements estimation and prediction methods for | |
7078 | hidden Markov and semi-Markov models for multiple observation sequences. Such | |
7079 | techniques are of interest when observed data is thought to be dependent on some | |
7080 | unobserved (or hidden) state. Also, this package is suitable for equidistant | |
7081 | time series data, with multivariate and/or missing data. Allows user defined | |
7082 | emission distributions.") | |
7083 | (license license:gpl2+))) | |
16c5285a | 7084 | |
7085 | (define-public r-nleqslv | |
7086 | (package | |
7087 | (name "r-nleqslv") | |
7088 | (version "3.3.2") | |
7089 | (source | |
7090 | (origin | |
7091 | (method url-fetch) | |
7092 | (uri (cran-uri "nleqslv" version)) | |
7093 | (sha256 | |
7094 | (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) | |
7095 | (build-system r-build-system) | |
7096 | (native-inputs `(("gfortran" ,gfortran))) | |
7097 | (home-page "https://cran.r-project.org/web/packages/nleqslv/") | |
7098 | (synopsis "Solve systems of nonlinear equations") | |
7099 | (description | |
7100 | "The @code{r-nleqslv} package solves a system of nonlinear equations using a | |
7101 | Broyden or a Newton method with a choice of global strategies such as line | |
7102 | search and trust region. There are options for using a numerical or user | |
7103 | supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a | |
7104 | singular or ill-conditioned Jacobian.") | |
7105 | (license license:gpl2+))) | |
63ec2c50 | 7106 | |
7107 | (define-public r-physicalactivity | |
7108 | (package | |
7109 | (name "r-physicalactivity") | |
7110 | (version "0.2-2") | |
7111 | (source | |
7112 | (origin | |
7113 | (method url-fetch) | |
7114 | (uri (cran-uri "PhysicalActivity" version)) | |
7115 | (sha256 | |
7116 | (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln")))) | |
7117 | (properties | |
7118 | `((upstream-name . "PhysicalActivity"))) | |
7119 | (build-system r-build-system) | |
7120 | (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") | |
7121 | (synopsis "Procesing accelerometer data for physical activity measurement") | |
7122 | (description | |
7123 | "This @code{r-physicalactivity} package provides a function @code{wearingMarking} | |
7124 | for classification of monitor wear and nonwear time intervals in accelerometer | |
7125 | data collected to assess physical activity. The package also contains functions | |
7126 | for making plots of accelerometer data and obtaining the summary of various | |
7127 | information including daily monitor wear time and the mean monitor wear time | |
7128 | during valid days. The revised package version 0.2-1 improved the functions | |
7129 | regarding speed, robustness and add better support for time zones and daylight | |
7130 | saving. In addition, several functions were added: | |
7131 | @enumerate | |
7132 | @item the @code{markDelivery} can classify days for ActiGraph delivery by mail; | |
7133 | @item the @code{markPAI} can categorize physical activity intensity level based | |
7134 | on user-defined cut-points of accelerometer counts. | |
7135 | @end enumerate | |
7136 | It also supports importing ActiGraph (AGD) files with @code{readActigraph} and | |
7137 | @code{queryActigraph} functions.") | |
7138 | (license license:gpl3+))) | |
f95d4542 | 7139 | |
7140 | (define-public r-acc | |
7141 | (package | |
7142 | (name "r-acc") | |
7143 | (version "1.3.3") | |
7144 | (source | |
7145 | (origin | |
7146 | (method url-fetch) | |
7147 | (uri (cran-uri "acc" version)) | |
7148 | (sha256 | |
7149 | (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) | |
7150 | (build-system r-build-system) | |
7151 | (propagated-inputs | |
7152 | `(("r-circlize" ,r-circlize) | |
7153 | ("r-dbi" ,r-dbi) | |
7154 | ("r-ggplot2" ,r-ggplot2) | |
7155 | ("r-iterators" ,r-iterators) | |
7156 | ("r-mhsmm" ,r-mhsmm) | |
7157 | ("r-nleqslv" ,r-nleqslv) | |
7158 | ("r-physicalactivity" ,r-physicalactivity) | |
7159 | ("r-plyr" ,r-plyr) | |
7160 | ("r-r-utils" ,r-r-utils) | |
7161 | ("r-rcpp" ,r-rcpp) | |
7162 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
7163 | ("r-rsqlite" ,r-rsqlite) | |
7164 | ("r-zoo" ,r-zoo))) | |
7165 | (home-page "https://cran.r-project.org/web/packages/acc/") | |
7166 | (synopsis "Exploring accelerometer data") | |
7167 | (description | |
7168 | "This package processes accelerometer data from uni-axial and tri-axial devices | |
7169 | and generates data summaries. Also, includes functions to plot, analyze, and | |
7170 | simulate accelerometer data.") | |
7171 | (license license:gpl2+))) | |
f6890c08 | 7172 | |
7173 | (define-public r-rbenchmark | |
7174 | (package | |
7175 | (name "r-rbenchmark") | |
7176 | (version "1.0.0") | |
7177 | (source | |
7178 | (origin | |
7179 | (method url-fetch) | |
7180 | (uri (cran-uri "rbenchmark" version)) | |
7181 | (sha256 | |
7182 | (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9")))) | |
7183 | (build-system r-build-system) | |
7184 | (home-page "https://cran.r-project.org/web/packages/rbenchmark/") | |
7185 | (synopsis "Benchmarking routine for R") | |
7186 | (description | |
7187 | "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark, | |
7188 | and is intended to facilitate benchmarking of arbitrary R code. The library | |
7189 | consists of just one function, benchmark, which is a simple wrapper around | |
7190 | system.time. Given a specification of the benchmarking process (counts of | |
7191 | replications, evaluation environment) and an arbitrary number of expressions, | |
7192 | benchmark evaluates each of the expressions in the specified environment, | |
7193 | replicating the evaluation as many times as specified, and returning the results | |
7194 | conveniently wrapped into a data frame.") | |
7195 | (license license:gpl2+))) | |
7196 | ||
dab3e92c RW |
7197 | (define-public r-magick |
7198 | (package | |
7199 | (name "r-magick") | |
7200 | (version "2.0") | |
7201 | (source | |
7202 | (origin | |
7203 | (method url-fetch) | |
7204 | (uri (cran-uri "magick" version)) | |
7205 | (sha256 | |
7206 | (base32 | |
7207 | "18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m")))) | |
7208 | (build-system r-build-system) | |
7209 | (inputs | |
7210 | `(("imagemagick" ,imagemagick) | |
7211 | ("zlib" ,zlib))) | |
7212 | (propagated-inputs | |
7213 | `(("r-curl" ,r-curl) | |
7214 | ("r-magrittr" ,r-magrittr) | |
7215 | ("r-rcpp" ,r-rcpp))) | |
7216 | (native-inputs | |
7217 | `(("pkg-config" ,pkg-config))) | |
7218 | (home-page "https://github.com/ropensci/magick") | |
7219 | (synopsis "Advanced graphics and image-processing in R") | |
7220 | (description | |
7221 | "This package provides bindings to ImageMagick, a comprehensive image | |
7222 | processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, | |
7223 | etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All | |
7224 | operations are vectorized via the Magick++ STL meaning they operate either on | |
7225 | a single frame or a series of frames for working with layers, collages, or | |
7226 | animation. In RStudio, images are automatically previewed when printed to the | |
7227 | console, resulting in an interactive editing environment.") | |
7228 | (license license:expat))) | |
7229 | ||
f0bff698 RW |
7230 | (define-public r-survey |
7231 | (package | |
7232 | (name "r-survey") | |
7233 | (version "3.35-1") | |
7234 | (source | |
7235 | (origin | |
7236 | (method url-fetch) | |
7237 | (uri (cran-uri "survey" version)) | |
7238 | (sha256 | |
7239 | (base32 | |
7240 | "1nv4sdfmidvyjgvp3zvn5iw35bb8w0v7095is2pdy8cckkgdvr8i")))) | |
7241 | (build-system r-build-system) | |
7242 | (propagated-inputs | |
7243 | `(("r-lattice" ,r-lattice) | |
7244 | ("r-matrix" ,r-matrix) | |
7245 | ("r-minqa" ,r-minqa) | |
7246 | ("r-numderiv" ,r-numderiv) | |
7247 | ("r-survival" ,r-survival))) | |
7248 | (home-page "http://r-survey.r-forge.r-project.org/survey/") | |
7249 | (synopsis "Analysis of complex survey samples") | |
7250 | (description | |
7251 | "This package provides tools for the analysis of complex survey samples. | |
7252 | The provided features include: summary statistics, two-sample tests, rank | |
7253 | tests, generalised linear models, cumulative link models, Cox models, | |
7254 | loglinear models, and general maximum pseudolikelihood estimation for | |
7255 | multistage stratified, cluster-sampled, unequally weighted survey samples; | |
7256 | variances by Taylor series linearisation or replicate weights; | |
7257 | post-stratification, calibration, and raking; two-phase subsampling designs; | |
7258 | graphics; PPS sampling without replacement; principal components, and factor | |
7259 | analysis.") | |
7260 | ;; Either version of the GPL. | |
7261 | (license (list license:gpl2 license:gpl3)))) | |
7262 | ||
7af2dd38 | 7263 | (define-public r-dvmisc |
7264 | (package | |
7265 | (name "r-dvmisc") | |
a6a87db8 | 7266 | (version "1.1.3") |
7af2dd38 | 7267 | (source |
7268 | (origin | |
7269 | (method url-fetch) | |
7270 | (uri (cran-uri "dvmisc" version)) | |
7271 | (sha256 | |
a6a87db8 | 7272 | (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv")))) |
7af2dd38 | 7273 | (build-system r-build-system) |
7274 | (propagated-inputs | |
a6a87db8 RW |
7275 | `(("r-cubature" ,r-cubature) |
7276 | ("r-data-table" ,r-data-table) | |
7277 | ("r-dplyr" ,r-dplyr) | |
7278 | ("r-ggplot2" ,r-ggplot2) | |
7279 | ("r-mass" ,r-mass) | |
7280 | ("r-mvtnorm" ,r-mvtnorm) | |
7281 | ("r-pracma" ,r-pracma) | |
7282 | ("r-purrr" ,r-purrr) | |
7af2dd38 | 7283 | ("r-rbenchmark" ,r-rbenchmark) |
a6a87db8 RW |
7284 | ("r-rcpp" ,r-rcpp) |
7285 | ("r-survey" ,r-survey))) | |
7af2dd38 | 7286 | (home-page "https://cran.r-project.org/web/packages/dvmisc/") |
7287 | (synopsis "Faster computation of common statistics and miscellaneous functions") | |
7288 | (description | |
7289 | "This package implements faster versions of base R functions (e.g. mean, standard | |
7290 | deviation, covariance, weighted mean), mostly written in C++, along with | |
7291 | miscellaneous functions for various purposes (e.g. create the histogram with | |
7292 | fitted probability density function or probability mass function curve, create | |
7293 | the body mass index groups, assess the linearity assumption in logistic | |
7294 | regression).") | |
7295 | (license license:gpl2))) | |
d8d8844e | 7296 | |
7297 | (define-public r-accelerometry | |
7298 | (package | |
7299 | (name "r-accelerometry") | |
7300 | (version "3.1.2") | |
7301 | (source | |
7302 | (origin | |
7303 | (method url-fetch) | |
7304 | (uri (cran-uri "accelerometry" version)) | |
7305 | (sha256 | |
7306 | (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) | |
7307 | (build-system r-build-system) | |
7308 | (propagated-inputs | |
7309 | `(("r-dvmisc" ,r-dvmisc) | |
7310 | ("r-rcpp" ,r-rcpp))) | |
7311 | (home-page "https://cran.r-project.org/web/packages/accelerometry/") | |
7312 | (synopsis "Functions for processing accelerometer data") | |
7313 | (description | |
7314 | "This package provides a collection of functions that perform operations on | |
7315 | time-series accelerometer data, such as identify the non-wear time, flag minutes | |
7316 | that are part of an activity bout, and find the maximum 10-minute average count | |
7317 | value. The functions are generally very flexible, allowing for a variety of | |
7318 | algorithms to be implemented.") | |
7319 | (license license:gpl3))) | |
1ddb2b5c | 7320 | |
7321 | (define-public r-absim | |
7322 | (package | |
7323 | (name "r-absim") | |
7324 | (version "0.2.6") | |
7325 | (source | |
7326 | (origin | |
7327 | (method url-fetch) | |
7328 | (uri (cran-uri "AbSim" version)) | |
7329 | (sha256 | |
7330 | (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) | |
7331 | (properties `((upstream-name . "AbSim"))) | |
7332 | (build-system r-build-system) | |
7333 | (propagated-inputs | |
7334 | `(("r-ape" ,r-ape) | |
7335 | ("r-powerlaw" ,r-powerlaw))) | |
7336 | (home-page "https://cran.r-project.org/web/packages/AbSim/") | |
7337 | (synopsis "Time resolved simulations of antibody repertoires") | |
7338 | (description | |
7339 | "This package provides simulation methods for the evolution of antibody repertoires. | |
7340 | The heavy and light chain variable region of both human and C57BL/6 mice can | |
7341 | be simulated in a time-dependent fashion. Both single lineages using one set of | |
7342 | V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins | |
7343 | with an initial V-D-J recombination event, starting the first phylogenetic tree. | |
7344 | Upon completion, the main loop of the algorithm begins, with each iteration | |
7345 | representing one simulated time step. Various mutation events are possible at | |
7346 | each time step, contributing to a diverse final repertoire.") | |
7347 | (license license:gpl2))) | |
c2ffc4fb | 7348 | |
b5a31005 MIP |
7349 | (define-public r-quic |
7350 | (package | |
7351 | (name "r-quic") | |
7352 | (version "1.1") | |
7353 | (source | |
7354 | (origin | |
7355 | (method url-fetch) | |
7356 | (uri (cran-uri "QUIC" version)) | |
7357 | (sha256 | |
7358 | (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c")))) | |
7359 | (properties `((upstream-name . "QUIC"))) | |
7360 | (build-system r-build-system) | |
7361 | (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/") | |
7362 | (synopsis "Regularized sparse inverse covariance matrix estimation") | |
7363 | (description | |
7364 | "This package implements the regularized Gaussian maximum likelihood | |
7365 | estimation of the inverse of a covariance matrix. It uses Newton's method and | |
7366 | coordinate descent to solve the regularized inverse covariance matrix | |
7367 | estimation problem.") | |
7368 | ;; The project home page states that the release is under GPLv3 or later. | |
7369 | ;; The CRAN page only says GPL-3. | |
7370 | (license license:gpl3+))) | |
7371 | ||
b509df82 MIP |
7372 | (define-public r-abundant |
7373 | (package | |
7374 | (name "r-abundant") | |
7375 | (version "1.1") | |
7376 | (source | |
7377 | (origin | |
7378 | (method url-fetch) | |
7379 | (uri (cran-uri "abundant" version)) | |
7380 | (sha256 | |
7381 | (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) | |
7382 | (build-system r-build-system) | |
7383 | (propagated-inputs | |
7384 | `(("r-quic" ,r-quic))) | |
7385 | (home-page "https://cran.r-project.org/web/packages/abundant/") | |
7386 | (synopsis "Abundant regression and high-dimensional principal fitted components") | |
7387 | (description | |
7388 | "This package provides tools to fit and predict with the high-dimensional | |
7389 | principal fitted components model. This model is described by Cook, Forzani, | |
7390 | and Rothman (2012) @url{doi:10.1214/11-AOS962}.") | |
7391 | ;; The DESCRIPTION file states GPL-2, but since it directly depends on a | |
7392 | ;; GPLv3+ package (QUIC) this likely means GPLv2+. | |
7393 | (license license:gpl2+))) | |
7394 | ||
c2ffc4fb | 7395 | (define-public r-ac3net |
7396 | (package | |
7397 | (name "r-ac3net") | |
7398 | (version "1.2.2") | |
7399 | (source | |
7400 | (origin | |
7401 | (method url-fetch) | |
7402 | (uri (cran-uri "Ac3net" version)) | |
7403 | (sha256 | |
7404 | (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) | |
7405 | (properties `((upstream-name . "Ac3net"))) | |
7406 | (build-system r-build-system) | |
7407 | (propagated-inputs | |
7408 | `(("r-data-table" ,r-data-table))) | |
7409 | (home-page "https://cran.r-project.org/web/packages/Ac3net/") | |
7410 | (synopsis "Inferring directional conservative causal core gene networks") | |
7411 | (description "This package infers directional Conservative causal core | |
7412 | (gene) networks (C3NET). This is a version of the algorithm C3NET with | |
7413 | directional network.") | |
7414 | (license license:gpl3+))) | |
da333859 | 7415 | |
7416 | (define-public r-aca | |
7417 | (package | |
7418 | (name "r-aca") | |
7419 | (version "1.1") | |
7420 | (source | |
7421 | (origin | |
7422 | (method url-fetch) | |
7423 | (uri (cran-uri "ACA" version)) | |
7424 | (sha256 | |
7425 | (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) | |
7426 | (properties `((upstream-name . "ACA"))) | |
7427 | (build-system r-build-system) | |
7428 | (home-page "https://cran.r-project.org/web/packages/ACA/") | |
7429 | (synopsis "Abrupt change-point or aberration detection in point series") | |
7430 | (description | |
7431 | "This package offers an interactive function for the detection of breakpoints in | |
7432 | series.") | |
7433 | ;; Any version of the GPL | |
7434 | (license (list license:gpl2+ license:gpl3+)))) | |
9c1c2108 | 7435 | |
7436 | (define-public r-acceptancesampling | |
7437 | (package | |
7438 | (name "r-acceptancesampling") | |
ddd168ff | 7439 | (version "1.0-6") |
9c1c2108 | 7440 | (source |
7441 | (origin | |
7442 | (method url-fetch) | |
7443 | (uri (cran-uri "AcceptanceSampling" version)) | |
7444 | (sha256 | |
ddd168ff | 7445 | (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9")))) |
9c1c2108 | 7446 | (properties |
7447 | `((upstream-name . "AcceptanceSampling"))) | |
7448 | (build-system r-build-system) | |
7449 | (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") | |
7450 | (synopsis "Creation and evaluation of acceptance sampling plans") | |
7451 | (description | |
7452 | "This @code{r-acceptancesampling} provides functionality for creating and evaluating | |
7453 | acceptance sampling plans. Acceptance sampling is a methodology commonly used | |
7454 | in quality control and improvement. International standards of acceptance | |
7455 | sampling provide sampling plans for specific circumstances. The aim of this | |
7456 | package is to provide an easy-to-use interface to visualize single, double or | |
7457 | multiple sampling plans. In addition, methods have been provided to enable the | |
7458 | user to assess sampling plans against pre-specified levels of performance, as | |
7459 | measured by the probability of acceptance for a given level of quality in the | |
7460 | lot.") | |
7461 | (license license:gpl3+))) | |
7462 | ||
63781c57 LF |
7463 | (define-public r-acclma |
7464 | (package | |
7465 | (name "r-acclma") | |
7466 | (version "1.0") | |
7467 | (source | |
7468 | (origin | |
7469 | (method url-fetch) | |
7470 | (uri (cran-uri "ACCLMA" version)) | |
7471 | (sha256 | |
7472 | (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) | |
7473 | (properties `((upstream-name . "ACCLMA"))) | |
7474 | (build-system r-build-system) | |
7475 | (home-page "https://cran.r-project.org/web/packages/ACCLMA/") | |
7476 | (synopsis "ACC & LMA graph plotting") | |
7477 | (description | |
666fb288 LC |
7478 | "This package contains a function that imports data from a @acronym{CSV, |
7479 | Comma-Separated Values} file, or uses manually entered data from the format (x, | |
7480 | y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration | |
7481 | Curve} vs @acronym{LOI, Line of Independence} graph and | |
7482 | @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main | |
7483 | function is @code{plotLMA} (source file, header) that takes a data set and plots the | |
63781c57 LF |
7484 | appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a |
7485 | string) was passed, a manual data entry window is opened. The header parameter | |
7486 | indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has | |
7487 | a header row or not. The dataset should contain only one independent variable | |
7488 | (x) and one dependent variable (y) and can contain a weight for each | |
7489 | observation.") | |
7490 | (license license:gpl2))) | |
b55697fb LL |
7491 | |
7492 | (define-public r-aspi | |
7493 | (package | |
7494 | (name "r-aspi") | |
7495 | (version "0.2.0") | |
7496 | (source | |
7497 | (origin | |
7498 | (method url-fetch) | |
7499 | (uri (cran-uri "aspi" version)) | |
7500 | (sha256 | |
7501 | (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) | |
7502 | (build-system r-build-system) | |
7503 | (home-page | |
7504 | "https://cran.r-project.org/web/packages/aspi/") | |
7505 | (synopsis | |
7506 | "Analysis of symmetry of parasitic infections") | |
7507 | (description | |
7508 | "This package provides tools for the analysis and visualization of bilateral | |
7509 | asymmetry in parasitic infections.") | |
7510 | (license license:gpl3+))) | |
302db585 RW |
7511 | |
7512 | (define-public r-sandwich | |
7513 | (package | |
7514 | (name "r-sandwich") | |
7515 | (version "2.5-0") | |
7516 | (source | |
7517 | (origin | |
7518 | (method url-fetch) | |
7519 | (uri (cran-uri "sandwich" version)) | |
7520 | (sha256 | |
7521 | (base32 | |
7522 | "168kq5kk34xbhfsxsanard9zriyp6cw0s09ralzb57kk42pl9hbc")))) | |
7523 | (build-system r-build-system) | |
7524 | (propagated-inputs | |
7525 | `(("r-zoo" ,r-zoo))) | |
7526 | (home-page "https://cran.r-project.org/web/packages/sandwich/") | |
7527 | (synopsis "Robust Covariance Matrix Estimators") | |
7528 | (description | |
7529 | "This package provides model-robust standard error estimators for | |
7530 | cross-sectional, time series, clustered, panel, and longitudinal data.") | |
7531 | ;; Either version of the license. | |
7532 | (license (list license:gpl2 license:gpl3)))) | |
6ce07cf9 RW |
7533 | |
7534 | (define-public r-th-data | |
7535 | (package | |
7536 | (name "r-th-data") | |
62595ee3 | 7537 | (version "1.0-10") |
6ce07cf9 RW |
7538 | (source |
7539 | (origin | |
7540 | (method url-fetch) | |
7541 | (uri (cran-uri "TH.data" version)) | |
7542 | (sha256 | |
7543 | (base32 | |
62595ee3 | 7544 | "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1")))) |
6ce07cf9 RW |
7545 | (properties `((upstream-name . "TH.data"))) |
7546 | (build-system r-build-system) | |
7547 | (propagated-inputs | |
7548 | `(("r-mass" ,r-mass) | |
7549 | ("r-survival" ,r-survival))) | |
7550 | (home-page "https://cran.r-project.org/web/packages/TH.data/") | |
7551 | (synopsis "Shared data sets") | |
7552 | (description | |
7553 | "This package contains supporting data sets that are used in other | |
7554 | packages maintained by Torsten Hothorn.") | |
7555 | (license license:gpl3))) | |
7753b543 RW |
7556 | |
7557 | (define-public r-multcomp | |
7558 | (package | |
7559 | (name "r-multcomp") | |
b1f39e8c | 7560 | (version "1.4-10") |
7753b543 RW |
7561 | (source |
7562 | (origin | |
7563 | (method url-fetch) | |
7564 | (uri (cran-uri "multcomp" version)) | |
7565 | (sha256 | |
7566 | (base32 | |
b1f39e8c | 7567 | "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19")))) |
7753b543 RW |
7568 | (build-system r-build-system) |
7569 | (propagated-inputs | |
7570 | `(("r-codetools" ,r-codetools) | |
7571 | ("r-mvtnorm" ,r-mvtnorm) | |
7572 | ("r-sandwich" ,r-sandwich) | |
7573 | ("r-survival" ,r-survival) | |
7574 | ("r-th-data" ,r-th-data))) | |
7575 | (home-page "https://cran.r-project.org/web/packages/multcomp/") | |
7576 | (synopsis "Simultaneous inference in general parametric models") | |
7577 | (description | |
7578 | "Simultaneous tests and confidence intervals for general linear | |
7579 | hypotheses in parametric models, including linear, generalized linear, linear | |
7580 | mixed effects, and survival models. The package includes demos reproducing | |
7581 | analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, | |
7582 | Hothorn, Westfall, 2010, CRC Press).") | |
7583 | (license license:gpl2))) | |
55a08dce RW |
7584 | |
7585 | (define-public r-emmeans | |
7586 | (package | |
7587 | (name "r-emmeans") | |
e0f86164 | 7588 | (version "1.3.3") |
55a08dce RW |
7589 | (source |
7590 | (origin | |
7591 | (method url-fetch) | |
7592 | (uri (cran-uri "emmeans" version)) | |
7593 | (sha256 | |
7594 | (base32 | |
e0f86164 | 7595 | "1hpal1vq6gryzvgfvv9f328idg0mgjvlfnhaj069dhb7zqfwhzlk")))) |
55a08dce RW |
7596 | (build-system r-build-system) |
7597 | (propagated-inputs | |
7598 | `(("r-estimability" ,r-estimability) | |
7599 | ("r-mvtnorm" ,r-mvtnorm) | |
e0f86164 | 7600 | ("r-numderiv" ,r-numderiv) |
55a08dce RW |
7601 | ("r-plyr" ,r-plyr) |
7602 | ("r-xtable" ,r-xtable))) | |
7603 | (home-page "https://github.com/rvlenth/emmeans") | |
7604 | (synopsis "Estimated marginal means, aka least-squares means") | |
7605 | (description | |
7606 | "This package provides tools to obtain @dfn{estimated marginal | |
7607 | means} (EMMs) for many linear, generalized linear, and mixed models. It can | |
7608 | be used to compute contrasts or linear functions of EMMs, trends, and | |
7609 | comparisons of slopes.") | |
7610 | ;; Either version of the license. | |
7611 | (license (list license:gpl2 license:gpl3)))) | |
63fcb88a RW |
7612 | |
7613 | (define-public r-pwr | |
7614 | (package | |
7615 | (name "r-pwr") | |
7616 | (version "1.2-2") | |
7617 | (source | |
7618 | (origin | |
7619 | (method url-fetch) | |
7620 | (uri (cran-uri "pwr" version)) | |
7621 | (sha256 | |
7622 | (base32 | |
7623 | "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm")))) | |
7624 | (build-system r-build-system) | |
7625 | (native-inputs | |
7626 | `(("r-knitr" ,r-knitr))) | |
7627 | (home-page "https://github.com/heliosdrm/pwr") | |
7628 | (synopsis "Basic functions for power analysis") | |
7629 | (description | |
7630 | "This package provides power analysis functions along the lines of | |
7631 | Cohen (1988).") | |
7632 | (license license:gpl3+))) | |
bd531e83 | 7633 | |
42f344fa RW |
7634 | (define-public r-libcoin |
7635 | (package | |
7636 | (name "r-libcoin") | |
7637 | (version "1.0-4") | |
7638 | (source | |
7639 | (origin | |
7640 | (method url-fetch) | |
7641 | (uri (cran-uri "libcoin" version)) | |
7642 | (sha256 | |
7643 | (base32 | |
7644 | "1i893ij9vkmc4y721npw1s3prmmcs2da5vf3ajm0j8ccmfhbmp4i")))) | |
7645 | (build-system r-build-system) | |
7646 | (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) | |
7647 | (home-page "https://cran.r-project.org/web/packages/libcoin") | |
7648 | (synopsis "Linear test statistics for permutation inference") | |
7649 | (description | |
7650 | "This package provides basic infrastructure for linear test statistics | |
7651 | and permutation inference in the framework of Strasser and Weber (1999).") | |
7652 | (license license:gpl2))) | |
7653 | ||
bd531e83 RW |
7654 | (define-public r-coin |
7655 | (package | |
7656 | (name "r-coin") | |
f69ba00f | 7657 | (version "1.3-0") |
bd531e83 RW |
7658 | (source |
7659 | (origin | |
7660 | (method url-fetch) | |
7661 | (uri (cran-uri "coin" version)) | |
7662 | (sha256 | |
7663 | (base32 | |
f69ba00f | 7664 | "1y0yl4mjaxca0jqz53sv1gcpdg89m099rq61iszxvpx7w0vvpkmd")))) |
bd531e83 RW |
7665 | (build-system r-build-system) |
7666 | (propagated-inputs | |
f69ba00f RW |
7667 | `(("r-libcoin" ,r-libcoin) |
7668 | ("r-matrixstats" ,r-matrixstats) | |
7669 | ("r-modeltools" ,r-modeltools) | |
bd531e83 RW |
7670 | ("r-multcomp" ,r-multcomp) |
7671 | ("r-mvtnorm" ,r-mvtnorm) | |
7672 | ("r-survival" ,r-survival))) | |
7673 | (home-page "http://coin.r-forge.r-project.org") | |
7674 | (synopsis "Conditional inference procedures in a permutation test framework") | |
7675 | (description | |
7676 | "This package provides conditional inference procedures for the general | |
7677 | independence problem including two-sample, K-sample (non-parametric ANOVA), | |
7678 | correlation, censored, ordered and multivariate problems.") | |
7679 | (license license:gpl2))) | |
9b3ecb60 RW |
7680 | |
7681 | (define-public r-bayesplot | |
7682 | (package | |
7683 | (name "r-bayesplot") | |
7684 | (version "1.6.0") | |
7685 | (source | |
7686 | (origin | |
7687 | (method url-fetch) | |
7688 | (uri (cran-uri "bayesplot" version)) | |
7689 | (sha256 | |
7690 | (base32 | |
7691 | "0in9cq2ybpa7njrwqx4l6nc8i01cjswsvzwlyiw465pi74aapr57")))) | |
7692 | (build-system r-build-system) | |
7693 | (inputs | |
7694 | `(("pandoc" ,ghc-pandoc) | |
7695 | ("pandoc-citeproc" ,ghc-pandoc-citeproc))) | |
7696 | (propagated-inputs | |
7697 | `(("r-dplyr" ,r-dplyr) | |
7698 | ("r-ggplot2" ,r-ggplot2) | |
7699 | ("r-ggridges" ,r-ggridges) | |
7700 | ("r-reshape2" ,r-reshape2) | |
7701 | ("r-rlang" ,r-rlang))) | |
7702 | (home-page "http://mc-stan.org/bayesplot") | |
7703 | (synopsis "Plotting for Bayesian models") | |
7704 | (description | |
7705 | "This package provides plotting functions for posterior analysis, model | |
7706 | checking, and MCMC diagnostics. The package is designed not only to provide | |
7707 | convenient functionality for users, but also a common set of functions that | |
7708 | can be easily used by developers working on a variety of R packages for | |
7709 | Bayesian modeling.") | |
7710 | (license license:gpl3+))) | |
3b8a3f55 RW |
7711 | |
7712 | (define-public r-tmb | |
7713 | (package | |
7714 | (name "r-tmb") | |
492ec498 | 7715 | (version "1.7.15") |
3b8a3f55 RW |
7716 | (source |
7717 | (origin | |
7718 | (method url-fetch) | |
7719 | (uri (cran-uri "TMB" version)) | |
7720 | (sha256 | |
7721 | (base32 | |
492ec498 | 7722 | "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs")))) |
3b8a3f55 RW |
7723 | (properties `((upstream-name . "TMB"))) |
7724 | (build-system r-build-system) | |
7725 | (propagated-inputs | |
7726 | `(("r-matrix" ,r-matrix) | |
7727 | ("r-rcppeigen" ,r-rcppeigen))) | |
7728 | (home-page "http://tmb-project.org") | |
7729 | (synopsis "Template model builder: a general random effect tool") | |
7730 | (description | |
7731 | "With this tool, a user should be able to quickly implement complex | |
7732 | random effect models through simple C++ templates. The package combines | |
7733 | @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated | |
7734 | matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available | |
7735 | from R) to obtain an efficient implementation of the applied Laplace | |
7736 | approximation with exact derivatives. Key features are: Automatic sparseness | |
7737 | detection, parallelism through BLAS and parallel user templates.") | |
7738 | (license license:gpl2))) | |
aa4bde0b RW |
7739 | |
7740 | (define-public r-sjstats | |
7741 | (package | |
7742 | (name "r-sjstats") | |
a7524f70 | 7743 | (version "0.17.4") |
aa4bde0b RW |
7744 | (source |
7745 | (origin | |
7746 | (method url-fetch) | |
7747 | (uri (cran-uri "sjstats" version)) | |
7748 | (sha256 | |
7749 | (base32 | |
a7524f70 | 7750 | "012hp9m17xzjnsfvjjz2wdfgxm3irsrfx0zmahfnfmgdrwxd5vk5")))) |
aa4bde0b RW |
7751 | (build-system r-build-system) |
7752 | (propagated-inputs | |
a7524f70 | 7753 | `(("r-broom" ,r-broom) |
aa4bde0b RW |
7754 | ("r-dplyr" ,r-dplyr) |
7755 | ("r-emmeans" ,r-emmeans) | |
a7524f70 | 7756 | ("r-insight" ,r-insight) |
aa4bde0b RW |
7757 | ("r-lme4" ,r-lme4) |
7758 | ("r-magrittr" ,r-magrittr) | |
7759 | ("r-mass" ,r-mass) | |
7760 | ("r-matrix" ,r-matrix) | |
7761 | ("r-modelr" ,r-modelr) | |
aa4bde0b | 7762 | ("r-purrr" ,r-purrr) |
aa4bde0b RW |
7763 | ("r-rlang" ,r-rlang) |
7764 | ("r-sjlabelled" ,r-sjlabelled) | |
7765 | ("r-sjmisc" ,r-sjmisc) | |
7766 | ("r-tidyr" ,r-tidyr))) | |
7767 | (home-page "https://github.com/strengejacke/sjstats") | |
7768 | (synopsis "Functions for common statistical computations") | |
7769 | (description | |
7770 | "This package provides a collection of convenient functions for common | |
7771 | statistical computations, which are not directly provided by R's @code{base} | |
7772 | or @code{stats} packages. This package aims at providing, first, shortcuts | |
7773 | for statistical measures, which otherwise could only be calculated with | |
7774 | additional effort. Second, these shortcut functions are generic, and can be | |
7775 | applied not only to vectors, but also to other objects as well. The focus of | |
7776 | most functions lies on summary statistics or fit measures for regression | |
7777 | models, including generalized linear models, mixed effects models and Bayesian | |
7778 | models.") | |
7779 | (license license:gpl3))) | |
41394423 RW |
7780 | |
7781 | (define-public r-glmmtmb | |
7782 | (package | |
7783 | (name "r-glmmtmb") | |
1afe5644 | 7784 | (version "0.2.3") |
41394423 RW |
7785 | (source |
7786 | (origin | |
7787 | (method url-fetch) | |
7788 | (uri (cran-uri "glmmTMB" version)) | |
7789 | (sha256 | |
7790 | (base32 | |
1afe5644 | 7791 | "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb")))) |
41394423 RW |
7792 | (properties `((upstream-name . "glmmTMB"))) |
7793 | (build-system r-build-system) | |
7794 | (propagated-inputs | |
7795 | `(("r-lme4" ,r-lme4) | |
7796 | ("r-matrix" ,r-matrix) | |
7797 | ("r-nlme" ,r-nlme) | |
7798 | ("r-rcppeigen" ,r-rcppeigen) | |
7799 | ("r-tmb" ,r-tmb))) | |
7800 | (native-inputs | |
1afe5644 | 7801 | `(("r-knitr" ,r-knitr))) ; for vignettes |
41394423 RW |
7802 | (home-page "https://github.com/glmmTMB") |
7803 | (synopsis "Generalized linear mixed models") | |
7804 | (description | |
7805 | "Fit linear and generalized linear mixed models with various extensions, | |
7806 | including zero-inflation. The models are fitted using maximum likelihood | |
7807 | estimation via the Template Model Builder. Random effects are assumed to be | |
7808 | Gaussian on the scale of the linear predictor and are integrated out using the | |
7809 | Laplace approximation. Gradients are calculated using automatic | |
7810 | differentiation.") | |
7811 | (license license:agpl3+))) | |
489a6178 RW |
7812 | |
7813 | (define-public r-ggeffects | |
7814 | (package | |
7815 | (name "r-ggeffects") | |
fef93da8 | 7816 | (version "0.9.0") |
489a6178 RW |
7817 | (source |
7818 | (origin | |
7819 | (method url-fetch) | |
7820 | (uri (cran-uri "ggeffects" version)) | |
7821 | (sha256 | |
7822 | (base32 | |
fef93da8 | 7823 | "1bbr44yk1j8pz4kcbw1cqrzcnbih9n6rsgf96a6py5094qcal2qd")))) |
489a6178 RW |
7824 | (build-system r-build-system) |
7825 | (propagated-inputs | |
fef93da8 RW |
7826 | `(("r-dplyr" ,r-dplyr) |
7827 | ("r-insight" ,r-insight) | |
489a6178 RW |
7828 | ("r-magrittr" ,r-magrittr) |
7829 | ("r-mass" ,r-mass) | |
489a6178 RW |
7830 | ("r-purrr" ,r-purrr) |
7831 | ("r-rlang" ,r-rlang) | |
7832 | ("r-scales" ,r-scales) | |
7833 | ("r-sjlabelled" ,r-sjlabelled) | |
fef93da8 | 7834 | ("r-sjmisc" ,r-sjmisc))) |
489a6178 RW |
7835 | (home-page "https://github.com/strengejacke/ggeffects") |
7836 | (synopsis "Create tidy data frames of marginal effects for ggplot") | |
7837 | (description | |
7838 | "This package provides tools to compute marginal effects from statistical | |
7839 | models and return the result as tidy data frames. These data frames are ready | |
7840 | to use with the @code{ggplot2} package. Marginal effects can be calculated | |
7841 | for many different models. Interaction terms, splines and polynomial terms | |
7842 | are also supported. The two main functions are @code{ggpredict()} and | |
7843 | @code{ggeffect()}. There is a generic @code{plot()} method to plot the | |
7844 | results using @code{ggplot2}.") | |
7845 | (license license:gpl3))) | |
7b63047c RW |
7846 | |
7847 | (define-public r-sjplot | |
7848 | (package | |
7849 | (name "r-sjplot") | |
fd730167 | 7850 | (version "2.6.2") |
7b63047c RW |
7851 | (source |
7852 | (origin | |
7853 | (method url-fetch) | |
7854 | (uri (cran-uri "sjPlot" version)) | |
7855 | (sha256 | |
7856 | (base32 | |
fd730167 | 7857 | "0x9pbchmz4qf4c9bi52dhhgv1phfj03q1hnxic8vndl6xwib63cy")))) |
7b63047c RW |
7858 | (properties `((upstream-name . "sjPlot"))) |
7859 | (build-system r-build-system) | |
7860 | (propagated-inputs | |
7861 | `(("r-broom" ,r-broom) | |
7862 | ("r-dplyr" ,r-dplyr) | |
7863 | ("r-forcats" ,r-forcats) | |
7864 | ("r-ggeffects" ,r-ggeffects) | |
7865 | ("r-ggplot2" ,r-ggplot2) | |
7866 | ("r-glmmtmb" ,r-glmmtmb) | |
7867 | ("r-knitr" ,r-knitr) | |
7868 | ("r-lme4" ,r-lme4) | |
7869 | ("r-magrittr" ,r-magrittr) | |
7870 | ("r-mass" ,r-mass) | |
7871 | ("r-modelr" ,r-modelr) | |
7872 | ("r-nlme" ,r-nlme) | |
7873 | ("r-psych" ,r-psych) | |
7874 | ("r-purrr" ,r-purrr) | |
7875 | ("r-rlang" ,r-rlang) | |
7876 | ("r-scales" ,r-scales) | |
7877 | ("r-sjlabelled" ,r-sjlabelled) | |
7878 | ("r-sjmisc" ,r-sjmisc) | |
7879 | ("r-sjstats" ,r-sjstats) | |
7880 | ("r-tidyr" ,r-tidyr))) | |
7881 | (home-page "https://strengejacke.github.io/sjPlot/") | |
7882 | (synopsis "Data visualization for statistics in social science") | |
7883 | (description | |
7884 | "This package represents a collection of plotting and table output | |
7885 | functions for data visualization. Results of various statistical | |
7886 | analyses (that are commonly used in social sciences) can be visualized using | |
7887 | this package, including simple and cross tabulated frequencies, histograms, | |
7888 | box plots, (generalized) linear models, mixed effects models, principal | |
7889 | component analysis and correlation matrices, cluster analyses, scatter plots, | |
7890 | stacked scales, effects plots of regression models (including interaction | |
7891 | terms) and much more. This package supports labelled data.") | |
7892 | (license license:gpl3))) | |
03f80112 RW |
7893 | |
7894 | (define-public r-ini | |
7895 | (package | |
7896 | (name "r-ini") | |
7897 | (version "0.3.1") | |
7898 | (source | |
7899 | (origin | |
7900 | (method url-fetch) | |
7901 | (uri (cran-uri "ini" version)) | |
7902 | (sha256 | |
7903 | (base32 | |
7904 | "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) | |
7905 | (build-system r-build-system) | |
7906 | (home-page "https://github.com/dvdscripter/ini") | |
7907 | (synopsis "Read and write configuration files") | |
7908 | (description | |
7909 | "This package provides tools to parse simple @code{.ini} configuration | |
7910 | files to an structured list. Users can manipulate this resulting list with | |
7911 | @code{lapply()} functions. This same structured list can be used to write | |
7912 | back to file after modifications.") | |
7913 | (license license:gpl3))) | |
21405e81 RW |
7914 | |
7915 | (define-public r-gh | |
7916 | (package | |
7917 | (name "r-gh") | |
7918 | (version "1.0.1") | |
7919 | (source | |
7920 | (origin | |
7921 | (method url-fetch) | |
7922 | (uri (cran-uri "gh" version)) | |
7923 | (sha256 | |
7924 | (base32 | |
7925 | "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k")))) | |
7926 | (build-system r-build-system) | |
7927 | (propagated-inputs | |
7928 | `(("r-httr" ,r-httr) | |
7929 | ("r-ini" ,r-ini) | |
7930 | ("r-jsonlite" ,r-jsonlite))) | |
7931 | (home-page "https://github.com/r-lib/gh#readme") | |
7932 | (synopsis "Access the GitHub API via R") | |
7933 | (description | |
7934 | "This package provides a minimal R client to access the GitHub API.") | |
7935 | (license license:expat))) | |
d6871153 RW |
7936 | |
7937 | (define-public r-fs | |
7938 | (package | |
7939 | (name "r-fs") | |
c9ba1155 | 7940 | (version "1.2.7") |
d6871153 RW |
7941 | (source |
7942 | (origin | |
7943 | (method url-fetch) | |
7944 | (uri (cran-uri "fs" version)) | |
7945 | (sha256 | |
7946 | (base32 | |
c9ba1155 | 7947 | "03aq2ill03ladsa4438nrz213ks2mqhxsrb9fjsp62bhk36v8k1a")))) |
d6871153 RW |
7948 | (build-system r-build-system) |
7949 | (propagated-inputs | |
7950 | `(("r-rcpp" ,r-rcpp))) | |
7951 | (native-inputs | |
7952 | `(("pkg-config" ,pkg-config))) | |
7953 | (home-page "http://fs.r-lib.org") | |
7954 | (synopsis "Cross-platform file system operations based on libuv") | |
7955 | (description | |
7956 | "This package provides a cross-platform interface to file system | |
7957 | operations, built on top of the libuv C library.") | |
7958 | (license license:gpl3))) | |
153e5b2d RW |
7959 | |
7960 | (define-public r-clisymbols | |
7961 | (package | |
7962 | (name "r-clisymbols") | |
7963 | (version "1.2.0") | |
7964 | (source | |
7965 | (origin | |
7966 | (method url-fetch) | |
7967 | (uri (cran-uri "clisymbols" version)) | |
7968 | (sha256 | |
7969 | (base32 | |
7970 | "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86")))) | |
7971 | (build-system r-build-system) | |
7972 | (home-page "https://github.com/gaborcsardi/clisymbols") | |
7973 | (synopsis "Unicode symbols at the R prompt") | |
7974 | (description | |
7975 | "This package provides a small subset of Unicode symbols, that are useful | |
7976 | when building command line applications. They fall back to alternatives on | |
7977 | terminals that do not support Unicode.") | |
7978 | (license license:expat))) | |
efefd3ec RW |
7979 | |
7980 | (define-public r-usethis | |
7981 | (package | |
7982 | (name "r-usethis") | |
7983 | (version "1.4.0") | |
7984 | (source | |
7985 | (origin | |
7986 | (method url-fetch) | |
7987 | (uri (cran-uri "usethis" version)) | |
7988 | (sha256 | |
7989 | (base32 | |
7990 | "1gadckx3sxz9gxvpkprj9x7zcgg2nz5m4q0vi76ya9li1v03rwwn")))) | |
7991 | (build-system r-build-system) | |
7992 | (propagated-inputs | |
7993 | `(("r-clipr" ,r-clipr) | |
7994 | ("r-clisymbols" ,r-clisymbols) | |
7995 | ("r-crayon" ,r-crayon) | |
7996 | ("r-curl" ,r-curl) | |
7997 | ("r-desc" ,r-desc) | |
7998 | ("r-fs" ,r-fs) | |
7999 | ("r-gh" ,r-gh) | |
8000 | ("r-git2r" ,r-git2r) | |
8001 | ("r-glue" ,r-glue) | |
8002 | ("r-rlang" ,r-rlang) | |
8003 | ("r-rprojroot" ,r-rprojroot) | |
8004 | ("r-rstudioapi" ,r-rstudioapi) | |
8005 | ("r-whisker" ,r-whisker))) | |
8006 | (home-page "https://github.com/r-lib/usethis") | |
8007 | (synopsis "Automate R package and project setup") | |
8008 | (description | |
8009 | "This package helps you to automate R package and project setup tasks | |
8010 | that are otherwise performed manually. This includes setting up unit testing, | |
8011 | test coverage, continuous integration, Git, GitHub integration, licenses, | |
8012 | Rcpp, RStudio projects, and more.") | |
8013 | (license license:gpl3))) | |
99342624 RW |
8014 | |
8015 | (define-public r-sessioninfo | |
8016 | (package | |
8017 | (name "r-sessioninfo") | |
3d6fa1a3 | 8018 | (version "1.1.1") |
99342624 RW |
8019 | (source |
8020 | (origin | |
8021 | (method url-fetch) | |
8022 | (uri (cran-uri "sessioninfo" version)) | |
8023 | (sha256 | |
8024 | (base32 | |
3d6fa1a3 | 8025 | "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn")))) |
99342624 RW |
8026 | (build-system r-build-system) |
8027 | (propagated-inputs | |
8028 | `(("r-cli" ,r-cli) | |
8029 | ("r-withr" ,r-withr))) | |
8030 | (home-page "https://github.com/r-lib/sessioninfo#readme") | |
8031 | (synopsis "R session information") | |
8032 | (description | |
8033 | "This package provides tools to query and print information about the | |
8034 | current R session. It is similar to @code{utils::sessionInfo()}, but includes | |
8035 | more information about packages, and where they were installed from.") | |
8036 | (license license:gpl2))) | |
cbc8e6dd RW |
8037 | |
8038 | (define-public r-remotes | |
8039 | (package | |
8040 | (name "r-remotes") | |
fc532b45 | 8041 | (version "2.0.2") |
cbc8e6dd RW |
8042 | (source |
8043 | (origin | |
8044 | (method url-fetch) | |
8045 | (uri (cran-uri "remotes" version)) | |
8046 | (sha256 | |
8047 | (base32 | |
fc532b45 | 8048 | "0rsjxmhwpr51ilsdjfqn06mj8yr2d7nckcn3arv1ljn23qfkpcxa")))) |
cbc8e6dd RW |
8049 | (build-system r-build-system) |
8050 | (home-page "https://github.com/r-lib/remotes#readme") | |
8051 | (synopsis "R package installation from remote repositories") | |
8052 | (description | |
8053 | "Download and install R packages stored in GitHub, BitBucket, or plain | |
8054 | subversion or git repositories. This package is a lightweight replacement of | |
8055 | the @code{install_*} functions in the @code{devtools} package. Indeed most of | |
8056 | the code was copied over from @code{devtools}.") | |
8057 | (license license:gpl2+))) | |
7d8f3470 RW |
8058 | |
8059 | (define-public r-xopen | |
8060 | (package | |
8061 | (name "r-xopen") | |
8062 | (version "1.0.0") | |
8063 | (source | |
8064 | (origin | |
8065 | (method url-fetch) | |
8066 | (uri (cran-uri "xopen" version)) | |
8067 | (sha256 | |
8068 | (base32 | |
8069 | "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) | |
8070 | (build-system r-build-system) | |
8071 | (propagated-inputs | |
8072 | `(("r-processx" ,r-processx))) | |
8073 | (home-page "https://github.com/r-lib/xopen#readme") | |
8074 | (synopsis "Open system files, URLs, anything") | |
8075 | (description | |
8076 | "This package provides a cross-platform solution to open files, | |
8077 | directories or URLs with their associated programs.") | |
8078 | (license license:expat))) | |
5df4e27f RW |
8079 | |
8080 | (define-public r-rcmdcheck | |
8081 | (package | |
8082 | (name "r-rcmdcheck") | |
06910a86 | 8083 | (version "1.3.2") |
5df4e27f RW |
8084 | (source |
8085 | (origin | |
8086 | (method url-fetch) | |
8087 | (uri (cran-uri "rcmdcheck" version)) | |
8088 | (sha256 | |
8089 | (base32 | |
06910a86 | 8090 | "0ys1nd7690mhwzslyzg8fq1wxr28nz8g6av5iykkrshb8lkxg7ly")))) |
5df4e27f RW |
8091 | (build-system r-build-system) |
8092 | (propagated-inputs | |
8093 | `(("r-callr" ,r-callr) | |
8094 | ("r-cli" ,r-cli) | |
8095 | ("r-crayon" ,r-crayon) | |
8096 | ("r-desc" ,r-desc) | |
8097 | ("r-digest" ,r-digest) | |
8098 | ("r-pkgbuild" ,r-pkgbuild) | |
8099 | ("r-prettyunits" ,r-prettyunits) | |
8100 | ("r-r6" ,r-r6) | |
8101 | ("r-rprojroot" ,r-rprojroot) | |
7466c3bb | 8102 | ("r-sessioninfo" ,r-sessioninfo) |
5df4e27f RW |
8103 | ("r-withr" ,r-withr) |
8104 | ("r-xopen" ,r-xopen))) | |
8105 | (home-page "https://github.com/r-Lib/rcmdcheck#readme") | |
8106 | (synopsis "Run R CMD check from R and capture results") | |
8107 | (description | |
8108 | "Run @code{R CMD check} from R programmatically, and capture the results | |
8109 | of the individual checks.") | |
8110 | (license license:expat))) | |
9b02d1a1 RW |
8111 | |
8112 | (define-public r-rapportools | |
8113 | (package | |
8114 | (name "r-rapportools") | |
8115 | (version "1.0") | |
8116 | (source | |
8117 | (origin | |
8118 | (method url-fetch) | |
8119 | (uri (cran-uri "rapportools" version)) | |
8120 | (sha256 | |
8121 | (base32 | |
8122 | "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) | |
8123 | (build-system r-build-system) | |
8124 | (propagated-inputs | |
8125 | `(("r-pander" ,r-pander) | |
8126 | ("r-plyr" ,r-plyr) | |
8127 | ("r-reshape" ,r-reshape))) | |
8128 | (home-page "https://cran.r-project.org/web/packages/rapportools/") | |
8129 | (synopsis "Miscellaneous helper functions with sane defaults for reporting") | |
8130 | (description | |
8131 | "This package provides helper functions that act as wrappers to more | |
8132 | advanced statistical methods with the advantage of having sane defaults for | |
8133 | quick reporting.") | |
8134 | (license license:agpl3+))) | |
319a80ce RW |
8135 | |
8136 | (define-public r-pander | |
8137 | (package | |
8138 | (name "r-pander") | |
a44f8b00 | 8139 | (version "0.6.3") |
319a80ce RW |
8140 | (source |
8141 | (origin | |
8142 | (method url-fetch) | |
8143 | (uri (cran-uri "pander" version)) | |
8144 | (sha256 | |
8145 | (base32 | |
a44f8b00 | 8146 | "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi")))) |
319a80ce RW |
8147 | (build-system r-build-system) |
8148 | (propagated-inputs | |
8149 | `(("r-digest" ,r-digest) | |
8150 | ("r-rcpp" ,r-rcpp))) | |
8151 | (home-page "https://rapporter.github.io/pander") | |
8152 | (synopsis "Render R objects into Pandoc's markdown") | |
8153 | (description | |
8154 | "The main aim of the pander R package is to provide a minimal and easy | |
8155 | tool for rendering R objects into Pandoc's markdown. The package is also | |
8156 | capable of exporting/converting complex Pandoc documents (reports) in various | |
8157 | ways.") | |
8158 | ;; This package is licensed under either the AGPLv3+ or the very rarely | |
8159 | ;; used OSL 3.0. | |
8160 | (license license:agpl3+))) | |
74cc74e4 RW |
8161 | |
8162 | (define-public r-summarytools | |
8163 | (package | |
8164 | (name "r-summarytools") | |
5093cbdc | 8165 | (version "0.9.2") |
74cc74e4 RW |
8166 | (source |
8167 | (origin | |
8168 | (method url-fetch) | |
8169 | (uri (cran-uri "summarytools" version)) | |
8170 | (sha256 | |
8171 | (base32 | |
5093cbdc | 8172 | "1q83kii6prqf9z5v8cxj1q2944kx9x7dcxyqix3m883a94dmgivy")))) |
74cc74e4 RW |
8173 | (build-system r-build-system) |
8174 | (propagated-inputs | |
5093cbdc RW |
8175 | `(("r-checkmate" ,r-checkmate) |
8176 | ("r-dplyr" ,r-dplyr) | |
8177 | ("r-htmltools" ,r-htmltools) | |
74cc74e4 | 8178 | ("r-lubridate" ,r-lubridate) |
5093cbdc | 8179 | ("r-magick" ,r-magick) |
74cc74e4 RW |
8180 | ("r-matrixstats" ,r-matrixstats) |
8181 | ("r-pander" ,r-pander) | |
8182 | ("r-pryr" ,r-pryr) | |
8183 | ("r-rapportools" ,r-rapportools) | |
5093cbdc RW |
8184 | ("r-rcurl" ,r-rcurl) |
8185 | ("r-tidyr" ,r-tidyr))) | |
74cc74e4 RW |
8186 | (home-page "https://github.com/dcomtois/summarytools") |
8187 | (synopsis "Tools to quickly and neatly summarize data") | |
8188 | (description | |
8189 | "This package provides tools for data frame summaries, cross-tabulations, | |
8190 | weight-enabled frequency tables and common univariate statistics in concise | |
8191 | tables available in a variety of formats (plain ASCII, Markdown and HTML). A | |
8192 | good point-of-entry for exploring data, both for experienced and new R | |
8193 | users.") | |
8194 | (license license:gpl2))) | |
7c7ee6cf RW |
8195 | |
8196 | (define-public r-lsei | |
8197 | (package | |
8198 | (name "r-lsei") | |
8199 | (version "1.2-0") | |
8200 | (source | |
8201 | (origin | |
8202 | (method url-fetch) | |
8203 | (uri (cran-uri "lsei" version)) | |
8204 | (sha256 | |
8205 | (base32 | |
8206 | "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7")))) | |
8207 | (build-system r-build-system) | |
8208 | (native-inputs | |
8209 | `(("gfortran" ,gfortran))) | |
8210 | (home-page "https://www.stat.auckland.ac.nz/~yongwang") | |
8211 | (synopsis "Solve regression problems under equality/inequality constraints") | |
8212 | (description | |
8213 | "It contains functions that solve least squares linear regression | |
8214 | problems under linear equality/inequality constraints. Functions for solving | |
8215 | quadratic programming problems are also available, which transform such | |
8216 | problems into least squares ones first.") | |
8217 | (license license:gpl2+))) | |
2ea75a83 RW |
8218 | |
8219 | (define-public r-npsurv | |
8220 | (package | |
8221 | (name "r-npsurv") | |
8222 | (version "0.4-0") | |
8223 | (source | |
8224 | (origin | |
8225 | (method url-fetch) | |
8226 | (uri (cran-uri "npsurv" version)) | |
8227 | (sha256 | |
8228 | (base32 | |
8229 | "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20")))) | |
8230 | (build-system r-build-system) | |
8231 | (propagated-inputs | |
8232 | `(("r-lsei" ,r-lsei))) | |
8233 | (home-page "https://www.stat.auckland.ac.nz/~yongwang") | |
8234 | (synopsis "Nonparametric survival analysis") | |
8235 | (description | |
8236 | "This package contains functions for non-parametric survival analysis of | |
8237 | exact and interval-censored observations.") | |
8238 | (license license:gpl2+))) | |
32499b26 RW |
8239 | |
8240 | (define-public r-clusteval | |
8241 | (package | |
8242 | (name "r-clusteval") | |
8243 | (version "0.1") | |
8244 | (source | |
8245 | (origin | |
8246 | (method url-fetch) | |
8247 | (uri (cran-uri "clusteval" version)) | |
8248 | (sha256 | |
8249 | (base32 | |
8250 | "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) | |
8251 | (build-system r-build-system) | |
8252 | (propagated-inputs | |
8253 | `(("r-mvtnorm" ,r-mvtnorm) | |
8254 | ("r-rcpp" ,r-rcpp))) | |
8255 | (home-page "https://cran.r-project.org/web/packages/clusteval/") | |
8256 | (synopsis "Evaluation of clustering algorithms") | |
8257 | (description | |
8258 | "This R package provides a suite of tools to evaluate clustering | |
8259 | algorithms, clusterings, and individual clusters.") | |
8260 | (license license:expat))) | |
373cef0a RW |
8261 | |
8262 | (define-public r-tweedie | |
8263 | (package | |
8264 | (name "r-tweedie") | |
8265 | (version "2.3.2") | |
8266 | (source | |
8267 | (origin | |
8268 | (method url-fetch) | |
8269 | (uri (cran-uri "tweedie" version)) | |
8270 | (sha256 | |
8271 | (base32 | |
8272 | "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls")))) | |
8273 | (build-system r-build-system) | |
8274 | (native-inputs `(("gfortran" ,gfortran))) | |
8275 | (home-page "https://cran.r-project.org/web/packages/tweedie/") | |
8276 | (synopsis "Evaluation of Tweedie exponential family models") | |
8277 | (description | |
8278 | "Maximum likelihood computations for Tweedie families, including the | |
8279 | series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and | |
8280 | the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), | |
8281 | and related methods.") | |
8282 | (license license:gpl2+))) | |
4fb35ebd RW |
8283 | |
8284 | (define-public r-rcppgsl | |
8285 | (package | |
8286 | (name "r-rcppgsl") | |
8287 | (version "0.3.6") | |
8288 | (source | |
8289 | (origin | |
8290 | (method url-fetch) | |
8291 | (uri (cran-uri "RcppGSL" version)) | |
8292 | (sha256 | |
8293 | (base32 | |
8294 | "16pdapq31729db53agnb48jkvdm97167n3bigy5zazc3q3isis1m")))) | |
8295 | (properties `((upstream-name . "RcppGSL"))) | |
8296 | (build-system r-build-system) | |
8297 | (propagated-inputs | |
8298 | `(("r-rcpp" ,r-rcpp) | |
8299 | ("gsl" ,gsl))) | |
8300 | (native-inputs | |
8301 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
8302 | (home-page "https://cran.r-project.org/web/packages/RcppGSL/") | |
8303 | (synopsis "Rcpp integration for GSL vectors and matrices") | |
8304 | (description | |
8305 | "The GNU Scientific Library (or GSL) is a collection of numerical | |
8306 | routines for scientific computing. It is particularly useful for C and C++ | |
8307 | programs as it provides a standard C interface to a wide range of mathematical | |
8308 | routines. There are over 1000 functions in total with an extensive test | |
8309 | suite. The RcppGSL package provides an easy-to-use interface between GSL data | |
8310 | structures and R using concepts from Rcpp which is itself a package that eases | |
8311 | the interfaces between R and C++.") | |
8312 | (license license:gpl2+))) | |
20ff6e3a RW |
8313 | |
8314 | (define-public r-mvabund | |
8315 | (package | |
8316 | (name "r-mvabund") | |
48102ce1 | 8317 | (version "4.0.1") |
20ff6e3a RW |
8318 | (source |
8319 | (origin | |
8320 | (method url-fetch) | |
8321 | (uri (cran-uri "mvabund" version)) | |
8322 | (sha256 | |
8323 | (base32 | |
48102ce1 | 8324 | "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k")))) |
20ff6e3a RW |
8325 | (build-system r-build-system) |
8326 | (propagated-inputs | |
8327 | `(("r-mass" ,r-mass) | |
8328 | ("r-rcpp" ,r-rcpp) | |
8329 | ("r-rcppgsl" ,r-rcppgsl) | |
8330 | ("r-statmod" ,r-statmod) | |
8331 | ("r-tweedie" ,r-tweedie))) | |
8332 | (home-page "https://cran.r-project.org/web/packages/mvabund/") | |
8333 | (synopsis "Statistical methods for analysing multivariate abundance data") | |
8334 | (description | |
8335 | "This package provides a set of tools for displaying, modeling and | |
8336 | analysing multivariate abundance data in community ecology.") | |
8337 | (license license:lgpl2.1+))) | |
49863fd6 RW |
8338 | |
8339 | (define-public r-afex | |
8340 | (package | |
8341 | (name "r-afex") | |
e2fee46f | 8342 | (version "0.23-0") |
49863fd6 RW |
8343 | (source |
8344 | (origin | |
8345 | (method url-fetch) | |
8346 | (uri (cran-uri "afex" version)) | |
8347 | (sha256 | |
8348 | (base32 | |
e2fee46f | 8349 | "0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7")))) |
49863fd6 RW |
8350 | (build-system r-build-system) |
8351 | (propagated-inputs | |
8352 | `(("r-car" ,r-car) | |
8353 | ("r-lme4" ,r-lme4) | |
8354 | ("r-lmertest" ,r-lmertest) | |
8355 | ("r-pbkrtest" ,r-pbkrtest) | |
8356 | ("r-reshape2" ,r-reshape2))) | |
8357 | (home-page "https://afex.singmann.science/") | |
8358 | (synopsis "Analysis of factorial experiments") | |
8359 | (description | |
8360 | "This package provides convenience functions for analyzing factorial | |
8361 | experiments using ANOVA or mixed models.") | |
8362 | (license license:gpl2+))) | |
7c02dd62 RW |
8363 | |
8364 | (define-public r-lmertest | |
8365 | (package | |
8366 | (name "r-lmertest") | |
f18ca07e | 8367 | (version "3.1-0") |
7c02dd62 RW |
8368 | (source |
8369 | (origin | |
8370 | (method url-fetch) | |
8371 | (uri (cran-uri "lmerTest" version)) | |
8372 | (sha256 | |
8373 | (base32 | |
f18ca07e | 8374 | "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b")))) |
7c02dd62 RW |
8375 | (properties `((upstream-name . "lmerTest"))) |
8376 | (build-system r-build-system) | |
8377 | (propagated-inputs | |
8378 | `(("r-ggplot2" ,r-ggplot2) | |
8379 | ("r-lme4" ,r-lme4) | |
8380 | ("r-mass" ,r-mass) | |
8381 | ("r-numderiv" ,r-numderiv))) | |
8382 | (home-page "https://github.com/runehaubo/lmerTestR") | |
8383 | (synopsis "Tests in linear mixed effects models") | |
8384 | (description | |
8385 | "This package provides p-values in type I, II or III anova and summary | |
8386 | tables for @code{lmer} model fits via Satterthwaite's degrees of freedom | |
8387 | method. A Kenward-Roger method is also available via the @code{pbkrtest} | |
8388 | package. Model selection methods include step, drop1 and anova-like tables | |
8389 | for random effects (ranova). Methods for Least-Square means (LS-means) and | |
8390 | tests of linear contrasts of fixed effects are also available.") | |
8391 | (license license:gpl2+))) | |
fd649d1e RW |
8392 | |
8393 | (define-public r-r2glmm | |
8394 | (package | |
8395 | (name "r-r2glmm") | |
8396 | (version "0.1.2") | |
8397 | (source | |
8398 | (origin | |
8399 | (method url-fetch) | |
8400 | (uri (cran-uri "r2glmm" version)) | |
8401 | (sha256 | |
8402 | (base32 | |
8403 | "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) | |
8404 | (build-system r-build-system) | |
8405 | (propagated-inputs | |
8406 | `(("r-afex" ,r-afex) | |
8407 | ("r-data-table" ,r-data-table) | |
8408 | ("r-dplyr" ,r-dplyr) | |
8409 | ("r-ggplot2" ,r-ggplot2) | |
8410 | ("r-gridextra" ,r-gridextra) | |
8411 | ("r-lmertest" ,r-lmertest) | |
8412 | ("r-mass" ,r-mass) | |
8413 | ("r-matrix" ,r-matrix) | |
8414 | ("r-mgcv" ,r-mgcv) | |
8415 | ("r-pbkrtest" ,r-pbkrtest))) | |
8416 | (home-page "https://github.com/bcjaeger/r2glmm") | |
8417 | (synopsis "Compute R squared for mixed (multilevel) models") | |
8418 | (description | |
8419 | "This package computes model and semi partial R squared with confidence | |
8420 | limits for the linear and generalized linear mixed model (LMM and GLMM). The | |
8421 | R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM | |
8422 | using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et | |
8423 | al. (2016)).") | |
8424 | (license license:gpl2))) | |
cddc0300 | 8425 | |
8426 | (define-public r-weights | |
8427 | (package | |
8428 | (name "r-weights") | |
8429 | (version "1.0") | |
8430 | (source | |
8431 | (origin | |
8432 | (method url-fetch) | |
8433 | (uri (cran-uri "weights" version)) | |
8434 | (sha256 | |
8435 | (base32 | |
8436 | "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c")))) | |
8437 | (build-system r-build-system) | |
8438 | (propagated-inputs | |
8439 | `(("r-gdata" ,r-gdata) | |
8440 | ("r-hmisc" ,r-hmisc) | |
8441 | ("r-mice" ,r-mice))) | |
8442 | (home-page | |
8443 | "https://cran.r-project.org/web/packages/weights/") | |
8444 | (synopsis "Weighting and weighted statistics") | |
8445 | (description "This package Provides a variety of functions for producing | |
8446 | simple weighted statistics, such as weighted Pearson's correlations, partial | |
8447 | correlations, Chi-Squared statistics, histograms, and t-tests. Also now | |
8448 | includes some software for quickly recoding survey data and plotting point | |
8449 | estimates from interaction terms in regressions (and multiply imputed | |
8450 | regressions). NOTE: Weighted partial correlation calculations pulled to | |
8451 | address a bug.") | |
8452 | (license license:gpl2+))) | |
bfa5662e RW |
8453 | |
8454 | (define-public r-rcppannoy | |
8455 | (package | |
8456 | (name "r-rcppannoy") | |
8457 | (version "0.0.11") | |
8458 | (source | |
8459 | (origin | |
8460 | (method url-fetch) | |
8461 | (uri (cran-uri "RcppAnnoy" version)) | |
8462 | (sha256 | |
8463 | (base32 | |
8464 | "1ik50ancfgcvh03n4jsqwjk8lf056rbgd70q4l4didmvh5kcyjd1")))) | |
8465 | (properties `((upstream-name . "RcppAnnoy"))) | |
8466 | (build-system r-build-system) | |
8467 | (propagated-inputs | |
8468 | `(("r-rcpp" ,r-rcpp))) | |
8469 | (native-inputs | |
8470 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
8471 | (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") | |
8472 | (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") | |
8473 | (description | |
8474 | "Annoy is a small C++ library for Approximate Nearest Neighbors written | |
8475 | for efficient memory usage as well an ability to load from and save to disk. | |
8476 | This package provides an R interface.") | |
8477 | ;; Annoy is released under ASL 2.0, but this wrapper is released under | |
8478 | ;; GPLv2+. | |
8479 | (license (list license:gpl2+ license:asl2.0)))) | |
b58940cb RW |
8480 | |
8481 | (define-public r-ncdf4 | |
8482 | (package | |
8483 | (name "r-ncdf4") | |
1adcbeda | 8484 | (version "1.16.1") |
b58940cb RW |
8485 | (source |
8486 | (origin | |
8487 | (method url-fetch) | |
8488 | (uri (cran-uri "ncdf4" version)) | |
8489 | (sha256 | |
8490 | (base32 | |
1adcbeda | 8491 | "083sb24anyd4sw0il3x07pqn9rbx5y5ayqass6mz8x443rnjvphd")))) |
b58940cb RW |
8492 | (build-system r-build-system) |
8493 | (inputs | |
8494 | `(("netcdf" ,netcdf) | |
8495 | ("zlib" ,zlib))) | |
8496 | (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") | |
8497 | (synopsis "R interface to Unidata netCDF format data files") | |
8498 | (description | |
8499 | "This package provides a high-level R interface to data files written | |
8500 | using Unidata's netCDF library (version 4 or earlier), which are binary data | |
8501 | files that are portable across platforms and include metadata information in | |
8502 | addition to the data sets. Using this package, netCDF files can be opened and | |
8503 | data sets read in easily. It is also easy to create new netCDF dimensions, | |
8504 | variables, and files, in either version 3 or 4 format, and manipulate existing | |
8505 | netCDF files.") | |
8506 | (license license:gpl3+))) | |
1e605c03 RW |
8507 | |
8508 | (define-public r-biocmanager | |
8509 | (package | |
8510 | (name "r-biocmanager") | |
749872a5 | 8511 | (version "1.30.4") |
1e605c03 RW |
8512 | (source |
8513 | (origin | |
8514 | (method url-fetch) | |
8515 | (uri (cran-uri "BiocManager" version)) | |
8516 | (sha256 | |
8517 | (base32 | |
749872a5 | 8518 | "0kxs76pixk1d2lpvkyrq6nnvv1rqf55ph5f7igkadyyqirf3y2ah")))) |
1e605c03 RW |
8519 | (properties `((upstream-name . "BiocManager"))) |
8520 | (build-system r-build-system) | |
8521 | (home-page "https://cran.r-project.org/web/packages/BiocManager/") | |
8522 | (synopsis "Access the Bioconductor project package repository") | |
8523 | (description | |
8524 | "This package provides a convenient tool to install and update | |
8525 | Bioconductor packages.") | |
8526 | (license license:artistic2.0))) | |
f338e480 RW |
8527 | |
8528 | (define-public r-rgl | |
8529 | (package | |
8530 | (name "r-rgl") | |
8aef1ea6 | 8531 | (version "0.100.19") |
f338e480 RW |
8532 | (source |
8533 | (origin | |
8534 | (method url-fetch) | |
8535 | (uri (cran-uri "rgl" version)) | |
8536 | (sha256 | |
8537 | (base32 | |
8aef1ea6 | 8538 | "09bhvx8aq104yzysfgd7wlnq4vrvmnd4jzgj0c32whjfal10fqsh")))) |
f338e480 RW |
8539 | (build-system r-build-system) |
8540 | (native-inputs | |
8541 | `(("pkg-config" ,pkg-config))) | |
8542 | (inputs | |
8543 | `(("freetype" ,freetype) | |
8544 | ("libpng" ,libpng) | |
8545 | ("glu" ,glu) | |
8546 | ("libx11" ,libx11) | |
8547 | ("ghc-pandoc" ,ghc-pandoc) | |
8548 | ("zlib" ,zlib))) | |
8549 | (propagated-inputs | |
8550 | `(("r-crosstalk" ,r-crosstalk) | |
8551 | ("r-htmltools" ,r-htmltools) | |
8552 | ("r-htmlwidgets" ,r-htmlwidgets) | |
8553 | ("r-jsonlite" ,r-jsonlite) | |
8554 | ("r-knitr" ,r-knitr) | |
8555 | ("r-magrittr" ,r-magrittr) | |
8556 | ("r-manipulatewidget" ,r-manipulatewidget) | |
8557 | ("r-shiny" ,r-shiny))) | |
8558 | (home-page "https://r-forge.r-project.org/projects/rgl/") | |
8559 | (synopsis "3D visualization using OpenGL") | |
8560 | (description | |
8561 | "This package provides medium to high level functions for 3D interactive graphics, | |
8562 | including functions modelled on base graphics (@code{plot3d()}, etc.) as well | |
8563 | as functions for constructing representations of geometric | |
8564 | objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to | |
8565 | various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D | |
8566 | image formats, including PNG, Postscript, SVG, PGF.") | |
8567 | ;; Any version of the GPL. | |
8568 | (license (list license:gpl2+ license:gpl3+)))) | |
213e72a1 RW |
8569 | |
8570 | (define-public r-multicool | |
8571 | (package | |
8572 | (name "r-multicool") | |
8573 | (version "0.1-10") | |
8574 | (source | |
8575 | (origin | |
8576 | (method url-fetch) | |
8577 | (uri (cran-uri "multicool" version)) | |
8578 | (sha256 | |
8579 | (base32 | |
8580 | "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v")))) | |
8581 | (build-system r-build-system) | |
8582 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
8583 | (home-page "https://cran.r-project.org/web/packages/multicool/") | |
8584 | (synopsis "Permutations of multisets in cool-lex order") | |
8585 | (description | |
8586 | "This package provides a set of tools to permute multisets without loops | |
8587 | or hash tables and to generate integer partitions. Cool-lex order is similar | |
8588 | to colexicographical order.") | |
8589 | (license license:gpl2))) | |
4106e6ad RW |
8590 | |
8591 | (define-public r-misc3d | |
8592 | (package | |
8593 | (name "r-misc3d") | |
8594 | (version "0.8-4") | |
8595 | (source | |
8596 | (origin | |
8597 | (method url-fetch) | |
8598 | (uri (cran-uri "misc3d" version)) | |
8599 | (sha256 | |
8600 | (base32 | |
8601 | "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) | |
8602 | (build-system r-build-system) | |
8603 | (home-page "https://cran.r-project.org/web/packages/misc3d/") | |
8604 | (synopsis "Miscellaneous 3D Plots") | |
8605 | (description | |
8606 | "This package provides a collection of miscellaneous 3d plots, including | |
8607 | isosurfaces.") | |
8608 | ;; Any version of the GPL. | |
8609 | (license (list license:gpl2+ license:gpl3+)))) | |
da256afb RW |
8610 | |
8611 | (define-public r-ks | |
8612 | (package | |
8613 | (name "r-ks") | |
91f0b745 | 8614 | (version "1.11.4") |
da256afb RW |
8615 | (source |
8616 | (origin | |
8617 | (method url-fetch) | |
8618 | (uri (cran-uri "ks" version)) | |
8619 | (sha256 | |
8620 | (base32 | |
91f0b745 | 8621 | "0d5i8458s8ri9pcx2jm003z1ajk7ha3pmw1sr6lgn6a8d7wgmvqb")))) |
da256afb RW |
8622 | (build-system r-build-system) |
8623 | (propagated-inputs | |
8624 | `(("r-fnn" ,r-fnn) | |
8625 | ("r-kernlab" ,r-kernlab) | |
8626 | ("r-kernsmooth" ,r-kernsmooth) | |
8627 | ("r-matrix" ,r-matrix) | |
8628 | ("r-mclust" ,r-mclust) | |
8629 | ("r-mgcv" ,r-mgcv) | |
da256afb RW |
8630 | ("r-multicool" ,r-multicool) |
8631 | ("r-mvtnorm" ,r-mvtnorm))) | |
8632 | (home-page "http://www.mvstat.net/tduong/") | |
8633 | (synopsis "Kernel smoothing") | |
8634 | (description | |
8635 | "This package provides kernel smoothers for univariate and multivariate | |
8636 | data, including density functions, density derivatives, cumulative | |
8637 | distributions, modal clustering, discriminant analysis, and two-sample | |
8638 | hypothesis testing.") | |
8639 | ;; Either version of the GPL. | |
8640 | (license (list license:gpl2 license:gpl3)))) | |
cf383cf0 RW |
8641 | |
8642 | (define-public r-feature | |
8643 | (package | |
8644 | (name "r-feature") | |
8645 | (version "1.2.13") | |
8646 | (source | |
8647 | (origin | |
8648 | (method url-fetch) | |
8649 | (uri (cran-uri "feature" version)) | |
8650 | (sha256 | |
8651 | (base32 | |
8652 | "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra")))) | |
8653 | (build-system r-build-system) | |
8654 | (propagated-inputs | |
8655 | `(("r-ks" ,r-ks) | |
8656 | ("r-misc3d" ,r-misc3d) | |
8657 | ("r-rgl" ,r-rgl))) | |
8658 | (home-page "http://www.mvstat.net/tduong/") | |
8659 | (synopsis "Inferential feature significance for kernel density estimation") | |
8660 | (description | |
8661 | "The feature package contains functions to display and compute kernel | |
8662 | density estimates, significant gradient and significant curvature regions. | |
8663 | Significant gradient and/or curvature regions often correspond to significant | |
8664 | features (e.g. local modes).") | |
8665 | ;; Either version of the GPL. | |
8666 | (license (list license:gpl2 license:gpl3)))) | |
06bc7b82 RW |
8667 | |
8668 | (define-public r-arm | |
8669 | (package | |
8670 | (name "r-arm") | |
8671 | (version "1.10-1") | |
8672 | (source | |
8673 | (origin | |
8674 | (method url-fetch) | |
8675 | (uri (cran-uri "arm" version)) | |
8676 | (sha256 | |
8677 | (base32 | |
8678 | "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg")))) | |
8679 | (build-system r-build-system) | |
8680 | (propagated-inputs | |
8681 | `(("r-abind" ,r-abind) | |
8682 | ("r-coda" ,r-coda) | |
8683 | ("r-lme4" ,r-lme4) | |
8684 | ("r-mass" ,r-mass) | |
8685 | ("r-matrix" ,r-matrix) | |
8686 | ("r-nlme" ,r-nlme))) | |
8687 | (home-page "https://cran.r-project.org/web/packages/arm/") | |
8688 | (synopsis "Data analysis using regression and multilevel/hierarchical models") | |
8689 | (description | |
8690 | "This package provides functions to accompany A. Gelman and J. Hill, | |
8691 | Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge | |
8692 | University Press, 2007.") | |
8693 | (license license:gpl3+))) | |
3cef715a RW |
8694 | |
8695 | (define-public r-circular | |
8696 | (package | |
8697 | (name "r-circular") | |
8698 | (version "0.4-93") | |
8699 | (source | |
8700 | (origin | |
8701 | (method url-fetch) | |
8702 | (uri (cran-uri "circular" version)) | |
8703 | (sha256 | |
8704 | (base32 | |
8705 | "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) | |
8706 | (build-system r-build-system) | |
8707 | (propagated-inputs | |
8708 | `(("r-boot" ,r-boot) | |
8709 | ("r-mvtnorm" ,r-mvtnorm))) | |
8710 | (native-inputs | |
8711 | `(("gfortran" ,gfortran))) | |
8712 | (home-page "https://cran.r-project.org/web/packages/circular/") | |
8713 | (synopsis "Circular statistics") | |
8714 | (description | |
8715 | "This package provides tools for circular statistics, from \"Topics in | |
8716 | circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World | |
8717 | Scientific.") | |
8718 | (license license:gpl2+))) | |
10483a64 RW |
8719 | |
8720 | (define-public r-activity | |
8721 | (package | |
8722 | (name "r-activity") | |
0207ad9e | 8723 | (version "1.2") |
10483a64 RW |
8724 | (source |
8725 | (origin | |
8726 | (method url-fetch) | |
8727 | (uri (cran-uri "activity" version)) | |
8728 | (sha256 | |
8729 | (base32 | |
0207ad9e | 8730 | "11w2bz6p9xbzdh6773dmbbh6rws0h5dj18p8m0ivzizgq932vdzs")))) |
10483a64 RW |
8731 | (build-system r-build-system) |
8732 | (propagated-inputs | |
8733 | `(("r-circular" ,r-circular) | |
10483a64 RW |
8734 | ("r-pbapply" ,r-pbapply))) |
8735 | (home-page "https://cran.r-project.org/web/packages/activity/") | |
8736 | (synopsis "Animal activity statistics") | |
8737 | (description | |
8738 | "This package provides functions to fit kernel density functions to | |
8739 | animal activity time data; plot activity distributions; quantify overall | |
8740 | levels of activity; statistically compare activity metrics through | |
8741 | bootstrapping; and evaluate variation in linear variables with time (or other | |
8742 | circular variables).") | |
8743 | (license license:gpl3))) | |
e4f4a04a RW |
8744 | |
8745 | (define-public r-ouch | |
8746 | (package | |
8747 | (name "r-ouch") | |
8748 | (version "2.11-1") | |
8749 | (source | |
8750 | (origin | |
8751 | (method url-fetch) | |
8752 | (uri (cran-uri "ouch" version)) | |
8753 | (sha256 | |
8754 | (base32 | |
8755 | "0xkwwi62vdahlcg3k32zb1nfwsx87zdssk79mvcxgfsw9bw4gahx")))) | |
8756 | (build-system r-build-system) | |
8757 | (propagated-inputs `(("r-subplex" ,r-subplex))) | |
8758 | (home-page "http://kingaa.github.io/ouch/") | |
8759 | (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") | |
8760 | (description | |
8761 | "This package provides tools to fit and compare Ornstein-Uhlenbeck models | |
8762 | for evolution along a phylogenetic tree.") | |
8763 | (license license:gpl2+))) | |
705ea5bf RW |
8764 | |
8765 | (define-public r-fmsb | |
8766 | (package | |
8767 | (name "r-fmsb") | |
8768 | (version "0.6.3") | |
8769 | (source | |
8770 | (origin | |
8771 | (method url-fetch) | |
8772 | (uri (cran-uri "fmsb" version)) | |
8773 | (sha256 | |
8774 | (base32 | |
8775 | "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5")))) | |
8776 | (build-system r-build-system) | |
8777 | (home-page "http://minato.sip21c.org/msb/") | |
8778 | (synopsis "Functions for medical statistics book with demographic data") | |
8779 | (description | |
8780 | "This package provides several utility functions for the book entitled | |
8781 | \"Practices of Medical and Health Data Analysis using R\" (Pearson Education | |
8782 | Japan, 2007) with Japanese demographic data and some demographic analysis | |
8783 | related functions.") | |
8784 | (license license:gpl2+))) | |
ced51a20 RW |
8785 | |
8786 | (define-public r-stabledist | |
8787 | (package | |
8788 | (name "r-stabledist") | |
8789 | (version "0.7-1") | |
8790 | (source | |
8791 | (origin | |
8792 | (method url-fetch) | |
8793 | (uri (cran-uri "stabledist" version)) | |
8794 | (sha256 | |
8795 | (base32 | |
8796 | "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86")))) | |
8797 | (build-system r-build-system) | |
8798 | (home-page "http://www.rmetrics.org") | |
8799 | (synopsis "Stable distribution functions") | |
8800 | (description | |
8801 | "This package provides density, probability and quantile functions, and | |
8802 | random number generation for (skew) stable distributions, using the | |
8803 | parametrizations of Nolan.") | |
8804 | (license license:gpl2+))) | |
a50abb36 RW |
8805 | |
8806 | (define-public r-gsl | |
8807 | (package | |
8808 | (name "r-gsl") | |
6bdce94f | 8809 | (version "2.1-6") |
a50abb36 RW |
8810 | (source |
8811 | (origin | |
8812 | (method url-fetch) | |
8813 | (uri (cran-uri "gsl" version)) | |
8814 | (sha256 | |
8815 | (base32 | |
6bdce94f | 8816 | "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m")))) |
a50abb36 RW |
8817 | (build-system r-build-system) |
8818 | (inputs | |
8819 | `(("gsl" ,gsl))) | |
8820 | (home-page "https://cran.r-project.org/web/packages/gsl") | |
8821 | (synopsis "Wrapper for the GNU Scientific Library") | |
8822 | (description | |
8823 | "This package provides an R wrapper for the special functions and quasi | |
8824 | random number generators of the GNU Scientific Library.") | |
8825 | (license license:gpl2+))) | |
03a3ec5e RW |
8826 | |
8827 | (define-public r-adgoftest | |
8828 | (package | |
8829 | (name "r-adgoftest") | |
8830 | (version "0.3") | |
8831 | (source | |
8832 | (origin | |
8833 | (method url-fetch) | |
8834 | (uri (cran-uri "ADGofTest" version)) | |
8835 | (sha256 | |
8836 | (base32 | |
8837 | "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) | |
8838 | (properties `((upstream-name . "ADGofTest"))) | |
8839 | (build-system r-build-system) | |
8840 | (home-page "https://cran.r-project.org/web/packages/ADGofTest") | |
8841 | (synopsis "Anderson-Darling GoF test") | |
8842 | (description | |
8843 | "This package provides an implementation of the Anderson-Darling GoF test | |
8844 | with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the | |
8845 | Anderson-Darling Distribution\".") | |
8846 | ;; Any version of the GPL. | |
8847 | (license license:gpl3+))) | |
71601a5d RW |
8848 | |
8849 | (define-public r-softimpute | |
8850 | (package | |
8851 | (name "r-softimpute") | |
8852 | (version "1.4") | |
8853 | (source | |
8854 | (origin | |
8855 | (method url-fetch) | |
8856 | (uri (cran-uri "softImpute" version)) | |
8857 | (sha256 | |
8858 | (base32 | |
8859 | "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq")))) | |
8860 | (properties `((upstream-name . "softImpute"))) | |
8861 | (build-system r-build-system) | |
8862 | (propagated-inputs | |
8863 | `(("r-matrix" ,r-matrix))) | |
8864 | (native-inputs | |
8865 | `(("gfortran" ,gfortran))) | |
8866 | (home-page "https://cran.r-project.org/web/packages/softImpute") | |
8867 | (synopsis "Matrix completion via iterative soft-thresholded SVD") | |
8868 | (description | |
8869 | "This package provides iterative methods for matrix completion that use | |
8870 | nuclear-norm regularization. The package includes procedures for centering | |
8871 | and scaling rows, columns or both, and for computing low-rank @dfn{single | |
8872 | value decompositions} (SVDs) on large sparse centered matrices (i.e. principal | |
8873 | components).") | |
8874 | (license license:gpl2))) | |
44b0c5b5 RW |
8875 | |
8876 | (define-public r-fftwtools | |
8877 | (package | |
8878 | (name "r-fftwtools") | |
8879 | (version "0.9-8") | |
8880 | (source | |
8881 | (origin | |
8882 | (method url-fetch) | |
8883 | (uri (cran-uri "fftwtools" version)) | |
8884 | (sha256 | |
8885 | (base32 | |
8886 | "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6")))) | |
8887 | (build-system r-build-system) | |
8888 | (inputs `(("fftw" ,fftw))) | |
8889 | (home-page "https://github.com/krahim/fftwtools") | |
8890 | (synopsis "Wrapper for FFTW3") | |
8891 | (description | |
8892 | "This package provides a wrapper for several FFTW functions. It provides | |
8893 | access to the two-dimensional FFT, the multivariate FFT, and the | |
8894 | one-dimensional real to complex FFT using the FFTW3 library. The package | |
8895 | includes the functions @code{fftw()} and @code{mvfftw()} which are designed to | |
8896 | mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. | |
8897 | The FFT functions have a parameter that allows them to not return the | |
8898 | redundant complex conjugate when the input is real data.") | |
8899 | (license license:gpl2+))) | |
db084d79 RW |
8900 | |
8901 | (define-public r-tiff | |
8902 | (package | |
8903 | (name "r-tiff") | |
8904 | (version "0.1-5") | |
8905 | (source | |
8906 | (origin | |
8907 | (method url-fetch) | |
8908 | (uri (cran-uri "tiff" version)) | |
8909 | (sha256 | |
8910 | (base32 | |
8911 | "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) | |
8912 | (build-system r-build-system) | |
8913 | (inputs | |
8914 | `(("libtiff" ,libtiff) | |
8915 | ("libjpeg" ,libjpeg) | |
8916 | ("zlib" ,zlib))) | |
8917 | (home-page "http://www.rforge.net/tiff/") | |
8918 | (synopsis "Read and write TIFF images") | |
8919 | (description | |
8920 | "This package provides an easy and simple way to read, write and display | |
8921 | bitmap images stored in the TIFF format. It can read and write both files and | |
8922 | in-memory raw vectors.") | |
8923 | ;; Either of these two license versions. | |
8924 | (license (list license:gpl2 license:gpl3)))) | |
f3949fec RW |
8925 | |
8926 | (define-public r-waveslim | |
8927 | (package | |
8928 | (name "r-waveslim") | |
61cb2e31 | 8929 | (version "1.7.5.1") |
f3949fec RW |
8930 | (source |
8931 | (origin | |
8932 | (method url-fetch) | |
8933 | (uri (cran-uri "waveslim" version)) | |
8934 | (sha256 | |
8935 | (base32 | |
61cb2e31 | 8936 | "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk")))) |
f3949fec RW |
8937 | (build-system r-build-system) |
8938 | (native-inputs | |
8939 | `(("gfortran" ,gfortran))) | |
8940 | (home-page "http://waveslim.blogspot.com") | |
8941 | (synopsis "Basic wavelet routines for signal processing") | |
8942 | (description | |
8943 | "This package provides basic wavelet routines for time series (1D), | |
8944 | image (2D) and array (3D) analysis. The code provided here is based on | |
8945 | wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk | |
8946 | and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from | |
8947 | Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet | |
8948 | pairs (Selesnick 2001, 2002).") | |
8949 | (license license:bsd-3))) | |
e37935e4 RW |
8950 | |
8951 | (define-public r-wordcloud | |
8952 | (package | |
8953 | (name "r-wordcloud") | |
8954 | (version "2.6") | |
8955 | (source | |
8956 | (origin | |
8957 | (method url-fetch) | |
8958 | (uri (cran-uri "wordcloud" version)) | |
8959 | (sha256 | |
8960 | (base32 | |
8961 | "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) | |
8962 | (build-system r-build-system) | |
8963 | (propagated-inputs | |
8964 | `(("r-rcolorbrewer" ,r-rcolorbrewer) | |
8965 | ("r-rcpp" ,r-rcpp))) | |
8966 | (home-page "https://cran.r-project.org/web/packages/wordcloud") | |
8967 | (synopsis "Word clouds") | |
8968 | (description | |
8969 | "This package provides functionality to create pretty word clouds, | |
8970 | visualize differences and similarity between documents, and avoid | |
8971 | over-plotting in scatter plots with text.") | |
8972 | (license license:lgpl2.1))) | |
a6e4413d RW |
8973 | |
8974 | (define-public r-colorramps | |
8975 | (package | |
8976 | (name "r-colorramps") | |
8977 | (version "2.3") | |
8978 | (source | |
8979 | (origin | |
8980 | (method url-fetch) | |
8981 | (uri (cran-uri "colorRamps" version)) | |
8982 | (sha256 | |
8983 | (base32 | |
8984 | "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z")))) | |
8985 | (properties `((upstream-name . "colorRamps"))) | |
8986 | (build-system r-build-system) | |
8987 | (home-page "https://cran.r-project.org/web/packages/colorRamps") | |
8988 | (synopsis "Build color tables") | |
8989 | (description "This package provides features to build gradient color | |
8990 | maps.") | |
8991 | ;; Any version of the GPL | |
8992 | (license license:gpl3+))) | |
61d73349 RW |
8993 | |
8994 | (define-public r-tidytree | |
8995 | (package | |
8996 | (name "r-tidytree") | |
0b14b100 | 8997 | (version "0.2.4") |
61d73349 RW |
8998 | (source |
8999 | (origin | |
9000 | (method url-fetch) | |
9001 | (uri (cran-uri "tidytree" version)) | |
9002 | (sha256 | |
9003 | (base32 | |
0b14b100 | 9004 | "04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w")))) |
61d73349 RW |
9005 | (build-system r-build-system) |
9006 | (propagated-inputs | |
9007 | `(("r-ape" ,r-ape) | |
9008 | ("r-dplyr" ,r-dplyr) | |
9009 | ("r-lazyeval" ,r-lazyeval) | |
9010 | ("r-magrittr" ,r-magrittr) | |
9011 | ("r-rlang" ,r-rlang) | |
9012 | ("r-tibble" ,r-tibble))) | |
9013 | (home-page "https://github.com/GuangchuangYu/tidytree") | |
9014 | (synopsis "Tidy tool for phylogenetic tree data manipulation") | |
9015 | (description | |
9016 | "Phylogenetic trees generally contain multiple components including nodes, | |
9017 | edges, branches and associated data. This package provides an approach to | |
9018 | convert tree objects to tidy data frames. It also provides tidy interfaces to | |
9019 | manipulate tree data.") | |
9020 | (license license:artistic2.0))) | |
45b469a4 RW |
9021 | |
9022 | (define-public r-rvcheck | |
9023 | (package | |
9024 | (name "r-rvcheck") | |
9025 | (version "0.1.3") | |
9026 | (source | |
9027 | (origin | |
9028 | (method url-fetch) | |
9029 | (uri (cran-uri "rvcheck" version)) | |
9030 | (sha256 | |
9031 | (base32 | |
9032 | "1i2g6gyiqyd1pn6y0h6vmlcmg1qb5pv7rym8mkw8jnyc3in9hn8b")))) | |
9033 | (build-system r-build-system) | |
9034 | (propagated-inputs | |
9035 | `(("r-rlang" ,r-rlang))) | |
9036 | (home-page "https://cran.r-project.org/web/packages/rvcheck") | |
9037 | (synopsis "R package version check") | |
9038 | (description | |
9039 | "This package provides tools to check the latest release version of R and | |
9040 | R packages (on CRAN, Bioconductor or Github).") | |
9041 | (license license:artistic2.0))) | |
fbebccf7 RW |
9042 | |
9043 | (define-public r-docopt | |
9044 | (package | |
9045 | (name "r-docopt") | |
9046 | (version "0.6.1") | |
9047 | (source | |
9048 | (origin | |
9049 | (method url-fetch) | |
9050 | (uri (cran-uri "docopt" version)) | |
9051 | (sha256 | |
9052 | (base32 | |
9053 | "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068")))) | |
9054 | (build-system r-build-system) | |
9055 | (home-page "https://github.com/docopt/docopt.R") | |
9056 | (synopsis "Command-line interface specification language") | |
9057 | (description | |
9058 | "This package enables you to define a command-line interface by just | |
9059 | giving it a description in the specific format.") | |
9060 | (license license:expat))) | |
b614009e RW |
9061 | |
9062 | (define-public r-sparsesvd | |
9063 | (package | |
9064 | (name "r-sparsesvd") | |
9065 | (version "0.1-4") | |
9066 | (source | |
9067 | (origin | |
9068 | (method url-fetch) | |
9069 | (uri (cran-uri "sparsesvd" version)) | |
9070 | (sha256 | |
9071 | (base32 | |
9072 | "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam")))) | |
9073 | (build-system r-build-system) | |
9074 | (propagated-inputs `(("r-matrix" ,r-matrix))) | |
9075 | (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") | |
9076 | (synopsis "Sparse truncated singular value decomposition") | |
9077 | (description | |
9078 | "This package provides a Wrapper around the SVDLIBC library | |
9079 | for (truncated) singular value decomposition of a sparse matrix. Currently, | |
9080 | only sparse real matrices in Matrix package format are supported.") | |
9081 | ;; SVDLIBC is released under BSD-2. The R interface is released under | |
9082 | ;; BSD-3. | |
9083 | (license (list license:bsd-3 license:bsd-2)))) | |
13f5837b RW |
9084 | |
9085 | (define-public r-densityclust | |
9086 | (package | |
9087 | (name "r-densityclust") | |
9088 | (version "0.3") | |
9089 | (source | |
9090 | (origin | |
9091 | (method url-fetch) | |
9092 | (uri (cran-uri "densityClust" version)) | |
9093 | (sha256 | |
9094 | (base32 | |
9095 | "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13")))) | |
9096 | (properties `((upstream-name . "densityClust"))) | |
9097 | (build-system r-build-system) | |
9098 | (propagated-inputs | |
9099 | `(("r-fnn" ,r-fnn) | |
9100 | ("r-ggplot2" ,r-ggplot2) | |
9101 | ("r-ggrepel" ,r-ggrepel) | |
9102 | ("r-gridextra" ,r-gridextra) | |
9103 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9104 | ("r-rcpp" ,r-rcpp) | |
9105 | ("r-rtsne" ,r-rtsne))) | |
9106 | (home-page "https://cran.r-project.org/web/packages/densityClust") | |
9107 | (synopsis "Clustering by fast search and find of density peaks") | |
9108 | (description | |
9109 | "This package provides an improved implementation (based on k-nearest | |
9110 | neighbors) of the density peak clustering algorithm, originally described by | |
9111 | Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle | |
9112 | large datasets (> 100,000 samples) very efficiently.") | |
9113 | (license license:gpl2+))) | |
58bc8857 RW |
9114 | |
9115 | (define-public r-combinat | |
9116 | (package | |
9117 | (name "r-combinat") | |
9118 | (version "0.0-8") | |
9119 | (source | |
9120 | (origin | |
9121 | (method url-fetch) | |
9122 | (uri (cran-uri "combinat" version)) | |
9123 | (sha256 | |
9124 | (base32 | |
9125 | "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) | |
9126 | (build-system r-build-system) | |
9127 | (home-page "https://cran.r-project.org/web/packages/combinat") | |
9128 | (synopsis "Combinatorics utilities") | |
9129 | (description "This package provides assorted routines for combinatorics.") | |
9130 | (license license:gpl2))) | |
9f33d76c RW |
9131 | |
9132 | (define-public r-qlcmatrix | |
9133 | (package | |
9134 | (name "r-qlcmatrix") | |
9135 | (version "0.9.7") | |
9136 | (source | |
9137 | (origin | |
9138 | (method url-fetch) | |
9139 | (uri (cran-uri "qlcMatrix" version)) | |
9140 | (sha256 | |
9141 | (base32 | |
9142 | "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) | |
9143 | (properties `((upstream-name . "qlcMatrix"))) | |
9144 | (build-system r-build-system) | |
9145 | (propagated-inputs | |
9146 | `(("r-docopt" ,r-docopt) | |
9147 | ("r-matrix" ,r-matrix) | |
9148 | ("r-slam" ,r-slam) | |
9149 | ("r-sparsesvd" ,r-sparsesvd))) | |
9150 | (home-page "https://cran.r-project.org/web/packages/qlcMatrix") | |
9151 | (synopsis "Sparse matrix functions for quantitative language comparison") | |
9152 | (description | |
9153 | "This package provides an extension of the functionality of the Matrix | |
9154 | package for using sparse matrices. Some of the functions are very general, | |
9155 | while other are highly specific for the special data format used for | |
9156 | @dfn{quantitative language comparison} (QLC).") | |
9157 | (license license:gpl3))) | |
e3bb0766 RW |
9158 | |
9159 | (define-public r-ddrtree | |
9160 | (package | |
9161 | (name "r-ddrtree") | |
9162 | (version "0.1.5") | |
9163 | (source | |
9164 | (origin | |
9165 | (method url-fetch) | |
9166 | (uri (cran-uri "DDRTree" version)) | |
9167 | (sha256 | |
9168 | (base32 | |
9169 | "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) | |
9170 | (properties `((upstream-name . "DDRTree"))) | |
9171 | (build-system r-build-system) | |
9172 | (propagated-inputs | |
9173 | `(("r-bh" ,r-bh) | |
9174 | ("r-irlba" ,r-irlba) | |
9175 | ("r-rcpp" ,r-rcpp) | |
9176 | ("r-rcppeigen" ,r-rcppeigen))) | |
9177 | (home-page "https://cran.r-project.org/web/packages/DDRTree") | |
9178 | (synopsis "Learning principal graphs with DDRTree") | |
9179 | (description | |
9180 | "This package provides an implementation of the framework of | |
9181 | @dfn{reversed graph embedding} (RGE) which projects data into a reduced | |
9182 | dimensional space while constructs a principal tree which passes through the | |
9183 | middle of the data simultaneously. DDRTree shows superiority to | |
9184 | alternatives (Wishbone, DPT) for inferring the ordering as well as the | |
9185 | intrinsic structure of single cell genomics data. In general, it could be | |
9186 | used to reconstruct the temporal progression as well as the bifurcation | |
9187 | structure of any data type.") | |
9188 | (license license:asl2.0))) | |
d53b2317 RW |
9189 | |
9190 | (define-public r-corpcor | |
9191 | (package | |
9192 | (name "r-corpcor") | |
9193 | (version "1.6.9") | |
9194 | (source | |
9195 | (origin | |
9196 | (method url-fetch) | |
9197 | (uri (cran-uri "corpcor" version)) | |
9198 | (sha256 | |
9199 | (base32 | |
9200 | "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf")))) | |
9201 | (build-system r-build-system) | |
9202 | (home-page "http://strimmerlab.org/software/corpcor/") | |
9203 | (synopsis "Efficient estimation of covariance and (partial) correlation") | |
9204 | (description | |
9205 | "This package implements a James-Stein-type shrinkage estimator for the | |
9206 | covariance matrix, with separate shrinkage for variances and correlations. | |
9207 | Furthermore, functions are available for fast singular value decomposition, | |
9208 | for computing the pseudoinverse, and for checking the rank and positive | |
9209 | definiteness of a matrix.") | |
9210 | (license license:gpl3+))) | |
3088b3fc RW |
9211 | |
9212 | (define-public r-rspectra | |
9213 | (package | |
9214 | (name "r-rspectra") | |
9215 | (version "0.13-1") | |
9216 | (source | |
9217 | (origin | |
9218 | (method url-fetch) | |
9219 | (uri (cran-uri "RSpectra" version)) | |
9220 | (sha256 | |
9221 | (base32 | |
9222 | "1sw80chwyyjzf5px278l6xmp94yhwrlj5xh8d3wlw3dnvdkycca7")))) | |
9223 | (properties `((upstream-name . "RSpectra"))) | |
9224 | (build-system r-build-system) | |
9225 | (propagated-inputs | |
9226 | `(("r-matrix" ,r-matrix) | |
9227 | ("r-rcpp" ,r-rcpp) | |
9228 | ("r-rcppeigen" ,r-rcppeigen))) | |
9229 | (home-page "https://github.com/yixuan/RSpectra") | |
9230 | (synopsis "Solvers for large-scale Eigenvalue and SVD problems") | |
9231 | (description | |
9232 | "This package provides an R interface to the Spectra library for | |
9233 | large-scale eigenvalue and SVD problems. It is typically used to compute a | |
9234 | few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, | |
9235 | which is usually more efficient than @code{eigen()} if k << n.") | |
9236 | ;; MPL 2 or later. | |
9237 | (license license:mpl2.0))) | |
029425cb RW |
9238 | |
9239 | (define-public r-vbsr | |
9240 | (package | |
9241 | (name "r-vbsr") | |
9242 | (version "0.0.5") | |
9243 | (source | |
9244 | (origin | |
9245 | (method url-fetch) | |
9246 | (uri (cran-uri "vbsr" version)) | |
9247 | (sha256 | |
9248 | (base32 | |
9249 | "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) | |
9250 | (build-system r-build-system) | |
9251 | (home-page "https://cran.r-project.org/web/packages/vbsr") | |
9252 | (synopsis "Variational Bayes spike regression regularized linear models") | |
9253 | (description | |
9254 | "This package provides an efficient algorithm for solving ultra-sparse | |
9255 | regularized regression models using a variational Bayes algorithm with a spike | |
9256 | prior. The algorithm is solved on a path, with coordinate updates, and is | |
9257 | capable of generating very sparse models. Very general model | |
9258 | diagnostics for controlling type-1 errors are also provided.") | |
9259 | (license license:gpl2))) | |
3d62d98e RW |
9260 | |
9261 | (define-public r-flare | |
9262 | (package | |
9263 | (name "r-flare") | |
9264 | (version "1.6.0") | |
9265 | (source | |
9266 | (origin | |
9267 | (method url-fetch) | |
9268 | (uri (cran-uri "flare" version)) | |
9269 | (sha256 | |
9270 | (base32 | |
9271 | "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1")))) | |
9272 | (build-system r-build-system) | |
9273 | (propagated-inputs | |
9274 | `(("r-igraph" ,r-igraph) | |
9275 | ("r-lattice" ,r-lattice) | |
9276 | ("r-mass" ,r-mass) | |
9277 | ("r-matrix" ,r-matrix))) | |
9278 | (home-page "https://cran.r-project.org/web/packages/flare") | |
9279 | (synopsis "Family of Lasso regression implementations") | |
9280 | (description | |
9281 | "This packages provides implementations of a family of Lasso variants | |
9282 | including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating | |
9283 | high dimensional sparse linear models.") | |
9284 | (license license:gpl2))) | |
5f0fbfc0 RW |
9285 | |
9286 | (define-public r-lassopv | |
9287 | (package | |
9288 | (name "r-lassopv") | |
9289 | (version "0.2.0") | |
9290 | (source | |
9291 | (origin | |
9292 | (method url-fetch) | |
9293 | (uri (cran-uri "lassopv" version)) | |
9294 | (sha256 | |
9295 | (base32 | |
9296 | "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) | |
9297 | (build-system r-build-system) | |
9298 | (propagated-inputs `(("r-lars" ,r-lars))) | |
9299 | (home-page "https://github.com/lingfeiwang/lassopv") | |
9300 | (synopsis "Non-parametric p-value estimation for predictors in Lasso") | |
9301 | (description | |
9302 | "This package enables you to estimate the p-values for predictors x | |
9303 | against target variable y in Lasso regression, using the regularization | |
9304 | strength when each predictor enters the active set of regularization path for | |
9305 | the first time as the statistic.") | |
9306 | (license license:gpl3))) | |
adcd0cc8 RW |
9307 | |
9308 | (define-public r-splitstackshape | |
9309 | (package | |
9310 | (name "r-splitstackshape") | |
9311 | (version "1.4.6") | |
9312 | (source | |
9313 | (origin | |
9314 | (method url-fetch) | |
9315 | (uri (cran-uri "splitstackshape" version)) | |
9316 | (sha256 | |
9317 | (base32 | |
9318 | "03w6h64ga4zqilffdway4l38l5cbman4yrspkzhbigds12aqz25r")))) | |
9319 | (build-system r-build-system) | |
9320 | (propagated-inputs | |
9321 | `(("r-data-table" ,r-data-table))) | |
9322 | (home-page "https://github.com/mrdwab/splitstackshape") | |
9323 | (synopsis "Stack and reshape datasets after splitting concatenated values") | |
9324 | (description | |
9325 | "Online data collection tools like Google Forms often export | |
9326 | multiple-response questions with data concatenated in cells. The | |
9327 | @code{concat.split} (cSplit) family of functions provided by this package | |
9328 | splits such data into separate cells. This package also includes functions to | |
9329 | stack groups of columns and to reshape wide data, even when the data are | |
9330 | \"unbalanced\"---something which @code{reshape} (from base R) does not handle, | |
9331 | and which @code{melt} and @code{dcast} from @code{reshape2} do not easily | |
9332 | handle.") | |
9333 | (license license:gpl3))) | |
b2e777b2 RW |
9334 | |
9335 | (define-public r-tfmpvalue | |
9336 | (package | |
9337 | (name "r-tfmpvalue") | |
9338 | (version "0.0.8") | |
9339 | (source | |
9340 | (origin | |
9341 | (method url-fetch) | |
9342 | (uri (cran-uri "TFMPvalue" version)) | |
9343 | (sha256 | |
9344 | (base32 | |
9345 | "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) | |
9346 | (properties `((upstream-name . "TFMPvalue"))) | |
9347 | (build-system r-build-system) | |
9348 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
9349 | (home-page "https://github.com/ge11232002/TFMPvalue") | |
9350 | (synopsis "P-value computation for position weight matrices") | |
9351 | (description | |
9352 | "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) | |
9353 | identification from sequence/alignments, we are interested in the significance | |
9354 | of certain match scores. TFMPvalue provides the accurate calculation of a | |
9355 | p-value with a score threshold for position weight matrices, or the score with | |
9356 | a given p-value. It is an interface to code originally made available by | |
9357 | Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. | |
9358 | Touzet and Varre (2007).") | |
9359 | (license license:gpl2))) | |
f79e63a5 RW |
9360 | |
9361 | (define-public r-rnifti | |
9362 | (package | |
9363 | (name "r-rnifti") | |
9364 | (version "0.10.0") | |
9365 | (source | |
9366 | (origin | |
9367 | (method url-fetch) | |
9368 | (uri (cran-uri "RNifti" version)) | |
9369 | (sha256 | |
9370 | (base32 | |
9371 | "07sfzps4yg5zdhbxh6i4rbjvbjvvf2d8i9jcf64ywbmi557sw1zv")))) | |
9372 | (properties `((upstream-name . "RNifti"))) | |
9373 | (build-system r-build-system) | |
9374 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
9375 | (home-page "https://github.com/jonclayden/RNifti") | |
9376 | (synopsis "Fast R and C++ access to NIfTI images") | |
9377 | (description | |
9378 | "This package provides very fast read and write access to images stored | |
9379 | in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between | |
9380 | compiled C and interpreted R code. It also provides a C/C++ API that can be | |
9381 | used by other packages.") | |
9382 | (license license:gpl2))) | |
6e09f506 RW |
9383 | |
9384 | (define-public r-shades | |
9385 | (package | |
9386 | (name "r-shades") | |
16d296bb | 9387 | (version "1.3.1") |
6e09f506 RW |
9388 | (source |
9389 | (origin | |
9390 | (method url-fetch) | |
9391 | (uri (cran-uri "shades" version)) | |
9392 | (sha256 | |
9393 | (base32 | |
16d296bb | 9394 | "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv")))) |
6e09f506 RW |
9395 | (build-system r-build-system) |
9396 | (home-page "https://github.com/jonclayden/shades") | |
9397 | (synopsis "Simple color manipulation") | |
9398 | (description | |
9399 | "This package provides functions for easily manipulating colors, | |
9400 | creating color scales and calculating color distances.") | |
9401 | (license license:bsd-3))) | |
cb03d6c6 RW |
9402 | |
9403 | (define-public r-ore | |
9404 | (package | |
9405 | (name "r-ore") | |
9406 | (version "1.6.2") | |
9407 | (source | |
9408 | (origin | |
9409 | (method url-fetch) | |
9410 | (uri (cran-uri "ore" version)) | |
9411 | (sha256 | |
9412 | (base32 | |
9413 | "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m")))) | |
9414 | (build-system r-build-system) | |
9415 | (home-page "https://github.com/jonclayden/ore") | |
9416 | (synopsis "R interface to the Onigmo regular expression library") | |
9417 | (description | |
9418 | "This package provides an alternative to R's built-in functionality for | |
9419 | handling regular expressions, based on the Onigmo library. It offers | |
9420 | first-class compiled regex objects, partial matching and function-based | |
9421 | substitutions, amongst other features.") | |
9422 | (license license:bsd-3))) | |
b98662c5 RW |
9423 | |
9424 | (define-public r-reportr | |
9425 | (package | |
9426 | (name "r-reportr") | |
9427 | (version "1.3.0") | |
9428 | (source | |
9429 | (origin | |
9430 | (method url-fetch) | |
9431 | (uri (cran-uri "reportr" version)) | |
9432 | (sha256 | |
9433 | (base32 | |
9434 | "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) | |
9435 | (build-system r-build-system) | |
9436 | (propagated-inputs `(("r-ore" ,r-ore))) | |
9437 | (home-page "https://github.com/jonclayden/reportr") | |
9438 | (synopsis "General message and error reporting system") | |
9439 | (description | |
9440 | "This package provides a system for reporting messages, which offers | |
9441 | certain useful features over the standard R system, such as the incorporation | |
9442 | of output consolidation, message filtering, assertions, expression | |
9443 | substitution, automatic generation of stack traces for debugging, and | |
9444 | conditional reporting based on the current \"output level\".") | |
9445 | (license license:gpl2))) | |
7eec973e RW |
9446 | |
9447 | (define-public r-tractor-base | |
9448 | (package | |
9449 | (name "r-tractor-base") | |
9450 | (version "3.3.0") | |
9451 | (source | |
9452 | (origin | |
9453 | (method url-fetch) | |
9454 | (uri (cran-uri "tractor.base" version)) | |
9455 | (sha256 | |
9456 | (base32 | |
9457 | "0i62dwra0yh565ryz75byfgqv22bqwz7138zs48w46yj2h8q9hyj")))) | |
9458 | (properties `((upstream-name . "tractor.base"))) | |
9459 | (build-system r-build-system) | |
9460 | (propagated-inputs | |
9461 | `(("r-ore" ,r-ore) | |
9462 | ("r-reportr" ,r-reportr) | |
9463 | ("r-rnifti" ,r-rnifti) | |
9464 | ("r-shades" ,r-shades))) | |
9465 | (home-page "http://www.tractor-mri.org.uk") | |
9466 | (synopsis "Read, manipulate and visualize magnetic resonance images") | |
9467 | (description | |
9468 | "This package provides functions for working with magnetic resonance | |
9469 | images. It supports reading and writing of popular file formats (DICOM, | |
9470 | Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive | |
9471 | visualization; flexible image manipulation; metadata and sparse image | |
9472 | handling.") | |
9473 | (license license:gpl2))) | |
d0eb09a1 RW |
9474 | |
9475 | (define-public r-grimport | |
9476 | (package | |
9477 | (name "r-grimport") | |
9ad5f4ba | 9478 | (version "0.9-1.1") |
d0eb09a1 RW |
9479 | (source |
9480 | (origin | |
9481 | (method url-fetch) | |
9482 | (uri (cran-uri "grImport" version)) | |
9483 | (sha256 | |
9484 | (base32 | |
9ad5f4ba | 9485 | "19d05ygpiv47lfzhfih35pdfll0axbrgd6p86l59mmg2d0j0s8bd")))) |
d0eb09a1 RW |
9486 | (properties `((upstream-name . "grImport"))) |
9487 | (build-system r-build-system) | |
9488 | (inputs | |
9489 | `(("ghostscript" ,ghostscript))) | |
9490 | (propagated-inputs | |
9491 | `(("r-xml" ,r-xml))) | |
9492 | (home-page "https://cran.r-project.org/web/packages/grImport") | |
9493 | (synopsis "Convert, import, and draw PostScript pictures") | |
9494 | (description | |
9495 | "This package provides functions for converting, importing, and drawing | |
9496 | PostScript pictures in R plots.") | |
9497 | (license license:gpl2+))) | |
2871b670 RW |
9498 | |
9499 | (define-public r-kohonen | |
9500 | (package | |
9501 | (name "r-kohonen") | |
9502 | (version "3.0.8") | |
9503 | (source | |
9504 | (origin | |
9505 | (method url-fetch) | |
9506 | (uri (cran-uri "kohonen" version)) | |
9507 | (sha256 | |
9508 | (base32 | |
9509 | "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q")))) | |
9510 | (build-system r-build-system) | |
9511 | (propagated-inputs | |
9512 | `(("r-mass" ,r-mass) | |
9513 | ("r-rcpp" ,r-rcpp))) | |
9514 | (home-page "https://cran.r-project.org/web/packages/kohonen") | |
9515 | (synopsis "Supervised and unsupervised self-organising maps") | |
9516 | (description | |
9517 | "This package provides functions to train @dfn{self-organising | |
9518 | maps} (SOMs). Also interrogation of the maps and prediction using trained | |
9519 | maps are supported. The name of the package refers to Teuvo Kohonen, the | |
9520 | inventor of the SOM.") | |
9521 | (license license:gpl2+))) | |
00436e2c RW |
9522 | |
9523 | (define-public r-nnls | |
9524 | (package | |
9525 | (name "r-nnls") | |
9526 | (version "1.4") | |
9527 | (source | |
9528 | (origin | |
9529 | (method url-fetch) | |
9530 | (uri (cran-uri "nnls" version)) | |
9531 | (sha256 | |
9532 | (base32 | |
9533 | "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) | |
9534 | (build-system r-build-system) | |
9535 | (native-inputs `(("gfortran" ,gfortran))) | |
9536 | (home-page "https://cran.r-project.org/web/packages/nnls") | |
9537 | (synopsis "Lawson-Hanson algorithm for non-negative least squares") | |
9538 | (description | |
9539 | "This package provides an R interface to the Lawson-Hanson implementation | |
9540 | of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows | |
9541 | the combination of non-negative and non-positive constraints.") | |
9542 | (license license:gpl2+))) | |
25861356 RW |
9543 | |
9544 | (define-public r-iso | |
9545 | (package | |
9546 | (name "r-iso") | |
9547 | (version "0.0-17") | |
9548 | (source | |
9549 | (origin | |
9550 | (method url-fetch) | |
9551 | (uri (cran-uri "Iso" version)) | |
9552 | (sha256 | |
9553 | (base32 | |
9554 | "0lljc99sdzdqj6d56qbsggibr6pkdwkh821bj70ianikyvmdc1y0")))) | |
9555 | (properties `((upstream-name . "Iso"))) | |
9556 | (build-system r-build-system) | |
9557 | (native-inputs `(("gfortran" ,gfortran))) | |
9558 | (home-page "http://www.stat.auckland.ac.nz/~rolf/") | |
9559 | (synopsis "Functions to perform isotonic regression") | |
9560 | (description | |
9561 | "This package provides support for linear order and unimodal | |
9562 | order (univariate) isotonic regression and bivariate isotonic regression with | |
9563 | linear order on both variables.") | |
9564 | (license license:gpl2+))) | |
9401f56b RW |
9565 | |
9566 | (define-public r-chemometricswithr | |
9567 | (package | |
9568 | (name "r-chemometricswithr") | |
e0417402 | 9569 | (version "0.1.13") |
9401f56b RW |
9570 | (source |
9571 | (origin | |
9572 | (method url-fetch) | |
9573 | (uri (cran-uri "ChemometricsWithR" version)) | |
9574 | (sha256 | |
9575 | (base32 | |
e0417402 | 9576 | "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) |
9401f56b RW |
9577 | (properties |
9578 | `((upstream-name . "ChemometricsWithR"))) | |
9579 | (build-system r-build-system) | |
9580 | (propagated-inputs | |
9581 | `(("r-devtools" ,r-devtools) | |
9582 | ("r-kohonen" ,r-kohonen) | |
9583 | ("r-mass" ,r-mass) | |
9584 | ("r-pls" ,r-pls))) | |
9585 | (home-page "https://github.com/rwehrens/CWR") | |
9586 | (synopsis "Chemometrics with R") | |
9587 | (description | |
9588 | "This package provides functions and scripts used in the book | |
9589 | \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and | |
9590 | Life Sciences\" by Ron Wehrens, Springer (2011).") | |
9591 | (license license:gpl2+))) | |
d28be7b7 RW |
9592 | |
9593 | (define-public r-als | |
9594 | (package | |
9595 | (name "r-als") | |
9596 | (version "0.0.6") | |
9597 | (source | |
9598 | (origin | |
9599 | (method url-fetch) | |
9600 | (uri (cran-uri "ALS" version)) | |
9601 | (sha256 | |
9602 | (base32 | |
9603 | "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) | |
9604 | (properties `((upstream-name . "ALS"))) | |
9605 | (build-system r-build-system) | |
9606 | (propagated-inputs | |
9607 | `(("r-iso" ,r-iso) | |
9608 | ("r-nnls" ,r-nnls))) | |
9609 | (home-page "https://cran.r-project.org/web/packages/ALS") | |
9610 | (synopsis "Multivariate curve resolution alternating least squares") | |
9611 | (description | |
9612 | "Alternating least squares is often used to resolve components | |
9613 | contributing to data with a bilinear structure; the basic technique may be | |
9614 | extended to alternating constrained least squares. This package provides an | |
9615 | implementation of @dfn{multivariate curve resolution alternating least | |
9616 | squares} (MCR-ALS). | |
9617 | ||
9618 | Commonly applied constraints include unimodality, non-negativity, and | |
9619 | normalization of components. Several data matrices may be decomposed | |
9620 | simultaneously by assuming that one of the two matrices in the bilinear | |
9621 | decomposition is shared between datasets.") | |
9622 | (license license:gpl2+))) | |
895efece RW |
9623 | |
9624 | (define-public r-strucchange | |
9625 | (package | |
9626 | (name "r-strucchange") | |
9627 | (version "1.5-1") | |
9628 | (source | |
9629 | (origin | |
9630 | (method url-fetch) | |
9631 | (uri (cran-uri "strucchange" version)) | |
9632 | (sha256 | |
9633 | (base32 | |
9634 | "0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl")))) | |
9635 | (build-system r-build-system) | |
9636 | (propagated-inputs | |
9637 | `(("r-sandwich" ,r-sandwich) | |
9638 | ("r-zoo" ,r-zoo))) | |
9639 | (home-page "https://cran.r-project.org/web/packages/strucchange") | |
9640 | (synopsis "Testing, monitoring, and dating structural changes") | |
9641 | (description | |
9642 | "This package provides tools for testing, monitoring and dating | |
9643 | structural changes in (linear) regression models. It features tests/methods | |
9644 | from the generalized fluctuation test framework as well as from the F | |
9645 | test (Chow test) framework. This includes methods to fit, plot and test | |
9646 | fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F | |
9647 | statistics, respectively. It is possible to monitor incoming data online | |
9648 | using fluctuation processes. Finally, the breakpoints in regression models | |
9649 | with structural changes can be estimated together with confidence intervals. | |
9650 | Emphasis is always given to methods for visualizing the data.") | |
9651 | ;; Either of these two GPL versions | |
9652 | (license (list license:gpl2 license:gpl3)))) | |
e7176ac5 RW |
9653 | |
9654 | (define-public r-pixmap | |
9655 | (package | |
9656 | (name "r-pixmap") | |
9657 | (version "0.4-11") | |
9658 | (source | |
9659 | (origin | |
9660 | (method url-fetch) | |
9661 | (uri (cran-uri "pixmap" version)) | |
9662 | (sha256 | |
9663 | (base32 | |
9664 | "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) | |
9665 | (build-system r-build-system) | |
9666 | (home-page "https://cran.r-project.org/web/packages/pixmap") | |
9667 | (synopsis "Tools for bitmap images") | |
9668 | (description | |
9669 | "This package provides functions for importing, exporting, plotting and | |
9670 | other manipulations of bitmapped images.") | |
9671 | (license license:gpl2))) | |
9170eb7f RW |
9672 | |
9673 | (define-public r-rapidjsonr | |
9674 | (package | |
9675 | (name "r-rapidjsonr") | |
9676 | (version "1.1") | |
9677 | (source | |
9678 | (origin | |
9679 | (method url-fetch) | |
9680 | (uri (cran-uri "rapidjsonr" version)) | |
9681 | (sha256 | |
9682 | (base32 | |
9683 | "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd")))) | |
9684 | (build-system r-build-system) | |
9685 | (home-page "https://cran.r-project.org/web/packages/rapidjsonr") | |
9686 | (synopsis "JSON parser") | |
9687 | (description | |
9688 | "This package provides JSON parsing capability through the Rapidjson | |
9689 | library.") | |
9690 | (license license:expat))) | |
ad6fea16 RW |
9691 | |
9692 | (define-public r-ontologyindex | |
9693 | (package | |
9694 | (name "r-ontologyindex") | |
209e504b | 9695 | (version "2.5") |
ad6fea16 RW |
9696 | (source |
9697 | (origin | |
9698 | (method url-fetch) | |
9699 | (uri (cran-uri "ontologyIndex" version)) | |
9700 | (sha256 | |
9701 | (base32 | |
209e504b | 9702 | "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) |
ad6fea16 RW |
9703 | (properties `((upstream-name . "ontologyIndex"))) |
9704 | (build-system r-build-system) | |
9705 | (home-page "https://cran.r-project.org/web/packages/ontologyIndex") | |
9706 | (synopsis "Functions for processing ontologies in R") | |
9707 | (description | |
9708 | "This package provides functions for reading ontologies into R as lists | |
9709 | and manipulating sets of ontological terms.") | |
9710 | (license license:gpl2+))) | |
dfd09f7b RW |
9711 | |
9712 | (define-public r-bigrquery | |
9713 | (package | |
9714 | (name "r-bigrquery") | |
4bc5d451 | 9715 | (version "1.1.0") |
dfd09f7b RW |
9716 | (source |
9717 | (origin | |
9718 | (method url-fetch) | |
9719 | (uri (cran-uri "bigrquery" version)) | |
9720 | (sha256 | |
9721 | (base32 | |
4bc5d451 | 9722 | "0h2nzyn1w0padpl61l467j7vlkc2wair7sh6p26p94z4zfsnv0i1")))) |
dfd09f7b RW |
9723 | (build-system r-build-system) |
9724 | (propagated-inputs | |
9725 | `(("r-assertthat" ,r-assertthat) | |
4bc5d451 | 9726 | ("r-bit64" ,r-bit64) |
dfd09f7b RW |
9727 | ("r-curl" ,r-curl) |
9728 | ("r-dbi" ,r-dbi) | |
9729 | ("r-glue" ,r-glue) | |
9730 | ("r-httr" ,r-httr) | |
9731 | ("r-jsonlite" ,r-jsonlite) | |
9732 | ("r-prettyunits" ,r-prettyunits) | |
9733 | ("r-progress" ,r-progress) | |
9734 | ("r-rapidjsonr" ,r-rapidjsonr) | |
9735 | ("r-rcpp" ,r-rcpp) | |
9736 | ("r-tibble" ,r-tibble))) | |
9737 | (home-page "https://github.com/rstats-db/bigrquery") | |
9738 | (synopsis "R interface to Google's BigQuery API") | |
9739 | (description | |
9740 | "This package provides an R interface to Google's BigQuery database.") | |
9741 | (license license:gpl3))) | |
1ab51604 RW |
9742 | |
9743 | (define-public r-gmp | |
9744 | (package | |
9745 | (name "r-gmp") | |
83bfddd1 | 9746 | (version "0.5-13.5") |
1ab51604 RW |
9747 | (source |
9748 | (origin | |
9749 | (method url-fetch) | |
9750 | (uri (cran-uri "gmp" version)) | |
9751 | (sha256 | |
9752 | (base32 | |
83bfddd1 | 9753 | "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn")))) |
1ab51604 RW |
9754 | (build-system r-build-system) |
9755 | (arguments | |
9756 | '(#:phases | |
9757 | (modify-phases %standard-phases | |
9758 | (add-after 'unpack 'set-CC | |
9759 | (lambda _ (setenv "CC" "gcc") #t))))) | |
9760 | (inputs `(("gmp" ,gmp))) | |
9761 | (home-page "https://cran.r-project.org/web/packages/gmp") | |
9762 | (synopsis "Multiple precision arithmetic") | |
9763 | (description | |
9764 | "This package supports multiple precision arithmetic (big integers and | |
9765 | rationals, prime number tests, matrix computation), \"arithmetic without | |
9766 | limitations\" using the GNU Multiple Precision library.") | |
9767 | ;; Any version of the GPL. | |
9768 | (license license:gpl3+))) | |
a536c7c9 RW |
9769 | |
9770 | (define-public r-rmpfr | |
9771 | (package | |
9772 | (name "r-rmpfr") | |
df00ca25 | 9773 | (version "0.7-2") |
a536c7c9 RW |
9774 | (source |
9775 | (origin | |
9776 | (method url-fetch) | |
9777 | (uri (cran-uri "Rmpfr" version)) | |
9778 | (sha256 | |
9779 | (base32 | |
df00ca25 | 9780 | "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc")))) |
a536c7c9 RW |
9781 | (properties `((upstream-name . "Rmpfr"))) |
9782 | (build-system r-build-system) | |
9783 | (inputs | |
9784 | `(("mpfr" ,mpfr))) | |
9785 | (propagated-inputs | |
9786 | `(("r-gmp" ,r-gmp))) | |
9787 | (home-page "http://rmpfr.r-forge.r-project.org/") | |
9788 | (synopsis "R bindings to the MPFR library") | |
9789 | (description | |
9790 | "This package supports arithmetic (via S4 classes and methods) for | |
9791 | arbitrary precision floating point numbers, including transcendental | |
9792 | functions. To this end, the package interfaces with the @dfn{Multiple | |
9793 | Precision Floating-Point Reliable} (MPFR) library.") | |
9794 | (license license:gpl2+))) | |
8004bb24 RW |
9795 | |
9796 | (define-public r-assertive-base | |
9797 | (package | |
9798 | (name "r-assertive-base") | |
9799 | (version "0.0-7") | |
9800 | (source | |
9801 | (origin | |
9802 | (method url-fetch) | |
9803 | (uri (cran-uri "assertive.base" version)) | |
9804 | (sha256 | |
9805 | (base32 | |
9806 | "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh")))) | |
9807 | (properties | |
9808 | `((upstream-name . "assertive.base"))) | |
9809 | (build-system r-build-system) | |
9810 | (home-page "https://bitbucket.org/richierocks/assertive.base") | |
9811 | (synopsis "Core of the assertive package") | |
9812 | (description | |
9813 | "This package provides a minimal set of predicates and assertions used by | |
9814 | the assertive package. This is mainly for use by other package developers who | |
9815 | want to include run-time testing features in their own packages.") | |
9816 | (license license:gpl3+))) | |
4b2d17ed RW |
9817 | |
9818 | (define-public r-assertive-properties | |
9819 | (package | |
9820 | (name "r-assertive-properties") | |
9821 | (version "0.0-4") | |
9822 | (source | |
9823 | (origin | |
9824 | (method url-fetch) | |
9825 | (uri (cran-uri "assertive.properties" version)) | |
9826 | (sha256 | |
9827 | (base32 | |
9828 | "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw")))) | |
9829 | (properties | |
9830 | `((upstream-name . "assertive.properties"))) | |
9831 | (build-system r-build-system) | |
9832 | (propagated-inputs | |
9833 | `(("r-assertive-base" ,r-assertive-base))) | |
9834 | (home-page "https://bitbucket.org/richierocks/assertive.properties") | |
9835 | (synopsis "Assertions to check properties of variables") | |
9836 | (description | |
9837 | "This package provides a set of predicates and assertions for checking | |
9838 | the properties of variables, such as length, names and attributes. This is | |
9839 | mainly for use by other package developers who want to include run-time | |
9840 | testing features in their own packages.") | |
9841 | (license license:gpl3+))) | |
dac9c1f6 RW |
9842 | |
9843 | (define-public r-assertive-numbers | |
9844 | (package | |
9845 | (name "r-assertive-numbers") | |
9846 | (version "0.0-2") | |
9847 | (source | |
9848 | (origin | |
9849 | (method url-fetch) | |
9850 | (uri (cran-uri "assertive.numbers" version)) | |
9851 | (sha256 | |
9852 | (base32 | |
9853 | "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds")))) | |
9854 | (properties | |
9855 | `((upstream-name . "assertive.numbers"))) | |
9856 | (build-system r-build-system) | |
9857 | (propagated-inputs | |
9858 | `(("r-assertive-base" ,r-assertive-base))) | |
9859 | (home-page "https://bitbucket.org/richierocks/assertive.numbers") | |
9860 | (synopsis "Assertions to check properties of numbers") | |
9861 | (description | |
9862 | "This package provides a set of predicates and assertions for checking | |
9863 | the properties of numbers. This is mainly for use by other package developers | |
9864 | who want to include run-time testing features in their own packages.") | |
9865 | (license license:gpl3+))) | |
2da2d2f6 RW |
9866 | |
9867 | (define-public r-assertive-sets | |
9868 | (package | |
9869 | (name "r-assertive-sets") | |
9870 | (version "0.0-3") | |
9871 | (source | |
9872 | (origin | |
9873 | (method url-fetch) | |
9874 | (uri (cran-uri "assertive.sets" version)) | |
9875 | (sha256 | |
9876 | (base32 | |
9877 | "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7")))) | |
9878 | (properties | |
9879 | `((upstream-name . "assertive.sets"))) | |
9880 | (build-system r-build-system) | |
9881 | (propagated-inputs | |
9882 | `(("r-assertive-base" ,r-assertive-base))) | |
9883 | (home-page "https://bitbucket.org/richierocks/assertive.sets") | |
9884 | (synopsis "Assertions to check properties of sets") | |
9885 | (description | |
9886 | "This package provides a set of predicates and assertions for checking | |
9887 | the properties of sets. This is mainly for use by other package developers | |
9888 | who want to include run-time testing features in their own packages.") | |
9889 | (license license:gpl3+))) | |
905aa46a RW |
9890 | |
9891 | (define-public r-assertive-matrices | |
9892 | (package | |
9893 | (name "r-assertive-matrices") | |
9894 | (version "0.0-2") | |
9895 | (source | |
9896 | (origin | |
9897 | (method url-fetch) | |
9898 | (uri (cran-uri "assertive.matrices" version)) | |
9899 | (sha256 | |
9900 | (base32 | |
9901 | "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil")))) | |
9902 | (properties | |
9903 | `((upstream-name . "assertive.matrices"))) | |
9904 | (build-system r-build-system) | |
9905 | (propagated-inputs | |
9906 | `(("r-assertive-base" ,r-assertive-base))) | |
9907 | (home-page "https://bitbucket.org/richierocks/assertive.matrices") | |
9908 | (synopsis "Assertions to check properties of matrices") | |
9909 | (description | |
9910 | "This package provides a set of predicates and assertions for checking | |
9911 | the properties of matrices. This is mainly for use by other package | |
9912 | developers who want to include run-time testing features in their own | |
9913 | packages.") | |
9914 | (license license:gpl3+))) | |
c358b5d4 RW |
9915 | |
9916 | (define-public r-assertive-models | |
9917 | (package | |
9918 | (name "r-assertive-models") | |
9919 | (version "0.0-2") | |
9920 | (source | |
9921 | (origin | |
9922 | (method url-fetch) | |
9923 | (uri (cran-uri "assertive.models" version)) | |
9924 | (sha256 | |
9925 | (base32 | |
9926 | "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr")))) | |
9927 | (properties | |
9928 | `((upstream-name . "assertive.models"))) | |
9929 | (build-system r-build-system) | |
9930 | (propagated-inputs | |
9931 | `(("r-assertive-base" ,r-assertive-base))) | |
9932 | (home-page "https://bitbucket.org/richierocks/assertive.models") | |
9933 | (synopsis "Assertions to check properties of models") | |
9934 | (description | |
9935 | "This package provides a set of predicates and assertions for checking | |
9936 | the properties of models. This is mainly for use by other package developers | |
9937 | who want to include run-time testing features in their own packages.") | |
9938 | (license license:gpl3+))) | |
dcafcfb4 RW |
9939 | |
9940 | (define-public r-assertive-reflection | |
9941 | (package | |
9942 | (name "r-assertive-reflection") | |
9943 | (version "0.0-4") | |
9944 | (source | |
9945 | (origin | |
9946 | (method url-fetch) | |
9947 | (uri (cran-uri "assertive.reflection" version)) | |
9948 | (sha256 | |
9949 | (base32 | |
9950 | "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj")))) | |
9951 | (properties | |
9952 | `((upstream-name . "assertive.reflection"))) | |
9953 | (build-system r-build-system) | |
9954 | (propagated-inputs | |
9955 | `(("r-assertive-base" ,r-assertive-base))) | |
9956 | (home-page "https://bitbucket.org/richierocks/assertive.reflection") | |
9957 | (synopsis "Assertions for checking the state of R") | |
9958 | (description | |
9959 | "This package provides a set of predicates and assertions for checking | |
9960 | the state and capabilities of R, the operating system it is running on, and | |
9961 | the IDE being used. This is mainly for use by other package developers who | |
9962 | want to include run-time testing features in their own packages.") | |
9963 | (license license:gpl3+))) | |
5e3bd355 RW |
9964 | |
9965 | (define-public r-assertive-types | |
9966 | (package | |
9967 | (name "r-assertive-types") | |
9968 | (version "0.0-3") | |
9969 | (source | |
9970 | (origin | |
9971 | (method url-fetch) | |
9972 | (uri (cran-uri "assertive.types" version)) | |
9973 | (sha256 | |
9974 | (base32 | |
9975 | "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb")))) | |
9976 | (properties | |
9977 | `((upstream-name . "assertive.types"))) | |
9978 | (build-system r-build-system) | |
9979 | (propagated-inputs | |
9980 | `(("r-assertive-base" ,r-assertive-base) | |
9981 | ("r-assertive-properties" ,r-assertive-properties) | |
9982 | ("r-codetools" ,r-codetools))) | |
9983 | (home-page "https://bitbucket.org/richierocks/assertive.types") | |
9984 | (synopsis "Assertions to check types of variables") | |
9985 | (description | |
9986 | "This package provides a set of predicates and assertions for checking | |
9987 | the types of variables. This is mainly for use by other package developers | |
9988 | who want to include run-time testing features in their own packages.") | |
9989 | (license license:gpl3+))) | |
1f0a761a RW |
9990 | |
9991 | (define-public r-assertive-files | |
9992 | (package | |
9993 | (name "r-assertive-files") | |
9994 | (version "0.0-2") | |
9995 | (source | |
9996 | (origin | |
9997 | (method url-fetch) | |
9998 | (uri (cran-uri "assertive.files" version)) | |
9999 | (sha256 | |
10000 | (base32 | |
10001 | "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy")))) | |
10002 | (properties | |
10003 | `((upstream-name . "assertive.files"))) | |
10004 | (build-system r-build-system) | |
10005 | (propagated-inputs | |
10006 | `(("r-assertive-base" ,r-assertive-base) | |
10007 | ("r-assertive-numbers" ,r-assertive-numbers))) | |
10008 | (home-page "https://bitbucket.org/richierocks/assertive.files") | |
10009 | (synopsis "Assertions to check properties of files") | |
10010 | (description | |
10011 | "This package provides a set of predicates and assertions for checking | |
10012 | the properties of files and connections. This is mainly for use by other | |
10013 | package developers who want to include run-time testing features in their own | |
10014 | packages.") | |
10015 | (license license:gpl3+))) | |
50ce8b1e RW |
10016 | |
10017 | (define-public r-assertive-code | |
10018 | (package | |
10019 | (name "r-assertive-code") | |
10020 | (version "0.0-3") | |
10021 | (source | |
10022 | (origin | |
10023 | (method url-fetch) | |
10024 | (uri (cran-uri "assertive.code" version)) | |
10025 | (sha256 | |
10026 | (base32 | |
10027 | "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) | |
10028 | (properties | |
10029 | `((upstream-name . "assertive.code"))) | |
10030 | (build-system r-build-system) | |
10031 | (propagated-inputs | |
10032 | `(("r-assertive-base" ,r-assertive-base) | |
10033 | ("r-assertive-properties" ,r-assertive-properties) | |
10034 | ("r-assertive-types" ,r-assertive-types))) | |
10035 | (home-page "https://bitbucket.org/richierocks/assertive.code") | |
10036 | (synopsis "Assertions to check properties of code") | |
10037 | (description | |
10038 | "This package provides a set of predicates and assertions for checking | |
10039 | the properties of code. This is mainly for use by other package developers | |
10040 | who want to include run-time testing features in their own packages.") | |
10041 | (license license:gpl3+))) | |
29d9a2af RW |
10042 | |
10043 | (define-public r-assertive-datetimes | |
10044 | (package | |
10045 | (name "r-assertive-datetimes") | |
10046 | (version "0.0-2") | |
10047 | (source | |
10048 | (origin | |
10049 | (method url-fetch) | |
10050 | (uri (cran-uri "assertive.datetimes" version)) | |
10051 | (sha256 | |
10052 | (base32 | |
10053 | "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78")))) | |
10054 | (properties | |
10055 | `((upstream-name . "assertive.datetimes"))) | |
10056 | (build-system r-build-system) | |
10057 | (propagated-inputs | |
10058 | `(("r-assertive-base" ,r-assertive-base) | |
10059 | ("r-assertive-types" ,r-assertive-types))) | |
10060 | (home-page "https://bitbucket.org/richierocks/assertive.datetimes") | |
10061 | (synopsis "Assertions to check properties of dates and times") | |
10062 | (description | |
10063 | "This package provides a set of predicates and assertions for checking | |
10064 | the properties of dates and times. This is mainly for use by other package | |
10065 | developers who want to include run-time testing features in their own | |
10066 | packages.") | |
10067 | (license license:gpl3+))) | |
66d0a0a7 RW |
10068 | |
10069 | (define-public r-assertive-strings | |
10070 | (package | |
10071 | (name "r-assertive-strings") | |
10072 | (version "0.0-3") | |
10073 | (source | |
10074 | (origin | |
10075 | (method url-fetch) | |
10076 | (uri (cran-uri "assertive.strings" version)) | |
10077 | (sha256 | |
10078 | (base32 | |
10079 | "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm")))) | |
10080 | (properties | |
10081 | `((upstream-name . "assertive.strings"))) | |
10082 | (build-system r-build-system) | |
10083 | (propagated-inputs | |
10084 | `(("r-assertive-base" ,r-assertive-base) | |
10085 | ("r-assertive-types" ,r-assertive-types) | |
10086 | ("r-stringi" ,r-stringi))) | |
10087 | (home-page "https://bitbucket.org/richierocks/assertive.strings") | |
10088 | (synopsis "Assertions to check properties of strings") | |
10089 | (description | |
10090 | "This package provides a set of predicates and assertions for checking | |
10091 | the properties of strings. This is mainly for use by other package developers | |
10092 | who want to include run-time testing features in their own packages.") | |
10093 | (license license:gpl3+))) | |
6d3702e5 RW |
10094 | |
10095 | (define-public r-assertive-data-us | |
10096 | (package | |
10097 | (name "r-assertive-data-us") | |
10098 | (version "0.0-2") | |
10099 | (source | |
10100 | (origin | |
10101 | (method url-fetch) | |
10102 | (uri (cran-uri "assertive.data.us" version)) | |
10103 | (sha256 | |
10104 | (base32 | |
10105 | "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq")))) | |
10106 | (properties | |
10107 | `((upstream-name . "assertive.data.us"))) | |
10108 | (build-system r-build-system) | |
10109 | (propagated-inputs | |
10110 | `(("r-assertive-base" ,r-assertive-base) | |
10111 | ("r-assertive-strings" ,r-assertive-strings))) | |
10112 | (home-page "https://bitbucket.org/richierocks/assertive.data.us") | |
10113 | (synopsis "Assertions to check properties of strings") | |
10114 | (description | |
10115 | "This package provides a set of predicates and assertions for checking | |
10116 | the properties of US-specific complex data types. This is mainly for use by | |
10117 | other package developers who want to include run-time testing features in | |
10118 | their own packages.") | |
10119 | (license license:gpl3+))) | |
39ef8e09 RW |
10120 | |
10121 | (define-public r-assertive-data-uk | |
10122 | (package | |
10123 | (name "r-assertive-data-uk") | |
10124 | (version "0.0-2") | |
10125 | (source | |
10126 | (origin | |
10127 | (method url-fetch) | |
10128 | (uri (cran-uri "assertive.data.uk" version)) | |
10129 | (sha256 | |
10130 | (base32 | |
10131 | "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b")))) | |
10132 | (properties | |
10133 | `((upstream-name . "assertive.data.uk"))) | |
10134 | (build-system r-build-system) | |
10135 | (propagated-inputs | |
10136 | `(("r-assertive-base" ,r-assertive-base) | |
10137 | ("r-assertive-strings" ,r-assertive-strings))) | |
10138 | (home-page "https://bitbucket.org/richierocks/assertive.data.uk") | |
10139 | (synopsis "Assertions to check properties of strings") | |
10140 | (description | |
10141 | "This package provides a set of predicates and assertions for checking | |
10142 | the properties of UK-specific complex data types. This is mainly for use by | |
10143 | other package developers who want to include run-time testing features in | |
10144 | their own packages.") | |
10145 | (license license:gpl3+))) | |
39231abf RW |
10146 | |
10147 | (define-public r-assertive-data | |
10148 | (package | |
10149 | (name "r-assertive-data") | |
10150 | (version "0.0-3") | |
10151 | (source | |
10152 | (origin | |
10153 | (method url-fetch) | |
10154 | (uri (cran-uri "assertive.data" version)) | |
10155 | (sha256 | |
10156 | (base32 | |
10157 | "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s")))) | |
10158 | (properties | |
10159 | `((upstream-name . "assertive.data"))) | |
10160 | (build-system r-build-system) | |
10161 | (propagated-inputs | |
10162 | `(("r-assertive-base" ,r-assertive-base) | |
10163 | ("r-assertive-strings" ,r-assertive-strings))) | |
10164 | (home-page "https://bitbucket.org/richierocks/assertive.data") | |
10165 | (synopsis "Assertions to check properties of data") | |
10166 | (description | |
10167 | "This package provides a set of predicates and assertions for checking | |
10168 | the properties of (country independent) complex data types. This is mainly | |
10169 | for use by other package developers who want to include run-time testing | |
10170 | features in their own packages.") | |
10171 | (license license:gpl3+))) | |
658b2b62 RW |
10172 | |
10173 | (define-public r-assertive | |
10174 | (package | |
10175 | (name "r-assertive") | |
10176 | (version "0.3-5") | |
10177 | (source | |
10178 | (origin | |
10179 | (method url-fetch) | |
10180 | (uri (cran-uri "assertive" version)) | |
10181 | (sha256 | |
10182 | (base32 | |
10183 | "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3")))) | |
10184 | (build-system r-build-system) | |
10185 | (propagated-inputs | |
10186 | `(("r-assertive-base" ,r-assertive-base) | |
10187 | ("r-assertive-code" ,r-assertive-code) | |
10188 | ("r-assertive-data" ,r-assertive-data) | |
10189 | ("r-assertive-data-uk" ,r-assertive-data-uk) | |
10190 | ("r-assertive-data-us" ,r-assertive-data-us) | |
10191 | ("r-assertive-datetimes" ,r-assertive-datetimes) | |
10192 | ("r-assertive-files" ,r-assertive-files) | |
10193 | ("r-assertive-matrices" ,r-assertive-matrices) | |
10194 | ("r-assertive-models" ,r-assertive-models) | |
10195 | ("r-assertive-numbers" ,r-assertive-numbers) | |
10196 | ("r-assertive-properties" ,r-assertive-properties) | |
10197 | ("r-assertive-reflection" ,r-assertive-reflection) | |
10198 | ("r-assertive-sets" ,r-assertive-sets) | |
10199 | ("r-assertive-strings" ,r-assertive-strings) | |
10200 | ("r-assertive-types" ,r-assertive-types) | |
10201 | ("r-knitr" ,r-knitr))) | |
10202 | (home-page "https://bitbucket.org/richierocks/assertive") | |
10203 | (synopsis "Readable check functions to ensure code integrity") | |
10204 | (description | |
10205 | "This package provides lots of predicates (@code{is_*} functions) to | |
10206 | check the state of your variables, and assertions (@code{assert_*} functions) | |
10207 | to throw errors if they aren't in the right form.") | |
10208 | (license license:gpl3+))) | |
f51dcc27 RW |
10209 | |
10210 | (define-public r-dotcall64 | |
10211 | (package | |
10212 | (name "r-dotcall64") | |
10213 | (version "1.0-0") | |
10214 | (source | |
10215 | (origin | |
10216 | (method url-fetch) | |
10217 | (uri (cran-uri "dotCall64" version)) | |
10218 | (sha256 | |
10219 | (base32 | |
10220 | "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) | |
10221 | (properties `((upstream-name . "dotCall64"))) | |
10222 | (build-system r-build-system) | |
10223 | (native-inputs `(("gfortran" ,gfortran))) | |
10224 | (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") | |
10225 | (synopsis "Enhanced foreign function interface supporting long vectors") | |
10226 | (description | |
10227 | "This package provides @code{.C64()}, an enhanced version of @code{.C()} | |
10228 | and @code{.Fortran()} from the R foreign function interface. @code{.C64()} | |
10229 | supports long vectors, arguments of type 64-bit integer, and provides a | |
10230 | mechanism to avoid unnecessary copies of read-only and write-only arguments. | |
10231 | This makes it a convenient and fast interface to C/C++ and Fortran code.") | |
10232 | (license license:gpl2+))) | |
90104ecd RW |
10233 | |
10234 | (define-public r-spam | |
10235 | (package | |
10236 | (name "r-spam") | |
6cea61eb | 10237 | (version "2.2-2") |
90104ecd RW |
10238 | (source |
10239 | (origin | |
10240 | (method url-fetch) | |
10241 | (uri (cran-uri "spam" version)) | |
10242 | (sha256 | |
10243 | (base32 | |
6cea61eb | 10244 | "024dgfnjfxvsiymbzrhadinamj6qy509f4sbd1zxql8ymkyxn7vi")))) |
90104ecd RW |
10245 | (build-system r-build-system) |
10246 | (propagated-inputs | |
10247 | `(("r-dotcall64" ,r-dotcall64))) | |
10248 | (native-inputs `(("gfortran" ,gfortran))) | |
10249 | (home-page "https://www.math.uzh.ch/pages/spam/") | |
10250 | (synopsis "Sparse matrix algebra") | |
10251 | (description | |
10252 | "This package provides a set of functions for sparse matrix algebra. | |
10253 | Differences with other sparse matrix packages are: | |
10254 | ||
10255 | @enumerate | |
10256 | @item it only supports (essentially) one sparse matrix format; | |
10257 | @item it is based on transparent and simple structure(s); | |
10258 | @item it is tailored for MCMC calculations within G(M)RF; | |
10259 | @item and it is fast and scalable (with the extension package @code{spam64}). | |
10260 | @end enumerate\n") | |
10261 | ;; Either of these licenses | |
10262 | (license (list license:bsd-3 license:lgpl2.0)))) | |
32725458 RW |
10263 | |
10264 | (define-public r-fields | |
10265 | (package | |
10266 | (name "r-fields") | |
10267 | (version "9.6") | |
10268 | (source | |
10269 | (origin | |
10270 | (method url-fetch) | |
10271 | (uri (cran-uri "fields" version)) | |
10272 | (sha256 | |
10273 | (base32 | |
10274 | "1v7z48a8jmdcil28rj8c3455k6rssr5v9qi6dyhhpbb193bj8121")))) | |
10275 | (build-system r-build-system) | |
10276 | (propagated-inputs | |
10277 | `(("r-maps" ,r-maps) | |
10278 | ("r-spam" ,r-spam))) | |
10279 | (native-inputs | |
10280 | `(("gfortran" ,gfortran))) | |
10281 | (home-page "http://www.image.ucar.edu/fields") | |
10282 | (synopsis "Tools for spatial data") | |
10283 | (description | |
10284 | "This is a package for curve, surface and function fitting with an | |
10285 | emphasis on splines, spatial data and spatial statistics. The major methods | |
10286 | include cubic, and thin plate splines, Kriging, and compactly supported | |
10287 | covariance functions for large data sets.") | |
10288 | (license license:gpl2+))) | |
99c164a5 RW |
10289 | |
10290 | (define-public r-spatialextremes | |
10291 | (package | |
10292 | (name "r-spatialextremes") | |
10293 | (version "2.0-7") | |
10294 | (source | |
10295 | (origin | |
10296 | (method url-fetch) | |
10297 | (uri (cran-uri "SpatialExtremes" version)) | |
10298 | (sha256 | |
10299 | (base32 | |
10300 | "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050")))) | |
10301 | (properties | |
10302 | `((upstream-name . "SpatialExtremes"))) | |
10303 | (build-system r-build-system) | |
10304 | (propagated-inputs | |
10305 | `(("r-fields" ,r-fields) | |
10306 | ("r-maps" ,r-maps))) | |
10307 | (home-page "http://spatialextremes.r-forge.r-project.org/") | |
10308 | (synopsis "Modelling spatial extremes") | |
10309 | (description | |
10310 | "This package provides tools for the statistical modelling of spatial | |
10311 | extremes using max-stable processes, copula or Bayesian hierarchical models. | |
10312 | More precisely, this package allows (conditional) simulations from various | |
10313 | parametric max-stable models, analysis of the extremal spatial dependence, the | |
10314 | fitting of such processes using composite likelihoods or least square (simple | |
10315 | max-stable processes only), model checking and selection and prediction.") | |
10316 | (license license:gpl2+))) | |
c2d6e866 RW |
10317 | |
10318 | (define-public r-drc | |
10319 | (package | |
10320 | (name "r-drc") | |
10321 | (version "3.0-1") | |
10322 | (source | |
10323 | (origin | |
10324 | (method url-fetch) | |
10325 | (uri (cran-uri "drc" version)) | |
10326 | (sha256 | |
10327 | (base32 | |
10328 | "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) | |
10329 | (build-system r-build-system) | |
10330 | (propagated-inputs | |
10331 | `(("r-car" ,r-car) | |
10332 | ("r-gtools" ,r-gtools) | |
10333 | ("r-mass" ,r-mass) | |
10334 | ("r-multcomp" ,r-multcomp) | |
10335 | ("r-plotrix" ,r-plotrix) | |
10336 | ("r-scales" ,r-scales))) | |
10337 | (home-page "https://cran.r-project.org/web/packages/drc") | |
10338 | (synopsis "Analysis of dose-response curves") | |
10339 | (description | |
10340 | "This package provides a suite of flexible and versatile model fitting | |
10341 | and after-fitting functions for the analysis of dose-response data.") | |
10342 | (license license:gpl2+))) | |
4fcbd7ea RW |
10343 | |
10344 | (define-public r-rmeta | |
10345 | (package | |
10346 | (name "r-rmeta") | |
10347 | (version "3.0") | |
10348 | (source | |
10349 | (origin | |
10350 | (method url-fetch) | |
10351 | (uri (cran-uri "rmeta" version)) | |
10352 | (sha256 | |
10353 | (base32 | |
10354 | "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) | |
10355 | (build-system r-build-system) | |
10356 | (home-page "https://cran.r-project.org/web/packages/rmeta") | |
10357 | (synopsis "Tools for meta-analysis") | |
10358 | (description | |
10359 | "This package provides functions for simple fixed and random effects | |
10360 | meta-analysis for two-sample comparisons and cumulative meta-analyses. It | |
10361 | draws standard summary plots, funnel plots, and computes summaries and tests | |
10362 | for association and heterogeneity.") | |
10363 | (license license:gpl2))) | |
afc0d815 RW |
10364 | |
10365 | (define-public r-bootstrap | |
10366 | (package | |
10367 | (name "r-bootstrap") | |
10368 | (version "2017.2") | |
10369 | (source | |
10370 | (origin | |
10371 | (method url-fetch) | |
10372 | (uri (cran-uri "bootstrap" version)) | |
10373 | (sha256 | |
10374 | (base32 | |
10375 | "08lmsy7k8wsgv89yc904c6fidcymr1ma2ry4fl0p69p21v4iiwa4")))) | |
10376 | (build-system r-build-system) | |
10377 | (native-inputs `(("gfortran" ,gfortran))) | |
10378 | (home-page "https://cran.r-project.org/web/packages/bootstrap") | |
10379 | (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") | |
10380 | (description | |
10381 | "This package provides software and data for the book \"An Introduction | |
10382 | to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. | |
10383 | This package is primarily provided for projects already based on it, and for | |
10384 | support of the book. New projects should preferentially use the recommended | |
10385 | package \"boot\".") | |
10386 | (license license:bsd-3))) | |
1ea708af RW |
10387 | |
10388 | (define-public r-survivalroc | |
10389 | (package | |
10390 | (name "r-survivalroc") | |
10391 | (version "1.0.3") | |
10392 | (source | |
10393 | (origin | |
10394 | (method url-fetch) | |
10395 | (uri (cran-uri "survivalROC" version)) | |
10396 | (sha256 | |
10397 | (base32 | |
10398 | "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) | |
10399 | (properties `((upstream-name . "survivalROC"))) | |
10400 | (build-system r-build-system) | |
10401 | (home-page "https://cran.r-project.org/web/packages/survivalROC") | |
10402 | (synopsis "Time-dependent ROC curve estimation from censored survival data") | |
10403 | (description | |
10404 | "Compute time-dependent ROC curve from censored survival data using | |
10405 | Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, | |
10406 | Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") | |
10407 | (license license:gpl2+))) | |
6a5bfe09 RW |
10408 | |
10409 | (define-public r-longitudinal | |
10410 | (package | |
10411 | (name "r-longitudinal") | |
10412 | (version "1.1.12") | |
10413 | (source | |
10414 | (origin | |
10415 | (method url-fetch) | |
10416 | (uri (cran-uri "longitudinal" version)) | |
10417 | (sha256 | |
10418 | (base32 | |
10419 | "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l")))) | |
10420 | (build-system r-build-system) | |
10421 | (propagated-inputs `(("r-corpcor" ,r-corpcor))) | |
10422 | (home-page "http://strimmerlab.org/software/longitudinal/") | |
10423 | (synopsis "Analysis of multiple time course data") | |
10424 | (description | |
10425 | "This package contains general data structures and functions for | |
10426 | longitudinal data with multiple variables, repeated measurements, and | |
10427 | irregularly spaced time points. It also implements a shrinkage estimator of | |
10428 | dynamical correlation and dynamical covariance.") | |
10429 | (license license:gpl3+))) | |
e50722c8 RW |
10430 | |
10431 | (define-public r-genenet | |
10432 | (package | |
10433 | (name "r-genenet") | |
10434 | (version "1.2.13") | |
10435 | (source | |
10436 | (origin | |
10437 | (method url-fetch) | |
10438 | (uri (cran-uri "GeneNet" version)) | |
10439 | (sha256 | |
10440 | (base32 | |
10441 | "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p")))) | |
10442 | (properties `((upstream-name . "GeneNet"))) | |
10443 | (build-system r-build-system) | |
10444 | (propagated-inputs | |
10445 | `(("r-corpcor" ,r-corpcor) | |
10446 | ("r-fdrtool" ,r-fdrtool) | |
10447 | ("r-longitudinal" ,r-longitudinal))) | |
10448 | (home-page "http://strimmerlab.org/software/genenet/") | |
10449 | (synopsis "Modeling and inferring gene networks") | |
10450 | (description | |
10451 | "This package analyzes gene expression (time series) data with focus on | |
10452 | the inference of gene networks. In particular, GeneNet implements the methods | |
10453 | of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) | |
10454 | for learning large-scale gene association networks (including assignment of | |
10455 | putative directions).") | |
10456 | (license license:gpl3+))) | |
fe4e9f03 RW |
10457 | |
10458 | (define-public r-rbamtools | |
10459 | (package | |
10460 | (name "r-rbamtools") | |
10461 | (version "2.16.11.2") | |
10462 | (source | |
10463 | (origin | |
10464 | (method url-fetch) | |
10465 | (uri (cran-uri "rbamtools" version)) | |
10466 | (sha256 | |
10467 | (base32 | |
10468 | "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj")))) | |
10469 | (build-system r-build-system) | |
10470 | (inputs `(("zlib" ,zlib))) | |
10471 | (propagated-inputs | |
10472 | `(("r-refgenome" ,r-refgenome))) | |
10473 | (home-page "https://cran.r-project.org/web/packages/rbamtools") | |
10474 | (synopsis "Read and write BAM (binary alignment) files") | |
10475 | (description | |
10476 | "This package provides an R interface to functions of the SAMtools | |
10477 | library.") | |
10478 | (license license:artistic2.0))) | |
e3c0e3e3 RW |
10479 | |
10480 | (define-public r-protviz | |
10481 | (package | |
10482 | (name "r-protviz") | |
c3e5b456 | 10483 | (version "0.4.0") |
e3c0e3e3 RW |
10484 | (source |
10485 | (origin | |
10486 | (method url-fetch) | |
10487 | (uri (cran-uri "protViz" version)) | |
10488 | (sha256 | |
10489 | (base32 | |
c3e5b456 | 10490 | "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1")))) |
e3c0e3e3 RW |
10491 | (properties `((upstream-name . "protViz"))) |
10492 | (build-system r-build-system) | |
10493 | (inputs | |
10494 | `(("perl" ,perl) | |
10495 | ("python-2" ,python-2))) | |
10496 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
10497 | (home-page "https://github.com/protViz/protViz/") | |
10498 | (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") | |
10499 | (description | |
10500 | "This package helps with quality checks, visualizations and analysis of | |
10501 | mass spectrometry data, coming from proteomics experiments. The package is | |
10502 | developed, tested and used at the Functional Genomics Center Zurich, where it | |
10503 | is used mainly for prototyping, teaching, and having fun with proteomics data. | |
10504 | But it can also be used to do data analysis for small scale data sets.") | |
10505 | (license license:gpl3))) | |
7aeec0cf RW |
10506 | |
10507 | (define-public r-cmprsk | |
10508 | (package | |
10509 | (name "r-cmprsk") | |
10510 | (version "2.2-7") | |
10511 | (source | |
10512 | (origin | |
10513 | (method url-fetch) | |
10514 | (uri (cran-uri "cmprsk" version)) | |
10515 | (sha256 | |
10516 | (base32 | |
10517 | "1imr3wpnj4g57n2x4ryahl4lk8lvq9y2r7319zv3k82mznha8bcm")))) | |
10518 | (build-system r-build-system) | |
10519 | (propagated-inputs | |
10520 | `(("r-survival" ,r-survival))) | |
10521 | (native-inputs | |
10522 | `(("gfortran" ,gfortran))) | |
10523 | (home-page "https://cran.r-project.org/web/packages/cmprsk") | |
10524 | (synopsis "Subdistribution analysis of competing risks") | |
10525 | (description | |
10526 | "This package provides tool for estimation, testing and regression | |
10527 | modeling of subdistribution functions in competing risks, as described in | |
10528 | Gray (1988), A class of K-sample tests for comparing the cumulative incidence | |
10529 | of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), | |
10530 | A proportional hazards model for the subdistribution of a competing risk, | |
10531 | JASA, 94:496-509.") | |
10532 | (license license:gpl2+))) | |
728012da RW |
10533 | |
10534 | (define-public r-etm | |
10535 | (package | |
10536 | (name "r-etm") | |
10537 | (version "1.0.4") | |
10538 | (source | |
10539 | (origin | |
10540 | (method url-fetch) | |
10541 | (uri (cran-uri "etm" version)) | |
10542 | (sha256 | |
10543 | (base32 | |
10544 | "0ws103b3pmli0z4xbyfxkly2wnnnxnnwc0r66qjjqjrlvm7pffl1")))) | |
10545 | (build-system r-build-system) | |
10546 | (propagated-inputs | |
10547 | `(("r-data-table" ,r-data-table) | |
10548 | ("r-lattice" ,r-lattice) | |
10549 | ("r-rcpp" ,r-rcpp) | |
10550 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
10551 | ("r-survival" ,r-survival))) | |
10552 | (home-page "https://cran.r-project.org/web/packages/etm") | |
10553 | (synopsis "Empirical transition matrix") | |
10554 | (description | |
10555 | "The @dfn{empirical transition matrix} (etm) package permits to estimate | |
10556 | the matrix of transition probabilities for any time-inhomogeneous multistate | |
10557 | model with finite state space using the Aalen-Johansen estimator.") | |
10558 | (license license:expat))) | |
17932a0f RW |
10559 | |
10560 | (define-public r-epi | |
10561 | (package | |
10562 | (name "r-epi") | |
83ef38b0 | 10563 | (version "2.35") |
17932a0f RW |
10564 | (source |
10565 | (origin | |
10566 | (method url-fetch) | |
10567 | (uri (cran-uri "Epi" version)) | |
10568 | (sha256 | |
10569 | (base32 | |
83ef38b0 | 10570 | "1z3959761ryv54y6vsrxxvhrwzz50xrxn55pqh5y7lrxh91zdsvl")))) |
17932a0f RW |
10571 | (properties `((upstream-name . "Epi"))) |
10572 | (build-system r-build-system) | |
10573 | (propagated-inputs | |
10574 | `(("r-cmprsk" ,r-cmprsk) | |
10575 | ("r-data-table" ,r-data-table) | |
10576 | ("r-etm" ,r-etm) | |
10577 | ("r-mass" ,r-mass) | |
10578 | ("r-matrix" ,r-matrix) | |
10579 | ("r-mgcv" ,r-mgcv) | |
10580 | ("r-numderiv" ,r-numderiv) | |
10581 | ("r-plyr" ,r-plyr) | |
10582 | ("r-survival" ,r-survival) | |
10583 | ("r-zoo" ,r-zoo))) | |
10584 | (home-page "http://BendixCarstensen.com/Epi/") | |
10585 | (synopsis "Statistical analysis in epidemiology") | |
10586 | (description | |
10587 | "This package provides functions for demographic and epidemiological | |
10588 | analysis in the Lexis diagram, i.e. register and cohort follow-up data, in | |
10589 | particular representation, manipulation and simulation of multistate data - | |
10590 | the Lexis suite of functions, which includes interfaces to the @code{mstate}, | |
10591 | @code{etm} and @code{cmprsk} packages. It also contains functions for | |
10592 | Age-Period-Cohort and Lee-Carter modeling and a function for interval censored | |
10593 | data and some useful functions for tabulation and plotting, as well as a | |
10594 | number of epidemiological data sets.") | |
10595 | (license license:gpl2))) | |
879a1520 RW |
10596 | |
10597 | (define-public r-ppls | |
10598 | (package | |
10599 | (name "r-ppls") | |
10600 | (version "1.6-1.1") | |
10601 | (source | |
10602 | (origin | |
10603 | (method url-fetch) | |
10604 | (uri (cran-uri "ppls" version)) | |
10605 | (sha256 | |
10606 | (base32 | |
10607 | "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) | |
10608 | (build-system r-build-system) | |
10609 | (propagated-inputs `(("r-mass" ,r-mass))) | |
10610 | (home-page "https://cran.r-project.org/web/packages/ppls") | |
10611 | (synopsis "Penalized partial least squares") | |
10612 | (description | |
10613 | "This package contains linear and nonlinear regression methods based on | |
10614 | partial least squares and penalization techniques. Model parameters are | |
10615 | selected via cross-validation, and confidence intervals ans tests for the | |
10616 | regression coefficients can be conducted via jackknifing.") | |
10617 | (license license:gpl2+))) | |
0af9616d RW |
10618 | |
10619 | (define-public r-huge | |
10620 | (package | |
10621 | (name "r-huge") | |
20b375ec | 10622 | (version "1.3.1") |
0af9616d RW |
10623 | (source |
10624 | (origin | |
10625 | (method url-fetch) | |
10626 | (uri (cran-uri "huge" version)) | |
10627 | (sha256 | |
10628 | (base32 | |
20b375ec | 10629 | "06s22i2cdn6g2r8kq5csyspinayh8dxxg9gkwcf4sa1lmrgb0bf9")))) |
0af9616d RW |
10630 | (build-system r-build-system) |
10631 | (propagated-inputs | |
10632 | `(("r-igraph" ,r-igraph) | |
0af9616d | 10633 | ("r-mass" ,r-mass) |
7706a98c RW |
10634 | ("r-matrix" ,r-matrix) |
10635 | ("r-rcpp" ,r-rcpp) | |
10636 | ("r-rcppeigen" ,r-rcppeigen))) | |
0af9616d RW |
10637 | (home-page "https://cran.r-project.org/web/packages/huge") |
10638 | (synopsis "High-dimensional undirected graph estimation") | |
10639 | (description | |
10640 | "This package provides a general framework for high-dimensional | |
10641 | undirected graph estimation. It integrates data preprocessing, neighborhood | |
10642 | screening, graph estimation, and model selection techniques into a pipeline.") | |
10643 | (license license:gpl2))) | |
39274ab4 RW |
10644 | |
10645 | (define-public r-parcor | |
10646 | (package | |
10647 | (name "r-parcor") | |
10648 | (version "0.2-6") | |
10649 | (source | |
10650 | (origin | |
10651 | (method url-fetch) | |
10652 | (uri (cran-uri "parcor" version)) | |
10653 | (sha256 | |
10654 | (base32 | |
10655 | "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) | |
10656 | (build-system r-build-system) | |
10657 | (propagated-inputs | |
10658 | `(("r-epi" ,r-epi) | |
10659 | ("r-genenet" ,r-genenet) | |
10660 | ("r-glmnet" ,r-glmnet) | |
10661 | ("r-mass" ,r-mass) | |
10662 | ("r-ppls" ,r-ppls))) | |
10663 | (home-page "https://cran.r-project.org/web/packages/parcor") | |
10664 | (synopsis "Regularized estimation of partial correlation matrices") | |
10665 | (description | |
10666 | "This package estimates the matrix of partial correlations based on | |
10667 | different regularized regression methods: lasso, adaptive lasso, PLS, and | |
10668 | Ridge Regression. In addition, the package provides model selection for | |
10669 | lasso, adaptive lasso and Ridge regression based on cross-validation.") | |
10670 | (license license:gpl2+))) | |
cba08f60 RW |
10671 | |
10672 | (define-public r-mcmc | |
10673 | (package | |
10674 | (name "r-mcmc") | |
ae7e6f06 | 10675 | (version "0.9-6") |
cba08f60 RW |
10676 | (source |
10677 | (origin | |
10678 | (method url-fetch) | |
10679 | (uri (cran-uri "mcmc" version)) | |
10680 | (sha256 | |
10681 | (base32 | |
ae7e6f06 | 10682 | "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4")))) |
cba08f60 RW |
10683 | (build-system r-build-system) |
10684 | (home-page "http://www.stat.umn.edu/geyer/mcmc/") | |
10685 | (synopsis "Markov chain Monte Carlo") | |
10686 | (description | |
10687 | "This package simulates continuous distributions of random vectors using | |
10688 | @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R | |
10689 | function that evaluates the log unnormalized density. Algorithms are random | |
10690 | walk Metropolis algorithm (function @code{metrop}), simulated | |
10691 | tempering (function @code{temper}), and morphometric random walk | |
10692 | Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity | |
10693 | by change of variable.") | |
10694 | (license license:expat))) | |
cf4cd8bc RW |
10695 | |
10696 | (define-public r-listenv | |
10697 | (package | |
10698 | (name "r-listenv") | |
10699 | (version "0.7.0") | |
10700 | (source | |
10701 | (origin | |
10702 | (method url-fetch) | |
10703 | (uri (cran-uri "listenv" version)) | |
10704 | (sha256 | |
10705 | (base32 | |
10706 | "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1")))) | |
10707 | (build-system r-build-system) | |
10708 | (native-inputs | |
10709 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
10710 | (home-page "https://github.com/HenrikBengtsson/listenv") | |
10711 | (synopsis "Environments behaving (almost) as lists") | |
10712 | (description | |
10713 | "This package implements list environments. List environments are | |
10714 | environments that have list-like properties. For instance, the elements of a | |
10715 | list environment are ordered and can be accessed and iterated over using index | |
10716 | subsetting.") | |
10717 | (license license:lgpl2.1+))) | |
226294a4 RW |
10718 | |
10719 | (define-public r-globals | |
10720 | (package | |
10721 | (name "r-globals") | |
10722 | (version "0.12.4") | |
10723 | (source | |
10724 | (origin | |
10725 | (method url-fetch) | |
10726 | (uri (cran-uri "globals" version)) | |
10727 | (sha256 | |
10728 | (base32 | |
10729 | "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br")))) | |
10730 | (build-system r-build-system) | |
10731 | (propagated-inputs | |
10732 | `(("r-codetools" ,r-codetools))) | |
10733 | (home-page "https://github.com/HenrikBengtsson/globals") | |
10734 | (synopsis "Identify global objects in R expressions") | |
10735 | (description | |
10736 | "This package provides tools to identify global (\"unknown\" or \"free\") | |
10737 | objects in R expressions by code inspection using various strategies, e.g. | |
10738 | conservative or liberal. The objective of this package is to make it as | |
10739 | simple as possible to identify global objects for the purpose of exporting | |
10740 | them in distributed compute environments.") | |
10741 | (license license:lgpl2.1+))) | |
b3080cdd RW |
10742 | |
10743 | (define-public r-future | |
10744 | (package | |
10745 | (name "r-future") | |
1a38c314 | 10746 | (version "1.12.0") |
b3080cdd RW |
10747 | (source |
10748 | (origin | |
10749 | (method url-fetch) | |
10750 | (uri (cran-uri "future" version)) | |
10751 | (sha256 | |
10752 | (base32 | |
1a38c314 | 10753 | "12hq7hsfydlscwrb37ns9a8561bzpsp82nn7jrcyj0ydk610nipm")))) |
b3080cdd RW |
10754 | (build-system r-build-system) |
10755 | (propagated-inputs | |
10756 | `(("r-digest" ,r-digest) | |
10757 | ("r-globals" ,r-globals) | |
10758 | ("r-listenv" ,r-listenv))) | |
10759 | (native-inputs | |
10760 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
10761 | (home-page "https://github.com/HenrikBengtsson/future") | |
10762 | (synopsis "Unified parallel and distributed processing in R") | |
10763 | (description | |
10764 | "The purpose of this package is to provide a lightweight and unified | |
10765 | Future API for sequential and parallel processing of R expression via futures. | |
10766 | This package implements sequential, multicore, multisession, and cluster | |
10767 | futures. With these, R expressions can be evaluated on the local machine, in | |
10768 | parallel a set of local machines, or distributed on a mix of local and remote | |
10769 | machines. Extensions to this package implement additional backends for | |
10770 | processing futures via compute cluster schedulers etc. Because of its unified | |
10771 | API, there is no need to modify any code in order to switch from sequential on | |
10772 | the local machine to, say, distributed processing on a remote compute cluster.") | |
10773 | (license license:lgpl2.1+))) | |
9680047c RW |
10774 | |
10775 | (define-public r-future-apply | |
10776 | (package | |
10777 | (name "r-future-apply") | |
d1c2fd8e | 10778 | (version "1.2.0") |
9680047c RW |
10779 | (source |
10780 | (origin | |
10781 | (method url-fetch) | |
10782 | (uri (cran-uri "future.apply" version)) | |
10783 | (sha256 | |
10784 | (base32 | |
d1c2fd8e | 10785 | "00ma43ma3byrf9vfqqn9g8sn18c71ryhk7lpza5h7817f1kibw1h")))) |
9680047c RW |
10786 | (properties `((upstream-name . "future.apply"))) |
10787 | (build-system r-build-system) | |
10788 | (propagated-inputs | |
10789 | `(("r-future" ,r-future) | |
10790 | ("r-globals" ,r-globals))) | |
10791 | (native-inputs | |
10792 | `(("r-r-rsp" ,r-r-rsp))) ; vignette builder | |
10793 | (home-page "https://github.com/HenrikBengtsson/future.apply") | |
10794 | (synopsis "Apply function to elements in parallel using futures") | |
10795 | (description | |
10796 | "This package provides implementations of @code{apply()}, | |
10797 | @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()}, | |
10798 | @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that | |
10799 | can be resolved using any future-supported backend, e.g. parallel on the local | |
10800 | machine or distributed on a compute cluster.") | |
10801 | (license license:gpl2+))) | |
867e2b1b RW |
10802 | |
10803 | (define-public r-rsvd | |
10804 | (package | |
10805 | (name "r-rsvd") | |
10806 | (version "1.0.0") | |
10807 | (source | |
10808 | (origin | |
10809 | (method url-fetch) | |
10810 | (uri (cran-uri "rsvd" version)) | |
10811 | (sha256 | |
10812 | (base32 | |
10813 | "0vjhrvnkl9rmvl8sv2kac5sd10z3fgxymb676ynxzc2pmhydy3an")))) | |
10814 | (build-system r-build-system) | |
10815 | (propagated-inputs | |
10816 | `(("r-matrix" ,r-matrix))) | |
10817 | (home-page "https://github.com/erichson/rSVD") | |
10818 | (synopsis "Randomized singular value decomposition") | |
10819 | (description | |
10820 | "Low-rank matrix decompositions are fundamental tools and widely used for | |
10821 | data analysis, dimension reduction, and data compression. Classically, highly | |
10822 | accurate deterministic matrix algorithms are used for this task. However, the | |
10823 | emergence of large-scale data has severely challenged our computational | |
10824 | ability to analyze big data. The concept of randomness has been demonstrated | |
10825 | as an effective strategy to quickly produce approximate answers to familiar | |
10826 | problems such as the @dfn{singular value decomposition} (SVD). This package | |
10827 | provides several randomized matrix algorithms such as the randomized singular | |
10828 | value decomposition (@code{rsvd}), randomized principal component | |
10829 | analysis (@code{rpca}), randomized robust principal component | |
10830 | analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}), | |
10831 | and the randomized CUR decomposition (@code{rcur}). In addition several plot | |
10832 | functions are provided.") | |
10833 | (license license:gpl3+))) | |
14afee3e BG |
10834 | |
10835 | (define-public r-sloop | |
10836 | (package | |
10837 | (name "r-sloop") | |
10838 | (version "1.0.1") | |
10839 | (source | |
10840 | (origin | |
10841 | (method url-fetch) | |
10842 | (uri (cran-uri "sloop" version)) | |
10843 | (sha256 | |
10844 | (base32 | |
10845 | "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j")))) | |
10846 | (build-system r-build-system) | |
10847 | (propagated-inputs | |
10848 | `(("r-codetools" ,r-codetools) | |
10849 | ("r-crayon" ,r-crayon) | |
10850 | ("r-purrr" ,r-purrr) | |
10851 | ("r-rlang" ,r-rlang) | |
10852 | ("r-tibble" ,r-tibble))) | |
10853 | (home-page "https://github.com/r-lib/sloop") | |
10854 | (synopsis "Helpers for object-oriented programming in R") | |
10855 | (description | |
10856 | "This package provides a collection of helper functions designed to | |
10857 | help you to better understand object oriented programming in R, particularly | |
10858 | using @code{S3}.") | |
10859 | (license license:gpl3))) | |
4254b480 RW |
10860 | |
10861 | (define-public r-capushe | |
10862 | (package | |
10863 | (name "r-capushe") | |
10864 | (version "1.1.1") | |
10865 | (source | |
10866 | (origin | |
10867 | (method url-fetch) | |
10868 | (uri (cran-uri "capushe" version)) | |
10869 | (sha256 | |
10870 | (base32 | |
10871 | "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc")))) | |
10872 | (build-system r-build-system) | |
10873 | (propagated-inputs `(("r-mass" ,r-mass))) | |
10874 | (home-page "https://cran.r-project.org/web/packages/capushe/index.html") | |
10875 | (synopsis "Calibrating penalities using slope heuristics") | |
10876 | (description | |
10877 | "This package provides tools for the calibration of penalized criteria | |
10878 | for model selection. The calibration methods available are based on the slope | |
10879 | heuristics.") | |
10880 | (license license:gpl2+))) | |
c691c607 RW |
10881 | |
10882 | (define-public r-dorng | |
10883 | (package | |
10884 | (name "r-dorng") | |
10885 | (version "1.7.1") | |
10886 | (source | |
10887 | (origin | |
10888 | (method url-fetch) | |
10889 | (uri (cran-uri "doRNG" version)) | |
10890 | (sha256 | |
10891 | (base32 | |
10892 | "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7")))) | |
10893 | (properties `((upstream-name . "doRNG"))) | |
10894 | (build-system r-build-system) | |
10895 | (propagated-inputs | |
10896 | `(("r-foreach" ,r-foreach) | |
10897 | ("r-iterators" ,r-iterators) | |
10898 | ("r-pkgmaker" ,r-pkgmaker) | |
10899 | ("r-rngtools" ,r-rngtools))) | |
10900 | (home-page "https://renozao.github.io/doRNG/") | |
10901 | (synopsis "Generic reproducible parallel backend for foreach loops") | |
10902 | (description | |
10903 | "This package provides functions to perform reproducible parallel | |
10904 | @code{foreach} loops, using independent random streams as generated by | |
10905 | L'Ecuyer's combined multiple-recursive generator. It enables to easily | |
10906 | convert standard @code{%dopar%} loops into fully reproducible loops, | |
10907 | independently of the number of workers, the task scheduling strategy, or the | |
10908 | chosen parallel environment and associated foreach backend.") | |
10909 | (license license:gpl2+))) | |
f3233bee RW |
10910 | |
10911 | (define-public r-blockmodeling | |
10912 | (package | |
10913 | (name "r-blockmodeling") | |
10914 | (version "0.3.4") | |
10915 | (source | |
10916 | (origin | |
10917 | (method url-fetch) | |
10918 | (uri (cran-uri "blockmodeling" version)) | |
10919 | (sha256 | |
10920 | (base32 | |
10921 | "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2")))) | |
10922 | (build-system r-build-system) | |
10923 | (propagated-inputs | |
10924 | `(("r-doparallel" ,r-doparallel) | |
10925 | ("r-dorng" ,r-dorng) | |
10926 | ("r-foreach" ,r-foreach) | |
10927 | ("r-matrix" ,r-matrix))) | |
10928 | (native-inputs `(("gfortran" ,gfortran))) | |
10929 | (home-page "https://cran.r-project.org/web/packages/blockmodeling") | |
10930 | (synopsis "Generalized and classical blockmodeling of valued networks") | |
10931 | (description | |
10932 | "This package is primarily meant as an implementation of generalized | |
10933 | blockmodeling for valued networks. In addition, measures of similarity or | |
10934 | dissimilarity based on structural equivalence and regular equivalence (REGE | |
10935 | algorithms) can be computed and partitioned matrices can be plotted.") | |
10936 | (license license:gpl2+))) | |
4af186a9 RW |
10937 | |
10938 | (define-public r-upsetr | |
10939 | (package | |
10940 | (name "r-upsetr") | |
10941 | (version "1.3.3") | |
10942 | (source | |
10943 | (origin | |
10944 | (method url-fetch) | |
10945 | (uri (cran-uri "UpSetR" version)) | |
10946 | (sha256 | |
10947 | (base32 | |
10948 | "08vj7l92b8fpqyqwxshll2mhk3yhgyr74axvr2lf29z78bapymhz")))) | |
10949 | (properties `((upstream-name . "UpSetR"))) | |
10950 | (build-system r-build-system) | |
10951 | (propagated-inputs | |
10952 | `(("r-ggplot2" ,r-ggplot2) | |
10953 | ("r-gridextra" ,r-gridextra) | |
10954 | ("r-plyr" ,r-plyr) | |
10955 | ("r-scales" ,r-scales))) | |
10956 | (home-page "https://github.com/hms-dbmi/UpSetR") | |
10957 | (synopsis "Visualize intersecting sets") | |
10958 | (description | |
10959 | "This package provides a more scalable alternative to Venn and Euler | |
10960 | diagrams for visualizing intersecting sets. Create visualizations of | |
10961 | intersecting sets using a novel matrix design, along with visualizations of | |
10962 | several common set, element and attribute related tasks.") | |
10963 | (license license:expat))) | |
1901a532 | 10964 | |
849350fb RW |
10965 | ;; This package includes a JavaScript file, which is not minified. When |
10966 | ;; upgrading please check that there are no new minified JavaScript files. | |
10967 | (define-public r-shinybs | |
10968 | (package | |
10969 | (name "r-shinybs") | |
10970 | (version "0.61") | |
10971 | (source | |
10972 | (origin | |
10973 | (method url-fetch) | |
10974 | (uri (cran-uri "shinyBS" version)) | |
10975 | (sha256 | |
10976 | (base32 | |
10977 | "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji")))) | |
10978 | (properties `((upstream-name . "shinyBS"))) | |
10979 | (build-system r-build-system) | |
10980 | ;; The tests spawn Shiny browser apps. They cannot be run | |
10981 | ;; non-interactively. | |
10982 | (arguments '(#:tests? #f)) | |
10983 | (propagated-inputs | |
10984 | `(("r-htmltools" ,r-htmltools) | |
10985 | ("r-shiny" ,r-shiny))) | |
10986 | (home-page "https://ebailey78.github.io/shinyBS/") | |
10987 | (synopsis "Twitter Bootstrap components for Shiny") | |
10988 | (description | |
10989 | "This package adds additional Twitter Bootstrap components to Shiny.") | |
10990 | (license license:gpl3))) | |
10991 | ||
1901a532 RW |
10992 | (define-public r-outliers |
10993 | (package | |
10994 | (name "r-outliers") | |
10995 | (version "0.14") | |
10996 | (source | |
10997 | (origin | |
10998 | (method url-fetch) | |
10999 | (uri (cran-uri "outliers" version)) | |
11000 | (sha256 | |
11001 | (base32 | |
11002 | "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn")))) | |
11003 | (build-system r-build-system) | |
11004 | (home-page "https://cran.r-project.org/web/packages/outliers/index.html") | |
11005 | (synopsis "Tests for outliers") | |
11006 | (description | |
11007 | "This package provides a collection of some tests commonly used for | |
11008 | identifying outliers.") | |
11009 | (license license:gpl2+))) | |
8cd3f49d RW |
11010 | |
11011 | (define-public r-bayesm | |
11012 | (package | |
11013 | (name "r-bayesm") | |
11014 | (version "3.1-1") | |
11015 | (source | |
11016 | (origin | |
11017 | (method url-fetch) | |
11018 | (uri (cran-uri "bayesm" version)) | |
11019 | (sha256 | |
11020 | (base32 | |
11021 | "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28")))) | |
11022 | (build-system r-build-system) | |
11023 | (propagated-inputs | |
11024 | `(("r-rcpp" ,r-rcpp) | |
11025 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
11026 | (home-page "http://www.perossi.org/home/bsm-1") | |
11027 | (synopsis "Bayesian inference for marketing/micro-econometrics") | |
11028 | (description | |
11029 | "This package covers many important models used in marketing and | |
11030 | micro-econometrics applications, including Bayes Regression (univariate or | |
11031 | multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and | |
11032 | Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), | |
11033 | Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate | |
11034 | Mixtures of Normals (including clustering), Dirichlet Process Prior Density | |
11035 | Estimation with normal base, Hierarchical Linear Models with normal prior and | |
11036 | covariates, Hierarchical Linear Models with a mixture of normals prior and | |
11037 | covariates, Hierarchical Multinomial Logits with a mixture of normals prior | |
11038 | and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior | |
11039 | and covariates, Hierarchical Negative Binomial Regression Models, Bayesian | |
11040 | analysis of choice-based conjoint data, Bayesian treatment of linear | |
11041 | instrumental variables models, Analysis of Multivariate Ordinal survey data | |
11042 | with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random | |
11043 | Coefficient Logit Models.") | |
11044 | (license license:gpl2+))) | |
262ab4b1 RW |
11045 | |
11046 | (define-public r-tensora | |
11047 | (package | |
11048 | (name "r-tensora") | |
11049 | (version "0.36.1") | |
11050 | (source | |
11051 | (origin | |
11052 | (method url-fetch) | |
11053 | (uri (cran-uri "tensorA" version)) | |
11054 | (sha256 | |
11055 | (base32 | |
11056 | "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7")))) | |
11057 | (properties `((upstream-name . "tensorA"))) | |
11058 | (build-system r-build-system) | |
11059 | (home-page "http://www.stat.boogaart.de/tensorA") | |
11060 | (synopsis "Advanced tensor arithmetic with named indices") | |
11061 | (description | |
11062 | "This package provides convenience functions for advanced linear algebra | |
11063 | with tensors and computation with datasets of tensors on a higher level | |
11064 | abstraction. It includes Einstein and Riemann summing conventions, dragging, | |
11065 | co- and contravariate indices, and parallel computations on sequences of | |
11066 | tensors.") | |
11067 | (license license:gpl2+))) | |
7d779142 RW |
11068 | |
11069 | (define-public r-rarpack | |
11070 | (package | |
11071 | (name "r-rarpack") | |
11072 | (version "0.11-0") | |
11073 | (source | |
11074 | (origin | |
11075 | (method url-fetch) | |
11076 | (uri (cran-uri "rARPACK" version)) | |
11077 | (sha256 | |
11078 | (base32 | |
11079 | "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) | |
11080 | (properties `((upstream-name . "rARPACK"))) | |
11081 | (build-system r-build-system) | |
11082 | (propagated-inputs `(("r-rspectra" ,r-rspectra))) | |
11083 | (home-page "https://github.com/yixuan/rARPACK") | |
11084 | (synopsis "Solvers for large scale eigenvalue and SVD problems") | |
11085 | (description | |
11086 | "This package was previously an R wrapper of the ARPACK library, and now | |
11087 | a shell of the R package RSpectra, an R interface to the Spectra library for | |
11088 | solving large scale eigenvalue/vector problems. The current version of | |
11089 | rARPACK simply imports and exports the functions provided by RSpectra. New | |
11090 | users of rARPACK are advised to switch to the RSpectra package.") | |
11091 | (license license:bsd-3))) | |
5fde35b3 RW |
11092 | |
11093 | (define-public r-compositions | |
11094 | (package | |
11095 | (name "r-compositions") | |
11096 | (version "1.40-2") | |
11097 | (source | |
11098 | (origin | |
11099 | (method url-fetch) | |
11100 | (uri (cran-uri "compositions" version)) | |
11101 | (sha256 | |
11102 | (base32 | |
11103 | "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i")))) | |
11104 | (build-system r-build-system) | |
11105 | (propagated-inputs | |
11106 | `(("r-bayesm" ,r-bayesm) | |
11107 | ("r-energy" ,r-energy) | |
11108 | ("r-robustbase" ,r-robustbase) | |
11109 | ("r-tensora" ,r-tensora))) | |
11110 | (home-page "http://www.stat.boogaart.de/compositions") | |
11111 | (synopsis "Compositional data analysis") | |
11112 | (description | |
11113 | "This package provides functions for the consistent analysis of | |
11114 | compositional data (e.g. portions of substances) and positive | |
11115 | numbers (e.g. concentrations).") | |
11116 | (license license:gpl2+))) | |
5f673e2c RW |
11117 | |
11118 | (define-public r-cobs | |
11119 | (package | |
11120 | (name "r-cobs") | |
11121 | (version "1.3-3") | |
11122 | (source | |
11123 | (origin | |
11124 | (method url-fetch) | |
11125 | (uri (cran-uri "cobs" version)) | |
11126 | (sha256 | |
11127 | (base32 | |
11128 | "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb")))) | |
11129 | (build-system r-build-system) | |
11130 | (propagated-inputs | |
11131 | `(("r-quantreg" ,r-quantreg) | |
11132 | ("r-sparsem" ,r-sparsem))) | |
11133 | (home-page "https://cran.r-project.org/web/packages/cobs") | |
11134 | (synopsis "Constrained B-Splines (sparse matrix based)") | |
11135 | (description | |
11136 | "This package provides qualitatively constrained (regression) smoothing | |
11137 | splines via linear programming and sparse matrices.") | |
11138 | (license license:gpl2+))) | |
c60e3e10 RW |
11139 | |
11140 | (define-public r-drimpute | |
11141 | (package | |
11142 | (name "r-drimpute") | |
11143 | (version "1.0") | |
11144 | (source | |
11145 | (origin | |
11146 | (method url-fetch) | |
11147 | (uri (cran-uri "DrImpute" version)) | |
11148 | (sha256 | |
11149 | (base32 | |
11150 | "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b")))) | |
11151 | (properties `((upstream-name . "DrImpute"))) | |
11152 | (build-system r-build-system) | |
11153 | (propagated-inputs | |
11154 | `(("r-rcpp" ,r-rcpp) | |
11155 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
11156 | (home-page "https://github.com/ikwak2/DrImpute") | |
11157 | (synopsis "Imputing dropout events in single-cell RNA-Seq data") | |
11158 | (description | |
11159 | "This is an R package for imputing dropout events. Many statistical | |
11160 | methods in cell type identification, visualization and lineage reconstruction | |
11161 | do not account for dropout events. DrImpute can improve the performance of | |
11162 | such software by imputing dropout events.") | |
11163 | (license license:gpl3))) | |
061a4b68 RW |
11164 | |
11165 | (define-public r-gamlss-dist | |
11166 | (package | |
11167 | (name "r-gamlss-dist") | |
7e6c5ebb | 11168 | (version "5.1-3") |
061a4b68 RW |
11169 | (source |
11170 | (origin | |
11171 | (method url-fetch) | |
11172 | (uri (cran-uri "gamlss.dist" version)) | |
11173 | (sha256 | |
11174 | (base32 | |
7e6c5ebb | 11175 | "0154pm1f3g77krj0gxh9icz207pshdrxihb6gjv1k5aph8y69zc7")))) |
061a4b68 RW |
11176 | (properties `((upstream-name . "gamlss.dist"))) |
11177 | (build-system r-build-system) | |
11178 | (propagated-inputs `(("r-mass" ,r-mass))) | |
11179 | (home-page "http://www.gamlss.org/") | |
11180 | (synopsis "Distributions for Generalized Additive Models for location scale and shape") | |
11181 | (description | |
11182 | "This package provides a set of distributions which can be used for | |
11183 | modelling the response variables in Generalized Additive Models for Location | |
11184 | Scale and Shape. The distributions can be continuous, discrete or mixed | |
11185 | distributions. Extra distributions can be created, by transforming, any | |
11186 | continuous distribution defined on the real line, to a distribution defined on | |
11187 | ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} | |
11188 | transformation, respectively.") | |
11189 | ;; Either version of the GPL. | |
11190 | (license (list license:gpl2 license:gpl3)))) | |
4fd99443 | 11191 | |
5146a24e RW |
11192 | ;; This package includes JavaScript files, which are not minified. When |
11193 | ;; upgrading please check that there are no new minified JavaScript files. | |
11194 | (define-public r-shinyjs | |
11195 | (package | |
11196 | (name "r-shinyjs") | |
11197 | (version "1.0") | |
11198 | (source | |
11199 | (origin | |
11200 | (method url-fetch) | |
11201 | (uri (cran-uri "shinyjs" version)) | |
11202 | (sha256 | |
11203 | (base32 | |
11204 | "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8")))) | |
11205 | (build-system r-build-system) | |
11206 | (propagated-inputs | |
11207 | `(("r-digest" ,r-digest) | |
11208 | ("r-htmltools" ,r-htmltools) | |
11209 | ("r-jsonlite" ,r-jsonlite) | |
11210 | ("r-shiny" ,r-shiny))) | |
11211 | (home-page "https://deanattali.com/shinyjs") | |
11212 | (synopsis "Improve the user experience of your Shiny apps") | |
11213 | (description | |
11214 | "Perform common useful JavaScript operations in Shiny apps that will | |
11215 | greatly improve your apps without having to know any JavaScript. Examples | |
11216 | include: hiding an element, disabling an input, resetting an input back to its | |
11217 | original value, delaying code execution by a few seconds, and many more useful | |
11218 | functions for both the end user and the developer. Shinyjs can also be used | |
11219 | to easily call your own custom JavaScript functions from R.") | |
11220 | (license license:agpl3+))) | |
11221 | ||
c27927db RW |
11222 | ;; This package includes minified JavaScript files. When upgrading please |
11223 | ;; check that there are no new minified JavaScript files. | |
11224 | (define-public r-colourpicker | |
11225 | (package | |
11226 | (name "r-colourpicker") | |
11227 | (version "1.0") | |
11228 | (source | |
11229 | (origin | |
11230 | (method url-fetch) | |
11231 | (uri (cran-uri "colourpicker" version)) | |
11232 | (sha256 | |
11233 | (base32 | |
11234 | "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi")))) | |
11235 | (build-system r-build-system) | |
11236 | (arguments | |
11237 | `(#:modules ((guix build utils) | |
11238 | (guix build r-build-system) | |
11239 | (srfi srfi-1) | |
11240 | (ice-9 popen)) | |
11241 | #:phases | |
11242 | (modify-phases %standard-phases | |
11243 | (add-after 'unpack 'process-javascript | |
11244 | (lambda* (#:key inputs #:allow-other-keys) | |
11245 | (with-directory-excursion "inst" | |
11246 | (call-with-values | |
11247 | (lambda () | |
11248 | (unzip2 | |
11249 | `((,(assoc-ref inputs "js-salvattore") | |
11250 | "examples/colourInput/www/salvattore.min.js") | |
11251 | (,(assoc-ref inputs "js-jquery") | |
11252 | "htmlwidgets/lib/jquery/jquery.min.js") | |
11253 | ("www/shared/colourpicker/js/colourpicker.js" | |
11254 | "www/shared/colourpicker/js/colourpicker.min.js")))) | |
11255 | (lambda (sources targets) | |
11256 | (for-each (lambda (source target) | |
11257 | (format #t "Processing ~a --> ~a~%" | |
11258 | source target) | |
11259 | (delete-file target) | |
11260 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
11261 | (call-with-output-file target | |
11262 | (lambda (port) | |
11263 | (dump-port minified port))))) | |
11264 | sources targets)))) | |
11265 | #t))))) | |
11266 | (propagated-inputs | |
11267 | `(("r-ggplot2" ,r-ggplot2) | |
11268 | ("r-htmltools" ,r-htmltools) | |
11269 | ("r-htmlwidgets" ,r-htmlwidgets) | |
11270 | ("r-jsonlite" ,r-jsonlite) | |
11271 | ("r-miniui" ,r-miniui) | |
11272 | ("r-shiny" ,r-shiny) | |
11273 | ("r-shinyjs" ,r-shinyjs))) | |
11274 | (native-inputs | |
11275 | `(("uglify-js" ,uglify-js) | |
11276 | ("js-jquery" | |
11277 | ,(origin | |
11278 | (method url-fetch) | |
11279 | (uri "https://code.jquery.com/jquery-3.3.1.js") | |
11280 | (sha256 | |
11281 | (base32 | |
11282 | "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) | |
11283 | ("js-salvattore" | |
11284 | ,(origin | |
11285 | (method url-fetch) | |
11286 | (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js") | |
11287 | (sha256 | |
11288 | (base32 | |
11289 | "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5")))))) | |
11290 | (home-page "https://github.com/daattali/colourpicker") | |
11291 | (synopsis "Color picker tool for Shiny and for selecting colors in plots") | |
11292 | (description | |
11293 | "This package provides a color picker that can be used as an input in | |
11294 | Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, | |
11295 | custom color palettes, and many more options. A plot color helper tool is | |
11296 | available as an RStudio Addin, which helps you pick colors to use in your | |
11297 | plots. A more generic color picker RStudio Addin is also provided to let you | |
11298 | select colors to use in your R code.") | |
11299 | (license license:expat))) | |
11300 | ||
30f53ec8 RW |
11301 | (define-public r-ggextra |
11302 | (package | |
11303 | (name "r-ggextra") | |
11304 | (version "0.8") | |
11305 | (source | |
11306 | (origin | |
11307 | (method url-fetch) | |
11308 | (uri (cran-uri "ggExtra" version)) | |
11309 | (sha256 | |
11310 | (base32 | |
11311 | "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b")))) | |
11312 | (properties `((upstream-name . "ggExtra"))) | |
11313 | (build-system r-build-system) | |
11314 | (propagated-inputs | |
11315 | `(("r-colourpicker" ,r-colourpicker) | |
11316 | ("r-ggplot2" ,r-ggplot2) | |
11317 | ("r-gtable" ,r-gtable) | |
11318 | ("r-miniui" ,r-miniui) | |
11319 | ("r-scales" ,r-scales) | |
11320 | ("r-shiny" ,r-shiny) | |
11321 | ("r-shinyjs" ,r-shinyjs))) | |
11322 | (home-page "https://github.com/daattali/ggExtra") | |
11323 | (synopsis "Marginal histograms for ggplot2 and other enhancements") | |
11324 | (description | |
11325 | "This package is a collection of functions and layers to enhance ggplot2. | |
11326 | The flagship function is @code{ggMarginal()}, which can be used to add | |
11327 | marginal histograms/boxplots/density plots to ggplot2 scatterplots.") | |
11328 | (license license:expat))) | |
11329 | ||
4fd99443 RW |
11330 | (define-public r-minpack-lm |
11331 | (package | |
11332 | (name "r-minpack-lm") | |
11333 | (version "1.2-1") | |
11334 | (source | |
11335 | (origin | |
11336 | (method url-fetch) | |
11337 | (uri (cran-uri "minpack.lm" version)) | |
11338 | (sha256 | |
11339 | (base32 | |
11340 | "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) | |
11341 | (properties `((upstream-name . "minpack.lm"))) | |
11342 | (build-system r-build-system) | |
11343 | (native-inputs `(("gfortran" ,gfortran))) | |
11344 | (home-page "https://cran.r-project.org/web/packages/minpack.lm") | |
11345 | (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") | |
11346 | (description | |
11347 | "The @code{nls.lm} function provides an R interface to @code{lmder} and | |
11348 | @code{lmdif} from the MINPACK library, for solving nonlinear least-squares | |
11349 | problems by a modification of the Levenberg-Marquardt algorithm, with support | |
11350 | for lower and upper parameter bounds. The implementation can be used via | |
2f041a4c | 11351 | @code{nls}-like calls using the @code{nlsLM} function.") |
4fd99443 | 11352 | (license license:gpl3))) |
01fe44cb RW |
11353 | |
11354 | (define-public r-moments | |
11355 | (package | |
11356 | (name "r-moments") | |
11357 | (version "0.14") | |
11358 | (source | |
11359 | (origin | |
11360 | (method url-fetch) | |
11361 | (uri (cran-uri "moments" version)) | |
11362 | (sha256 | |
11363 | (base32 | |
11364 | "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra")))) | |
11365 | (build-system r-build-system) | |
11366 | (home-page "https://cran.r-project.org/web/packages/moments") | |
11367 | (synopsis "Moments, cumulants, skewness, kurtosis and related tests") | |
11368 | (description | |
11369 | "This package provides functions to calculate: moments, Pearson's | |
11370 | kurtosis, Geary's kurtosis and skewness; it also includes tests related to | |
11371 | them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") | |
11372 | (license license:gpl2+))) | |
9e2ff342 RW |
11373 | |
11374 | (define-public r-msir | |
11375 | (package | |
11376 | (name "r-msir") | |
5ccf16c7 | 11377 | (version "1.3.2") |
9e2ff342 RW |
11378 | (source |
11379 | (origin | |
11380 | (method url-fetch) | |
11381 | (uri (cran-uri "msir" version)) | |
11382 | (sha256 | |
11383 | (base32 | |
5ccf16c7 | 11384 | "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb")))) |
9e2ff342 RW |
11385 | (build-system r-build-system) |
11386 | (propagated-inputs | |
5ccf16c7 | 11387 | `(("r-mclust" ,r-mclust))) |
9e2ff342 RW |
11388 | (home-page "https://cran.r-project.org/web/packages/msir") |
11389 | (synopsis "Model-based sliced inverse regression") | |
11390 | (description | |
11391 | "This is an R package for dimension reduction based on finite Gaussian | |
11392 | mixture modeling of inverse regression.") | |
11393 | (license license:gpl2+))) | |
e8be5a00 RW |
11394 | |
11395 | (define-public r-pbivnorm | |
11396 | (package | |
11397 | (name "r-pbivnorm") | |
11398 | (version "0.6.0") | |
11399 | (source | |
11400 | (origin | |
11401 | (method url-fetch) | |
11402 | (uri (cran-uri "pbivnorm" version)) | |
11403 | (sha256 | |
11404 | (base32 | |
11405 | "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) | |
11406 | (build-system r-build-system) | |
11407 | (native-inputs `(("gfortran" ,gfortran))) | |
11408 | (home-page "https://github.com/brentonk/pbivnorm") | |
11409 | (synopsis "Vectorized bivariate normal CDF") | |
11410 | (description | |
11411 | "This package provides a vectorized R function for calculating | |
11412 | probabilities from a standard bivariate normal CDF.") | |
11413 | (license license:gpl2+))) | |
ca3f1370 RW |
11414 | |
11415 | (define-public r-lavaan | |
11416 | (package | |
11417 | (name "r-lavaan") | |
11418 | (version "0.6-3") | |
11419 | (source | |
11420 | (origin | |
11421 | (method url-fetch) | |
11422 | (uri (cran-uri "lavaan" version)) | |
11423 | (sha256 | |
11424 | (base32 | |
11425 | "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz")))) | |
11426 | (build-system r-build-system) | |
11427 | (propagated-inputs | |
11428 | `(("r-mass" ,r-mass) | |
11429 | ("r-mnormt" ,r-mnormt) | |
11430 | ("r-numderiv" ,r-numderiv) | |
11431 | ("r-pbivnorm" ,r-pbivnorm))) | |
11432 | (home-page "http://lavaan.ugent.be") | |
11433 | (synopsis "Latent variable analysis") | |
11434 | (description | |
11435 | "This package provides tools to fit a variety of latent variable models, | |
11436 | including confirmatory factor analysis, structural equation modeling and | |
11437 | latent growth curve models.") | |
11438 | (license license:gpl2+))) | |
4d1f19e0 RW |
11439 | |
11440 | (define-public r-nonnest2 | |
11441 | (package | |
11442 | (name "r-nonnest2") | |
11443 | (version "0.5-2") | |
11444 | (source | |
11445 | (origin | |
11446 | (method url-fetch) | |
11447 | (uri (cran-uri "nonnest2" version)) | |
11448 | (sha256 | |
11449 | (base32 | |
11450 | "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6")))) | |
11451 | (build-system r-build-system) | |
11452 | (propagated-inputs | |
11453 | `(("r-compquadform" ,r-compquadform) | |
11454 | ("r-lavaan" ,r-lavaan) | |
11455 | ("r-mvtnorm" ,r-mvtnorm) | |
11456 | ("r-sandwich" ,r-sandwich))) | |
11457 | (home-page "https://cran.r-project.org/web/packages/nonnest2/") | |
11458 | (synopsis "Tests of non-nested models") | |
11459 | (description | |
11460 | "This package allows for testing of non-nested models. It includes tests | |
11461 | of model distinguishability and of model fit that can be applied to both | |
11462 | nested and non-nested models. The package also includes functionality to | |
11463 | obtain confidence intervals associated with AIC and BIC.") | |
11464 | ;; Either version of the GPL. | |
11465 | (license (list license:gpl2 license:gpl3)))) | |
be0777ba RW |
11466 | |
11467 | (define-public r-penalized | |
11468 | (package | |
11469 | (name "r-penalized") | |
11470 | (version "0.9-51") | |
11471 | (source | |
11472 | (origin | |
11473 | (method url-fetch) | |
11474 | (uri (cran-uri "penalized" version)) | |
11475 | (sha256 | |
11476 | (base32 | |
11477 | "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) | |
11478 | (build-system r-build-system) | |
11479 | (propagated-inputs | |
11480 | `(("r-rcpp" ,r-rcpp) | |
11481 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
11482 | ("r-survival" ,r-survival))) | |
11483 | (home-page "https://cran.r-project.org/web/packages/penalized/") | |
11484 | (synopsis "Penalized estimation in GLMs and in the Cox model") | |
11485 | (description | |
11486 | "This package provides tools for fitting possibly high dimensional | |
11487 | penalized regression models. The penalty structure can be any combination of | |
11488 | an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity | |
11489 | constraint on the regression coefficients. The supported regression models | |
11490 | are linear, logistic and Poisson regression and the Cox Proportional Hazards | |
11491 | model. Cross-validation routines allow optimization of the tuning | |
11492 | parameters.") | |
11493 | (license license:gpl2+))) | |
5570804a RW |
11494 | |
11495 | (define-public r-zim | |
11496 | (package | |
11497 | (name "r-zim") | |
11498 | (version "1.1.0") | |
11499 | (source | |
11500 | (origin | |
11501 | (method url-fetch) | |
11502 | (uri (cran-uri "ZIM" version)) | |
11503 | (sha256 | |
11504 | (base32 | |
11505 | "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) | |
11506 | (properties `((upstream-name . "ZIM"))) | |
11507 | (build-system r-build-system) | |
11508 | (propagated-inputs `(("r-mass" ,r-mass))) | |
11509 | (home-page "https://github.com/biostatstudio/ZIM") | |
11510 | (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") | |
11511 | (description | |
11512 | "Analyze count time series with excess zeros. Two types of statistical | |
11513 | models are supported: Markov regression and state-space models. They are also | |
11514 | known as observation-driven and parameter-driven models respectively in the | |
11515 | time series literature. The functions used for Markov regression or | |
11516 | observation-driven models can also be used to fit ordinary regression models | |
11517 | with independent data under the zero-inflated Poisson (ZIP) or zero-inflated | |
11518 | negative binomial (ZINB) assumption. The package also contains miscellaneous | |
11519 | functions to compute density, distribution, quantile, and generate random | |
11520 | numbers from ZIP and ZINB distributions.") | |
11521 | (license license:gpl3))) | |
026dd77c RW |
11522 | |
11523 | (define-public r-nor1mix | |
11524 | (package | |
11525 | (name "r-nor1mix") | |
11526 | (version "1.2-3") | |
11527 | (source | |
11528 | (origin | |
11529 | (method url-fetch) | |
11530 | (uri (cran-uri "nor1mix" version)) | |
11531 | (sha256 | |
11532 | (base32 | |
11533 | "1bvk888qml9qr7q703s7qzgm0sqfchcjdjqwqllm5vrjx0cnapj3")))) | |
11534 | (build-system r-build-system) | |
11535 | (home-page "https://cran.r-project.org/web/packages/nor1mix/") | |
11536 | (synopsis "Normal (1-d) mixture models") | |
11537 | (description | |
11538 | "This package provides S3 classes and methods for one-dimensional normal | |
11539 | mixture models, for, e.g., density estimation or clustering algorithms | |
11540 | research and teaching; it provides the widely used Marron-Wand densities. It | |
11541 | also provides tools for efficient random number generation and graphics.") | |
11542 | (license license:gpl2+))) | |
648dbd27 RW |
11543 | |
11544 | (define-public r-beanplot | |
11545 | (package | |
11546 | (name "r-beanplot") | |
11547 | (version "1.2") | |
11548 | (source | |
11549 | (origin | |
11550 | (method url-fetch) | |
11551 | (uri (cran-uri "beanplot" version)) | |
11552 | (sha256 | |
11553 | (base32 | |
11554 | "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9")))) | |
11555 | (build-system r-build-system) | |
11556 | (home-page "https://cran.r-project.org/web/packages/beanplot/") | |
11557 | (synopsis "Visualization via beanplots") | |
11558 | (description | |
11559 | "This package provides beanplots, an alternative to | |
11560 | boxplot/stripchart/violin plots. It can be used to plot univariate comparison | |
11561 | graphs.") | |
11562 | (license license:gpl2))) | |
f313baf0 RW |
11563 | |
11564 | (define-public r-pbdzmq | |
11565 | (package | |
11566 | (name "r-pbdzmq") | |
11567 | (version "0.3-3") | |
11568 | (source | |
11569 | (origin | |
11570 | (method url-fetch) | |
11571 | (uri (cran-uri "pbdZMQ" version)) | |
11572 | (sha256 | |
11573 | (base32 | |
11574 | "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf")))) | |
11575 | (properties `((upstream-name . "pbdZMQ"))) | |
11576 | (build-system r-build-system) | |
11577 | (inputs | |
11578 | `(("zeromq" ,zeromq) | |
11579 | ("zlib" ,zlib))) | |
11580 | (native-inputs | |
11581 | `(("pkg-config" ,pkg-config))) | |
11582 | (home-page "https://pbdr.org/") | |
11583 | (synopsis "R interface to ZeroMQ") | |
11584 | (description | |
11585 | "ZeroMQ is a well-known library for high-performance asynchronous | |
11586 | messaging in scalable, distributed applications. This package provides high | |
11587 | level R wrapper functions to easily utilize ZeroMQ. The main focus is on | |
11588 | interactive client/server programming frameworks. A few wrapper functions | |
11589 | compatible with @code{rzmq} are also provided.") | |
11590 | (license license:gpl3))) | |
d17186d6 RW |
11591 | |
11592 | (define-public r-repr | |
11593 | (package | |
11594 | (name "r-repr") | |
11595 | (version "0.19.2") | |
11596 | (source | |
11597 | (origin | |
11598 | (method url-fetch) | |
11599 | (uri (cran-uri "repr" version)) | |
11600 | (sha256 | |
11601 | (base32 | |
11602 | "1mhhzakkagb8z568yx3p2ixs8fcifm7f8l2yq285zrz8jmnpckfx")))) | |
11603 | (build-system r-build-system) | |
11604 | (propagated-inputs | |
11605 | `(("r-base64enc" ,r-base64enc) | |
11606 | ("r-htmltools" ,r-htmltools) | |
11607 | ("r-jsonlite" ,r-jsonlite))) | |
11608 | (home-page "https://cran.r-project.org/web/packages/repr/") | |
11609 | (synopsis "Serializable representations") | |
11610 | (description | |
11611 | "This package provides string and binary representations of objects for | |
11612 | several formats and MIME types.") | |
11613 | (license license:gpl3))) | |
664dedd5 RW |
11614 | |
11615 | (define-public r-irdisplay | |
11616 | (package | |
11617 | (name "r-irdisplay") | |
11618 | (version "0.7.0") | |
11619 | (source | |
11620 | (origin | |
11621 | (method url-fetch) | |
11622 | (uri (cran-uri "IRdisplay" version)) | |
11623 | (sha256 | |
11624 | (base32 | |
11625 | "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli")))) | |
11626 | (properties `((upstream-name . "IRdisplay"))) | |
11627 | (build-system r-build-system) | |
11628 | (propagated-inputs | |
11629 | `(("r-repr" ,r-repr))) | |
11630 | (home-page "https://cran.r-project.org/web/packages/IRdisplay/") | |
11631 | (synopsis "Jupyter display machinery") | |
11632 | (description | |
11633 | "This package provides an interface to the rich display capabilities of | |
11634 | Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a | |
11635 | running IRkernel session.") | |
11636 | (license license:expat))) | |
984a8aa6 RW |
11637 | |
11638 | (define-public r-irkernel | |
11639 | (package | |
11640 | (name "r-irkernel") | |
11641 | (version "0.8.15") | |
11642 | (source | |
11643 | (origin | |
11644 | (method url-fetch) | |
11645 | (uri (cran-uri "IRkernel" version)) | |
11646 | (sha256 | |
11647 | (base32 | |
11648 | "1n0nc3paij8fgbp7l2b4405zk9k4y3gdi2bz6z8x6j0h5mi6k6a6")))) | |
11649 | (properties `((upstream-name . "IRkernel"))) | |
11650 | (build-system r-build-system) | |
11651 | (arguments | |
11652 | `(#:phases | |
11653 | (modify-phases %standard-phases | |
11654 | (add-after 'install 'install-kernelspec | |
11655 | (lambda* (#:key outputs #:allow-other-keys) | |
11656 | (let ((out (assoc-ref outputs "out"))) | |
11657 | (setenv "HOME" "/tmp") | |
11658 | (invoke "jupyter" "kernelspec" "install" | |
11659 | "--name" "ir" | |
11660 | "--prefix" out | |
11661 | (string-append out "/site-library/IRkernel/kernelspec")) | |
11662 | #t)))))) | |
11663 | (inputs | |
11664 | `(("jupyter" ,jupyter))) | |
11665 | (propagated-inputs | |
11666 | `(("r-crayon" ,r-crayon) | |
11667 | ("r-digest" ,r-digest) | |
11668 | ("r-evaluate" ,r-evaluate) | |
11669 | ("r-irdisplay" ,r-irdisplay) | |
11670 | ("r-jsonlite" ,r-jsonlite) | |
11671 | ("r-pbdzmq" ,r-pbdzmq) | |
11672 | ("r-repr" ,r-repr) | |
11673 | ("r-uuid" ,r-uuid))) | |
11674 | (home-page "https://cran.r-project.org/web/packages/IRkernel/") | |
11675 | (synopsis "Native R kernel for Jupyter") | |
11676 | (description | |
11677 | "The R kernel for the Jupyter environment executes R code which the | |
11678 | front-end (Jupyter Notebook or other front-ends) submits to the kernel via the | |
11679 | network.") | |
11680 | (license license:expat))) | |
51df4340 RW |
11681 | |
11682 | (define-public r-gmodels | |
11683 | (package | |
11684 | (name "r-gmodels") | |
11685 | (version "2.18.1") | |
11686 | (source | |
11687 | (origin | |
11688 | (method url-fetch) | |
11689 | (uri (cran-uri "gmodels" version)) | |
11690 | (sha256 | |
11691 | (base32 | |
11692 | "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) | |
11693 | (build-system r-build-system) | |
11694 | (propagated-inputs | |
11695 | `(("r-gdata" ,r-gdata) | |
11696 | ("r-mass" ,r-mass))) | |
11697 | (home-page "https://cran.r-project.org/web/packages/gmodels/") | |
11698 | (synopsis "Various R programming tools for model fitting") | |
11699 | (description | |
11700 | "This package provides various R programming tools for model fitting.") | |
11701 | (license license:gpl2))) | |
3942bf5e RW |
11702 | |
11703 | (define-public r-apcluster | |
11704 | (package | |
11705 | (name "r-apcluster") | |
11706 | (version "1.4.7") | |
11707 | (source | |
11708 | (origin | |
11709 | (method url-fetch) | |
11710 | (uri (cran-uri "apcluster" version)) | |
11711 | (sha256 | |
11712 | (base32 | |
11713 | "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s")))) | |
11714 | (build-system r-build-system) | |
11715 | (propagated-inputs | |
11716 | `(("r-matrix" ,r-matrix) | |
11717 | ("r-rcpp" ,r-rcpp))) | |
11718 | (home-page "https://cran.r-project.org/web/packages/apcluster/") | |
11719 | (synopsis "Affinity propagation clustering") | |
11720 | (description | |
11721 | "This package implements affinity propagation clustering introduced by | |
11722 | Frey and Dueck (2007). The package further provides leveraged affinity | |
11723 | propagation and an algorithm for exemplar-based agglomerative clustering that | |
11724 | can also be used to join clusters obtained from affinity propagation. Various | |
11725 | plotting functions are available for analyzing clustering results.") | |
11726 | (license license:gpl2+))) | |
a97796cd RW |
11727 | |
11728 | (define-public r-valr | |
11729 | (package | |
11730 | (name "r-valr") | |
11731 | (version "0.5.0") | |
11732 | (source | |
11733 | (origin | |
11734 | (method url-fetch) | |
11735 | (uri (cran-uri "valr" version)) | |
11736 | (sha256 | |
11737 | (base32 | |
11738 | "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika")))) | |
11739 | (build-system r-build-system) | |
11740 | (propagated-inputs | |
11741 | `(("r-broom" ,r-broom) | |
11742 | ("r-dplyr" ,r-dplyr) | |
11743 | ("r-ggplot2" ,r-ggplot2) | |
11744 | ("r-rcpp" ,r-rcpp) | |
11745 | ("r-readr" ,r-readr) | |
11746 | ("r-rlang" ,r-rlang) | |
11747 | ("r-stringr" ,r-stringr) | |
11748 | ("r-tibble" ,r-tibble))) | |
11749 | (home-page "http://github.com/rnabioco/valr") | |
11750 | (synopsis "Genome interval arithmetic in R") | |
11751 | (description | |
11752 | "This package enables you to read and manipulate genome intervals and | |
11753 | signals. It provides functionality similar to command-line tool suites within | |
11754 | R, enabling interactive analysis and visualization of genome-scale data.") | |
11755 | (license license:expat))) | |
100f5602 NB |
11756 | |
11757 | (define-public r-rematch2 | |
11758 | (package | |
11759 | (name "r-rematch2") | |
11760 | (version "2.0.1") | |
11761 | (source | |
11762 | (origin | |
11763 | (method url-fetch) | |
11764 | (uri (cran-uri "rematch2" version)) | |
11765 | (sha256 | |
11766 | (base32 | |
11767 | "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6")))) | |
11768 | (build-system r-build-system) | |
11769 | (propagated-inputs | |
11770 | `(("r-tibble" ,r-tibble))) | |
11771 | (home-page "https://github.com/r-lib/rematch2") | |
11772 | (synopsis "Tidy output from regular expression matching") | |
11773 | (description | |
11774 | "This package provides wrappers on @code{regexpr} and @code{gregexpr} to | |
11775 | return the match results in tidy data frames.") | |
11776 | (license license:expat))) | |
0c02f94f RW |
11777 | |
11778 | (define-public r-picante | |
11779 | (package | |
11780 | (name "r-picante") | |
11781 | (version "1.8") | |
11782 | (source | |
11783 | (origin | |
11784 | (method url-fetch) | |
11785 | (uri (cran-uri "picante" version)) | |
11786 | (sha256 | |
11787 | (base32 | |
11788 | "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1")))) | |
11789 | (build-system r-build-system) | |
11790 | (propagated-inputs | |
11791 | `(("r-ape" ,r-ape) | |
11792 | ("r-nlme" ,r-nlme) | |
11793 | ("r-vegan" ,r-vegan))) | |
11794 | (home-page "https://cran.r-project.org/web/packages/picante/") | |
11795 | (synopsis "Integrating phylogenies and ecology") | |
11796 | (description | |
11797 | "This package provides functions for phylocom integration, community | |
11798 | analyses, null-models, traits and evolution. It implements numerous | |
11799 | ecophylogenetic approaches including measures of community phylogenetic and | |
11800 | trait diversity, phylogenetic signal, estimation of trait values for | |
11801 | unobserved taxa, null models for community and phylogeny randomizations, and | |
11802 | utility functions for data input/output and phylogeny plotting. A full | |
11803 | description of package functionality and methods are provided by Kembel et | |
11804 | al. (2010).") | |
11805 | (license license:gpl2))) | |
93f178b5 RW |
11806 | |
11807 | (define-public r-reinforcelearn | |
11808 | (package | |
11809 | (name "r-reinforcelearn") | |
11810 | (version "0.2.0") | |
11811 | (source | |
11812 | (origin | |
11813 | (method url-fetch) | |
11814 | (uri (cran-uri "reinforcelearn" version)) | |
11815 | (sha256 | |
11816 | (base32 | |
11817 | "0naakmyb14d2cf7cy5ir52qh3bp51gvs6hyhfi3f72yl2jfnnpzg")))) | |
11818 | (build-system r-build-system) | |
11819 | (propagated-inputs | |
11820 | `(("r-checkmate" ,r-checkmate) | |
11821 | ("r-nnet" ,r-nnet) | |
11822 | ("r-purrr" ,r-purrr) | |
11823 | ("r-r6" ,r-r6))) | |
11824 | (home-page "https://markusdumke.github.io/reinforcelearn") | |
11825 | (synopsis "Reinforcement learning") | |
11826 | (description | |
11827 | "This package implements reinforcement learning environments and | |
11828 | algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm | |
11829 | can be used with function approximation, eligibility traces (Singh & Sutton, | |
11830 | 1996) and experience replay (Mnih et al., 2013).") | |
11831 | (license license:expat))) | |
f98d97c6 RW |
11832 | |
11833 | (define-public r-lemon | |
11834 | (package | |
11835 | (name "r-lemon") | |
11836 | (version "0.4.3") | |
11837 | (source | |
11838 | (origin | |
11839 | (method url-fetch) | |
11840 | (uri (cran-uri "lemon" version)) | |
11841 | (sha256 | |
11842 | (base32 | |
11843 | "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw")))) | |
11844 | (build-system r-build-system) | |
11845 | (propagated-inputs | |
11846 | `(("r-ggplot2" ,r-ggplot2) | |
11847 | ("r-gridextra" ,r-gridextra) | |
11848 | ("r-gtable" ,r-gtable) | |
11849 | ("r-knitr" ,r-knitr) | |
11850 | ("r-lattice" ,r-lattice) | |
11851 | ("r-plyr" ,r-plyr) | |
11852 | ("r-scales" ,r-scales))) | |
11853 | (home-page "https://github.com/stefanedwards/lemon") | |
11854 | (synopsis "Freshen up your ggplot2 plots") | |
11855 | (description | |
11856 | "This package provides functions for working with legends and axis lines | |
11857 | of ggplot2, facets that repeat axis lines on all panels, and some knitr | |
11858 | extensions.") | |
11859 | (license license:gpl3))) | |
79db3a1a RW |
11860 | |
11861 | (define-public r-wgaim | |
11862 | (package | |
11863 | (name "r-wgaim") | |
11864 | (version "1.4-11") | |
11865 | (source | |
11866 | (origin | |
11867 | (method url-fetch) | |
11868 | (uri (cran-uri "wgaim" version)) | |
11869 | (sha256 | |
11870 | (base32 | |
11871 | "1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg")))) | |
11872 | (build-system r-build-system) | |
11873 | (propagated-inputs | |
11874 | `(("r-lattice" ,r-lattice) | |
11875 | ("r-qtl" ,r-qtl))) | |
11876 | (home-page "https://cran.r-project.org/web/packages/wgaim") | |
11877 | (synopsis "Whole genome average interval mapping for QTL detection") | |
11878 | (description | |
11879 | "This package integrates sophisticated mixed modelling methods with a | |
11880 | whole genome approach to detecting significant QTL in linkage maps.") | |
11881 | (license license:gpl2+))) | |
f33cb7ab RW |
11882 | |
11883 | (define-public r-bedr | |
11884 | (package | |
11885 | (name "r-bedr") | |
11886 | (version "1.0.6") | |
11887 | (source | |
11888 | (origin | |
11889 | (method url-fetch) | |
11890 | (uri (cran-uri "bedr" version)) | |
11891 | (sha256 | |
11892 | (base32 | |
11893 | "0q790695h8bls0qw284n1zn7lxzym1dnnj095fsbjga2p116z4yv")))) | |
11894 | (build-system r-build-system) | |
11895 | (propagated-inputs | |
11896 | `(("r-data-table" ,r-data-table) | |
11897 | ("r-r-utils" ,r-r-utils) | |
11898 | ("r-testthat" ,r-testthat) | |
11899 | ("r-venndiagram" ,r-venndiagram) | |
11900 | ("r-yaml" ,r-yaml) | |
11901 | ("bedops" ,bedops) | |
11902 | ("bedtools" ,bedtools) | |
11903 | ("htslib" ,htslib))) ; for tabix | |
11904 | (native-inputs | |
11905 | `(("r-knitr" ,r-knitr))) ; for vignettes | |
11906 | (home-page "https://cran.r-project.org/web/packages/bedr") | |
11907 | (synopsis "Genomic region processing") | |
11908 | (description | |
11909 | "This package is for genomic regions processing using command line tools | |
11910 | such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient | |
11911 | utilities to perform genome arithmetic e.g indexing, formatting and merging. | |
11912 | The bedr package's API enhances access to these tools as well as offers | |
11913 | additional utilities for genomic regions processing.") | |
11914 | (license license:gpl2))) | |
459dcb95 RW |
11915 | |
11916 | (define-public r-partitions | |
11917 | (package | |
11918 | (name "r-partitions") | |
11919 | (version "1.9-19") | |
11920 | (source | |
11921 | (origin | |
11922 | (method url-fetch) | |
11923 | (uri (cran-uri "partitions" version)) | |
11924 | (sha256 | |
11925 | (base32 | |
11926 | "1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx")))) | |
11927 | (build-system r-build-system) | |
11928 | (propagated-inputs | |
11929 | `(("r-gmp" ,r-gmp) | |
11930 | ("r-polynom" ,r-polynom))) | |
11931 | (home-page "https://cran.r-project.org/web/packages/partitions") | |
11932 | (synopsis "Additive partitions of integers") | |
11933 | (description | |
11934 | "This package provides tools to enumerates the partitions, unequal | |
11935 | partitions, and restricted partitions of an integer; the three corresponding | |
11936 | partition functions are also given.") | |
11937 | ;; Any version of the GPL | |
11938 | (license license:gpl2+))) | |
761c097f RW |
11939 | |
11940 | (define-public r-brobdingnag | |
11941 | (package | |
11942 | (name "r-brobdingnag") | |
11943 | (version "1.2-6") | |
11944 | (source | |
11945 | (origin | |
11946 | (method url-fetch) | |
11947 | (uri (cran-uri "Brobdingnag" version)) | |
11948 | (sha256 | |
11949 | (base32 | |
11950 | "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r")))) | |
11951 | (properties `((upstream-name . "Brobdingnag"))) | |
11952 | (build-system r-build-system) | |
11953 | (home-page "https://github.com/RobinHankin/Brobdingnag.git") | |
11954 | (synopsis "Very large numbers in R") | |
11955 | (description | |
11956 | "This package handles very large numbers in R. Real numbers are held | |
11957 | using their natural logarithms, plus a logical flag indicating sign. The | |
11958 | package includes a vignette that gives a step-by-step introduction to using S4 | |
11959 | methods.") | |
11960 | ;; Any version of the GPL | |
11961 | (license license:gpl2+))) | |
c30be23a RW |
11962 | |
11963 | (define-public r-untb | |
11964 | (package | |
11965 | (name "r-untb") | |
11966 | (version "1.7-4") | |
11967 | (source | |
11968 | (origin | |
11969 | (method url-fetch) | |
11970 | (uri (cran-uri "untb" version)) | |
11971 | (sha256 | |
11972 | (base32 | |
11973 | "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6")))) | |
11974 | (build-system r-build-system) | |
11975 | (propagated-inputs | |
11976 | `(("r-brobdingnag" ,r-brobdingnag) | |
11977 | ("r-partitions" ,r-partitions) | |
11978 | ("r-polynom" ,r-polynom))) | |
11979 | (home-page "https://github.com/RobinHankin/untb.git") | |
11980 | (synopsis "Ecological drift under the UNTB") | |
11981 | (description | |
11982 | "This package provides numerical simulations, and visualizations, of | |
11983 | Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).") | |
11984 | (license license:gpl2+))) | |
ea87b4e3 RW |
11985 | |
11986 | (define-public r-stepwise | |
11987 | (package | |
11988 | (name "r-stepwise") | |
11989 | (version "0.3") | |
11990 | (source | |
11991 | (origin | |
11992 | (method url-fetch) | |
11993 | (uri (cran-uri "stepwise" version)) | |
11994 | (sha256 | |
11995 | (base32 | |
11996 | "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2")))) | |
11997 | (build-system r-build-system) | |
11998 | (home-page "http://stat.sfu.ca/statgen/research/stepwise.html") | |
11999 | (synopsis "Stepwise detection of recombination breakpoints") | |
12000 | (description | |
12001 | "This package provides a stepwise approach to identifying recombination | |
12002 | breakpoints in a genomic sequence alignment.") | |
12003 | (license license:gpl2+))) | |
2a35bb15 RW |
12004 | |
12005 | (define-public r-snpmaxsel | |
12006 | (package | |
12007 | (name "r-snpmaxsel") | |
12008 | (version "1.0-3") | |
12009 | (source | |
12010 | (origin | |
12011 | (method url-fetch) | |
12012 | (uri (cran-uri "SNPmaxsel" version)) | |
12013 | (sha256 | |
12014 | (base32 | |
12015 | "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z")))) | |
12016 | (properties `((upstream-name . "SNPmaxsel"))) | |
12017 | (build-system r-build-system) | |
12018 | (propagated-inputs | |
12019 | `(("r-combinat" ,r-combinat) | |
12020 | ("r-mvtnorm" ,r-mvtnorm))) | |
12021 | (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") | |
12022 | (synopsis "Maximally selected statistics for SNP data") | |
12023 | (description | |
12024 | "This package implements asymptotic methods related to maximally selected | |
12025 | statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP) | |
12026 | data.") | |
12027 | (license license:gpl2+))) | |
7002c44f | 12028 | |
49a48c49 RW |
12029 | (define-public r-acsnminer |
12030 | (package | |
12031 | (name "r-acsnminer") | |
12032 | (version "0.16.8.25") | |
12033 | (source (origin | |
12034 | (method url-fetch) | |
12035 | (uri (cran-uri "ACSNMineR" version)) | |
12036 | (sha256 | |
12037 | (base32 | |
12038 | "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) | |
12039 | (properties `((upstream-name . "ACSNMineR"))) | |
12040 | (build-system r-build-system) | |
12041 | (propagated-inputs | |
12042 | `(("r-ggplot2" ,r-ggplot2) | |
12043 | ("r-gridextra" ,r-gridextra))) | |
12044 | (home-page "https://cran.r-project.org/web/packages/ACSNMineR") | |
12045 | (synopsis "Gene enrichment analysis") | |
12046 | (description | |
12047 | "This package provides tools to compute and represent gene set enrichment | |
12048 | or depletion from your data based on pre-saved maps from the @dfn{Atlas of | |
12049 | Cancer Signalling Networks} (ACSN) or user imported maps. The gene set | |
12050 | enrichment can be run with hypergeometric test or Fisher exact test, and can | |
12051 | use multiple corrections. Visualization of data can be done either by | |
12052 | barplots or heatmaps.") | |
12053 | (license license:gpl2+))) | |
12054 | ||
c4d521ba RW |
12055 | (define-public r-seqinr |
12056 | (package | |
12057 | (name "r-seqinr") | |
12058 | (version "3.4-5") | |
12059 | (source | |
12060 | (origin | |
12061 | (method url-fetch) | |
12062 | (uri (cran-uri "seqinr" version)) | |
12063 | (sha256 | |
12064 | (base32 | |
12065 | "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn")))) | |
12066 | (build-system r-build-system) | |
12067 | (propagated-inputs | |
12068 | `(("r-ade4" ,r-ade4) | |
12069 | ("r-segmented" ,r-segmented))) | |
12070 | (inputs | |
12071 | `(("zlib" ,zlib))) | |
12072 | (home-page "http://seqinr.r-forge.r-project.org/") | |
12073 | (synopsis "Biological sequences retrieval and analysis") | |
12074 | (description | |
12075 | "This package provides tools for exploratory data analysis and data | |
12076 | visualization of biological sequence (DNA and protein) data. It also includes | |
12077 | utilities for sequence data management under the ACNUC system.") | |
12078 | (license license:gpl2+))) | |
12079 | ||
7002c44f RW |
12080 | (define-public r-units |
12081 | (package | |
12082 | (name "r-units") | |
12083 | (version "0.6-2") | |
12084 | (source | |
12085 | (origin | |
12086 | (method url-fetch) | |
12087 | (uri (cran-uri "units" version)) | |
12088 | (sha256 | |
12089 | (base32 | |
12090 | "0w7iwp8c66d5gj4rsb8c87vb0ja39hym6fmfnqaqwb3is1snfa2y")))) | |
12091 | (build-system r-build-system) | |
12092 | (inputs | |
12093 | `(("udunits" ,udunits))) | |
12094 | (propagated-inputs | |
12095 | `(("r-rcpp" ,r-rcpp))) | |
12096 | (home-page "https://github.com/r-quantities/units/") | |
12097 | (synopsis "Measurement Units for R Vectors") | |
12098 | (description | |
12099 | "This package provides support for measurement units in R vectors, | |
12100 | matrices and arrays: automatic propagation, conversion, derivation and | |
12101 | simplification of units; raising errors in case of unit incompatibility. It | |
12102 | is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} | |
12103 | classes.") | |
12104 | (license license:gpl2))) | |
518c1dea RW |
12105 | |
12106 | (define-public r-classint | |
12107 | (package | |
12108 | (name "r-classint") | |
12109 | (version "0.3-1") | |
12110 | (source | |
12111 | (origin | |
12112 | (method url-fetch) | |
12113 | (uri (cran-uri "classInt" version)) | |
12114 | (sha256 | |
12115 | (base32 | |
12116 | "1fcjrb593bzvx1z57hq1sjs2gp6g7sm4d4xrhasfrps4nmbzirp2")))) | |
12117 | (properties `((upstream-name . "classInt"))) | |
12118 | (build-system r-build-system) | |
12119 | (propagated-inputs | |
12120 | `(("r-class" ,r-class) | |
12121 | ("r-e1071" ,r-e1071))) | |
12122 | (native-inputs `(("gfortran" ,gfortran))) | |
12123 | (home-page "https://github.com/r-spatial/classInt/") | |
12124 | (synopsis "Choose univariate class intervals") | |
12125 | (description | |
12126 | "This package provides selected commonly used methods for choosing | |
12127 | univariate class intervals for mapping or other graphics purposes.") | |
12128 | (license license:gpl2+))) | |
66c08ff4 RW |
12129 | |
12130 | (define-public r-spdata | |
12131 | (package | |
12132 | (name "r-spdata") | |
12133 | (version "0.3.0") | |
12134 | (source | |
12135 | (origin | |
12136 | (method url-fetch) | |
12137 | (uri (cran-uri "spData" version)) | |
12138 | (sha256 | |
12139 | (base32 | |
12140 | "162cqb331ki43jx4r8lpkjpn2l712figd896rnawg9j1jmjyl96y")))) | |
12141 | (properties `((upstream-name . "spData"))) | |
12142 | (build-system r-build-system) | |
12143 | (home-page "https://github.com/Nowosad/spData") | |
12144 | (synopsis "Datasets for spatial analysis") | |
12145 | (description | |
12146 | "This a package containing diverse spatial datasets for demonstrating, | |
12147 | benchmarking and teaching spatial data analysis. It includes R data of class | |
12148 | @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a | |
12149 | range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some | |
12150 | of the datasets are designed to illustrate specific analysis techniques. | |
12151 | @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to | |
12152 | illustrate point pattern analysis techniques.") | |
12153 | (license license:cc0))) | |
e5228273 RW |
12154 | |
12155 | (define-public r-learnbayes | |
12156 | (package | |
12157 | (name "r-learnbayes") | |
12158 | (version "2.15.1") | |
12159 | (source | |
12160 | (origin | |
12161 | (method url-fetch) | |
12162 | (uri (cran-uri "LearnBayes" version)) | |
12163 | (sha256 | |
12164 | (base32 | |
12165 | "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv")))) | |
12166 | (properties `((upstream-name . "LearnBayes"))) | |
12167 | (build-system r-build-system) | |
12168 | (home-page "https://cran.r-project.org/web/packages/LearnBayes") | |
12169 | (synopsis "Functions for learning Bayesian inference") | |
12170 | (description | |
12171 | "This package provides a collection of functions helpful in learning the | |
12172 | basic tenets of Bayesian statistical inference. It contains functions for | |
12173 | summarizing basic one and two parameter posterior distributions and predictive | |
12174 | distributions. It contains MCMC algorithms for summarizing posterior | |
12175 | distributions defined by the user. It also contains functions for regression | |
12176 | models, hierarchical models, Bayesian tests, and illustrations of Gibbs | |
12177 | sampling.") | |
12178 | (license license:gpl2+))) | |
dcc50286 RW |
12179 | |
12180 | (define-public r-deldir | |
12181 | (package | |
12182 | (name "r-deldir") | |
12183 | (version "0.1-16") | |
12184 | (source | |
12185 | (origin | |
12186 | (method url-fetch) | |
12187 | (uri (cran-uri "deldir" version)) | |
12188 | (sha256 | |
12189 | (base32 | |
12190 | "0549kj0hlkdyvm5axsm3np30wg53fm2pxybijzw0avlgsd2y2n2q")))) | |
12191 | (build-system r-build-system) | |
12192 | (native-inputs `(("gfortran" ,gfortran))) | |
12193 | (home-page "https://cran.r-project.org/web/packages/deldir") | |
12194 | (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") | |
12195 | (description | |
12196 | "This package provides tools for calculating the Delaunay triangulation | |
12197 | and the Dirichlet or Voronoi tessellation (with respect to the entire plane) | |
12198 | of a planar point set. It plots triangulations and tessellations in various | |
12199 | ways, clips tessellations to sub-windows, calculates perimeters of | |
12200 | tessellations, and summarizes information about the tiles of the | |
12201 | tessellation.") | |
12202 | (license license:gpl2+))) | |
d884e407 RW |
12203 | |
12204 | (define-public r-sf | |
12205 | (package | |
12206 | (name "r-sf") | |
12207 | (version "0.7-3") | |
12208 | (source | |
12209 | (origin | |
12210 | (method url-fetch) | |
12211 | (uri (cran-uri "sf" version)) | |
12212 | (sha256 | |
12213 | (base32 | |
12214 | "1b9lbid0hmmz8m5vhg8mi2mi2rclia6qwzd1jr8s81i2l0md828d")))) | |
12215 | (build-system r-build-system) | |
12216 | (inputs | |
12217 | `(("gdal" ,gdal) | |
12218 | ("geos" ,geos) | |
12219 | ("proj" ,proj.4) | |
12220 | ("zlib" ,zlib))) | |
12221 | (propagated-inputs | |
12222 | `(("r-classint" ,r-classint) | |
12223 | ("r-dbi" ,r-dbi) | |
12224 | ("r-magrittr" ,r-magrittr) | |
12225 | ("r-rcpp" ,r-rcpp) | |
12226 | ("r-units" ,r-units))) | |
12227 | (native-inputs `(("pkg-config" ,pkg-config))) | |
12228 | (home-page "https://github.com/r-spatial/sf/") | |
12229 | (synopsis "Simple features for R") | |
12230 | (description | |
12231 | "This package provides support for simple features, a standardized way to | |
12232 | encode spatial vector data. It binds to GDAL for reading and writing data, to | |
12233 | GEOS for geometrical operations, and to PROJ for projection conversions and | |
12234 | datum transformations.") | |
12235 | ;; Either of these licenses | |
12236 | (license (list license:gpl2 license:expat)))) | |
e371e534 RW |
12237 | |
12238 | (define-public r-spdep | |
12239 | (package | |
12240 | (name "r-spdep") | |
12241 | (version "1.0-2") | |
12242 | (source | |
12243 | (origin | |
12244 | (method url-fetch) | |
12245 | (uri (cran-uri "spdep" version)) | |
12246 | (sha256 | |
12247 | (base32 | |
12248 | "1ciqn5xslm4ryad10nm6fqy1qhq3qhd4hx9bj94kphfm8x1zm7kg")))) | |
12249 | (build-system r-build-system) | |
12250 | (propagated-inputs | |
12251 | `(("r-boot" ,r-boot) | |
12252 | ("r-coda" ,r-coda) | |
12253 | ("r-deldir" ,r-deldir) | |
12254 | ("r-expm" ,r-expm) | |
12255 | ("r-gmodels" ,r-gmodels) | |
12256 | ("r-learnbayes" ,r-learnbayes) | |
12257 | ("r-mass" ,r-mass) | |
12258 | ("r-matrix" ,r-matrix) | |
12259 | ("r-nlme" ,r-nlme) | |
12260 | ("r-sf" ,r-sf) | |
12261 | ("r-sp" ,r-sp) | |
12262 | ("r-spdata" ,r-spdata))) | |
12263 | (home-page "https://github.com/r-spatial/spdep/") | |
12264 | (synopsis "Spatial dependence: weighting schemes, statistics and models") | |
12265 | (description | |
12266 | "This package provides a collection of functions to create spatial | |
12267 | weights matrix objects from polygon contiguities, from point patterns by | |
12268 | distance and tessellations, for summarizing these objects, and for permitting | |
12269 | their use in spatial data analysis, including regional aggregation by minimum | |
12270 | spanning tree.") | |
12271 | (license license:gpl2+))) | |
91c1fbdf RW |
12272 | |
12273 | (define-public r-adegenet | |
12274 | (package | |
12275 | (name "r-adegenet") | |
12276 | (version "2.1.1") | |
12277 | (source | |
12278 | (origin | |
12279 | (method url-fetch) | |
12280 | (uri (cran-uri "adegenet" version)) | |
12281 | (sha256 | |
12282 | (base32 | |
12283 | "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh")))) | |
12284 | (build-system r-build-system) | |
12285 | (propagated-inputs | |
12286 | `(("r-ade4" ,r-ade4) | |
12287 | ("r-ape" ,r-ape) | |
12288 | ("r-boot" ,r-boot) | |
12289 | ("r-dplyr" ,r-dplyr) | |
12290 | ("r-ggplot2" ,r-ggplot2) | |
12291 | ("r-igraph" ,r-igraph) | |
12292 | ("r-mass" ,r-mass) | |
12293 | ("r-reshape2" ,r-reshape2) | |
12294 | ("r-seqinr" ,r-seqinr) | |
12295 | ("r-shiny" ,r-shiny) | |
12296 | ("r-spdep" ,r-spdep) | |
12297 | ("r-vegan" ,r-vegan))) | |
12298 | (home-page "https://github.com/thibautjombart/adegenet") | |
12299 | (synopsis "Exploratory analysis of genetic and genomic data") | |
12300 | (description | |
12301 | "This package provides a toolset for the exploration of genetic and | |
12302 | genomic data. Adegenet provides formal (S4) classes for storing and handling | |
12303 | various genetic data, including genetic markers with varying ploidy and | |
12304 | hierarchical population structure (@code{genind} class), alleles counts by | |
12305 | populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It | |
12306 | also implements original multivariate methods (DAPC, sPCA), graphics, | |
12307 | statistical tests, simulation tools, distance and similarity measures, and | |
12308 | several spatial methods. A range of both empirical and simulated datasets is | |
12309 | also provided to illustrate various methods.") | |
12310 | (license license:gpl2+))) | |
3d2bc817 RW |
12311 | |
12312 | (define-public r-pegas | |
12313 | (package | |
12314 | (name "r-pegas") | |
12315 | (version "0.11") | |
12316 | (source | |
12317 | (origin | |
12318 | (method url-fetch) | |
12319 | (uri (cran-uri "pegas" version)) | |
12320 | (sha256 | |
12321 | (base32 | |
12322 | "0l21bapzbjcvblbvks3jh9rpy9hng1ccd7f0glhqw695lc737bpx")))) | |
12323 | (build-system r-build-system) | |
12324 | (propagated-inputs | |
12325 | `(("r-adegenet" ,r-adegenet) | |
12326 | ("r-ape" ,r-ape))) | |
12327 | (home-page "http://ape-package.ird.fr/pegas.html") | |
12328 | (synopsis "Population and evolutionary genetics analysis system") | |
12329 | (description | |
12330 | "This package provides functions for reading, writing, plotting, | |
12331 | analysing, and manipulating allelic and haplotypic data, including from VCF | |
12332 | files, and for the analysis of population nucleotide sequences and | |
12333 | micro-satellites including coalescent analyses, linkage disequilibrium, | |
12334 | population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, | |
12335 | minimum spanning tree and network, and median-joining networks.") | |
12336 | (license license:gpl2+))) | |
cd977b35 RW |
12337 | |
12338 | (define-public r-rmetasim | |
12339 | (package | |
12340 | (name "r-rmetasim") | |
12341 | (version "3.1.7") | |
12342 | (source | |
12343 | (origin | |
12344 | (method url-fetch) | |
12345 | (uri (cran-uri "rmetasim" version)) | |
12346 | (sha256 | |
12347 | (base32 | |
12348 | "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r")))) | |
12349 | (build-system r-build-system) | |
12350 | (propagated-inputs | |
12351 | `(("r-ade4" ,r-ade4) | |
12352 | ("r-adegenet" ,r-adegenet) | |
12353 | ("r-gtools" ,r-gtools) | |
12354 | ("r-pegas" ,r-pegas))) | |
12355 | (home-page "https://cran.r-project.org/web/packages/rmetasim") | |
12356 | (synopsis "Individual-based population genetic simulation environment") | |
12357 | (description | |
12358 | "This package provides an interface between R and the metasim simulation | |
12359 | engine. The simulation environment is documented in: Strand, A.(2002), | |
12360 | Metasim 1.0: an individual-based environment for simulating population | |
12361 | genetics of complex population dynamics.") | |
12362 | ;; Any GPL version | |
12363 | (license license:gpl2+))) | |
601ddf02 RW |
12364 | |
12365 | (define-public r-genetics | |
12366 | (package | |
12367 | (name "r-genetics") | |
12368 | (version "1.3.8.1.1") | |
12369 | (source | |
12370 | (origin | |
12371 | (method url-fetch) | |
12372 | (uri (cran-uri "genetics" version)) | |
12373 | (sha256 | |
12374 | (base32 | |
12375 | "0p59r4vxhy68d7cv2s2k4vbgnkxji21naz9jmdry9wxclrg7fw28")))) | |
12376 | (build-system r-build-system) | |
12377 | (propagated-inputs | |
12378 | `(("r-combinat" ,r-combinat) | |
12379 | ("r-gdata" ,r-gdata) | |
12380 | ("r-gtools" ,r-gtools) | |
12381 | ("r-mass" ,r-mass) | |
12382 | ("r-mvtnorm" ,r-mvtnorm))) | |
12383 | (home-page "https://cran.r-project.org/web/packages/genetics/") | |
12384 | (synopsis "Population genetics") | |
12385 | (description | |
12386 | "This package provides classes and methods for handling genetic data. | |
12387 | It includes classes to represent genotypes and haplotypes at single markers up | |
12388 | to multiple markers on multiple chromosomes. Function include allele | |
12389 | frequencies, flagging homo/heterozygotes, flagging carriers of certain | |
12390 | alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating | |
12391 | and testing for linkage disequilibrium, ...") | |
12392 | ;; Any GPL version. | |
12393 | (license license:gpl2+))) | |
5ef7d057 RW |
12394 | |
12395 | (define-public r-snp-plotter | |
12396 | (package | |
12397 | (name "r-snp-plotter") | |
12398 | (version "0.5.1") | |
12399 | (source | |
12400 | (origin | |
12401 | (method url-fetch) | |
12402 | (uri (cran-uri "snp.plotter" version)) | |
12403 | (sha256 | |
12404 | (base32 | |
12405 | "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) | |
12406 | (properties `((upstream-name . "snp.plotter"))) | |
12407 | (build-system r-build-system) | |
12408 | (propagated-inputs `(("r-genetics" ,r-genetics))) | |
12409 | (home-page "https://cran.r-project.org/web/packages/snp.plotter/") | |
12410 | (synopsis "Plot p-values using single SNP and/or haplotype data") | |
12411 | (description | |
12412 | "This package helps you create plots of p-values using single SNP and/or | |
12413 | haplotype data. Main features of the package include options to display a | |
12414 | @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple | |
12415 | datasets simultaneously. Plots can be created using global and/or individual | |
12416 | haplotype p-values along with single SNP p-values. Images are created as | |
12417 | either PDF/EPS files.") | |
12418 | (license license:gpl2+))) | |
6a472af3 RW |
12419 | |
12420 | (define-public r-polspline | |
12421 | (package | |
12422 | (name "r-polspline") | |
12423 | (version "1.1.14") | |
12424 | (source | |
12425 | (origin | |
12426 | (method url-fetch) | |
12427 | (uri (cran-uri "polspline" version)) | |
12428 | (sha256 | |
12429 | (base32 | |
12430 | "0g4s5nwi13yfs6b169yw8vrs48nvjyc014k2v7ybcxarl8z81va0")))) | |
12431 | (build-system r-build-system) | |
12432 | (native-inputs `(("gfortran" ,gfortran))) | |
12433 | (home-page "https://cran.r-project.org/web/packages/polspline/") | |
12434 | (synopsis "Polynomial spline routines") | |
12435 | (description | |
12436 | "This package provides routines for the polynomial spline fitting | |
12437 | routines hazard regression, hazard estimation with flexible tails, logspline, | |
12438 | lspec, polyclass, and polymars.") | |
12439 | (license license:gpl2+))) | |
a8c965cf RW |
12440 | |
12441 | (define-public r-rms | |
12442 | (package | |
12443 | (name "r-rms") | |
12444 | (version "5.1-3") | |
12445 | (source | |
12446 | (origin | |
12447 | (method url-fetch) | |
12448 | (uri (cran-uri "rms" version)) | |
12449 | (sha256 | |
12450 | (base32 | |
12451 | "1sw9a0iqiips580jpbk7yiqgyiswihvaqbnq4ybsmd4ki86i5isz")))) | |
12452 | (build-system r-build-system) | |
12453 | (propagated-inputs | |
12454 | `(("r-ggplot2" ,r-ggplot2) | |
12455 | ("r-hmisc" ,r-hmisc) | |
12456 | ("r-htmltable" ,r-htmltable) | |
12457 | ("r-htmltools" ,r-htmltools) | |
12458 | ("r-lattice" ,r-lattice) | |
12459 | ("r-multcomp" ,r-multcomp) | |
12460 | ("r-nlme" ,r-nlme) | |
12461 | ("r-polspline" ,r-polspline) | |
12462 | ("r-quantreg" ,r-quantreg) | |
12463 | ("r-rpart" ,r-rpart) | |
12464 | ("r-sparsem" ,r-sparsem) | |
12465 | ("r-survival" ,r-survival))) | |
12466 | (native-inputs `(("gfortran" ,gfortran))) | |
12467 | (home-page "http://biostat.mc.vanderbilt.edu/rms") | |
12468 | (synopsis "Regression modeling strategies") | |
12469 | (description | |
12470 | "This is a package for regression modeling, testing, estimation, | |
12471 | validation, graphics, prediction, and typesetting by storing enhanced model | |
12472 | design attributes in the fit. The rms package is a collection of functions | |
12473 | that assist with and streamline modeling. It also contains functions for | |
12474 | binary and ordinal logistic regression models, ordinal models for continuous Y | |
12475 | with a variety of distribution families, and the Buckley-James multiple | |
12476 | regression model for right-censored responses, and implements penalized | |
12477 | maximum likelihood estimation for logistic and ordinary linear models. The | |
12478 | package works with almost any regression model, but it was especially written | |
12479 | to work with binary or ordinal regression models, Cox regression, accelerated | |
12480 | failure time models, ordinary linear models, the Buckley-James model, | |
12481 | generalized least squares for serially or spatially correlated observations, | |
12482 | generalized linear models, and quantile regression.") | |
12483 | (license license:gpl2+))) | |
cd47dcf6 RW |
12484 | |
12485 | (define-public r-haplo-stats | |
12486 | (package | |
12487 | (name "r-haplo-stats") | |
12488 | (version "1.7.9") | |
12489 | (source | |
12490 | (origin | |
12491 | (method url-fetch) | |
12492 | (uri (cran-uri "haplo.stats" version)) | |
12493 | (sha256 | |
12494 | (base32 | |
12495 | "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx")))) | |
12496 | (properties `((upstream-name . "haplo.stats"))) | |
12497 | (build-system r-build-system) | |
12498 | (propagated-inputs | |
12499 | `(("r-rms" ,r-rms))) | |
12500 | (native-inputs | |
12501 | `(("r-r-rsp" ,r-r-rsp))) ; for vignettes | |
12502 | (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") | |
12503 | (synopsis "Analysis of haplotypes when linkage phase is ambiguous") | |
12504 | (description | |
12505 | "This package provides routines for the analysis of indirectly measured | |
12506 | haplotypes. The statistical methods assume that all subjects are unrelated | |
12507 | and that haplotypes are ambiguous (due to unknown linkage phase of the genetic | |
12508 | markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()}, | |
12509 | @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed | |
12510 | examples in the vignette.") | |
12511 | (license license:gpl2+))) | |
bffb5826 RW |
12512 | |
12513 | (define-public r-bqtl | |
12514 | (package | |
12515 | (name "r-bqtl") | |
12516 | (version "1.0-32") | |
12517 | (source | |
12518 | (origin | |
12519 | (method url-fetch) | |
12520 | (uri (cran-uri "bqtl" version)) | |
12521 | (sha256 | |
12522 | (base32 | |
12523 | "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci")))) | |
12524 | (build-system r-build-system) | |
12525 | (native-inputs `(("gfortran" ,gfortran))) | |
12526 | (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") | |
12527 | (synopsis "Bayesian QTL mapping toolkit") | |
12528 | (description | |
12529 | "This is a QTL mapping toolkit for inbred crosses and recombinant inbred | |
12530 | lines. It includes maximum likelihood and Bayesian tools.") | |
12531 | (license license:gpl2+))) | |
73fcd222 RW |
12532 | |
12533 | (define-public r-ibdreg | |
12534 | (package | |
12535 | (name "r-ibdreg") | |
12536 | (version "0.2.5") | |
12537 | (source | |
12538 | (origin | |
12539 | (method url-fetch) | |
12540 | (uri (cran-uri "ibdreg" version)) | |
12541 | (sha256 | |
12542 | (base32 | |
12543 | "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g")))) | |
12544 | (build-system r-build-system) | |
12545 | (home-page "https://www.mayo.edu/research/labs/\ | |
12546 | statistical-genetics-genetic-epidemiology/software") | |
12547 | (synopsis "Regression methods for IBD linkage with covariates") | |
12548 | (description | |
12549 | "This package provides a method to test genetic linkage with covariates | |
12550 | by regression methods with response IBD sharing for relative pairs. Account | |
12551 | for correlations of IBD statistics and covariates for relative pairs within | |
12552 | the same pedigree.") | |
12553 | (license license:gpl2+))) | |
d4a255a4 RW |
12554 | |
12555 | (define-public r-dlmap | |
12556 | (package | |
12557 | (name "r-dlmap") | |
12558 | (version "1.13") | |
12559 | (source | |
12560 | (origin | |
12561 | (method url-fetch) | |
12562 | (uri (cran-uri "dlmap" version)) | |
12563 | (sha256 | |
12564 | (base32 | |
12565 | "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) | |
12566 | (build-system r-build-system) | |
12567 | (propagated-inputs | |
12568 | `(("r-ibdreg" ,r-ibdreg) | |
12569 | ("r-mgcv" ,r-mgcv) | |
12570 | ("r-nlme" ,r-nlme) | |
12571 | ("r-qtl" ,r-qtl) | |
12572 | ("r-wgaim" ,r-wgaim))) | |
12573 | (home-page "https://cran.r-project.org/web/packages/dlmap/") | |
12574 | (synopsis "Detection localization mapping for QTL") | |
12575 | (description | |
12576 | "This is package for QTL mapping in a mixed model framework with separate | |
12577 | detection and localization stages. The first stage detects the number of QTL | |
12578 | on each chromosome based on the genetic variation due to grouped markers on | |
12579 | the chromosome; the second stage uses this information to determine the most | |
12580 | likely QTL positions. The mixed model can accommodate general fixed and | |
12581 | random effects, including spatial effects in field trials and pedigree | |
12582 | effects. It is applicable to backcrosses, doubled haploids, recombinant | |
12583 | inbred lines, F2 intercrosses, and association mapping populations.") | |
12584 | (license license:gpl2))) | |
1cdd9f0e RW |
12585 | |
12586 | (define-public r-ldheatmap | |
12587 | (package | |
12588 | (name "r-ldheatmap") | |
12589 | (version "0.99-5") | |
12590 | (source | |
12591 | (origin | |
12592 | (method url-fetch) | |
12593 | (uri (cran-uri "LDheatmap" version)) | |
12594 | (sha256 | |
12595 | (base32 | |
12596 | "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s")))) | |
12597 | (properties `((upstream-name . "LDheatmap"))) | |
12598 | (build-system r-build-system) | |
12599 | (propagated-inputs | |
12600 | `(("r-genetics" ,r-genetics) | |
12601 | ("r-snpstats" ,r-snpstats))) | |
12602 | (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html") | |
12603 | (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") | |
12604 | (description | |
12605 | "This package provides tools to produce a graphical display, as a heat | |
12606 | map, of measures of pairwise linkage disequilibria between SNPs. Users may | |
12607 | optionally include the physical locations or genetic map distances of each SNP | |
12608 | on the plot.") | |
12609 | (license license:gpl3))) | |
b8fea3c8 RW |
12610 | |
12611 | (define-public r-hwde | |
12612 | (package | |
12613 | (name "r-hwde") | |
12614 | (version "0.67") | |
12615 | (source | |
12616 | (origin | |
12617 | (method url-fetch) | |
12618 | (uri (cran-uri "hwde" version)) | |
12619 | (sha256 | |
12620 | (base32 | |
12621 | "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy")))) | |
12622 | (build-system r-build-system) | |
12623 | (home-page "https://cran.r-project.org/web/packages/hwde/") | |
12624 | (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium") | |
12625 | (description | |
12626 | "This package fits models for genotypic disequilibria, as described in | |
12627 | Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast | |
12628 | terms are available that account for first order interactions between loci. | |
12629 | It also implements, for a single locus in a single population, a conditional | |
12630 | exact test for Hardy-Weinberg equilibrium.") | |
12631 | (license license:gpl2+))) | |
7cd4ff2f RW |
12632 | |
12633 | (define-public r-tdthap | |
12634 | (package | |
12635 | (name "r-tdthap") | |
12636 | (version "1.1-9") | |
12637 | (source | |
12638 | (origin | |
12639 | (method url-fetch) | |
12640 | (uri (cran-uri "tdthap" version)) | |
12641 | (sha256 | |
12642 | (base32 | |
12643 | "0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r")))) | |
12644 | (build-system r-build-system) | |
12645 | (home-page "https://cran.r-project.org/web/packages/tdthap/") | |
12646 | (synopsis "TDT tests for extended haplotypes") | |
12647 | (description | |
12648 | "Functions and examples are provided for transmission/disequilibrium | |
12649 | tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) | |
12650 | \"Transmission/disequilibrium tests for extended marker haplotypes\".") | |
12651 | (license license:artistic2.0))) | |
469fb438 RW |
12652 | |
12653 | (define-public r-sparql | |
12654 | (package | |
12655 | (name "r-sparql") | |
12656 | (version "1.16") | |
12657 | (source (origin | |
12658 | (method url-fetch) | |
12659 | (uri (cran-uri "SPARQL" version)) | |
12660 | (sha256 | |
12661 | (base32 | |
12662 | "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) | |
12663 | (properties `((upstream-name . "SPARQL"))) | |
12664 | (build-system r-build-system) | |
12665 | (propagated-inputs | |
12666 | `(("r-rcurl" ,r-rcurl) | |
12667 | ("r-xml" ,r-xml))) | |
12668 | (home-page "https://cran.r-project.org/web/packages/SPARQL") | |
12669 | (synopsis "SPARQL client for R") | |
12670 | (description "This package provides an interface to use SPARQL to pose | |
12671 | SELECT or UPDATE queries to an end-point.") | |
12672 | ;; The only license indication is found in the DESCRIPTION file, | |
12673 | ;; which states GPL-3. So we cannot assume GPLv3+. | |
12674 | (license license:gpl3))) | |
0ef062b3 RW |
12675 | |
12676 | (define-public r-bookdown | |
12677 | (package | |
12678 | (name "r-bookdown") | |
12679 | (version "0.9") | |
12680 | (source (origin | |
12681 | (method url-fetch) | |
12682 | (uri (cran-uri "bookdown" version)) | |
12683 | (sha256 | |
12684 | (base32 | |
12685 | "0vg1s1w0l9pm95asqb21yf39mfk1nc9rdhmlys9xwr7p7i7rsz32")))) | |
12686 | (build-system r-build-system) | |
12687 | (propagated-inputs | |
12688 | `(("r-htmltools" ,r-htmltools) | |
12689 | ("r-knitr" ,r-knitr) | |
12690 | ("r-rmarkdown" ,r-rmarkdown) | |
12691 | ("r-tinytex" ,r-tinytex) | |
12692 | ("r-yaml" ,r-yaml) | |
12693 | ("r-xfun" ,r-xfun))) | |
12694 | (home-page "https://github.com/rstudio/bookdown") | |
12695 | (synopsis "Authoring books and technical documents with R markdown") | |
12696 | (description "This package provides output formats and utilities for | |
12697 | authoring books and technical documents with R Markdown.") | |
12698 | (license license:gpl3))) | |
72a216a9 RW |
12699 | |
12700 | (define-public r-optparse | |
12701 | (package | |
12702 | (name "r-optparse") | |
12703 | (version "1.6.1") | |
12704 | (source | |
12705 | (origin | |
12706 | (method url-fetch) | |
12707 | (uri (cran-uri "optparse" version)) | |
12708 | (sha256 | |
12709 | (base32 | |
12710 | "04vyb6dhcga30mvghsg1p052jmf69xqxkvh3hzqz7dscyppy76w1")))) | |
12711 | (build-system r-build-system) | |
12712 | (propagated-inputs | |
12713 | `(("r-getopt" ,r-getopt))) | |
12714 | (home-page "https://github.com/trevorld/optparse") | |
12715 | (synopsis "Command line option parser") | |
12716 | (description | |
12717 | "This package provides a command line parser inspired by Python's | |
12718 | @code{optparse} library to be used with Rscript to write shebang scripts | |
12719 | that accept short and long options.") | |
12720 | (license license:gpl2+))) | |
c5a2b518 RW |
12721 | |
12722 | (define-public r-wgcna | |
12723 | (package | |
12724 | (name "r-wgcna") | |
12725 | (version "1.66") | |
12726 | (source | |
12727 | (origin | |
12728 | (method url-fetch) | |
12729 | (uri (cran-uri "WGCNA" version)) | |
12730 | (sha256 | |
12731 | (base32 | |
12732 | "0rhnyhzfn93yp24jz9v6dzrmyizwzdw070a7idm0k33w1cm8sjqv")))) | |
12733 | (properties `((upstream-name . "WGCNA"))) | |
12734 | (build-system r-build-system) | |
12735 | (propagated-inputs | |
12736 | `(("r-annotationdbi" ,r-annotationdbi) | |
12737 | ("r-doparallel" ,r-doparallel) | |
12738 | ("r-dynamictreecut" ,r-dynamictreecut) | |
12739 | ("r-fastcluster" ,r-fastcluster) | |
12740 | ("r-foreach" ,r-foreach) | |
12741 | ("r-go-db" ,r-go-db) | |
12742 | ("r-hmisc" ,r-hmisc) | |
12743 | ("r-impute" ,r-impute) | |
12744 | ("r-rcpp" ,r-rcpp) | |
12745 | ("r-robust" ,r-robust) | |
12746 | ("r-survival" ,r-survival) | |
12747 | ("r-matrixstats" ,r-matrixstats) | |
12748 | ("r-preprocesscore" ,r-preprocesscore))) | |
12749 | (home-page | |
12750 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
12751 | (synopsis "Weighted correlation network analysis") | |
12752 | (description | |
12753 | "This package provides functions necessary to perform Weighted | |
12754 | Correlation Network Analysis on high-dimensional data. It includes functions | |
12755 | for rudimentary data cleaning, construction and summarization of correlation | |
12756 | networks, module identification and functions for relating both variables and | |
12757 | modules to sample traits. It also includes a number of utility functions for | |
12758 | data manipulation and visualization.") | |
12759 | (license license:gpl2+))) | |
bac0ca32 RW |
12760 | |
12761 | (define-public r-kernlab | |
12762 | (package | |
12763 | (name "r-kernlab") | |
12764 | (version "0.9-27") | |
12765 | (source | |
12766 | (origin | |
12767 | (method url-fetch) | |
12768 | (uri (cran-uri "kernlab" version)) | |
12769 | (sha256 | |
12770 | (base32 | |
12771 | "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn")))) | |
12772 | (build-system r-build-system) | |
12773 | (home-page "https://cran.r-project.org/web/packages/kernlab") | |
12774 | (synopsis "Kernel-based machine learning tools") | |
12775 | (description | |
12776 | "This package provides kernel-based machine learning methods for | |
12777 | classification, regression, clustering, novelty detection, quantile regression | |
12778 | and dimensionality reduction. Among other methods @code{kernlab} includes | |
12779 | Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes | |
12780 | and a QP solver.") | |
12781 | (license license:gpl2))) | |
a0583c0d RW |
12782 | |
12783 | (define-public r-hierfstat | |
12784 | (package | |
12785 | (name "r-hierfstat") | |
12786 | (version "0.04-22") | |
12787 | (source | |
12788 | (origin | |
12789 | (method url-fetch) | |
12790 | (uri (cran-uri "hierfstat" version)) | |
12791 | (sha256 | |
12792 | (base32 | |
12793 | "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx")))) | |
12794 | (build-system r-build-system) | |
12795 | (propagated-inputs | |
12796 | `(("r-ade4" ,r-ade4) | |
12797 | ("r-adegenet" ,r-adegenet) | |
12798 | ("r-gtools" ,r-gtools))) | |
12799 | (home-page "https://cran.r-project.org/web/packages/hierfstat/") | |
12800 | (synopsis "Estimation and tests of hierarchical F-statistics") | |
12801 | (description | |
12802 | "This package allows the estimation of hierarchical F-statistics from | |
12803 | haploid or diploid genetic data with any numbers of levels in the hierarchy, | |
12804 | following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions | |
12805 | are also given to test via randomisations the significance of each F and | |
12806 | variance components, using the likelihood-ratio statistics G.") | |
12807 | (license license:gpl2+))) | |
3080b81a RW |
12808 | |
12809 | (define-public r-hapassoc | |
12810 | (package | |
12811 | (name "r-hapassoc") | |
12812 | (version "1.2-8") | |
12813 | (source | |
12814 | (origin | |
12815 | (method url-fetch) | |
12816 | (uri (cran-uri "hapassoc" version)) | |
12817 | (sha256 | |
12818 | (base32 | |
12819 | "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s")))) | |
12820 | (build-system r-build-system) | |
12821 | (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html") | |
12822 | (synopsis "Inference of trait associations with SNP haplotypes") | |
12823 | (description | |
12824 | "Hapassoc performs likelihood inference of trait associations with | |
12825 | haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The | |
12826 | functions are developed primarily for data collected in cohort or | |
12827 | cross-sectional studies. They can accommodate uncertain haplotype phase and | |
12828 | handle missing genotypes at some SNPs.") | |
12829 | (license license:gpl2))) | |
7166b77a RW |
12830 | |
12831 | (define-public r-sampling | |
12832 | (package | |
12833 | (name "r-sampling") | |
12834 | (version "2.8") | |
12835 | (source | |
12836 | (origin | |
12837 | (method url-fetch) | |
12838 | (uri (cran-uri "sampling" version)) | |
12839 | (sha256 | |
12840 | (base32 | |
12841 | "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m")))) | |
12842 | (build-system r-build-system) | |
12843 | (propagated-inputs | |
12844 | `(("r-lpsolve" ,r-lpsolve) | |
12845 | ("r-mass" ,r-mass))) | |
12846 | (home-page "https://cran.r-project.org/web/packages/sampling/") | |
12847 | (synopsis "Survey sampling") | |
12848 | (description | |
12849 | "This package provides functions for drawing and calibrating samples.") | |
12850 | (license license:gpl2+))) | |
4f8b1fb3 RW |
12851 | |
12852 | (define-public r-r2html | |
12853 | (package | |
12854 | (name "r-r2html") | |
12855 | (version "2.3.2") | |
12856 | (source | |
12857 | (origin | |
12858 | (method url-fetch) | |
12859 | (uri (cran-uri "R2HTML" version)) | |
12860 | (sha256 | |
12861 | (base32 | |
12862 | "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9")))) | |
12863 | (properties `((upstream-name . "R2HTML"))) | |
12864 | (build-system r-build-system) | |
12865 | (home-page "https://github.com/nalimilan/R2HTML") | |
12866 | (synopsis "HTML export for R objects") | |
12867 | (description | |
12868 | "This package includes HTML functions and methods to write in an HTML | |
12869 | file. Thus, making HTML reports is easy. It includes a function that allows | |
12870 | redirection on the fly, which appears to be very useful for teaching purposes, | |
12871 | as the student can keep a copy of the produced output to keep all that they | |
12872 | did during the course. The package comes with a vignette describing how to | |
12873 | write HTML reports for statistical analysis. Finally, a driver for Sweave | |
12874 | allows to parse HTML flat files containing R code and to automatically write | |
12875 | the corresponding outputs (tables and graphs).") | |
12876 | (license license:gpl2+))) | |
3f6e6e98 RW |
12877 | |
12878 | (define-public r-rjava | |
12879 | (package | |
12880 | (name "r-rjava") | |
12881 | (version "0.9-10") | |
12882 | (source | |
12883 | (origin | |
12884 | (method url-fetch) | |
12885 | (uri (cran-uri "rJava" version)) | |
12886 | (sha256 | |
12887 | (base32 | |
12888 | "0y7yg70i3zwbwl4g36js4dqpl51cmwss5ymrsk24d1z07bflp4y9")))) | |
12889 | (properties `((upstream-name . "rJava"))) | |
12890 | (build-system r-build-system) | |
12891 | (arguments | |
12892 | `(#:modules ((guix build utils) | |
12893 | (guix build r-build-system) | |
12894 | (ice-9 match)) | |
12895 | #:phases | |
12896 | (modify-phases %standard-phases | |
12897 | (add-after 'unpack 'set-JAVA_HOME | |
12898 | (lambda* (#:key inputs #:allow-other-keys) | |
12899 | (let ((jdk (assoc-ref inputs "jdk"))) | |
12900 | (setenv "JAVA_HOME" jdk) | |
12901 | (setenv "JAVA" (which "java")) | |
12902 | (setenv "JAR" (which "jar")) | |
12903 | (setenv "JAVAC" (which "javac")) | |
12904 | (setenv "JAVAH" (which "javah")) | |
12905 | (setenv "JAVA_CPPFLAGS" | |
12906 | (string-append "-I" jdk "/include " | |
12907 | "-I" jdk "/include/linux")) | |
12908 | (match (find-files (string-append jdk "/jre/lib/") "libjvm.so") | |
12909 | ((lib) (setenv "JAVA_LIBS" lib)) | |
12910 | (_ (error "Could not find libjvm.so")))) | |
12911 | #t))))) | |
12912 | (inputs | |
12913 | `(("icu4c" ,icu4c) | |
12914 | ("jdk" ,icedtea-8 "jdk") | |
12915 | ("pcre" ,pcre) | |
12916 | ("zlib" ,zlib))) | |
12917 | (home-page "http://www.rforge.net/rJava/") | |
12918 | (synopsis "Low-Level R to Java interface") | |
12919 | (description | |
12920 | "This package provides a low-level interface to the Java VM very much | |
12921 | like .C/.Call and friends. It allows the creation of objects, calling methods | |
12922 | and accessing fields.") | |
12923 | (license license:gpl2))) | |
b9b177b3 RW |
12924 | |
12925 | (define-public r-svmisc | |
12926 | (package | |
12927 | (name "r-svmisc") | |
12928 | (version "1.1.0") | |
12929 | (source | |
12930 | (origin | |
12931 | (method url-fetch) | |
12932 | (uri (cran-uri "svMisc" version)) | |
12933 | (sha256 | |
12934 | (base32 | |
12935 | "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2")))) | |
12936 | (properties `((upstream-name . "svMisc"))) | |
12937 | (build-system r-build-system) | |
12938 | (home-page "https://github.com/SciViews/svMisc") | |
12939 | (synopsis "Miscellaneous functions for SciViews") | |
12940 | (description | |
12941 | "This package provides miscellaneous functions for SciViews or general | |
12942 | use, including tools to manage a temporary environment attached to the search | |
12943 | path for temporary variables you do not want to @code{save()} or | |
12944 | @code{load()}; test the current platform; showing progress bars, etc.") | |
12945 | (license license:gpl2))) | |
18c51cf3 RW |
12946 | |
12947 | (define-public r-xyz | |
12948 | (package | |
12949 | (name "r-xyz") | |
12950 | (version "0.2") | |
12951 | (source | |
12952 | (origin | |
12953 | (method url-fetch) | |
12954 | (uri (cran-uri "xyz" version)) | |
12955 | (sha256 | |
12956 | (base32 | |
12957 | "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) | |
12958 | (build-system r-build-system) | |
12959 | (propagated-inputs | |
12960 | `(("r-rcpp" ,r-rcpp))) | |
12961 | (home-page "https://cran.r-project.org/web/packages/xyz/") | |
12962 | (synopsis "Algorithm for fast interaction search in high-dimensional data") | |
12963 | (description | |
12964 | "High dimensional interaction search by brute force requires a quadratic | |
12965 | computational cost in the number of variables. The xyz algorithm provably | |
12966 | finds strong interactions in almost linear time. For details of the algorithm | |
12967 | see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast | |
12968 | interaction search in high-dimensional data.") | |
12969 | ;; Any version of the GPL. | |
12970 | (license license:gpl2+))) | |
81df4e1e RW |
12971 | |
12972 | (define-public r-rttf2pt1 | |
12973 | (package | |
12974 | (name "r-rttf2pt1") | |
12975 | (version "1.3.7") | |
12976 | (source | |
12977 | (origin | |
12978 | (method url-fetch) | |
12979 | (uri (cran-uri "Rttf2pt1" version)) | |
12980 | (sha256 | |
12981 | (base32 | |
12982 | "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja")))) | |
12983 | (properties `((upstream-name . "Rttf2pt1"))) | |
12984 | (build-system r-build-system) | |
12985 | (home-page "https://github.com/wch/Rttf2pt1") | |
12986 | (synopsis "Font conversion utility") | |
12987 | (description | |
12988 | "This package contains the program @code{ttf2pt1}, for use with the | |
12989 | @code{extrafont} package.") | |
12990 | ;; Most of the files are covered under the Expat license. Some files are | |
12991 | ;; covered under BSD-3. Deviations for individual files are recorded in | |
12992 | ;; the LICENSE file. | |
12993 | (license (list license:bsd-3 license:expat | |
12994 | (license:non-copyleft "file://LICENSE"))))) | |
b6933ea6 RW |
12995 | |
12996 | (define-public r-extrafontdb | |
12997 | (package | |
12998 | (name "r-extrafontdb") | |
12999 | (version "1.0") | |
13000 | (source | |
13001 | (origin | |
13002 | (method url-fetch) | |
13003 | (uri (cran-uri "extrafontdb" version)) | |
13004 | (sha256 | |
13005 | (base32 | |
13006 | "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs")))) | |
13007 | (build-system r-build-system) | |
13008 | (home-page "https://github.com/wch/extrafontdb") | |
13009 | (synopsis "Database for the extrafont package") | |
13010 | (description | |
13011 | "This package holds the database for the @code{extrafont} package.") | |
13012 | (license license:gpl2))) | |
2331bf2a RW |
13013 | |
13014 | (define-public r-extrafont | |
13015 | (package | |
13016 | (name "r-extrafont") | |
13017 | (version "0.17") | |
13018 | (source | |
13019 | (origin | |
13020 | (method url-fetch) | |
13021 | (uri (cran-uri "extrafont" version)) | |
13022 | (sha256 | |
13023 | (base32 | |
13024 | "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g")))) | |
13025 | (build-system r-build-system) | |
13026 | (propagated-inputs | |
13027 | `(("r-extrafontdb" ,r-extrafontdb) | |
13028 | ("r-rttf2pt1" ,r-rttf2pt1))) | |
13029 | (home-page "https://github.com/wch/extrafont") | |
13030 | (synopsis "Tools for using fonts in R") | |
13031 | (description | |
13032 | "The extrafont package makes it easier to use fonts other than the basic | |
13033 | PostScript fonts that R uses. Fonts that are imported into extrafont can be | |
13034 | used with PDF or PostScript output files. There are two hurdles for using | |
13035 | fonts in PDF (or Postscript) output files: | |
13036 | ||
13037 | @enumerate | |
13038 | @item Making R aware of the font and the dimensions of the characters. | |
13039 | @item Embedding the fonts in the PDF file so that the PDF can be displayed | |
13040 | properly on a device that doesn't have the font. This is usually needed if | |
13041 | you want to print the PDF file or share it with others. | |
13042 | @end enumerate | |
13043 | ||
13044 | The extrafont package makes both of these things easier.") | |
13045 | (license license:gpl2))) | |
2d704608 RW |
13046 | |
13047 | (define-public r-xkcd | |
13048 | (package | |
13049 | (name "r-xkcd") | |
13050 | (version "0.0.6") | |
13051 | (source | |
13052 | (origin | |
13053 | (method url-fetch) | |
13054 | (uri (cran-uri "xkcd" version)) | |
13055 | (sha256 | |
13056 | (base32 | |
13057 | "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) | |
13058 | (build-system r-build-system) | |
13059 | (propagated-inputs | |
13060 | `(("r-extrafont" ,r-extrafont) | |
13061 | ("r-ggplot2" ,r-ggplot2) | |
13062 | ("r-hmisc" ,r-hmisc))) | |
13063 | (home-page "https://cran.r-project.org/web/packages/xkcd/") | |
13064 | (synopsis "Plot ggplot2 graphics in the XKCD style") | |
13065 | (description | |
13066 | "This package provides the means to plot ggplot2 graphs in the style of | |
13067 | the XKCD web comic.") | |
13068 | (license license:gpl3))) | |
0d50d0df RW |
13069 | |
13070 | (define-public r-msigdbr | |
13071 | (package | |
13072 | (name "r-msigdbr") | |
13073 | (version "6.2.1") | |
13074 | (source | |
13075 | (origin | |
13076 | (method url-fetch) | |
13077 | (uri (cran-uri "msigdbr" version)) | |
13078 | (sha256 | |
13079 | (base32 | |
13080 | "1264j1hs74kq7hyh68vfynadfi6mdpq46qm1hnwzkzzhmbzpb9cg")))) | |
13081 | (build-system r-build-system) | |
13082 | (propagated-inputs | |
13083 | `(("r-dplyr" ,r-dplyr) | |
13084 | ("r-magrittr" ,r-magrittr) | |
13085 | ("r-rlang" ,r-rlang) | |
13086 | ("r-tibble" ,r-tibble))) | |
13087 | (home-page "https://github.com/igordot/msigdbr") | |
13088 | (synopsis "MSigDB gene sets for multiple organisms") | |
13089 | (description | |
13090 | "This package provides the @dfn{Molecular Signatures Database} (MSigDB) | |
13091 | gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA) | |
13092 | software in a standard R data frame with key-value pairs. Included are the | |
13093 | original human gene symbols and Entrez IDs as well as the equivalents for | |
13094 | various frequently studied model organisms such as mouse, rat, pig, fly, and | |
13095 | yeast.") | |
13096 | ;; The package is covered under the Expat license, but the upstream MSigDB | |
13097 | ;; files are made available under the Creative Commons Attribution 4.0 | |
13098 | ;; International license. | |
13099 | (license (list license:expat license:cc-by4.0)))) | |
585d5ae0 RW |
13100 | |
13101 | (define-public r-gridgraphics | |
13102 | (package | |
13103 | (name "r-gridgraphics") | |
13104 | (version "0.3-0") | |
13105 | (source | |
13106 | (origin | |
13107 | (method url-fetch) | |
13108 | (uri (cran-uri "gridGraphics" version)) | |
13109 | (sha256 | |
13110 | (base32 | |
13111 | "1p94flvq5h3x817pl1m0aj3sim87x6zdbpv9xrgdnqw3rxfzwgqs")))) | |
13112 | (properties `((upstream-name . "gridGraphics"))) | |
13113 | (build-system r-build-system) | |
13114 | (home-page "https://github.com/pmur002/gridgraphics") | |
13115 | (synopsis "Redraw base graphics using @code{grid} graphics") | |
13116 | (description | |
13117 | "This package provides functions to convert a page of plots drawn with | |
13118 | the @code{graphics} package into identical output drawn with the @code{grid} | |
13119 | package. The result looks like the original @code{graphics}-based plot, but | |
13120 | consists of @code{grid} grobs and viewports that can then be manipulated with | |
13121 | @code{grid} functions (e.g., edit grobs and revisit viewports).") | |
13122 | (license license:gpl2+))) | |
1c59ec70 RW |
13123 | |
13124 | (define-public r-farver | |
13125 | (package | |
13126 | (name "r-farver") | |
13127 | (version "1.1.0") | |
13128 | (source | |
13129 | (origin | |
13130 | (method url-fetch) | |
13131 | (uri (cran-uri "farver" version)) | |
13132 | (sha256 | |
13133 | (base32 | |
13134 | "1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0")))) | |
13135 | (build-system r-build-system) | |
13136 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
13137 | (home-page "https://github.com/thomasp85/farver") | |
13138 | (synopsis "Vectorized color conversion and comparison") | |
13139 | (description | |
13140 | "The encoding of color can be handled in many different ways, using | |
13141 | different color spaces. As different color spaces have different uses, | |
13142 | efficient conversion between these representations are important. This | |
13143 | package provides a set of functions that gives access to very fast color space | |
13144 | conversion and comparisons implemented in C++, and offers 100-fold speed | |
13145 | improvements over the @code{convertColor} function in the @code{grDevices} | |
13146 | package.") | |
13147 | (license license:expat))) | |
e2582883 RW |
13148 | |
13149 | (define-public r-ggplotify | |
13150 | (package | |
13151 | (name "r-ggplotify") | |
13152 | (version "0.0.3") | |
13153 | (source | |
13154 | (origin | |
13155 | (method url-fetch) | |
13156 | (uri (cran-uri "ggplotify" version)) | |
13157 | (sha256 | |
13158 | (base32 | |
13159 | "14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby")))) | |
13160 | (build-system r-build-system) | |
13161 | (propagated-inputs | |
13162 | `(("r-ggplot2" ,r-ggplot2) | |
13163 | ("r-gridgraphics" ,r-gridgraphics) | |
13164 | ("r-rvcheck" ,r-rvcheck))) | |
13165 | (home-page "https://github.com/GuangchuangYu/ggplotify") | |
13166 | (synopsis "Convert plots to @code{grob} or @code{ggplot} object") | |
13167 | (description | |
13168 | "This package provides tools to convert plot function calls (using | |
13169 | expression or formula) to @code{grob} or @code{ggplot} objects that are | |
13170 | compatible with the @code{grid} and @code{ggplot2} environment. With this | |
13171 | package, we are able to e.g. use @code{cowplot} to align plots produced by | |
13172 | @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by | |
13173 | converting them to @code{ggplot} objects.") | |
13174 | (license license:artistic2.0))) | |
85431ca3 RW |
13175 | |
13176 | (define-public r-triebeard | |
13177 | (package | |
13178 | (name "r-triebeard") | |
13179 | (version "0.3.0") | |
13180 | (source | |
13181 | (origin | |
13182 | (method url-fetch) | |
13183 | (uri (cran-uri "triebeard" version)) | |
13184 | (sha256 | |
13185 | (base32 | |
13186 | "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) | |
13187 | (build-system r-build-system) | |
13188 | (propagated-inputs `(("r-rcpp" ,r-rcpp))) | |
13189 | (home-page "https://github.com/Ironholds/triebeard/") | |
13190 | (synopsis "Radix trees in Rcpp") | |
13191 | (description | |
13192 | "Radix trees, or tries, are key-value data structures optimized for | |
13193 | efficient lookups, similar in purpose to hash tables. This package provides | |
13194 | an implementation of radix trees for use in R programming and in developing | |
13195 | packages with Rcpp.") | |
13196 | (license license:expat))) | |
91e06bed RW |
13197 | |
13198 | (define-public r-tweenr | |
13199 | (package | |
13200 | (name "r-tweenr") | |
13201 | (version "1.0.1") | |
13202 | (source | |
13203 | (origin | |
13204 | (method url-fetch) | |
13205 | (uri (cran-uri "tweenr" version)) | |
13206 | (sha256 | |
13207 | (base32 | |
13208 | "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg")))) | |
13209 | (build-system r-build-system) | |
13210 | (propagated-inputs | |
13211 | `(("r-farver" ,r-farver) | |
13212 | ("r-magrittr" ,r-magrittr) | |
13213 | ("r-rcpp" ,r-rcpp) | |
13214 | ("r-rlang" ,r-rlang))) | |
13215 | (home-page "https://github.com/thomasp85/tweenr") | |
13216 | (synopsis "Interpolate data for smooth animations") | |
13217 | (description | |
13218 | "In order to create smooth animation between states of data, tweening is | |
13219 | necessary. This package provides a range of functions for creating tweened | |
13220 | data that can be used as basis for animation. Furthermore it adds a number of | |
13221 | vectorized interpolaters for common R data types such as numeric, date and | |
13222 | color.") | |
13223 | (license license:expat))) | |
09dde7fb RW |
13224 | |
13225 | (define-public r-polyclip | |
13226 | (package | |
13227 | (name "r-polyclip") | |
13228 | (version "1.10-0") | |
13229 | (source | |
13230 | (origin | |
13231 | (method url-fetch) | |
13232 | (uri (cran-uri "polyclip" version)) | |
13233 | (sha256 | |
13234 | (base32 | |
13235 | "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl")))) | |
13236 | (build-system r-build-system) | |
13237 | (native-inputs `(("pkg-config" ,pkg-config))) | |
13238 | (home-page "http://www.angusj.com/delphi/clipper.php") | |
13239 | (synopsis "Polygon clipping") | |
13240 | (description | |
13241 | "This package provides an R port of the library Clipper. It performs | |
13242 | polygon clipping operations (intersection, union, set minus, set difference) | |
13243 | for polygonal regions of arbitrary complexity, including holes. It computes | |
13244 | offset polygons (spatial buffer zones, morphological dilations, Minkowski | |
13245 | dilations) for polygonal regions and polygonal lines. It computes the | |
13246 | Minkowski Sum of general polygons. There is a function for removing | |
13247 | self-intersections from polygon data.") | |
13248 | (license license:boost1.0))) | |
d4ff09af RW |
13249 | |
13250 | (define-public r-urltools | |
13251 | (package | |
13252 | (name "r-urltools") | |
13253 | (version "1.7.2") | |
13254 | (source | |
13255 | (origin | |
13256 | (method url-fetch) | |
13257 | (uri (cran-uri "urltools" version)) | |
13258 | (sha256 | |
13259 | (base32 | |
13260 | "18lp66f2l504b8q3j4xy8j9pyzzlljw9f112sn6qii1cg83072wm")))) | |
13261 | (build-system r-build-system) | |
13262 | (propagated-inputs | |
13263 | `(("r-rcpp" ,r-rcpp) | |
13264 | ("r-triebeard" ,r-triebeard))) | |
13265 | (home-page "https://github.com/Ironholds/urltools/") | |
13266 | (synopsis "Vectorized tools for URL handling and parsing") | |
13267 | (description | |
13268 | "This package provides a toolkit for all URL-handling needs, including | |
13269 | encoding and decoding, parsing, parameter extraction and modification. All | |
13270 | functions are designed to be both fast and entirely vectorized. It is | |
13271 | intended to be useful for people dealing with web-related datasets, such as | |
13272 | server-side logs, although may be useful for other situations involving large | |
13273 | sets of URLs.") | |
13274 | (license license:expat))) | |
83f43284 RW |
13275 | |
13276 | (define-public r-ggforce | |
13277 | (package | |
13278 | (name "r-ggforce") | |
13279 | (version "0.2.1") | |
13280 | (source | |
13281 | (origin | |
13282 | (method url-fetch) | |
13283 | (uri (cran-uri "ggforce" version)) | |
13284 | (sha256 | |
13285 | (base32 | |
13286 | "04rh9z58q288lbi933472lgl26wwbw58rfhpgfyijmw9ccz7i93m")))) | |
13287 | (build-system r-build-system) | |
13288 | (propagated-inputs | |
13289 | `(("r-ggplot2" ,r-ggplot2) | |
13290 | ("r-gtable" ,r-gtable) | |
13291 | ("r-mass" ,r-mass) | |
13292 | ("r-polyclip" ,r-polyclip) | |
13293 | ("r-rcpp" ,r-rcpp) | |
13294 | ("r-rcppeigen" ,r-rcppeigen) | |
13295 | ("r-rlang" ,r-rlang) | |
13296 | ("r-scales" ,r-scales) | |
13297 | ("r-tweenr" ,r-tweenr))) | |
13298 | (home-page "https://ggforce.data-imaginist.com") | |
13299 | (synopsis "Accelerating ggplot2") | |
13300 | (description | |
13301 | "The aim of the ggplot2 package is to aid in visual data investigations. | |
13302 | This focus has led to a lack of facilities for composing specialized plots. | |
13303 | Thi package aims to be a collection of mainly new statistics and geometries | |
13304 | that fills this gap.") | |
13305 | (license license:expat))) | |
b5b0a2ff RW |
13306 | |
13307 | (define-public r-europepmc | |
13308 | (package | |
13309 | (name "r-europepmc") | |
13310 | (version "0.3") | |
13311 | (source | |
13312 | (origin | |
13313 | (method url-fetch) | |
13314 | (uri (cran-uri "europepmc" version)) | |
13315 | (sha256 | |
13316 | (base32 | |
13317 | "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h")))) | |
13318 | (build-system r-build-system) | |
13319 | (propagated-inputs | |
13320 | `(("r-dplyr" ,r-dplyr) | |
13321 | ("r-httr" ,r-httr) | |
13322 | ("r-jsonlite" ,r-jsonlite) | |
13323 | ("r-plyr" ,r-plyr) | |
13324 | ("r-progress" ,r-progress) | |
13325 | ("r-purrr" ,r-purrr) | |
13326 | ("r-urltools" ,r-urltools) | |
13327 | ("r-xml2" ,r-xml2))) | |
13328 | (home-page "https://github.com/ropensci/europepmc/") | |
13329 | (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") | |
13330 | (description | |
13331 | "This package provides an R Client for the | |
13332 | @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web | |
13333 | Service}. It gives access to both metadata on life science literature and | |
13334 | open access full texts. Europe PMC indexes all PubMed content and other | |
13335 | literature sources including Agricola, a bibliographic database of citations | |
13336 | to the agricultural literature, or Biological Patents. In addition to | |
13337 | bibliographic metadata, the client allows users to fetch citations and | |
13338 | reference lists. Links between life-science literature and other EBI | |
13339 | databases, including ENA, PDB or ChEMBL are also accessible.") | |
13340 | (license license:gpl3))) | |
11f226e1 RW |
13341 | |
13342 | (define-public r-ggraph | |
13343 | (package | |
13344 | (name "r-ggraph") | |
13345 | (version "1.0.2") | |
13346 | (source | |
13347 | (origin | |
13348 | (method url-fetch) | |
13349 | (uri (cran-uri "ggraph" version)) | |
13350 | (sha256 | |
13351 | (base32 | |
13352 | "0fpmp326mryd1k1qvacjadksrnhbla8h960i18lmrimzrag7692c")))) | |
13353 | (build-system r-build-system) | |
13354 | (propagated-inputs | |
13355 | `(("r-digest" ,r-digest) | |
13356 | ("r-dplyr" ,r-dplyr) | |
13357 | ("r-ggforce" ,r-ggforce) | |
13358 | ("r-ggplot2" ,r-ggplot2) | |
13359 | ("r-ggrepel" ,r-ggrepel) | |
13360 | ("r-gtable" ,r-gtable) | |
13361 | ("r-igraph" ,r-igraph) | |
13362 | ("r-mass" ,r-mass) | |
13363 | ("r-plyr" ,r-plyr) | |
13364 | ("r-rcpp" ,r-rcpp) | |
13365 | ("r-scales" ,r-scales) | |
13366 | ("r-viridis" ,r-viridis))) | |
13367 | (home-page "https://cran.r-project.org/web/packages/ggraph/") | |
13368 | (synopsis "Implementation of grammar of graphics for graphs and networks") | |
13369 | (description | |
13370 | "The grammar of graphics as implemented in ggplot2 is a poor fit for | |
13371 | graph and network visualizations due to its reliance on tabular data input. | |
13372 | The ggraph package is an extension of the ggplot2 API tailored to graph | |
13373 | visualizations and provides the same flexible approach to building up plots | |
13374 | layer by layer.") | |
13375 | (license license:gpl3))) | |
1c0c4b54 RW |
13376 | |
13377 | (define-public r-varselrf | |
13378 | (package | |
13379 | (name "r-varselrf") | |
13380 | (version "0.7-8") | |
13381 | (source | |
13382 | (origin | |
13383 | (method url-fetch) | |
13384 | (uri (cran-uri "varSelRF" version)) | |
13385 | (sha256 | |
13386 | (base32 | |
13387 | "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i")))) | |
13388 | (properties `((upstream-name . "varSelRF"))) | |
13389 | (build-system r-build-system) | |
13390 | (propagated-inputs | |
13391 | `(("r-randomforest" ,r-randomforest))) | |
13392 | (home-page "http://ligarto.org/rdiaz/Software/Software.html") | |
13393 | (synopsis "Variable selection using random forests") | |
13394 | (description | |
13395 | "This package provides tools for the variable selection from random | |
13396 | forests using both backwards variable elimination (for the selection of small | |
13397 | sets of non-redundant variables) and selection based on the importance | |
13398 | spectrum (somewhat similar to scree plots; for the selection of large, | |
13399 | potentially highly-correlated variables). The main applications are in | |
13400 | high-dimensional data (e.g., microarray data, and other genomics and | |
13401 | proteomics applications).") | |
13402 | (license license:gpl2+))) | |
aae0b86d RW |
13403 | |
13404 | (define-public r-pamr | |
13405 | (package | |
13406 | (name "r-pamr") | |
13407 | (version "1.56") | |
13408 | (source | |
13409 | (origin | |
13410 | (method url-fetch) | |
13411 | (uri (cran-uri "pamr" version)) | |
13412 | (sha256 | |
13413 | (base32 | |
13414 | "03h1m5fkw76jjln1psdb7x913a499ghf7n48rcd8damr5vdyf961")))) | |
13415 | (build-system r-build-system) | |
13416 | (propagated-inputs | |
13417 | `(("r-cluster" ,r-cluster) | |
13418 | ("r-survival" ,r-survival))) | |
13419 | (native-inputs `(("gfortran" ,gfortran))) | |
13420 | (home-page "https://cran.r-project.org/web/packages/pamr/") | |
13421 | (synopsis "Prediction Analysis for Microarrays") | |
13422 | (description | |
13423 | "This package provides some functions for sample classification in | |
13424 | microarrays.") | |
13425 | (license license:gpl2))) | |
fe3fb4e7 RW |
13426 | |
13427 | (define-public r-rda | |
13428 | (package | |
13429 | (name "r-rda") | |
13430 | (version "1.0.2-2.1") | |
13431 | (source | |
13432 | (origin | |
13433 | (method url-fetch) | |
13434 | (uri (cran-uri "rda" version)) | |
13435 | (sha256 | |
13436 | (base32 | |
13437 | "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639")))) | |
13438 | (build-system r-build-system) | |
13439 | (home-page "https://cran.r-project.org/web/packages/rda/") | |
13440 | (synopsis "Shrunken centroids regularized discriminant analysis") | |
13441 | (description | |
13442 | "This package provides tools for shrunken centroids regularized | |
13443 | discriminant analysis for the purpose of classifying high dimensional data.") | |
13444 | (license license:gpl2+))) | |
8473597f RW |
13445 | |
13446 | (define-public r-ggvis | |
13447 | (package | |
13448 | (name "r-ggvis") | |
13449 | (version "0.4.4") | |
13450 | (source | |
13451 | (origin | |
13452 | (method url-fetch) | |
13453 | (uri (cran-uri "ggvis" version)) | |
13454 | (sha256 | |
13455 | (base32 | |
13456 | "1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk")))) | |
13457 | (build-system r-build-system) | |
13458 | (propagated-inputs | |
13459 | `(("r-assertthat" ,r-assertthat) | |
13460 | ("r-dplyr" ,r-dplyr) | |
13461 | ("r-htmltools" ,r-htmltools) | |
13462 | ("r-jsonlite" ,r-jsonlite) | |
13463 | ("r-lazyeval" ,r-lazyeval) | |
13464 | ("r-magrittr" ,r-magrittr) | |
13465 | ("r-shiny" ,r-shiny))) | |
13466 | (home-page "https://ggvis.rstudio.com/") | |
13467 | (synopsis "Interactive grammar of graphics") | |
13468 | (description | |
13469 | "This package is a data visualization package for R providing an | |
13470 | implementation of an interactive grammar of graphics, taking the best parts of | |
13471 | ggplot2, combining them with the reactive framework of Shiny and drawing web | |
13472 | graphics using Vega.") | |
13473 | (license license:gpl2))) | |
d59df334 RW |
13474 | |
13475 | (define-public r-gbm | |
13476 | (package | |
13477 | (name "r-gbm") | |
13478 | (version "2.1.5") | |
13479 | (source | |
13480 | (origin | |
13481 | (method url-fetch) | |
13482 | (uri (cran-uri "gbm" version)) | |
13483 | (sha256 | |
13484 | (base32 | |
13485 | "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6")))) | |
13486 | (build-system r-build-system) | |
13487 | (propagated-inputs | |
13488 | `(("r-gridextra" ,r-gridextra) | |
13489 | ("r-lattice" ,r-lattice) | |
13490 | ("r-survival" ,r-survival))) | |
13491 | (home-page "https://github.com/gbm-developers/gbm") | |
13492 | (synopsis "Generalized boosted regression models") | |
13493 | (description | |
13494 | "This package is an implementation of extensions to Freund and Schapire's | |
13495 | AdaBoost algorithm and Friedman's gradient boosting machine. It includes | |
13496 | regression methods for least squares, absolute loss, t-distribution loss, | |
13497 | quantile regression, logistic, multinomial logistic, Poisson, Cox proportional | |
13498 | hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, | |
13499 | and Learning to Rank measures (LambdaMart).") | |
13500 | (license license:gpl2+))) | |
efba5613 RW |
13501 | |
13502 | (define-public r-threejs | |
13503 | (package | |
13504 | (name "r-threejs") | |
13505 | (version "0.3.1") | |
13506 | (source | |
13507 | (origin | |
13508 | (method url-fetch) | |
13509 | (uri (cran-uri "threejs" version)) | |
13510 | (sha256 | |
13511 | (base32 | |
13512 | "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi")))) | |
13513 | (build-system r-build-system) | |
13514 | (arguments | |
13515 | `(#:modules ((guix build utils) | |
13516 | (guix build r-build-system) | |
13517 | (srfi srfi-1) | |
13518 | (ice-9 popen)) | |
13519 | #:phases | |
13520 | (modify-phases %standard-phases | |
13521 | (add-after 'unpack 'process-javascript | |
13522 | (lambda* (#:key inputs #:allow-other-keys) | |
13523 | (with-directory-excursion "inst" | |
13524 | (call-with-values | |
13525 | (lambda () | |
13526 | (unzip2 | |
13527 | `((,(assoc-ref inputs "js-jquery") | |
13528 | "htmlwidgets/lib/jquery/jquery.min.js") | |
13529 | (,(assoc-ref inputs "js-threejs-85") | |
13530 | "htmlwidgets/lib/threejs-85/three.min.js")))) | |
13531 | (lambda (sources targets) | |
13532 | (for-each (lambda (source target) | |
13533 | (format #t "Processing ~a --> ~a~%" | |
13534 | source target) | |
13535 | (delete-file target) | |
13536 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
13537 | (call-with-output-file target | |
13538 | (lambda (port) | |
13539 | (dump-port minified port))))) | |
13540 | sources targets)))) | |
13541 | #t))))) | |
13542 | (propagated-inputs | |
13543 | `(("r-base64enc" ,r-base64enc) | |
13544 | ("r-crosstalk" ,r-crosstalk) | |
13545 | ("r-htmlwidgets" ,r-htmlwidgets) | |
13546 | ("r-igraph" ,r-igraph))) | |
13547 | (native-inputs | |
13548 | `(("uglify-js" ,uglify-js) | |
13549 | ("js-jquery" | |
13550 | ,(origin | |
13551 | (method url-fetch) | |
13552 | (uri "https://code.jquery.com/jquery-3.3.1.js") | |
13553 | (sha256 | |
13554 | (base32 | |
13555 | "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) | |
13556 | ("js-threejs-85" | |
13557 | ,(origin | |
13558 | (method url-fetch) | |
13559 | (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js") | |
13560 | (sha256 | |
13561 | (base32 | |
13562 | "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl")))))) | |
13563 | (home-page "https://bwlewis.github.io/rthreejs") | |
13564 | (synopsis "Interactive 3D scatter plots, networks and globes") | |
13565 | (description | |
13566 | "Create interactive 3D scatter plots, network plots, and globes in R | |
13567 | using the three.js visualization library.") | |
13568 | (license license:expat))) | |
74cada8e RW |
13569 | |
13570 | (define-public r-mlbench | |
13571 | (package | |
13572 | (name "r-mlbench") | |
13573 | (version "2.1-1") | |
13574 | (source | |
13575 | (origin | |
13576 | (method url-fetch) | |
13577 | (uri (cran-uri "mlbench" version)) | |
13578 | (sha256 | |
13579 | (base32 | |
13580 | "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl")))) | |
13581 | (build-system r-build-system) | |
13582 | (home-page "https://cran.r-project.org/web/packages/mlbench/") | |
13583 | (synopsis "Machine learning benchmark problems") | |
13584 | (description | |
13585 | "This package provides a collection of artificial and real-world machine | |
13586 | learning benchmark problems, including, e.g., several data sets from the UCI | |
13587 | repository.") | |
13588 | (license license:gpl2))) | |
409a13fe RW |
13589 | |
13590 | (define-public r-mpm | |
13591 | (package | |
13592 | (name "r-mpm") | |
13593 | (version "1.0-22") | |
13594 | (source | |
13595 | (origin | |
13596 | (method url-fetch) | |
13597 | (uri (cran-uri "mpm" version)) | |
13598 | (sha256 | |
13599 | (base32 | |
13600 | "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk")))) | |
13601 | (build-system r-build-system) | |
13602 | (propagated-inputs | |
13603 | `(("r-kernsmooth" ,r-kernsmooth) | |
13604 | ("r-mass" ,r-mass))) | |
13605 | (home-page "http://mpm.r-forge.r-project.org") | |
13606 | (synopsis "Multivariate projection methods") | |
13607 | (description | |
13608 | "This is a package for exploratory graphical analysis of multivariate | |
13609 | data, specifically gene expression data with different projection methods: | |
13610 | principal component analysis, correspondence analysis, spectral map | |
13611 | analysis.") | |
13612 | (license license:gpl2+))) | |
d8a28332 | 13613 | |
d2aa2d24 RW |
13614 | (define-public r-png |
13615 | (package | |
13616 | (name "r-png") | |
13617 | (version "0.1-7") | |
13618 | (source (origin | |
13619 | (method url-fetch) | |
13620 | (uri (cran-uri "png" version)) | |
13621 | (sha256 | |
13622 | (base32 | |
13623 | "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) | |
13624 | (build-system r-build-system) | |
13625 | (inputs | |
13626 | `(("libpng" ,libpng) | |
13627 | ("zlib" ,zlib))) | |
13628 | (home-page "http://www.rforge.net/png/") | |
13629 | (synopsis "Read and write PNG images") | |
13630 | (description | |
13631 | "This package provides an easy and simple way to read, write and display | |
13632 | bitmap images stored in the PNG format. It can read and write both files and | |
13633 | in-memory raw vectors.") | |
13634 | ;; Any of these GPL versions. | |
13635 | (license (list license:gpl2 license:gpl3)))) | |
13636 | ||
d8a28332 RW |
13637 | (define-public r-ggcorrplot |
13638 | (package | |
13639 | (name "r-ggcorrplot") | |
13640 | (version "0.1.2") | |
13641 | (source | |
13642 | (origin | |
13643 | (method url-fetch) | |
13644 | (uri (cran-uri "ggcorrplot" version)) | |
13645 | (sha256 | |
13646 | (base32 | |
13647 | "12sxvd9kjgszpbk35m7fj1wv7x40bp79c0g0by1xax70r3495h93")))) | |
13648 | (build-system r-build-system) | |
13649 | (propagated-inputs | |
13650 | `(("r-ggplot2" ,r-ggplot2) | |
13651 | ("r-reshape2" ,r-reshape2))) | |
13652 | (home-page "http://www.sthda.com/english/wiki/ggcorrplot") | |
13653 | (synopsis "Visualization of a correlation matrix using ggplot2") | |
13654 | (description | |
13655 | "The ggcorrplot package can be used to visualize easily a correlation | |
13656 | matrix using ggplot2. It provides a solution for reordering the correlation | |
13657 | matrix and displays the significance level on the plot. It also includes a | |
13658 | function for computing a matrix of correlation p-values.") | |
13659 | (license license:gpl2))) | |
f084e41e RW |
13660 | |
13661 | (define-public r-flexdashboard | |
13662 | (package | |
13663 | (name "r-flexdashboard") | |
13664 | (version "0.5.1.1") | |
13665 | (source | |
13666 | (origin | |
13667 | (method url-fetch) | |
13668 | (uri (cran-uri "flexdashboard" version)) | |
13669 | (sha256 | |
13670 | (base32 | |
13671 | "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x")))) | |
13672 | (build-system r-build-system) | |
13673 | (arguments | |
13674 | `(#:modules ((guix build utils) | |
13675 | (guix build r-build-system) | |
13676 | (srfi srfi-1) | |
13677 | (srfi srfi-26) | |
13678 | (ice-9 popen) | |
13679 | (ice-9 textual-ports)) | |
13680 | #:phases | |
13681 | (modify-phases %standard-phases | |
13682 | (add-after 'unpack 'process-javascript | |
13683 | (lambda* (#:key inputs #:allow-other-keys) | |
13684 | (with-directory-excursion "inst" | |
13685 | ;; Concatenate all components of prism.js | |
13686 | (let ((contents (string-join | |
13687 | (map (lambda (name) | |
13688 | (call-with-input-file | |
13689 | (assoc-ref inputs name) | |
13690 | get-string-all)) | |
13691 | (list "js-prism" | |
13692 | "js-prism-r" | |
13693 | "js-prism-line-numbers")) | |
13694 | "\n"))) | |
13695 | (call-with-output-file "prism-src.js" | |
13696 | (cut display contents <>))) | |
13697 | (call-with-values | |
13698 | (lambda () | |
13699 | (unzip2 | |
13700 | `(("www/stickytableheaders/jquery.stickytableheaders.js" | |
13701 | "www/stickytableheaders/jquery.stickytableheaders.min.js") | |
13702 | ("www/sly/sly.js" | |
13703 | "www/sly/sly.min.js") | |
13704 | ("prism-src.js" | |
13705 | "www/prism/prism.js") | |
13706 | (,(assoc-ref inputs "js-raphael") | |
13707 | "htmlwidgets/lib/raphael/raphael-2.1.4.min.js") | |
13708 | (,(assoc-ref inputs "js-featherlight") | |
13709 | "www/featherlight/featherlight.min.js")))) | |
13710 | (lambda (sources targets) | |
13711 | (for-each (lambda (source target) | |
13712 | (format #t "Processing ~a --> ~a~%" | |
13713 | source target) | |
13714 | (delete-file target) | |
13715 | (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) | |
13716 | (call-with-output-file target | |
13717 | (lambda (port) | |
13718 | (dump-port minified port))))) | |
13719 | sources targets)))) | |
13720 | #t))))) | |
13721 | (propagated-inputs | |
13722 | `(("r-htmltools" ,r-htmltools) | |
13723 | ("r-htmlwidgets" ,r-htmlwidgets) | |
13724 | ("r-jsonlite" ,r-jsonlite) | |
13725 | ("r-knitr" ,r-knitr) | |
13726 | ("r-rmarkdown" ,r-rmarkdown) | |
13727 | ("r-shiny" ,r-shiny))) | |
13728 | (native-inputs | |
13729 | `(("uglify-js" ,uglify-js) | |
13730 | ("js-raphael" | |
13731 | ,(origin | |
13732 | (method url-fetch) | |
13733 | (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js") | |
13734 | (sha256 | |
13735 | (base32 | |
13736 | "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x")))) | |
13737 | ("js-prism" | |
13738 | ,(origin | |
13739 | (method url-fetch) | |
13740 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js") | |
13741 | (sha256 | |
13742 | (base32 | |
13743 | "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c")))) | |
13744 | ("js-prism-r" | |
13745 | ,(origin | |
13746 | (method url-fetch) | |
13747 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js") | |
13748 | (sha256 | |
13749 | (base32 | |
13750 | "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki")))) | |
13751 | ("js-prism-line-numbers" | |
13752 | ,(origin | |
13753 | (method url-fetch) | |
13754 | (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js") | |
13755 | (sha256 | |
13756 | (base32 | |
13757 | "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991")))) | |
13758 | ("js-featherlight" | |
13759 | ,(origin | |
13760 | (method url-fetch) | |
13761 | (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js") | |
13762 | (sha256 | |
13763 | (base32 | |
13764 | "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb")))))) | |
13765 | (home-page "https://rmarkdown.rstudio.com/flexdashboard") | |
13766 | (synopsis "R Markdown format for flexible dashboards") | |
13767 | (description | |
13768 | "This package provides an R Markdown format for converting an R Markdown | |
13769 | document to a grid-oriented dashboard. The dashboard flexibly adapts the size | |
13770 | of its components to the containing web page.") | |
13771 | (license license:expat))) | |
c54ab337 RW |
13772 | |
13773 | (define-public r-preseqr | |
13774 | (package | |
13775 | (name "r-preseqr") | |
13776 | (version "4.0.0") | |
13777 | (source | |
13778 | (origin | |
13779 | (method url-fetch) | |
13780 | (uri (cran-uri "preseqR" version)) | |
13781 | (sha256 | |
13782 | (base32 | |
13783 | "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1")))) | |
13784 | (properties `((upstream-name . "preseqR"))) | |
13785 | (build-system r-build-system) | |
13786 | (propagated-inputs | |
13787 | `(("r-polynom" ,r-polynom))) | |
13788 | (home-page "https://cran.r-project.org/web/packages/preseqR/") | |
13789 | (synopsis "Predicting species accumulation curves") | |
13790 | (description | |
13791 | "This package can be used to predict the r-species accumulation | |
13792 | curve (r-SAC), which is the number of species represented at least r times as | |
13793 | a function of the sampling effort. When r = 1, the curve is known as the | |
13794 | species accumulation curve, or the library complexity curve in high-throughput | |
13795 | genomic sequencing. The package includes both parametric and nonparametric | |
13796 | methods, as described by Deng C, et al. (2018).") | |
13797 | (license license:gpl3))) | |
1fab2cf8 RW |
13798 | |
13799 | (define-public r-mapplots | |
13800 | (package | |
13801 | (name "r-mapplots") | |
13802 | (version "1.5.1") | |
13803 | (source | |
13804 | (origin | |
13805 | (method url-fetch) | |
13806 | (uri (cran-uri "mapplots" version)) | |
13807 | (sha256 | |
13808 | (base32 | |
13809 | "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p")))) | |
13810 | (build-system r-build-system) | |
13811 | (home-page "https://cran.r-project.org/web/packages/mapplots/") | |
13812 | (synopsis "Data visualization on maps") | |
13813 | (description | |
13814 | "This package helps you create simple maps; add sub-plots like pie plots | |
13815 | to a map or any other plot; format, plot and export gridded data. The package | |
13816 | was developed for displaying fisheries data but most functions can be used for | |
13817 | more generic data visualisation.") | |
13818 | (license license:gpl2+))) | |
9563dd55 RW |
13819 | |
13820 | (define-public r-pmcmr | |
13821 | (package | |
13822 | (name "r-pmcmr") | |
13823 | (version "4.3") | |
13824 | (source | |
13825 | (origin | |
13826 | (method url-fetch) | |
13827 | (uri (cran-uri "PMCMR" version)) | |
13828 | (sha256 | |
13829 | (base32 | |
13830 | "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij")))) | |
13831 | (properties `((upstream-name . "PMCMR"))) | |
13832 | (build-system r-build-system) | |
13833 | (home-page "https://cran.r-project.org/web/packages/PMCMR/") | |
13834 | (synopsis "Calculate pairwise multiple comparisons of mean rank sums") | |
13835 | (description | |
13836 | "This is a deprecated package for calculating pairwise multiple | |
13837 | comparisons of mean rank sums. This package is superseded by the novel | |
13838 | PMCMRplus package. The PMCMR package is no longer maintained, but kept for | |
13839 | compatibility of reverse depending packages for some time.") | |
13840 | (license license:gpl3+))) | |
8d1990d4 RW |
13841 | |
13842 | (define-public r-downloader | |
13843 | (package | |
13844 | (name "r-downloader") | |
13845 | (version "0.4") | |
13846 | (source | |
13847 | (origin | |
13848 | (method url-fetch) | |
13849 | (uri (cran-uri "downloader" version)) | |
13850 | (sha256 | |
13851 | (base32 | |
13852 | "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q")))) | |
13853 | (build-system r-build-system) | |
13854 | (propagated-inputs | |
13855 | `(("r-digest" ,r-digest))) | |
13856 | (home-page "https://github.com/wch/downloader") | |
13857 | (synopsis "Download files over HTTP and HTTPS") | |
13858 | (description | |
13859 | "This package provides a wrapper for the @code{download.file} function, | |
13860 | making it possible to download files over HTTPS across platforms. The | |
13861 | @code{RCurl} package provides this functionality (and much more) but has | |
13862 | external dependencies. This package has is implemented purely in R.") | |
13863 | (license license:gpl2))) |